@article {560, title = {Perspective on Terahertz Applications in Bioscience and Biotechnology}, journal = {ACS Photonics}, volume = {9}, year = {2022}, pages = {1117-1126}, chapter = {1117}, abstract = {

Within the field of terahertz science and technology, one of the most active areas of current research focuses on the intersection of terahertz measurements and methods with the world of biology and medicine. Current activities revolve around numerous diverse questions, ranging from studies of the vibrational spectra of biomolecules and macromolecular complexes to biosensing to medical diagnostics based on noninvasive imaging techniques. Unlike many other areas in which terahertz science is now making inroads, this research domain has been plagued with a number of misleading ideas, which originated at least two decades ago and continue to crop up in current literature. In the worst case, these unfortunate notions can distract from, and even obscure, fascinating and meaningful results. The purpose of this Perspective is to highlight a few of these mistaken concepts and, more importantly, to distinguish them from the many interesting works that continue to emerge from the fruitful marriage of terahertz with biology and medicine.

}, doi = {10.1021/acsphotonics.2c00228}, url = {https://pubs.acs.org/doi/abs/10.1021/acsphotonics.2c00228}, author = {Markelz, A. G. and Mittleman, D. M.} } @conference {441, title = {Anisotropic Terahertz Microscopy of Lysozyme in Different CrystalLattice Systems}, booktitle = {Biophysical Journal}, year = {2021}, month = {02/2021}, abstract = {

Long-range vibrational modes of proteins at terahertz (THz) frequencies havebeen associated with protein function and allosteric control. The characteriza-tion of these motions has been challenging due to energy overlap with waterabsorption and a large vibrational density of states. Recently it has been demon-strated both experimentally and theoretically that vibrational bands can be iso-lated using stationary sample anisotropic terahertz microscopy (SSTAM) fororiented samples, typically realized using protein crystals [1, 2]. In those earlymeasurements, inhibitor binding contrast was demonstrated for high symmetrytetragonal crystals. While high symmetry crystals are ideal for structural deter-minations, they can limit the types of vibrations observable in the ATM mea-surements. Here we show a survey of ATM measurements of triclinic,monoclinic and tetragonal crystals, demonstrating the unique signaturesobservable for the different symmetry groups, leading to a more completedetermination of the vibrational hot spots that may contribute to enzymatic ef-ficiency. The SSATM spectra indicate the presence of conserved vibrationalmodes near 40 cm-1 and 55 cm-1 for CEWL in triclinic, monoclinic and tetrag-onal lattice systems respectively. For CEWL in the monoclinic lattice system, aprominent band at 20cm1was consistently observed in the SSATM spectrabut not in the triclinic or tetragonal systems. The conserved bands may repre-sent vibrational modes that are unperturbed by crystal contact forces while thedifferences may be related to unique molecular orientation in different crystalsystems.


1.Niessen, K., Y. Deng, and A.G. Markelz,Near-field THz micropo-larimetry.Opt Express, 2019.27(20): p. 28036-28047.

2.Romo, T.D., A.Grossfield, and A.G. MarkelzPersistent Protein Motions in a RuggedEnergy Landscape Revealed by Normal Mode Ensemble Analysis. AcceptedJournal of Chemical Information and Modeling, 2020.

}, doi = {10.1016/j.bpj.2020.11.972}, url = {https://www.cell.com/biophysj/fulltext/S0006-3495(20)31879-8}, author = {McKinney, J. A. and George, D. K. and Deng, Y. and Markelz, A. G.} } @article {559, title = {Apparatus and method for analyzing a sample }, year = {2021}, publisher = {USPTO}, address = {United States}, abstract = {
An apparatus and method for Crystal Anisotropy Terahertz Microscopy ({\textquotedblleft}CATM{\textquotedblright}) is provided. The apparatus includes an emitter configured to emit a THz pulse and a detector configured to detect the THz pulse after the pulse is transmitted through a sample disposed on a sample surface of the detector. A pulsed radiation generator generates a probe beam to interrogate the detector. The detector may include an electro-optical ({\textquotedblleft}EO{\textquotedblright}) crystal configured to change in birefringence according to the THz pulse. The sample surface of the detector may have a dielectric coating which is transmissive to THz and reflective to the probe beam. The sample is disposed on the dielectric coating.
}, issn = {11,125,685}, url = {https://patents.google.com/patent/US11125685B2/en}, author = {Markelz, Andrea G and Acbas, Gheorghe and Niessen, Katherine A.} } @article {545, title = {Functional-State Dependence of Picosecond Protein Dynamics}, journal = {J. Phys. Chem. B}, volume = {125}, year = {2021}, pages = {11134-11140}, chapter = {11134}, abstract = {

We examine temperature-dependent picosecond dynamics of two benchmarking proteins lysozyme and cytochrome c using temperature-dependent terahertz permittivity measurements. We find that a double Arrhenius temperature dependence with activation energies E1 \~{} 0.1 kJ/mol and E2 \~{} 10 kJ/mol fits the folded and ligand-free state response. The higher activation energy is consistent with the so-called protein dynamical transition associated with beta relaxations at the solvent{\textendash}protein interface. The lower activation energy is consistent with correlated structural motions. When the structure is removed by denaturing, the lower-activation-energy process is no longer present. Additionally, the lower-activation-energy process is diminished with ligand binding but not for changes in the internal oxidation state. We suggest that the lower-energy activation process is associated with collective structural motions that are no longer accessible with denaturing or binding.

}, doi = {10.1021/acs.jpcb.1c05018}, author = {George, D. K. and Chen, J. Y. and He, Yunfen and Knab, J. R. and Markelz, A. G.} } @article {329, title = {Near-Field Stationary Sample Terahertz Spectroscopic Polarimetry for Biomolecular Structural Dynamics Determination}, journal = {ACS Photonics}, volume = {8}, year = {2021}, month = {02/2021}, pages = {658-668}, chapter = {658}, abstract = {

THz polarimetry on environmentally sensitive and microscopic samples can provide unique insight into underlying mechanisms of complex phenomena. For example, near-field THz anisotropic absorption successfully isolated protein structural vibrations which are connected to biological function. However, to determine how these vibrations impact function requires high throughput measurements of these complex systems, which is challenged by the need for near field detection, sample environmental control and full polarization variation. Stationary sample anisotropic terahertz spectroscopy (SSATS) and near-field stationary sample anisotropic terahertz microscopy (SSATM) have been proposed using synchronous control of THz and electro optic probe polarizations along an iso-response curve. Here we realize these techniques through robust control and calibration of the THz and NIR polarization states. Both methods rapidly measure the linear dichroism in the far field and near field. Validation measurements using standard birefringent sucrose single crystals found the crystal orientation can be determined by scanning the reference polarization and the synchronous pump{\textendash}probe polarization settings can be optimized to eliminate artifacts. SSATM is then used to determine spectral reproducibility and dehydration effects for a series of chicken egg white lysozyme samples. Reproducible anisotropic absorbance bands are found at about 30, 44, 55, and 62 cm{\textendash}1. These bands initially sharpen with slow dehydration, similar to the increase in resolution achieved in X-ray crystallographic protein structure determination. The SSATM technique confirms the reliability of anisotropic absorption characterization of protein intramolecular vibrations and opens an avenue for rapid determination of how these long-range dynamics affect biological function.

}, doi = {10.1021/acsphotonics.0c01876}, url = {https://pubs.acs.org/doi/abs/10.1021/acsphotonics.0c01876}, author = {Deng, Y. and McKinney, J. A. and George, D. K. and Niessen, K. A. and Sharma, A. and Markelz, A.G.} } @article {520, title = {Phonon Kinetics of Fructose at the Melting Transition}, journal = {J. Phys. Chem. C}, volume = {125}, year = {2021}, pages = {12269-12276}, chapter = {12269}, abstract = {

Terahertz time domain spectroscopy (THz TDS) is used to measure the melting kinetics of fructose molecular crystals. Combining single-crystal anisotropy measurements with density functional calculations, we assign the phonon frequencies and interrogate how specific phonons behave with melting. While nearly all the low-frequency phonons continuously red-shift with heating and melting, the lowest-energy phonon polarized along the c-axis blue-shifts at the melting temperature, suggesting an initial structural change immediately before melting. We find that the kinetics follow a 3D growth model with large activation energies, consistent with previous differential scanning calorimetry (DSC) measurements. The large activation energies indicate that multiple H-bonds must break collectively for the transition. The results suggest the generality of the kinetics for molecular crystals and that THz TDS with picosecond resolution could be used to measure ultrafast kinetics.

}, doi = {10.1021/acs.jpcc.1c00610}, author = {A. Davie and F. Vandrevala and S. Dampf and Y. Deng and D. K. George and E. D. Sylvester and T. Korter and E. Einarsson and J. B. Benedict and A. G. Markelz} } @article {519, title = {Photo-Switching of Protein Dynamical Collectivity}, journal = {Photonics}, volume = {8}, year = {2021}, chapter = {302}, abstract = {

We examine changes in the picosecond structural dynamics with irreversible photobleaching of red fluorescent proteins (RFP) mCherry, mOrange2 and TagRFP-T. Measurements of the protein dynamical transition using terahertz time-domain spectroscopy show in all cases an increase in the turn-on temperature in the bleached state. The result is surprising given that there is little change in the protein surface, and thus, the solvent dynamics held responsible for the transition should not change. A spectral analysis of the measurements guided by quasiharmonic calculations of the protein absorbance reveals that indeed the solvent dynamical turn-on temperature is independent of the thermal stability/photostate however the protein dynamical turn-on temperature shifts to higher temperatures. This is the first demonstration of switching the protein dynamical turn-on temperature with protein functional state. The observed shift in protein dynamical turn-on temperature relative to the solvent indicates an increase in the required mobile waters necessary for the protein picosecond motions, that is, these motions are more collective. Melting-point measurements reveal that the photobleached state is more thermally stable, and structural analysis of related RFP{\textquoteright}s shows that there is an increase in internal water channels as well as a more uniform atomic root mean squared displacement. These observations are consistent with previous suggestions that water channels form with extended light excitation providing O2 access to the chromophore and subsequent fluorescence loss. We report that these same channels increase internal coupling enhancing thermal stability and collectivity of the picosecond protein motions. The terahertz spectroscopic characterization of the protein and solvent dynamical onsets can be applied generally to measure changes in collectivity of protein motions.

}, doi = {10.3390/photonics8080302}, url = {https://www.mdpi.com/2304-6732/8/8/302}, author = {M. Xu and D. George and R. Jimenez and A. Markelz} } @article {253, title = {Evidence of Intramolecular Structural Stabilization in Light Activated State of Orange Carotenoid Protein}, journal = {Biophysical Journal}, volume = {118}, number = {3}, year = {2020}, note = {ISI Document Delivery No.: KK8YX
Times Cited: 0
Cited Reference Count: 0
McKinney, Jeffrey A. Sharma, Akansha Crossen, Kimberly Deng, Yanting George, Deepu K. Lechno-Yossef, Sigal Kerfeld, Cheryl Markelz, Andrea G.
64th Annual Meeting of the Biophysical-Society
Feb 15-19, 2020
San Diego, CA
Biophys Soc
NSFNational Science Foundation (NSF) [DBI 1556359, MCB 1616529]; DOEUnited States Department of Energy (DOE) [DE-SC0016317]; NIH STTRUnited States Department of Health \& Human ServicesNational Institutes of Health (NIH) - USA [R41 GM125486]
This work is supported by NSF grants DBI 1556359 and MCB 1616529, DOE grant DE-SC0016317 and NIH STTR R41 GM125486.

1
2
Cell press
Cambridge
1542-0086}, month = {Feb}, pages = {208A-208A}, type = {Meeting Abstract}, abstract = {

Orange carotenoid protein (OCP) controls efficiency of the light harvesting antenna, the phycobilisome (PBS), in diverse cyanobacteria and prevents oxidative damage. It is the only known photoactive protein that uses a carotenoid, canthaxanthin, as its chromophore. The structure of OCP consists of two globular domains, connected by an unstructured loop, that forms a hydrophobic pocket for the carotenoid. In low light, canthaxanthin bound OCP is inactive and appears orange. Illumination by strong light results in an active state that interacts with the PBS to induce fluorescence quenching, a red appearance and conformational changes that include a 12{\r A} shift by canthaxanthin into the N-terminal domain. Terahertz (THz) dynamical transition measurements and anisotropic terahertz microscopy are used to measure the intramolecular structural dynamics in the inactive and active states, which can be induced by photoexcitation or chaotropic salts. The measurements indicate that the active state has a decrease in structural flexibility, which may be related to enhanced interactions with the PBS.

}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2019.11.1245}, author = {McKinney, J. A. and Sharma, A. and Crossen, K. and Deng, Y. and George, D. K. and Lechno-Yossef, S. and Kerfeld, C. and Markelz, A. G.} } @article {238, title = {Linear dichroism infrared resonance in overdoped, underdoped, and optimally doped cuprate superconductors}, journal = {Physical Review B}, volume = {102}, number = {5}, year = {2020}, note = {ISI Document Delivery No.: NE5GO
Times Cited: 0
Cited Reference Count: 30
Cited References:
Acbas G, 2009, PHYS REV LETT, V103, DOI 10.1103/PhysRevLett.103.137201
Armitage NP, 2014, PHYS REV B, V90, DOI 10.1103/PhysRevB.90.035135
Arpaia R, 2018, PHY REV MATER, V2, DOI 10.1103/PhysRevMaterials.2.024804
Basov DN, 2005, REV MOD PHYS, V77, P721, DOI 10.1103/RevModPhys.77.721
Blumberg G, 1996, PHYS REV B, V53, P11930, DOI 10.1103/PhysRevB.53.R11930
Cerne J, 2000, PHYS REV LETT, V84, P3418, DOI 10.1103/PhysRevLett.84.3418
Fauque B, 2006, PHYS REV LETT, V96, DOI 10.1103/PhysRevLett.96.197001
Fridman I, 2011, PHYS REV B, V84, DOI 10.1103/PhysRevB.84.104522
George DK, 2012, J OPT SOC AM B, V29, P1406, DOI 10.1364/JOSAB.29.001406
Halperin B. I., 1991, SPRINGER P PHYS, V60, P439
Humlicek J, 2000, PHYS REV B, V61, P14554, DOI 10.1103/PhysRevB.61.14554
KOREN G, 1989, APPL PHYS LETT, V54, P1054, DOI 10.1063/1.101559
Koren G, 2016, PHYS REV B, V94, DOI 10.1103/PhysRevB.94.174515
Lubashevsky Y, 2014, PHYS REV LETT, V112, DOI 10.1103/PhysRevLett.112.147001
Mukherjee A, 2019, PHYS REV B, V99, DOI 10.1103/PhysRevB.99.085440
Nie LM, 2014, P NATL ACAD SCI USA, V111, P7980, DOI 10.1073/pnas.1406019111
Orenstein J, 2011, PHYS REV LETT, V107, DOI 10.1103/PhysRevLett.107.067002
PISAREV RV, 1991, PHASE TRANSIT, V37, P63, DOI 10.1080/01411599108203448
Simon ME, 2002, PHYS REV LETT, V89, DOI 10.1103/PhysRevLett.89.247003
TROFIMOV IE, 1994, APPL PHYS LETT, V65, P2481, DOI 10.1063/1.112671
Varma CM, 2014, EPL-EUROPHYS LETT, V106, DOI 10.1209/0295-5075/106/27001
Varma CM, 1997, PHYS REV B, V55, P14554, DOI 10.1103/PhysRevB.55.14554
Wu J, 2017, NATURE, V547, P432, DOI 10.1038/nature23290
Xia J, 2008, PHYS REV LETT, V100, DOI 10.1103/PhysRevLett.100.127002
Yakes MK, 2010, NANO LETT, V10, P1559, DOI 10.1021/nl9035302
Yakovenko VM, 2015, PHYSICA B, V460, P159, DOI 10.1016/j.physb.2014.11.060
Zhang H, 2018, PHYS REV MATER, V2, DOI 10.1103/PhysRevMaterials.2.033803
Zhang J, 2018, SCI ADV, V4, DOI 10.1126/sciadv.aao5235
Zhao L, 2017, NAT PHYS, V13, P250, DOI [10.1038/nphys3962, 10.1038/NPHYS3962]
Zhao L., 2018, ENCY MODERN OPTICS, P207
Mukherjee, A. Seo, J. Arik, M. M. Zhang, H. Zhang, C. C. Kirzhner, T. George, D. K. Markelz, A. G. Armitage, N. P. Koren, G. Wei, J. Y. T. Cerne, J.
NSF-DMR GrantNational Science Foundation (NSF) [1410599]; NSFNational Science Foundation (NSF) [MCB 1616529, DMR 1905519]; DOEUnited States Department of Energy (DOE) [DE-SC0016317]; NSERCNatural Sciences and Engineering Research Council of Canada (NSERC); CFI-OITCanada Foundation for Innovation; Canadian Institute for Advanced ResearchCanadian Institute for Advanced Research (CIFAR)
We are indebted to D. Hsieh, S. A. Kivelson, C. M. Varma, and L. Zhao for helpful discussions. We gratefully acknowledge support from NSF-DMR Grant No. 1410599 (J.C.). A.G.M. and D.K.G. were supported by NSF Grant No. MCB 1616529 and DOE Grant No. DE-SC0016317. Work in Toronto was supported by NSERC, CFI-OIT, and the Canadian Institute for Advanced Research. J.Y.T.W. thanks Kejun Xu for laboratory assistance in Toronto. N.P.A. was supported by NSF Grant No. DMR 1905519.

9
Amer physical soc
College pk
2469-9969}, month = {Aug}, pages = {6}, type = {Article}, abstract = {

By measuring the polarization changes in terahertz, infrared, and visible radiation over an extended energy range (3-2330 meV), we observe symmetry breaking in cuprate high-temperature superconductors over wide energy, doping, and temperature ranges. We measure the polarization rotation (Re[theta(F)]) and ellipticity (Im[theta(F)]) of transmitted radiation through thin films as the sample is rotated. We observe a twofold rotational symmetry in theta(F), which is associated with linear dichroism (LD) and occurs when electromagnetic radiation polarized along one direction is absorbed more strongly than radiation polarized in the perpendicular direction. Such polarization anisotropies can be generally associated with symmetry breakings. We measure the amplitude of the LD signal and study its temperature, energy, and doping dependence. The LD signal shows a resonant behavior with a peak in the few hundred meV range, which is coincident with the midinfrared optical feature that has been associated with the formation of the pseudogap state. The strongest LD signal is found in underdoped films, although it is also observed in optimally and overdoped samples. The LD signal is consistent with an electronic nematic order which is decoupled from the crystallographic axes as well as novel magnetoelectric effects.

}, keywords = {Materials Science, Physics}, isbn = {2469-9950}, doi = {10.1103/PhysRevB.102.054520}, author = {Mukherjee, A. and Seo, J. and Arik, M. M. and Zhang, H. and Zhang, C. C. and Kirzhner, T. and George, D. K. and Markelz, A. G. and Armitage, N. P. and Koren, G. and Wei, J. Y. T. and Cerne, J.} } @article {252, title = {Long Range Correlated Motions of TIM and their Possible Influence on Enzyme Function}, journal = {Biophysical Journal}, volume = {118}, number = {3}, year = {2020}, note = {ISI Document Delivery No.: KK8YX
Times Cited: 0
Cited Reference Count: 4
Cited References:
Acbas G, 2014, NAT COMMUN, V5, DOI 10.1038/ncomms4076
Niessen K.A. M.Y., 2017, BIOPHYS J, DOI [10.1016/j.bpj.2016.12.049.3., DOI 10.1016/J.BPJ.2016.12.049.3]
Niessen K, 2019, OPT EXPRESS, V27, P28036, DOI 10.1364/OE.27.028036
Niessen KA, 2019, NAT COMMUN, V10, DOI 10.1038/s41467-019-08926-3
McKinney, Jeffrey A. Deng, Yanting George, Deepu K. Richard, John Markelz, Andrea G.
64th Annual Meeting of the Biophysical-Society
Feb 15-19, 2020
San Diego, CA
Biophys Soc
NSFNational Science Foundation (NSF) [DBI 1556359, MCB 1616529]; DOEUnited States Department of Energy (DOE) [DE-SC0016317]; NIH STTRUnited States Department of Health \& Human ServicesNational Institutes of Health (NIH) - USA [R41 GM125486.1]
This work is supported by NSF grants DBI 1556359 and MCB 1616529, DOE grant DE-SC0016317 and NIH STTR R41 GM125486.1.

1
Cell press
Cambridge
1542-0086}, month = {Feb}, pages = {207A-207A}, type = {Meeting Abstract}, abstract = {

The alpha-beta barrel structure of triosephosphate isomerase (TIM) is possibly the most common among enzymes. In the case of TIM, structural dynamics are known to be essential to function. In particular the stabilization of the binding pocket by a phosphodianion {\textquotedblleft}handle{\textquotedblright} of the substrate and the closing of catalytic site loops 6 and 7 over the substrate. Loop 6 moves by as much as 7 Angstroms with binding. Recently a mutant survey for human TIM (hsTIM) found kcat can change significantly for a single mutation distant from the catalytic site. Crystallographic measurements find no structural change with the mutation, suggesting a dynamical mechanism for the allosteric effect. Here we use Stationary Sample Anisotropic Terahertz Microscopy (SSATM) to measure the long-range intramolecular vibrations and determine if specific vibrations couple the allosteric and catalytic sites. SSATM isolated protein long-range structural vibrations based on the dominant displacement direction [1-4]. We examine if specific vibrational bands are associate with loop 6 and loop 7 flexibility.

}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2019.11.1240}, author = {McKinney, J. A. and Deng, Y. T. and George, D. K. and Richard, J. and Markelz, A. G.} } @article {241, title = {Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis}, journal = {Journal of Chemical Information and Modeling}, volume = {60}, number = {12}, year = {2020}, note = {ISI Document Delivery No.: PT8QA
Times Cited: 0
Cited Reference Count: 47
Cited References:
Acbas G, 2014, NAT COMMUN, V5, DOI 10.1038/ncomms4076
Bahar I, 2007, CURR OPIN STRUC BIOL, V17, P633, DOI 10.1016/j.sbi.2007.09.011
Balog E, 2011, J PHYS CHEM B, V115, P6811, DOI 10.1021/jp108493g
Castro-Camus E, 2008, CHEM PHYS LETT, V455, P289, DOI 10.1016/j.cplett.2008.02.084
Cerutti DS, 2008, BIOCHEMISTRY-US, V47, P12065, DOI 10.1021/bi800894u
Cerutti DS, 2019, WIRES COMPUT MOL SCI, V9, DOI 10.1002/wcms.1402
CHO M, 1994, J CHEM PHYS, V100, P6672, DOI 10.1063/1.467027
Choi JH, 2014, J PHYS CHEM B, V118, P12837, DOI 10.1021/jp508547y
Cote Y, 2017, BIOPHYS J, V112, P2575, DOI 10.1016/j.bpj.2017.05.018
Dong J, 1999, ACTA CRYSTALLOGR D, V55, P745, DOI 10.1107/S0907444998016047
ESSMANN U, 1995, J CHEM PHYS, V103, P8577, DOI 10.1063/1.470117
Falconer RJ, 2012, J INFRARED MILLIM TE, V33, P973, DOI 10.1007/s10762-012-9915-9
FELLER SE, 1995, J CHEM PHYS, V103, P4613, DOI 10.1063/1.470648
Gerek ZN, 2011, PLOS COMPUT BIOL, V7, DOI 10.1371/journal.pcbi.1002154
GO N, 1983, P NATL ACAD SCI-BIOL, V80, P3696, DOI 10.1073/pnas.80.12.3696
Grossfield A, 2019, LIVING J COMPUT MOL, V1, P5067, DOI DOI 10.33011/LIVEC0MS.1.1.5067
Grossfield A, 2009, ANN REP COMP CHEM, V5, P23, DOI 10.1016/S1574-1400(09)00502-7
He YF, 2011, BIOPHYS J, V100, P1058, DOI 10.1016/j.bpj.2010.12.3731
HORIUCHI T, 1991, PROTEINS, V10, P106, DOI 10.1002/prot.340100204
Huang J, 2013, J COMPUT CHEM, V34, P2135, DOI 10.1002/jcc.23354
Katebi AR, 2014, PROTEIN SCI, V23, P213, DOI 10.1002/pro.2407
Kindt JT, 1997, J CHEM PHYS, V106, P4389, DOI 10.1063/1.473486
Kroll J, 2007, VIB SPECTROSC, V43, P324, DOI 10.1016/j.vibspec.2006.03.010
Leioatts N, 2012, J CHEM THEORY COMPUT, V8, P2424, DOI 10.1021/ct3000316
Lerbret A, 2009, J CHEM PHYS, V131, DOI 10.1063/1.3273218
Meinhold L, 2007, PHYS REV LETT, V99, DOI 10.1103/PhysRevLett.99.138101
Miller DW, 1999, J MOL BIOL, V286, P267, DOI 10.1006/jmbi.1998.2445
Niessen KA, 2019, NAT COMMUN, V10, DOI 10.1038/s41467-019-08926-3
Niessen KA, 2017, BIOPHYS J, V112, P933, DOI 10.1016/j.bpj.2016.12.049
Phillips JC, 2005, J COMPUT CHEM, V26, P1781, DOI 10.1002/jcc.20289
Porter JR, 2019, BIOPHYS J, V116, P818, DOI 10.1016/j.bpj.2018.11.3144
Romo TD, 2014, J COMPUT CHEM, V35, P2305, DOI 10.1002/jcc.23753
Romo TD, 2009, IEEE ENG MED BIO, P2332, DOI 10.1109/IEMBS.2009.5335065
Sassi P, 2013, J CHEM PHYS, V139, DOI 10.1063/1.4838355
Singh R, 2012, J PHYS CHEM A, V116, P10359, DOI 10.1021/jp307288r
Stehle CU, 2012, J CHEM PHYS, V136, DOI 10.1063/1.3686886
STRAUB JE, 1994, J PHYS CHEM-US, V98, P10978, DOI 10.1021/j100093a046
Tehver R, 2009, J MOL BIOL, V387, P390, DOI 10.1016/j.jmb.2008.12.032
Thirumuruganandham SP, 2009, J MOL MODEL, V15, P959, DOI 10.1007/s00894-008-0446-1
Whitmire SE, 2003, BIOPHYS J, V85, P1269, DOI 10.1016/S0006-3495(03)74562-7
Xie AH, 2000, PHYS REV LETT, V84, P5435, DOI 10.1103/PhysRevLett.84.5435
Xu D, 1996, J PHYS CHEM-US, V100, P12108, DOI 10.1021/jp960076a
Yu X, 2005, J CHEM PHYS, V122, DOI 10.1063/1.1830431
Yu X, 2004, CHEM PHYS LETT, V391, P181, DOI 10.1016/j.cplett.2004.04.100
Zakaria HA, 2011, APPL SPECTROSC, V65, P260, DOI 10.1366/10-06162
Zhang HL, 2009, J MOL GRAPH MODEL, V27, P655, DOI 10.1016/j.jmgm.2008.10.005
Zorba A, 2019, P NATL ACAD SCI USA, V116, P13937, DOI 10.1073/pnas.1906024116
Romo, Tod D. Grossfield, Alan Markelz, Andrea G.
Grossfield, Alan/0000-0002-5877-2789
National Science FoundationNational Science Foundation (NSF) [MCB 1616529]; U.S. Department of EnergyUnited States Department of Energy (DOE) [DESC0016317]
Funding was provided by the National Science Foundation (MCB 1616529) and the U.S. Department of Energy (DESC0016317).

1
Amer chemical soc
Washington
1549-960x}, month = {Dec}, pages = {6419-6426}, type = {Article}, abstract = {

Proteins are allosteric machines that couple motions at distinct, often distant, sites to control biological function. Low-frequency structural vibrations are a mechanism of this long-distance connection and are often used computationally to predict correlations, but experimentally identifying the vibrations associated with specific motions has proved challenging. Spectroscopy is an ideal tool to explore these excitations, but measurements have been largely unable to identify important frequency bands. The result is at odds with some previous calculations and raises the question what methods could successfully characterize protein structural vibrations. Here we show the lack of spectral structure arises in part from the variations in protein structure as the protein samples the energy landscape. However, by averaging over the energy landscape as sampled using an aggregate 18.5 mu s of all-atom molecular dynamics simulation of hen egg white lysozyme and normal-mode analyses, we find vibrations with large overlap with functional displacements are surprisingly concentrated in narrow frequency bands. These bands are not apparent in either the ensemble averaged vibrational density of states or isotropic absorption. However, in the case of the ensemble averaged anisotropic absorption, there is persistent spectral structure and overlap between this structure and the functional displacement frequency bands. We systematically lay out heuristics for calculating the spectra robustly, including the need for statistical sampling of the protein and inclusion of adequate water in the spectral calculation. The results show the congested spectrum of these complex molecules obscures important frequency bands associated with function and reveal a method to overcome this congestion by combining structurally sensitive spectroscopy with robust normal mode ensemble analysis.

}, keywords = {Chemistry, Computer Science, molecular-dynamics, Pharmacology \& Pharmacy, photoactive yellow protein, spectroscopy, state, vibrational-modes}, isbn = {1549-9596}, doi = {10.1021/acs.jcim.0c00879}, author = {Romo, T. D. and Grossfield, A. and Markelz, A. G.} } @article {282, title = {Is the Protein Dynamical Transition useful?}, journal = {Biophysical Journal}, volume = {118}, year = {2020}, chapter = {521a}, doi = {10.1016/j.bpj.2019.11.2866}, author = {Sharma, A. and George, D. K. and Crossen, K. and McKinney, J. and Kerfeld, C. and Markelz, A.} } @proceedings {544, title = {Stabilization of Terahertz Vibrational Modes in Illuminated Orange Carotenoid Protein Crystals}, year = {2020}, address = {Buffalo, NY}, abstract = {

Orange carotenoid protein (OCP) controls efficiency of the phycobilisome (PBS), the light harvesting antenna in cyanobacteria, to prevent oxidative damage. The OCP switches from resting state to photo protective state with intense blue light illumination. Questions persist as to why OCPR interaction increases with the PBS over that with the OCPO. Here we examine the role of long-range intramolecular vibrations within OCP. Using Stationary Sample Anisotropic Terahertz Microscopy (SSATM) we measure changes in the intramolecular vibrations with photo switching. We report the first observation of switching in the intramolecular vibrations with photoexcitation. Results suggest that there is a stiffening of the molecule in the photo protective state. This increase in structural stability may enhance the interaction with the PBS change in OCP interaction with PBS. In low light, carotenoid bound OCP appears orange (OCP o ) and is inactive. Illumination by strong light converts OCP to the active, red (OCPR) state, which interacts with the PBS. A comparison of anisotropic THz microscopy measurements of dark adapted (OCP o ) and illuminated OCP crystals indicate differences in their vibrational modes that may be important for OCP-PBS interactions.

}, doi = {10.1109/IRMMW-THz46771.2020.9370827}, author = {McKinney, J. and Sharma, A. and Deng, Y. and George, D. and Lechno-Yossef, S. and Kerfeld, C. and Markelz, A.} } @proceedings {612, title = {THz Transmission through Submillimeter Apertures}, year = {2020}, month = {11/2020}, address = {Buffalo NY}, abstract = {
Terahertz near-field microspectroscopy is emerging as an essential tool for characterization of novel materials and biomolecules. It is important to ensure the near field geometry used does not introduce spectral artifacts. For example, many scanning techniques can be strongly influenced by the interaction between the scattering tip and the sample. Here we examine the spectroscopic effects of a 200 μm diameter aperture for THz near-field measurements. We use HFSS to model free-space transmission through samples with resonant absorbance as a function of sample thickness, lateral sample width, and aperture diameter. We examine the transmitted power and spectral fidelity for coupling of transmitted THz light onto a detector. These studies inform corrective post-measurement analysis algorithms and design of near-field detection systems.
}, doi = {10.1109/IRMMW-THz46771.2020.9370923}, url = {https://ieeexplore.ieee.org/document/9370923}, author = {LaFave, T. and Lee, A. and Kao, T.-Y. and Markelz, A.} } @proceedings {299, title = {Angular Distortion Removal of THz Anisotropic Dichroism Microscope}, year = {2019}, month = {2019}, pages = {1 - 2}, address = {Paris, France}, abstract = {

We have developed a stationary sample THz anisotropic dichroism microscope as a powerful tool for material characterization. The key innovation is the use of an iso-response curve defined by the terahertz and detection light polarizations. Here we show that following a continuous iso-response curve introduces angular distortion in the spectrum, and this distortion can be eliminated by using a discontinuous iso-response angle pairs avoiding large gradient regions. Employing this additional constraint on the relative polarizations provides a convenient technique for rapid anisotropic terahertz spectroscopy.

}, keywords = {absorption, angular distortion removal, Biomedical measurement, continuous iso-response curve, detection light polarizations, discontinuous iso-response angle pairs, Distortion, light polarisation, material characterization, Microscopy, proteins, rapid anisotropic terahertz spectroscopy, relative polarizations, spectroscopy, stationary sample, terahertz spectroscopy, terahertz wave spectra, THz anisotropic dichroism microscope, vibrations}, isbn = {2162-2035}, doi = {10.1109/IRMMW-THz.2019.8873793}, url = {https://ieeexplore.ieee.org/document/8873793}, author = {Y. Deng and K. Niessen and A. Markelz} } @proceedings {235, title = {Anisotropic Terahertz Microscopy of Protein Collective Vibrations: Crystal Symmetry and Hydration Dependence}, year = {2019}, note = {ISI Document Delivery No.: BQ4OX
Times Cited: 0
Cited Reference Count: 4
Cited References:
Acbas G, 2014, NAT COMMUN, V5, DOI 10.1038/ncomms4076
Legrand L, 2002, ACTA CRYSTALLOGR D, V58, P1564, DOI 10.1107/S0907444902014403
Niessen KA, 2019, NAT COMMUN, V10, DOI 10.1038/s41467-019-08926-3
Niessen KA, 2017, BIOPHYS J, V112, P933, DOI 10.1016/j.bpj.2016.12.049
McKinney, Jeffrey Deng, Yanting Sharma, Akansha George, D. K. Markelz, A. G.
Irmmw-thz
Proceedings Paper
44th International Conference on Infrared, Millimeter, and Terahertz Waves (IRMMW-THz)
Sep 01-06, 2019
Paris, FRANCE
Lytid, TYDEX, Swiss Terahertz, Fondat Maison Chimie, CNRS, Lab Physique ENS, Li2S, LUNA, MenloSystems, ENS, PSL Univ Paris, FYLA, ADVANTEST, Springer Nature, Soc Francaise Physique, Sorbonne Univ, Int Soc Infrared Millimeter \& Terahertz Waves, IEEE, GDR NANO THz MIR
NSFNational Science Foundation (NSF) [DBI 1556359, MCB 1616529]; DOEUnited States Department of Energy (DOE) [DE-SC0016317]; NIHUnited States Department of Health \& Human ServicesNational Institutes of Health (NIH) - USA [STTR R41 GM125486]
This work is supported by NSF grants DBI 1556359 and MCB 1616529, DOE grant DE-SC0016317 and NIH STTR R41 GM125486.
345 e 47th st, new york, ny 10017 usa
2162-2027}, publisher = {Ieee}, address = {New York}, abstract = {

A stationary sample anisotropic terahertz microscopy technique is used to characterize the intramolecular vibrations for lysozyme. Tetragonal and triclinic crystals are compared. We find excellent reproducibility within a single crystal symmetry group. Several resonant bands are present for both symmetry groups, indicating they originate with the intramolecular vibrations and not crystal lattice phonons. Bands become more pronounced and higher frequency resonant bands begin to emerge with slight dehydration.

}, isbn = {978-1-5386-8285-2}, doi = {https://doi.org/10.1109/IRMMW-THz.2019.8873722}, author = {McKinney, J. and Deng, Y. T. and Sharma, A. and George, D. K. and Markelz, A. G.} } @article {276, title = {Blue Shift of a Molecular Crystal Phonon at the Solid to Liquid Phase Transition}, journal = {Bulletin of the American Physical Society}, volume = {2019}, year = {2019}, author = {Davie, Alex and Vandrevala, Farah and Deng, Yanting and George, D. and Sylvester, Eric D. and Korter, T. and Einarsson, E. and Benedict, Jason B. and Markelz, Andrea} } @article {248, title = {Deuteration and Inhibitor Binding Dependence of Protein Collective Vibrations}, journal = {Biophysical Journal}, volume = {116}, number = {3}, year = {2019}, note = {ISI Document Delivery No.: HO2XG
Times Cited: 0
Cited Reference Count: 2
Cited References:
Mahajan S, 2015, ARCH BIOCHEM BIOPHYS, V567, P59, DOI 10.1016/j.abb.2014.12.020
Niessen KA, 2017, BIOPHYS J, V112, P933, DOI 10.1016/j.bpj.2016.12.049
Deng, Yanting Mckinney, Jeffrey Markelz, Andrea
63rd Annual Meeting of the Biophysical-Society
Mar 02-06, 2019
Baltimore, MD
Biophys Soc

8
Cell press
Cambridge
1542-0086
1}, month = {Feb}, pages = {488A-488A}, type = {Meeting Abstract}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2018.11.2633}, author = {Deng, Y. T. and McKinney, J. and Markelz, A.} } @article {251, title = {The Effect of Crystal Contact Forces on the Protein Global Motions}, journal = {Biophysical Journal}, volume = {116}, number = {3}, year = {2019}, note = {ISI Document Delivery No.: HO2XG
Times Cited: 0
Cited Reference Count: 1
Cited References:
Acbas G, 2014, NAT COMMUN, V5, DOI 10.1038/ncomms4076
McKinney, Jeffrey A. Deng, Yanting George, Deepu Markelz, Andrea
63rd Annual Meeting of the Biophysical-Society
Mar 02-06, 2019
Baltimore, MD
Biophys Soc

8
Cell press
Cambridge
1542-0086
1}, month = {Feb}, pages = {489A-489A}, type = {Meeting Abstract}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2018.11.2638}, author = {McKinney, J. A. and Deng, Y. T. and George, D. and Markelz, A.} } @article {239, title = {Near-field THz micropolarimetry}, journal = {Optics Express}, volume = {27}, number = {20}, year = {2019}, note = {ISI Document Delivery No.: JB0XT
Times Cited: 1
Cited Reference Count: 31
Cited References:
Acbas G, 2014, NAT COMMUN, V5, DOI 10.1038/ncomms4076
Antoniou D, 2011, J PHYS CHEM B, V115, P15147, DOI 10.1021/jp207876k
Bagsican FR, 2017, SCI REP-UK, V7, DOI 10.1038/s41598-017-01883-1
Baxter JB, 2006, J PHYS CHEM B, V110, P25229, DOI 10.1021/jp064399a
BROOKS B, 1985, P NATL ACAD SCI USA, V82, P4995, DOI 10.1073/pnas.82.15.4995
Chen JY, 2007, APPL PHYS LETT, V90, DOI 10.1063/1.2748852
Chhowalla M, 2013, NAT CHEM, V5, P263, DOI [10.1038/NCHEM.1589, 10.1038/nchem.1589]
Cote Y, 2017, BIOPHYS J, V112, P2575, DOI 10.1016/j.bpj.2017.05.018
Dhillon SS, 2017, J PHYS D APPL PHYS, V50, DOI 10.1088/1361-6463/50/4/043001
Docherty CJ, 2014, ACS NANO, V8, P11147, DOI 10.1021/nn5034746
Ebbinghaus S, 2007, P NATL ACAD SCI USA, V104, P20749, DOI 10.1073/pnas.0709207104
Fan ST, 2014, J PHYS D APPL PHYS, V47, DOI 10.1088/0022-3727/47/37/374009
George DK, 2012, J OPT SOC AM B, V29, P1406, DOI 10.1364/JOSAB.29.001406
GRISCHKOWSKY D, 1990, J OPT SOC AM B, V7, P2006, DOI 10.1364/JOSAB.7.002006
Hayes D, 2011, FARADAY DISCUSS, V150, P459, DOI 10.1039/c0fd00030b
Hirota Y, 2006, OPT EXPRESS, V14, P4486, DOI 10.1364/OE.14.004486
Huang B, 2017, NATURE, V546, P270, DOI 10.1038/nature22391
Jin WC, 2018, NAT COMMUN, V9, DOI 10.1038/s41467-018-07547-6
Lang D, 2018, REV SCI INSTRUM, V89, DOI 10.1063/1.5016281
Markelz A, 2002, PHYS MED BIOL, V47, P3797, DOI 10.1088/0031-9155/47/21/318
Meireles L, 2011, PROTEIN SCI, V20, P1645, DOI 10.1002/pro.711
Niessen KA, 2019, NAT COMMUN, V10, DOI 10.1038/s41467-019-08926-3
Niessen KA, 2017, BIOPHYS J, V112, P933, DOI 10.1016/j.bpj.2016.12.049
Niessen Katherine A, 2015, Biophys Rev, V7, P201, DOI 10.1007/s12551-015-0168-4
Ostroverkhova O, 2006, APPL PHYS LETT, V89, DOI 10.1063/1.2387135
Planken PCM, 2011, J INFRARED MILLIM TE, V32, P975, DOI 10.1007/s10762-011-9824-3
Planken PCM, 2001, J OPT SOC AM B, V18, P313, DOI 10.1364/JOSAB.18.000313
Serita K, 2019, PHOTONICS-BASEL, V6, DOI 10.3390/photonics6010012
Vinh NQ, 2011, J AM CHEM SOC, V133, P8942, DOI 10.1021/ja200566u
You JW, 2018, NANO CONVERG, V5, DOI 10.1186/s40580-018-0158-x
Zhao C, 2017, NAT NANOTECHNOL, V12, P757, DOI [10.1038/NNANO.2017.68, 10.1038/nnano.2017.68]
Niessen, Katherine Deng, Yanting Markelz, A. G.
National Science FoundationNational Science Foundation (NSF) [DBI 1556359, MCB 1616529]; U.S. Department of EnergyUnited States Department of Energy (DOE) [DE-SCO016317]; National Institute of General Medical SciencesUnited States Department of Health \& Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of General Medical Sciences (NIGMS) [STTR R41 GM125486]
National Science Foundation (DBI 1556359, MCB 1616529); U.S. Department of Energy DE-SCO016317); National Institute of General Medical Sciences (STTR R41 GM125486).
1
3
9
Optical soc amer
Washington}, month = {Sep}, pages = {28036-28047}, type = {Article}, abstract = {

We introduce a method for rapid determination of anisotropic terahertz absorption with sub micron resolution and high spectral integrity in the terahertz range. The method is ideal for microscopic and environmentally sensitive materials such as 2-D materials and protein crystals where the anisotropic absorption is critical to understanding underlying physics. We introduce the idea of using an iso-response relationship between the THz polarization and electro optic probe polarization to enable stationary sample polarization measurements covering a full 2 pi polarization dependence measurement. (C) 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

}, keywords = {binding, conductivity, dynamics, modes, Optics, polarization modulation, Terahertz, time-domain spectroscopy, wse2}, isbn = {1094-4087}, doi = {https://doi.org/10.1364/OE.27.028036}, author = {Niessen, K. and Deng, Y. T. and Markelz, A. G.} } @article {283, title = {Photo Switching of Protein Dynamical Collectivity}, journal = {arXiv:1906.00893}, year = {2019}, url = {https://arxiv.org/abs/1906.00893}, author = {Xu, M. and George, D. K. and Jimenez, R. and Markelz, A. G.} } @article {199, title = {Protein and RNA dynamical fingerprinting}, journal = {Nature communications}, volume = {10}, number = {1}, year = {2019}, pages = {1-10}, isbn = {2041-1723}, doi = {https://doi.org/10.1038/s41467-019-08926-3}, author = {Niessen, Katherine A and Xu, Mengyang and George, Deepu K and Chen, Michael C and Ferr{\'e}-D{\textquoteright}Amar{\'e}, Adrian R and Snell, Edward H and Cody, Vivian and Pace, James and Schmidt, Marius and Markelz, Andrea G} } @conference {306, title = {Protein Intramolecular Motions with Deuteration and Inhibitor Binding Dependence}, booktitle = {APS R63.003}, year = {2019}, month = {03/2019}, url = {https://meetings.aps.org/Meeting/MAR19/Session/R63.3}, author = {Deng, Y. and McKinney, J. and Romo, T. and Grossfield, A. and Markelz, A. G.} } @article {249, title = {Spectral Assignment of Lysozyme Collective Vibrations}, journal = {Biophysical Journal}, volume = {116}, number = {3}, year = {2019}, note = {ISI Document Delivery No.: HO2XG
Times Cited: 0
Cited Reference Count: 1
Cited References:
Niessen KA, 2017, BIOPHYS J, V112, P933, DOI 10.1016/j.bpj.2016.12.049
Deng, Yanting Mckinney, Jeffrey Romo, Tod Grossfield, Alan Markelz, Andrea
63rd Annual Meeting of the Biophysical-Society
Mar 02-06, 2019
Baltimore, MD
Biophys Soc

8
Cell press
Cambridge
1542-0086
1}, month = {Feb}, pages = {564A-564A}, type = {Meeting Abstract}, abstract = {
Global structural vibrations at terahertz (THz) frequencies have been associated with protein function and allosteric control. A chief obstacle to utilizing this control mechanism has been measurement of specific motions. Recently it was shown that while the vibrational density of states, and isotropic absorption spectra are broad and featureless, collective vibrations can be isolated based on their directionality using aligned samples (realized with protein crystals) and anisotropic THz microscopy [1]. However the assignment of resonant bands to specific structural motions was complicated by the high symmetry of the tetragonal crystals used, and the slow experimental method. To structurally map the vibrations of the chicken egg white lysozyme (CEWL) we measure anisotropic absorption of triclinic crystals using our new technique: ideal polarization varying anisotropic THz microscopy (IPV-ATM). The low symmetry triclinic crystals provide absolute protein orientation, and the near field IPV-ATM rapidly measures broadband terahertz linear dichroism of the microcrystals. All measurements were performed at room temperature under 100\% humidity conditions. The unit cell parameters of triclinic lysozyme nitrate crystals, α = 28.5A{\textdegree}, b = 32.7A{\textdegree}, c = 35.1A{\textdegree}, α = 88.2{\textdegree}, β = 108.9{\textdegree}, γ = 111.9{\textdegree}, belonging to the P1 space group, were determined by X-ray diffraction before and after THz measurements. The intramolecular vibrational absorbance of the triclinic crystals has a more complex polarization dependence than the higher symmetry tetragonal crystals, as expected. While the tetragonal crystals have two strong bands at 45cm-1 and 55cm-1, the triclinic crystals have a series of narrow bands between 40 and 60cm-1 and a prominent band at 30cm-1. We compare the measured spectra to normal mode ensemble averaged calculations to assign the observed resonances, and isolating which collective motions impact the catalytic site.
}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2018.11.3032}, author = {Deng, Y. T. and McKinney, J. and Romo, T. and Grossfield, A. and Markelz, A.} } @proceedings {230, title = {Stationary Sample Anisotropic THz Spectroscopy using Discretely Tunable THz Sources}, year = {2019}, note = {Irmmw-thz
44th International Conference on Infrared, Millimeter, and Terahertz Waves (IRMMW-THz)
Sep 01-06, 2019
Paris, FRANCE
Lytid; TYDEX; Swiss Terahertz; Fondat Maison Chimie; CNRS, Lab Physique ENS; Li2S; LUNA; MenloSystems; ENS; PSL Univ Paris; FYLA; ADVANTEST; Springer Nature; Soc Francaise Physique; Sorbonne Univ; Int Soc Infrared Millimeter \& Terahertz Waves; IEEE; GDR NANO THz MIR
2162-2027}, abstract = {

We demonstrate anisotropic THz spectroscopy of sucrose using newly developed compact discretely tunable THz sources for turn-key spectroscopic systems.

}, isbn = {978-1-5386-8285-2}, doi = {https://doi.org/10.1109/IRMMW-THz.2019.8874234}, author = {LaFave, T., Jr. and George, D. K. and Markelz, A. G. and McNee, Ian and Kozlov, Vladimir and Schunemann, Peter} } @proceedings {185, title = {Tunable Compact Narrow Band THz Sources for Frequency Domain THz Anisotropic Spectroscopy}, volume = {10983}, year = {2019}, note = {ISI Document Delivery No.: BN5PJ
Times Cited: 0
Cited Reference Count: 17
Cited References:
Acbas G, 2014, NAT COMMUN, V5, DOI 10.1038/ncomms4076
Chen JY, 2007, APPL PHYS LETT, V90, DOI 10.1063/1.2748852
Jepsen PU, 2011, LASER PHOTONICS REV, V5, P124, DOI 10.1002/lpor.201000011
Lee Y. S., 2006, APPL PHYS LETT, V89
Lee YS, 2000, APPL PHYS LETT, V76, P2505, DOI 10.1063/1.126390
Lin A., 2013, ANTIPHASE DOMAIN ANN
Niessen K. A., BIOPHYSICAL J, V112, P933
Niessen KA, 2019, NAT COMMUN, V10, DOI 10.1038/s41467-019-08926-3
Niessen Katherine A, 2015, Biophys Rev, V7, P201, DOI 10.1007/s12551-015-0168-4
PARSONS DF, 1971, APPL OPTICS, V10, P1683
Singh R., 2013, PHYSICS
Strachan CJ, 2005, J PHARM SCI-US, V94, P837, DOI 10.1002/jps.20281
Tassev V., 2013, SPIE LASE, V9
Tekavec P., 2017, FRONTIERS OPTICS 201
Tonouchi M, 2007, NAT PHOTONICS, V1, P97, DOI 10.1038/nphoton.2007.3
Walther M, 2003, CHEM PHYS, V288, P261, DOI 10.1016/S0301-0104(03)00031-4
Zeitler JA, 2009, EUR J PHARM BIOPHARM, V71, P2, DOI 10.1016/j.ejpb.2008.08.012
George, D. K. LaFave, T. J. Markelz, A. G. Mcnee, Ian Tekavec, Patrick Kozlov, Vladimir Schunemann, Peter
LaFave, Tim/0000-0003-2925-8657
NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCESUnited States Department of Health \& Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of General Medical Sciences (NIGMS) [R41GM125486] Funding Source: NIH RePORTER; NIGMS NIH HHSUnited States Department of Health \& Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of General Medical Sciences (NIGMS) [R41 GM125486] Funding Source: Medline
0277-786x
1098311}, month = {Apr 15-17}, publisher = {Spie-Int Soc Optical Engineering}, address = {Baltimore, MD}, abstract = {

We demonstrate frequency domain THz anisotropy signature detection for protein crystal models using newly developed compact tunable narrow band THz sources based on Orientation Patterned Gallium Phosphide for turn-key spectroscopic systems.

}, keywords = {anisotropy, biomolecules, femtosecond, optical rectification, orientation patterned gallium phosphide, Terahertz, THz generation}, isbn = {978-1-5106-2632-4}, doi = {https://doi.org/10.1117/12.2519878}, author = {George, D. K. and LaFave, T. J. and Markelz, A. G. and McNee, I. and Tekavec, P. and Kozlov, V. and Schunemann, P.} } @conference {305, title = {Tunable narrow band sources for anisotropic THz spectroscopy}, booktitle = {APS S23-002}, year = {2019}, month = {02/2019}, url = {https://meetings.aps.org/Meeting/MAR19/Session/S23.2}, author = {George, D. K. and McNee, I. and Tekavec, P. and Kozlov, V. and Schunemann, P. and Markelz, A. G.} } @proceedings {236, title = {Tunable narrowband THz generation in orientation patterned gallium phosphide for THz anisotropy identification}, volume = {10902}, year = {2019}, note = {ISI Document Delivery No.: BM9XB
Times Cited: 2
Cited Reference Count: 8
Cited References:
Fejer M. M., 2013, ANTIPHASE DOMAIN ANN, P258
Jepsen PU, 2011, LASER PHOTONICS REV, V5, P124, DOI 10.1002/lpor.201000011
Lee YS, 2000, APPL PHYS LETT, V76, P2505, DOI 10.1063/1.126390
Niessen K. A., BIOPHYSICAL J, V112, P933
PARSONS DF, 1971, APPL OPTICS, V10, P1683
Singh R., 2013, MODULATED ORIENTATIO
Tassev V., 2013, SPIE LASE, P9
Tekavec P., 2017, FRONTIERS OPTICS 201
McNee, Ian Tekavec, Patrick Kozlov, Vladimir Markelz, A. G. George, D. K. Schunemann, Peter
Proceedings Paper
Conference on Nonlinear Frequency Generation and Conversion - Materials and Devices XVIII
Feb 05-07, 2019
San Francisco, CA
Spie
1000 20th st, po box 10, bellingham, wa 98227-0010 usa
0277-786x
Unsp 1090218}, publisher = {Spie-Int Soc Optical Engineering}, address = {Bellingham}, abstract = {

We demonstrate tunable narrowband THz generation by optical rectification of a femtosecond pulse in Orientation Patterned Gallium Phosphide. Center frequencies of 0.9 - 3.8 THz with average power up to 15 mu W were achieved using a 1.064 mu m fiber laser for the pump laser. Biomolecular characterization for an early application of this system is also shown in this work by anisotropic spectroscopic signature detection of molecular crystals in the THz region.

}, keywords = {anisotropy, biomolecules, femtosecond, optical rectification, orientation patterned gallium phosphide, Terahertz, THz generation}, isbn = {978-1-5106-2447-4}, doi = {https://doi.org/10.1117/12.2510522}, author = {McNee, I. and Tekavec, P. and Kozlov, V. and Markelz, A. G. and George, D. K. and Schunemann, P.}, editor = {Schunemann, P. G. and Schepler, K. L.} } @article {247, title = {Increase in Dynamical Collectivity and Directionality of Orange Carotenoid Protein in the Photo-Protective State}, journal = {Biophysical Journal}, volume = {114}, number = {3}, year = {2018}, note = {ISI Document Delivery No.: GD5RB
Times Cited: 1
Cited Reference Count: 0
Deng, Yanting Luck, Catherine H. Romo, Tod D. Grossfield, Alan M. Bandara, Sepalika Ren, Zhong Yang, Xiaojing Markelz, Andrea G.
62nd Annual Meeting of the Biophysical-Society
Feb 17-21, 2018
San Francisco, CA
Biophys Soc
1

7
Cell press
Cambridge
1542-0086}, month = {Feb}, pages = {522A-522A}, type = {Meeting Abstract}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2017.11.2854}, author = {Deng, Y. T. and Luck, C. H. and Romo, T. D. and Grossfield, A. M. and Bandara, S. and Ren, Z. and Yang, X. J. and Markelz, A. G.} } @conference {286, title = {Investigation of the Isotope Shift in Protein Collective Vibrations}, booktitle = {APS 2018}, volume = {A50.013}, year = {2018}, url = {http://meetings.aps.org/link/BAPS.2018.MAR.A50.13}, author = {Luck, C. and Xu, M. and Markelz, A.} } @conference {284, title = {Measuring Protein Intramolecular Dynamics with Terahertz Light: Functional Changes and Relevance to Biology}, booktitle = {APS 2018}, volume = {H50.001}, year = {2018}, url = {http://meetings.aps.org/link/BAPS.2018.MAR.H50.1}, author = {Xu, M. and Deng, Y. and Luck, C. and Sharma, A. and Markelz, A.} } @conference {285, title = {Rapid Terahertz Dichroism Near Field Microscopy for Biomolecular Intramolecular Vibrational Spectroscopy}, booktitle = {APS 2018}, volume = {A50.008}, year = {2018}, url = {http://meetings.aps.org/link/BAPS.2018.MAR.A50.8}, author = {Deng, Y. and Niessen, K. and Markelz, A.} } @proceedings {182, title = {Terahertz Light Fingerprints Biomolecular Dynamics}, year = {2018}, pages = {SW3D. 5}, publisher = {Optical Society of America}, doi = {https://doi.org/10.1364/CLEO_SI.2018.SW3D.5}, author = {Deng, Yanting and Xu, Mengyang and Niessen, Katherine A and George, Deepu Koshy and Markelz, Andrea G} } @proceedings {226, title = {THz Anisotropy Identification using Tunable Compact Narrow Band THz Sources}, year = {2018}, note = {ISI Document Delivery No.: BL3GO
Times Cited: 0
Cited Reference Count: 6
Cited References:
Dhillon SS, 2017, J PHYS D APPL PHYS, V50, DOI 10.1088/1361-6463/50/4/043001
Lee YS, 2000, APPL PHYS LETT, V76, P2505, DOI 10.1063/1.126390
Lin A., 2013, ANTIPHASE DOMAIN ANN, P258
Niessen KA, 2017, BIOPHYS J, V112, P933, DOI 10.1016/j.bpj.2016.12.049
Tassev V., 2013, SPIE LASE, P9
Tekavec P., 2017, FRONTIERS OPTICS 201
George, D. K. Markelz, A. G. Mcnee, Ian Tekavec, Patrick Kozlov, Vladimir Schunemann, Peter
Irmmw-thz
Proceedings Paper
43rd International Conference on Infrared, Millimeter, and Terahertz Waves (IRMMW-THz)
Sep 09-14, 2018
Nagoya, JAPAN
IEEE Microwave Theory \& Tech Soc, TeraTech, JSPS, JSIR, Japan Soc Appl Phys, IEEJ, CSJ, AIP, APL Photon, AIP, Journal Appl Phys, EiC, SPSJ, Terahertz Syst Consortium, AICHI, Nagoya Convent \& Visitors Bur, ADVANTEST CORP, AmTechs Corp, Menlo Systems GmbH, Nippo Precigion Co Ltd, TeraMetrix LLC Div Luna, ATN Japan LTD, DAHENG NEW EPOCH TECHNOL INC, FEMTO Dev Inc, KYOWA FINTECH Co Ltd, Spectra Design Ltd, TeraView Ltd, TYDEX LLC, Virginia Diodes Inc, PNP, Tydex Res \& Ind Opt, Femtowave, Kyowa Fine Tech Co Ltd, Daheng Opt
345 e 47th st, new york, ny 10017 usa
2162-2027}, publisher = {Ieee}, address = {New York}, abstract = {

We demonstrate THz anisotropy signature determination of a protein crystal model using newly developed compact tunable narrow band THz sources for turn-key spectroscopic systems for the bio molecular community.

}, isbn = {978-1-5386-3809-5}, doi = {https://doi.org/10.1109/IRMMW-THz.2018.8510291}, author = {George, D. K. and Markelz, A. G. and McNee, I. and Tekavec, P. and Kozlov, V. and Schunemann, P.} } @article {224, title = {The 2017 terahertz science and technology roadmap}, journal = {Journal of Physics D-Applied Physics}, volume = {50}, number = {4}, year = {2017}, note = {ISI Document Delivery No.: EI0HL
Times Cited: 541
Cited Reference Count: 209
Cited References:
Adam AJL, 2011, J INFRARED MILLIM TE, V32, P976, DOI 10.1007/s10762-011-9809-2
Ahmed SS, 2012, IEEE MICROW MAG, V13, P26, DOI 10.1109/MMM.2012.2205772
Alliance N., 2015, CISC VIS NETW IND GL, P1
[Anonymous], 2013, 178512012 IEEE
[Anonymous], 2014, IEEE T ELECT DEVICES, V61
[Anonymous], 2012, 178522016 IEEE
[Anonymous], 2015, P17852 IEEE
Appleby R, 2015, P SOC PHOTO-OPT INS, V9462
Arnone DD, 1999, PROC SPIE, V3828, P209, DOI 10.1117/12.361037
Ashworth PC, 2009, OPT EXPRESS, V17, P12444, DOI 10.1364/OE.17.012444
AUSTON DH, 1988, IEEE J QUANTUM ELECT, V24, P184, DOI 10.1109/3.114
Barbieri S, 2011, NAT PHOTONICS, V5, P306, DOI [10.1038/NPHOTON.2011.49, 10.1038/nphoton.2011.49]
Barker RJ., 2005, MODERN MICROWAVE MIL
Basov DN, 2011, REV MOD PHYS, V83, P471, DOI 10.1103/RevModPhys.83.471
Bauwens M. F., 2014, P IEEEMTT S INT MICR, P1, DOI [10.1109/MWSYM.2014.68486 07, DOI 10.1109/MWSYM.2014.6848607]
Beard MC, 2002, NANO LETT, V2, P983, DOI 10.1021/nl0256210
Beard MC, 2000, PHYS REV B, V62, P15764, DOI 10.1103/PhysRevB.62.15764
Bechtel HA, 2014, P NATL ACAD SCI USA, V111, P7191, DOI 10.1073/pnas.1400502111
Belkin MA, 2008, OPT EXPRESS, V16, P3242, DOI 10.1364/OE.16.003242
Belkin MA, 2015, PHYS SCRIPTA, V90, DOI 10.1088/0031-8949/90/11/118002
Bell R., 2012, INTRO FOURIER TRANSF
Berry CW, 2013, NAT COMMUN, V4, DOI 10.1038/ncomms2638
Blanchard F, 2011, OPT EXPRESS, V19, P8277, DOI 10.1364/OE.19.008277
Blau J, 2013, P FREE EL LAS FEL 20, P486
Booske JH, 2011, IEEE T THZ SCI TECHN, V1, P54, DOI 10.1109/TTHZ.2011.2151610
Booske JH, 2008, PHYS PLASMAS, V15, DOI 10.1063/1.2838240
Boppel S, 2012, 2012 IEEE 12TH TOPICAL MEETING ON SILICON MONOLITHIC INTEGRATED CIRCUITS IN RF SYSTEMS (SIRF), P77, DOI 10.1109/SiRF.2012.6160142
Burghoff D, 2014, NAT PHOTONICS, V8, P462, DOI 10.1038/nphoton.2014.85
Busch SF, 2014, J INFRARED MILLIM TE, V35, P993, DOI 10.1007/s10762-014-0113-9
Byrne MB, 2011, APPL PHYS LETT, V98, DOI 10.1063/1.3579258
Carr GL, 2002, NATURE, V420, P153, DOI 10.1038/nature01175
Carranza IE, 2015, IEEE T THZ SCI TECHN, V5, P892, DOI 10.1109/TTHZ.2015.2463673
Castro-Camus E, 2007, OPT EXPRESS, V15, P7047, DOI 10.1364/OE.15.007047
Chan WL, 2007, REP PROG PHYS, V70, P1325, DOI 10.1088/0034-4885/70/8/R02
Chattopadhyay G, 2011, IEEE T THZ SCI TECHN, V1, P33, DOI 10.1109/TTHZ.2011.2159561
Chen HT, 2003, APPL PHYS LETT, V83, P3009, DOI 10.1063/1.1616668
Chen JN, 2012, NATURE, V487, P77, DOI 10.1038/nature11254
Cocker T L, 2016, J PHYS D, V16, P1421
Cocker TL, 2013, NAT PHOTONICS, V7, P620, DOI [10.1038/NPHOTON.2013.151, 10.1038/nphoton.2013.151]
Coleman B, 2001, Issue Brief (Public Policy Inst (Am Assoc Retired Pers)), P1
Cooper KB, 2014, IEEE MICROW MAG, V15, P51, DOI 10.1109/MMM.2014.2356092
Cruz F C, 2007, C MICR OPT
Cunningham J, 2010, ELECTRON LETT, V46, pS34, DOI 10.1049/el.2010.3317
Dean P, 2011, OPT LETT, V36, P2587, DOI 10.1364/OL.36.002587
Dietz RJB, 2014, OPT LETT, V39, P6482, DOI 10.1364/OL.39.006482
Dietz RJB, 2014, OPT EXPRESS, V22, P19411, DOI 10.1364/OE.22.019411
Dobrovolsky V, 2007, SEMICOND SCI TECH, V22, P103, DOI 10.1088/0268-1242/22/2/017
Ducournau G, 2014, IEEE T THZ SCI TECHN, V4, P328, DOI 10.1109/TTHZ.2014.2309006
Dunsmore J.P., 2012, HDB MICROWAVE COMPON
Duvillaret L, 1999, APPL OPTICS, V38, P409, DOI 10.1364/AO.38.000409
Eisele M, 2014, NAT PHOTONICS, V8, P841, DOI [10.1038/nphoton.2014.225, 10.1038/NPHOTON.2014.225]
Falconer RJ, 2012, J INFRARED MILLIM TE, V33, P973, DOI 10.1007/s10762-012-9915-9
Fathololoumi S, 2012, OPT EXPRESS, V20, P3866, DOI 10.1364/OE.20.003866
Fausti D, 2011, SCIENCE, V331, P189, DOI 10.1126/science.1197294
Federici J, 2010, J APPL PHYS, V107, DOI 10.1063/1.3386413
Fei Z, 2012, NATURE, V487, P82, DOI 10.1038/nature11253
FETTERMAN HR, 1974, APPL PHYS LETT, V24, P70, DOI 10.1063/1.1655098
Freeman JR, 2013, OPT EXPRESS, V21, P16162, DOI 10.1364/OE.21.016162
Frisk U, 2003, ASTRON ASTROPHYS, V402, pL27, DOI 10.1051/0004-6361:20030335
Garet F, 2014, APPL PHYS LETT, V105, DOI 10.1063/1.4890732
Gavrilov NG, 2007, NUCL INSTRUM METH A, V575, P54, DOI 10.1016/j.nima.2007.01.023
Gensch M., 2013, P 35 INT FREE EL LAS, P474
George DK, 2012, J OPT SOC AM B, V29, P1406, DOI 10.1364/JOSAB.29.001406
Giliberti V, 2013, APPL PHYS LETT, V103, DOI 10.1063/1.4819734
Grant J, 2013, LASER PHOTONICS REV, V7, P1043, DOI 10.1002/lpor.201300087
Green B, 2016, SCI REP-UK, V6, DOI 10.1038/srep22256
Griffith P.R., 2007, FOURIER TRANSFORM IN
GRISCHKOWSKY D, 1990, J OPT SOC AM B, V7, P2006, DOI 10.1364/JOSAB.7.002006
Gruene P, 2008, SCIENCE, V321, P674, DOI 10.1126/science.1161166
Han NR, 2014, OPT LETT, V39, P3480, DOI 10.1364/OL.39.003480
Han RN, 2013, IEEE J SOLID-ST CIRC, V48, P2296, DOI 10.1109/JSSC.2013.2269856
Hanham SM, 2015, APPL PHYS LETT, V107, DOI 10.1063/1.4927242
Hassel J, 2015, PROC SPIE, V9651, DOI 10.1117/12.2197522
Hauri CP, 2011, APPL PHYS LETT, V99, DOI 10.1063/1.3655331
He W, 2015, APPL PHYS LETT, V107, DOI 10.1063/1.4932099
Hebling J, 2002, OPT EXPRESS, V10, P1161, DOI 10.1364/OE.10.001161
Heinz E, 2015, J INFRARED MILLIM TE, V36, P879, DOI 10.1007/s10762-015-0170-8
Henry SC, 2012, OPT ENG, V51, DOI 10.1117/1.OE.51.9.091603
Hesler J L, 2006, P 7 INT S SPAC TER T, P215
Hintzsche H, 2012, CRIT REV ENV SCI TEC, V42, P2408, DOI 10.1080/10643389.2011.574206
Hishida M, 2011, PHYS REV LETT, V106, DOI 10.1103/PhysRevLett.106.158102
Ho IC, 2010, OPT EXPRESS, V18, P2872, DOI 10.1364/OE.18.002872
HU BB, 1995, OPT LETT, V20, P1716, DOI 10.1364/OL.20.001716
Huang C, 2012, PHYS REV B, V85
Huber R, 2001, NATURE, V414, P286, DOI 10.1038/35104522
Jankowiak A., 2013, Synchrotron Radiation News, V26, P22, DOI 10.1080/08940886.2013.791212
Jepsen PU, 2007, CHEM PHYS LETT, V442, P275, DOI 10.1016/j.cplett.2007.05.112
Jepsen PU, 2011, LASER PHOTONICS REV, V5, P124, DOI 10.1002/lpor.201000011
Jepsen PU, 2005, OPT LETT, V30, P29, DOI 10.1364/OL.30.000029
JUICE-Jupiter Icy Moons Explorer, 2014, SRE20141 JUICE EUR S, P1
Kallfass I, 2011, IEEE T THZ SCI TECHN, V1, P477, DOI 10.1109/TTHZ.2011.2160021
Kampfrath T, 2013, NAT PHOTONICS, V7, P680, DOI [10.1038/nphoton.2013.184, 10.1038/NPHOTON.2013.184]
Kan T, 2015, NAT COMMUN, V6, DOI 10.1038/ncomms9422
Karpowicz N, 2008, APPL PHYS LETT, V92, DOI 10.1063/1.2828709
Kehr SC, 2008, PHYS REV LETT, V100, DOI 10.1103/PhysRevLett.100.256403
Kemp MC, 2011, IEEE T THZ SCI TECHN, V1, P282, DOI 10.1109/TTHZ.2011.2159647
Khalid A, 2014, J APPL PHYS, V115, DOI 10.1063/1.4868705
Kirley MP, 2015, IEEE T THZ SCI TECHN, V5, P1012, DOI 10.1109/TTHZ.2015.2468074
Kiwa T, 2003, OPT LETT, V28, P2058, DOI 10.1364/OL.28.002058
Koch M, 2001, NATO SCI SER II MATH, V27, P241
Koenig S, 2013, NAT PHOTONICS, V7, P977, DOI [10.1038/nphoton.2013.275, 10.1038/NPHOTON.2013.275]
Kohler R, 2002, NATURE, V417, P156, DOI 10.1038/417156a
Koppens FHL, 2014, NAT NANOTECHNOL, V9, P780, DOI [10.1038/nnano.2014.215, 10.1038/NNANO.2014.215]
Kosarev A, 2010, SOLID STATE ELECTRON, V54, P417, DOI 10.1016/j.sse.2009.12.032
Kundu I, 2014, OPT EXPRESS, V22, P16595, DOI 10.1364/OE.22.016595
Kuznetsov SA, 2010, KEY ENG MATER, V437, P276, DOI 10.4028/www.scientific.net/KEM.437.276
Langevin Y, 2005, PAYLOAD MISSION DEFI
LaRue JL, 2015, PHYS REV LETT, V115, DOI 10.1103/PhysRevLett.115.036103
Leitenstorfer A, 2014, NEW J PHYS, V16, DOI 10.1088/1367-2630/16/4/045016
Leitner DM, 2006, INT REV PHYS CHEM, V25, P553, DOI 10.1080/01442350600862117
Li LH, 2014, ELECTRON LETT, V50, P309, DOI 10.1049/el.2013.4035
Liu L, 2010, IEEE MICROW WIREL CO, V20, P504, DOI 10.1109/LMWC.2010.2055553
Liu SC, 2016, OPT EXPRESS, V24, P2728, DOI 10.1364/OE.24.002728
Lu X H, 2008, P SOC PHOTO-OPT INS, V7277
Luukanen A, 2003, APPL PHYS LETT, V82, P3970, DOI 10.1063/1.1579562
Mann C, 2009, P SOC PHOTO-OPT INS, V7311, P3970
Mickan S, 2004, PROC SPIE, V5277, P54, DOI 10.1117/12.530386
Mineo M, 2010, IEEE T ELECTRON DEV, V57, P3169, DOI 10.1109/TED.2010.2071876
Mittleman DM, 1996, IEEE J SEL TOP QUANT, V2, P679, DOI 10.1109/2944.571768
Mittleman DM, 1999, APPL PHYS B-LASERS O, V68, P1085, DOI 10.1007/s003400050750
Moon K, 2012, APPL PHYS LETT, V101, DOI 10.1063/1.4733475
Muller AS, 2010, REV ACCEL SCI TECH, V3, P165, DOI 10.1142/S1793626810000427
Muller R, 2015, J INFRARED MILLIM TE, V36, P654, DOI 10.1007/s10762-015-0163-7
Naftaly M, 2015, TERAHERTZ METROLOGY, P1
Nagai M, 2015, OPT EXPRESS, V23, P4641, DOI 10.1364/OE.23.004641
Nagatsuma T, 2012, OPT EXPRESS, V21, P477
Nagel M, 2002, APPL PHYS LETT, V80, P154, DOI 10.1063/1.1428619
Navarro-Cia M, 2015, J INFRARED MILLIM TE, V36, P542, DOI 10.1007/s10762-015-0157-5
Nielsen K, 2009, OPT EXPRESS, V17, P8592, DOI 10.1364/OE.17.008592
Niessen Katherine A, 2015, Biophys Rev, V7, P201, DOI 10.1007/s12551-015-0168-4
Nordquist CD, 2011, IEEE J SEL TOP QUANT, V17, P130, DOI 10.1109/JSTQE.2010.2049095
Oh SJ, 2012, J INFRARED MILLIM TE, V33, P74, DOI 10.1007/s10762-011-9847-9
Ojefors E, 2009, IEEE J SOLID-ST CIRC, V44, P1968, DOI 10.1109/JSSC.2009.2021911
Ortolani M, 2008, PHYS REV LETT, V97
Ozerov M, 2014, PHYS REV LETT, V113, DOI 10.1103/PhysRevLett.113.157205
Paoloni C, 2013, IEEE T ELECTRON DEV, V60, P1236, DOI 10.1109/TED.2013.2240686
Parrott EPJ, 2015, APPL SPECTROSC, V69, P1, DOI 10.1366/14-07707
Patrashin M, 2015, IEEE T ELECTRON DEV, V62, P1068, DOI 10.1109/TED.2015.2393358
Peiponen K. E., 2013, TERAHERTZ SPECTROSCO, V171
Peng K, 2015, NANO LETT, V15, P206, DOI 10.1021/nl5033843
Pickwell E, 2004, APPL PHYS LETT, V84, P2190, DOI 10.1063/1.1688448
Ponnampalam L, 2011, J LIGHTWAVE TECHNOL, V29, P2229, DOI 10.1109/JLT.2011.2158186
Pupeza I, 2007, OPT EXPRESS, V15, P4335, DOI 10.1364/OE.15.004335
Rauter P, 2015, LASER PHOTONICS REV, V9, P452, DOI 10.1002/lpor.201500095
Reid CB, 2011, PHYS MED BIOL, V56, P4333, DOI 10.1088/0031-9155/56/14/008
Reid J R, 2012, IEEE 12 TOP M SIL MO, P17
Rosch M, 2015, NAT PHOTONICS, V9, P42, DOI [10.1038/nphoton.2014.279, 10.1038/NPHOTON.2014.279]
Rudd JV, 2000, PROC SPIE, V3934, P27, DOI 10.1117/12.386344
Rymanov V, 2015, PHOTONICS, V2, DOI 10.3390/photonics2041152
SANTOS Daisy Conceicao, 2014, THESIS
Scherger B, 2011, APPL OPTICS, V50, P2256, DOI 10.1364/AO.50.002256
Schleicher JM, 2009, J APPL PHYS, V105, DOI 10.1063/1.3133093
Schumann S, 2012, OPT EXPRESS, V20, P19200, DOI 10.1364/OE.20.019200
Seeds AJ, 2015, J LIGHTWAVE TECHNOL, V33, P579, DOI 10.1109/JLT.2014.2355137
Sell A, 2008, OPT LETT, V33, P2767, DOI 10.1364/OL.33.002767
Shams H, 2015, IEEE PHOTONICS J, V7, DOI 10.1109/JPHOT.2015.2438437
Shams H, 2014, OPT EXPRESS, V22, P23465, DOI 10.1364/OE.22.023465
Shen YC, 2004, APPL PHYS LETT, V85, P164, DOI 10.1063/1.1768313
Simoens F., 2014, PHILOS T A, V372, P1
Simoens F, 2011, 36 INT C INFR MILL T, P1
Singh A, 2015, OPT EXPRESS, V23, P6656, DOI 10.1364/OE.23.006656
Sirtori C, 2013, NAT PHOTONICS, V7, P691, DOI [10.1038/NPHOTON.2013.208, 10.1038/nphoton.2013.208]
SMITH PR, 1988, IEEE J QUANTUM ELECT, V24, P255, DOI 10.1109/3.121
Son JH, 2013, NANOTECHNOLOGY, V24, DOI 10.1088/0957-4484/24/21/214001
Swinyard B, 2013, SPIE SENSORS SYSTEMS
Sy S, 2010, PHYS MED BIOL, V55, P7587, DOI 10.1088/0031-9155/55/24/013
Taylor ZD, 2015, IEEE T THZ SCI TECHN, V5, P184, DOI 10.1109/TTHZ.2015.2392628
Teppati V, 2013, CAMB RF MICROW ENG, P1, DOI 10.1017/CBO9781139567626
Tewari P, 2012, P SPIE, V8261
Thomas B., 2014, P 39 INT C INFR MILL, P1
Thumm M, 2014, KIT SCI REPORTS, V7693
Tonouchi M, 2007, NAT PHOTONICS, V1, P97, DOI 10.1038/nphoton.2007.3
Truong BCQ, 2015, IEEE T BIO-MED ENG, V62, P699, DOI 10.1109/TBME.2014.2364025
Turcinkova D, 2015, APPL PHYS LETT, V106, DOI 10.1063/1.4916653
Turner GM, 2002, J PHYS CHEM B, V106, P11716, DOI 10.1021/jp025844e
van der Valk NCJ, 2002, APPL PHYS LETT, V81, P1558, DOI 10.1063/1.1503404
van Dijk F, 2014, IEEE PHOTONIC TECH L, V26, P965, DOI 10.1109/LPT.2014.2309353
Vicario C, 2014, PHYS REV LETT, V112, DOI 10.1103/PhysRevLett.112.213901
Vinh NQ, 2015, J CHEM PHYS, V142, DOI 10.1063/1.4918708
Vitiello MS, 2012, NAT PHOTONICS, V6, P525, DOI 10.1038/nphoton.2012.145
Vitiello MS, 2015, OPT EXPRESS, V23, P5167, DOI 10.1364/OE.23.005167
Vitiello MS, 2014, NAT COMMUN, V5, DOI 10.1038/ncomms6884
Wade A, 2009, NAT PHOTONICS, V3, P41, DOI 10.1038/NPHOTON.2008.251
Wallace B., 2015, SPIE NEWSROOM, DOI [10.1117/2.1201503.005871, DOI 10.1117/2.1201503.005871]
Wallace VP, 2004, BRIT J DERMATOL, V151, P424, DOI 10.1111/j.1365-2133.2004.06129.x
Wang FH, 2015, OPTICA, V2, P944, DOI 10.1364/OPTICA.2.000944
Weightman P, 2012, PHYS BIOL, V9, DOI 10.1088/1478-3975/9/5/053001
Wienold M, 2014, OPT EXPRESS, V22, P3334, DOI 10.1364/OE.22.003334
Wilk R, 2007, C LAS EL BALT MD
Williams BS, 2006, ELECTRON LETT, V42, P89, DOI 10.1049/el:20063921
Williams GP, 2006, REP PROG PHYS, V69, P301, DOI 10.1088/0034-4885/69/2/R01
Williams GP, 2008, NAT PHYS, V4, P356, DOI 10.1038/nphys958
Williams MRC, 2013, J PHYS CHEM B, V117, P10444, DOI 10.1021/jp406730a
Williams R, 2013, PHYS MED BIOL, V58, P373, DOI 10.1088/0031-9155/58/2/373
Withayachumnankul W, 2008, J OPT SOC AM B, V25, P1059, DOI 10.1364/JOSAB.25.001059
Woerner M, 2013, NEW J PHYS, V15, DOI 10.1088/1367-2630/15/2/025039
Woodward RM, 2003, J INVEST DERMATOL, V120, P72, DOI 10.1046/j.1523-1747.2003.12013.x
Wu X, OPT LETT, V39, P5403
Wu ZR, 2013, REV SCI INSTRUM, V84, DOI 10.1063/1.4790427
Xu J, 2003, PROC SPIE, V5268, P19, DOI 10.1117/12.518533
Yamashita M, 2011, OPT EXPRESS, V19, P10864, DOI 10.1364/OE.19.010864
Yan F, 2013, J INFRARED MILLIM TE, V34, P489, DOI 10.1007/s10762-013-0005-4
Yang SH, 2014, IEEE T THZ SCI TECHN, V4, P575, DOI 10.1109/TTHZ.2014.2342505
Yeh KL, 2007, APPL PHYS LETT, V90, DOI 10.1063/1.2734374
Zamora A, 2015, IEEE MTT S INT MICR
Zhao JF, 2011, IEEE T ELECTRON DEV, V58, P1221, DOI 10.1109/TED.2011.2109723
Zheludev NI, 2012, NAT MATER, V11, P917, DOI [10.1038/NMAT3431, 10.1038/nmat3431]
Zhou Y, 2010, PROG ELECTROMAGN RES, V105, P71, DOI 10.2528/PIER10041806
Zibik EA, 2009, NAT MATER, V8, P803, DOI [10.1038/nmat2511, 10.1038/NMAT2511]
Dhillon, S. S. Vitiello, M. S. Linfield, E. H. Davies, A. G. Hoffmann, Matthias C. Booske, John Paoloni, Claudio Gensch, M. Weightman, P. Williams, G. P. Castro-Camus, E. Cumming, D. R. S. Simoens, F. Escorcia-Carranza, I. Grant, J. Lucyszyn, Stepan Kuwata-Gonokami, Makoto Konishi, Kuniaki Koch, Martin Schmuttenmaer, Charles A. Cocker, Tyler L. Huber, Rupert Markelz, A. G. Taylor, Z. D. Wallace, Vincent P. Zeitler, J. Axel Sibik, Juraj Korter, Timothy M. Ellison, B. Rea, S. Goldsmith, P. Cooper, Ken B. Appleby, Roger Pardo, D. Huggard, P. G. Krozer, V. Shams, Haymen Fice, Martyn Renaud, Cyril Seeds, Alwyn Stoehr, Andreas Naftaly, Mira Ridler, Nick Clarke, Roland Cunningham, John E. Johnston, Michael B.
Huggard, Peter/U-2150-2019; Konishi, Kuniaki/AAN-3624-2020; Zeitler, J. Axel/B-4885-2008; Paoloni, Claudio/AAH-9824-2019; Hoffmann, Matthias C./N-1082-2019; Wallace, Vincent P/A-9320-2012; Johnston, Michael/B-9813-2008; Castro-Camus, Enrique/V-6861-2019; Krozer, Viktor/P-5623-2014; Hoffmann, Matthias C/B-3893-2009; PAOLONI, CLAUDIO/AAA-3211-2020; Gonokami, Makoto/F-3641-2012; Shams, Haymen/H-3754-2012; Ridler, Nick/AAN-9637-2020; Huber, Rupert/N-4126-2018
Konishi, Kuniaki/0000-0003-2389-9787; Zeitler, J. Axel/0000-0002-4958-0582; Hoffmann, Matthias C./0000-0002-3596-9853; Wallace, Vincent P/0000-0003-3814-5400; Johnston, Michael/0000-0002-0301-8033; Krozer, Viktor/0000-0002-2387-1947; Hoffmann, Matthias C/0000-0002-3596-9853; PAOLONI, CLAUDIO/0000-0002-0265-0862; Shams, Haymen/0000-0002-5333-6478; Huber, Rupert/0000-0001-6617-9283; Davies, Alexander/0000-0002-1987-4846; Seeds, Alwyn/0000-0002-5228-627X; Castro-Camus, Enrique/0000-0002-8218-9155; Cunningham, John/0000-0002-1805-9743; Naftaly, Mira/0000-0002-0671-822X; Cumming, David/0000-0002-7838-8362
Engineering and Physical Sciences Research CouncilUK Research \& Innovation (UKRI)Engineering \& Physical Sciences Research Council (EPSRC) [EP/P015883/1, EP/M00306X/1, EP/K023349/1, EP/M017095/1, EP/L026597/1, EP/J017671/1] Funding Source: researchfish; Natural Environment Research CouncilUK Research \& Innovation (UKRI)NERC Natural Environment Research Council [NER/Z/S/2003/00642, NE/L012375/1, NER/Z/S/2000/01292] Funding Source: researchfish; Science and Technology Facilities CouncilUK Research \& Innovation (UKRI)Science \& Technology Facilities Council (STFC) [ST/P002056/1] Funding Source: researchfish; Direct For Biological SciencesNational Science Foundation (NSF)NSF - Directorate for Biological Sciences (BIO) [1556359] Funding Source: National Science Foundation; Div Of Biological InfrastructureNational Science Foundation (NSF)NSF - Directorate for Biological Sciences (BIO) [1556359] Funding Source: National Science Foundation; Div Of Molecular and Cellular BioscienceNational Science Foundation (NSF)NSF - Directorate for Biological Sciences (BIO) [1616529] Funding Source: National Science Foundation
566
30
462
Iop publishing ltd
Bristol
1361-6463}, month = {Feb}, pages = {49}, type = {Review}, abstract = {

Science and technologies based on terahertz frequency electromagnetic radiation (100 GHz-30 THz) have developed rapidly over the last 30 years. For most of the 20th Century, terahertz radiation, then referred to as sub-millimeter wave or far-infrared radiation, was mainly utilized by astronomers and some spectroscopists. Following the development of laser based terahertz time-domain spectroscopy in the 1980s and 1990s the field of THz science and technology expanded rapidly, to the extent that it now touches many areas from fundamental science to {\textquoteright}real world{\textquoteright} applications. For example THz radiation is being used to optimize materials for new solar cells, and may also be a key technology for the next generation of airport security scanners. While the field was emerging it was possible to keep track of all new developments, however now the field has grown so much that it is increasingly difficult to follow the diverse range of new discoveries and applications that are appearing. At this point in time, when the field of THz science and technology is moving from an emerging to a more established and interdisciplinary field, it is apt to present a roadmap to help identify the breadth and future directions of the field. The aim of this roadmap is to present a snapshot of the present state of THz science and technology in 2017, and provide an opinion on the challenges and opportunities that the future holds. To be able to achieve this aim, we have invited a group of international experts to write 18 sections that cover most of the key areas of THz science and technology. We hope that The 2017 Roadmap on THz science and technology will prove to be a useful resource by providing a wide ranging introduction to the capabilities of THz radiation for those outside or just entering the field as well as providing perspective and breadth for those who are well established. We also feel that this review should serve as a useful guide for government and funding agencies.

}, keywords = {ex-vivo, generation, metal wave-guides, near-field, performance, photoconductive emitters, Physics, quantum-cascade lasers, radiation, semiconductors, Terahertz, thz, time-domain spectroscopy}, isbn = {0022-3727}, doi = {https://doi.org/10.1088/1361-6463/50/4/043001}, author = {Dhillon, S. S. and Vitiello, M. S. and Linfield, E. H. and Davies, A. G. and Hoffmann, M. C. and Booske, J. and Paoloni, C. and Gensch, M. and Weightman, P. and Williams, G. P. and Castro-Camus, E. and Cumming, D. R. S. and Simoens, F. and Escorcia-Carranza, I. and Grant, J. and Lucyszyn, S. and Kuwata-Gonokami, M. and Konishi, K. and Koch, M. and Schmuttenmaer, C. A. and Cocker, T. L. and Huber, R. and Markelz, A. G. and Taylor, Z. D. and Wallace, V. P. and Zeitler, J. A. and Sibik, J. and Korter, T. M. and Ellison, B. and Rea, S. and Goldsmith, P. and Cooper, K. B. and Appleby, R. and Pardo, D. and Huggard, P. G. and Krozer, V. and Shams, H. and Fice, M. and Renaud, C. and Seeds, A. and Stohr, A. and Naftaly, M. and Ridler, N. and Clarke, R. and Cunningham, J. E. and Johnston, M. B.} } @article {256, title = {Escaping the Water Cage: Protein Intramolecular Vibrations and the Dynamical Transition}, journal = {Biophysical Journal}, volume = {112}, number = {3}, year = {2017}, note = {ISI Document Delivery No.: EW3DR
Times Cited: 0
Cited Reference Count: 0
Xu, Mengyang Niessen, Katherine A. Deng, Yanting Michki, Nigel S. Markelz, Andrea G.
58th Annual Meeting of the Biophysical-Society
Feb 15-19, 2014
San Francisco, CA
Biophys Soc
NSFNational Science Foundation (NSF) [DBI 1556359, MCB 1616529]; DOEUnited States Department of Energy (DOE) [DE-SC0016317]
This work was supported by NSF (DBI 1556359 and MCB 1616529), and DOE DE-SC0016317.

7
Cell press
Cambridge
1542-0086
1}, month = {Feb}, pages = {318A-318A}, type = {Meeting Abstract}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2016.11.1723}, author = {Xu, M. Y. and Niessen, K. A. and Deng, Y. T. and Michki, N. S. and Markelz, A. G.} } @conference {288, title = {Global Picosecond Structural Dynamics of Orange Carotenoid Protein in Photo/Chemical Activated Signaling States}, booktitle = {APS 2017 S4.002}, year = {2017}, month = {03/2017}, url = {http://meetings.aps.org/link/BAPS.2017.MAR.S4.2}, author = {Deng, Y. and Xu, M. and Liu, H. and Blankenship, R. and Markelz, A.} } @article {254, title = {Importance of Protein Vibration Directionality on Function}, journal = {Biophysical Journal}, volume = {112}, number = {3}, year = {2017}, note = {Snell, Edward/G-2055-2018
Snell, Edward/0000-0001-8714-3191
1
58th Annual Meeting of the Biophysical-Society
Feb 15-19, 2014
San Francisco, CA
Biophys Soc
}, month = {Feb 3}, pages = {353A-353A}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2016.11.1916}, author = {Niessen, Katherine A. and Xu, Mengyang and Deng, Yanting and Snell, Edward H. and Markelz, Andrea G.} } @article {200, title = {Moving in the right direction: protein vibrations steering function}, journal = {Biophysical Journal}, volume = {112}, number = {5}, year = {2017}, pages = {933-942}, isbn = {0006-3495}, doi = {https://doi.org/10.1016/j.bpj.2016.12.049}, author = {Niessen, Katherine A and Xu, Mengyang and Paciaroni, Alessandro and Orecchini, Andrea and Snell, Edward H and Markelz, Andrea G} } @article {250, title = {Orange Carotenoid Protein Picosecond Dynamics Changes with Photo and Chemical Activation}, journal = {Biophysical Journal}, volume = {112}, number = {3}, year = {2017}, note = {ISI Document Delivery No.: EW3DS
Times Cited: 0
Cited Reference Count: 3
Cited References:
King JD, 2014, FEBS LETT, V588, P4561, DOI 10.1016/j.febslet.2014.10.024
Wilson A, 2006, PLANT CELL, V18, P992, DOI 10.1105/tpc.105.040121
Wilson A, 2008, P NATL ACAD SCI USA, V105, P12075, DOI 10.1073/pnas.0804636105
Deng, Yanting Xu, Mengyang Liu, Haijun Blankenship, Robert E. Markelz, Andrea G.
58th Annual Meeting of the Biophysical-Society
Feb 15-19, 2014
San Francisco, CA
Biophys Soc
Liu, Haijun/0000-0003-0537-0302

14
Cell press
Cambridge
1542-0086
1}, month = {Feb}, pages = {441A-441A}, type = {Meeting Abstract}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2016.11.2355}, author = {Deng, Y. T. and Xu, M. Y. and Liu, H. J. and Blankenship, R. E. and Markelz, A. G.} } @conference {287, title = {Temperature dependence of phonons in photosynthesis proteins}, booktitle = {APS 2017 S4.003}, year = {2017}, url = {http://meetings.aps.org/link/BAPS.2017.MAR.S4.3}, author = {Xu, M. and Myles, D. and Blankenship, R. and Markelz, A.} } @proceedings {246, title = {Anisotropic Absorption Measurements Reveal Protein Dynamical Transition in Intramolecular Vibrations}, year = {2016}, note = {ISI Document Delivery No.: BG7KC
Times Cited: 0
Cited Reference Count: 4
Cited References:
Acbas G, 2014, NAT COMMUN, V5, DOI 10.1038/ncomms4076
Niessen K., 2015, BIOPHYSICAL REV
PETHIG R, 1995, PROTEIN SOLVENT INTE, P265
RUPLEY JA, 1991, ADV PROTEIN CHEM, V41, P37
Xu, Mengyang Niessen, Katherine Michki, Nigel Deng, Yanting Snell, Edward Markelz, A. G.
Irmmw-thz
Proceedings Paper
41st International Conference on Infrared, Millimeter, and Terahertz Waves (IRMMW-THz)
Sep 25-30, 2016
Copenhagen, DENMARK
DTU, IEEE, QMC Instruments, Danish Ctr Laser Infrastructure, DTU Fotonik, Dept Photon Engn, ARL, Carl Sberg Fdn, AF Off Sci Res, Tech Univ Denmark, IEEE Microwave Theory \& Tech Soc, Azpect Photon, Ekspla, Hubner HF Syst Engn, I2S, Laser Quantum, Menlo Syst, Neaspec, Springer, TeraView, Virginia Diodes
Snell, Edward/G-2055-2018
Snell, Edward/0000-0001-8714-3191
345 e 47th st, new york, ny 10017 usa
2162-2027}, publisher = {Ieee}, address = {New York}, abstract = {

Modeling has predicted that intramolecular structural vibrations enables proteins to access functionally important structural change. We show that the vibrational density of states and the isotropic absorption in the terahertz range are only weakly dependent on the protein functional state for several bench marking proteins. At the same time the direction of motions changes dramatically with functional state and with a resulting impact on the anisotropic absorption. Our anisotropic THz microscopy (ATM) measurements confirm this sensitivity. Here we apply the technique to the question of whether the protein dynamical transition (DT) is important to protein function. We find a strong anisotropic resonance at 70 cm(-1) rapidly increases in strength at temperatures above the DT. As these intramolecular vibrations enable protein structure to change conformation, the results suggest function will cease below DT for those proteins that require large scale conformational change.

}, isbn = {978-1-4673-8485-8}, doi = {10.1109/IRMMW-THz.2016.7758347}, author = {Xu, M. Y. and Niessen, K. and Michki, N. and Deng, Y. T. and Snell, E. and Markelz, A. G.} } @conference {546, title = {Direct Measurements of the Long-Range Collective Vibrations of Photoactive Yellow Protein}, booktitle = {30th Anniversary Symposium of The Protein Society}, year = {2016}, address = {Baltimore MD}, abstract = {

Long-range collective vibrations are thought to be crucial to protein functions. In the case of photoactive protein family, modeling suggests the intramolecular vibrations provide an efficient means of energy relaxation[1], feedback for enhancement of chromophore vibrations that promote structural transitions[2] and can assist in charge energy transfer[3]. As a paradigm of this family, photoactive yellow protein (PYP) is a cytoplasmic photocycling protein related to negative phototactic response to blue light in purple photosynthetic bacteria. PYP has a p-coumaric acid chromophore binding to the cysteine residue via a thioester bond, whose vibrations were found to overlap calculated vibrations of the protein scaffold. Using our unique technique of anisotropic terahertz microscopy(ATM)[4], we measure the intramolecular vibrations for PYP for the first time, including cycling between ground and blue shift (pB) states. Room temperature ATM measurements are performed in the dark and with continuous wave illumination at 488nm, resulting in a steady pB state with approximately 5\% population conversion. In pB state, we find an overall decrease in the strength of resonant band in frequency range of 30-60 cm-1. Our calculated spectra using quasi-harmonic analysis indicate that our measurements are dominated by the protein vibrations, rather than the pCA chromophore, allowing us to characterize how the scaffold dynamics changes with functional states and mutations.

1. Levantino, M., et al. Nat Commun, 2015. 6.

2. Mataga, N., et al. Chem. Phys. Lett., 2002. 352(3-4): p. 220-225.

3. Fokas, A.S., et al. Photosynth. Res., 2014. 122

}, doi = {10.1002/pro.3026}, url = {https://onlinelibrary.wiley.com/doi/10.1002/pro.3026}, author = {Deng, Yanting and Xu, Mengyang and Niessen, Katherine A. and Schmidt, Marius and Markelz, Andrea G.} } @article {242, title = {Modulated orientation-sensitive terahertz spectroscopy}, journal = {Photonics Research}, volume = {4}, number = {3}, year = {2016}, note = {ISI Document Delivery No.: DM9BJ
Times Cited: 6
Cited Reference Count: 40
Cited References:
Acbas G, 2014, NAT COMMUN, V5, DOI 10.1038/ncomms4076
Aguilar RV, 2012, PHYS REV LETT, V108, DOI 10.1103/PhysRevLett.108.087403
Aschaffenburg DJ, 2012, APPL PHYS LETT, V100, DOI 10.1063/1.4729148
Bahar I, 2005, CURR OPIN STRUC BIOL, V15, P586, DOI 10.1016/j.sbi.2005.08.007
Benkovic SJ, 2003, SCIENCE, V301, P1196, DOI 10.1126/science.1085515
Boehr DD, 2006, CHEM REV, V106, P3055, DOI 10.1021/cr050312q
Chen JY, 2005, PHYS REV E, V72, DOI 10.1103/PhysRevE.72.040901
Chen Q, 1999, APPL PHYS LETT, V74, P3435, DOI 10.1063/1.124119
Daniel RM, 2003, ANNU REV BIOPH BIOM, V32, P69, DOI 10.1146/annurev.biophys.32.110601.142445
Diehl M, 1997, BIOPHYS J, V73, P2726, DOI 10.1016/S0006-3495(97)78301-2
Ebbinghaus S, 2007, P NATL ACAD SCI USA, V104, P20749, DOI 10.1073/pnas.0709207104
Falconer RJ, 2012, J INFRARED MILLIM TE, V33, P973, DOI 10.1007/s10762-012-9915-9
Fan ST, 2014, J PHYS D APPL PHYS, V47, DOI 10.1088/0022-3727/47/37/374009
Frauenfelder H, 2006, P NATL ACAD SCI USA, V103, P15469, DOI 10.1073/pnas.0607168103
Gabel F, 2002, Q REV BIOPHYS, V35, P327, DOI 10.1017/S0033583502003840
George DK, 2012, J OPT SOC AM B, V29, P1406, DOI 10.1364/JOSAB.29.001406
Giraud G, 2003, BIOPHYS J, V85, P1903, DOI 10.1016/S0006-3495(03)74618-9
Hammes GG, 2011, BIOCHEMISTRY-US, V50, P10422, DOI 10.1021/bi201486f
Jackson J.D., 1975, CLASSICAL ELECTRODYN
Jenkins GS, 2010, REV SCI INSTRUM, V81, DOI 10.1063/1.3480554
Jepsen PU, 2007, CHEM PHYS LETT, V442, P275, DOI 10.1016/j.cplett.2007.05.112
Karplus M, 2005, P NATL ACAD SCI USA, V102, P6679, DOI 10.1073/pnas.0408930102
Kim SJ, 2008, ANGEW CHEM INT EDIT, V47, P6486, DOI 10.1002/anie.200802281
Kindt JT, 1996, J PHYS CHEM-US, V100, P10373, DOI 10.1021/jp960141g
King MD, 2010, J PHYS CHEM A, V114, P7127, DOI 10.1021/jp101935n
Kroll J, 2007, VIB SPECTROSC, V43, P324, DOI 10.1016/j.vibspec.2006.03.010
Leitner DM, 2008, HFSP J, V2, P314, DOI 10.2976/1.2976661
Li M, 2011, OPT LETT, V36, P3633, DOI 10.1364/OL.36.003633
Liu D, 2008, PHYS REV LETT, V101, DOI 10.1103/PhysRevLett.101.135501
Niessen Katherine A, 2015, Biophys Rev, V7, P201, DOI 10.1007/s12551-015-0168-4
PETHIG R, 1995, PROTEIN SOLVENT INTE, P265
Planken PCM, 2001, J OPT SOC AM B, V18, P313, DOI 10.1364/JOSAB.18.000313
Rheinstadter MC, 2009, PHYS REV LETT, V103, DOI 10.1103/PhysRevLett.103.128104
RUPLEY JA, 1991, ADV PROTEIN CHEM, V41, P37
Singh R, 2012, J PHYS CHEM A, V116, P10359, DOI 10.1021/jp307288r
TORGESEN JL, 1964, SCIENCE, V146, P53, DOI 10.1126/science.146.3640.53
Vinh NQ, 2011, J AM CHEM SOC, V133, P8942, DOI 10.1021/ja200566u
Walther M, 2003, CHEM PHYS, V288, P261, DOI 10.1016/S0301-0104(03)00031-4
Xu J, 2006, J PHYS CHEM B, V110, P24255, DOI 10.1021/jp064830w
Yasumatsu N, 2012, REV SCI INSTRUM, V83, DOI 10.1063/1.3683570
Singh, Rohit George, Deepu Koshy Bae, Chejin Niessen, K. A. Markelz, A. G.
George, Deepu/J-9882-2014
George, Deepu/0000-0003-0021-0705
National Science Foundation (NSF)National Science Foundation (NSF) [DBI2959989]; University at Buffalo (UB) [1126960-1-68255]; Los Alamos National Laboratory (LANL)United States Department of Energy (DOE)Los Alamos National Laboratory [1125895-1-71842]; Direct For Biological SciencesNational Science Foundation (NSF)NSF - Directorate for Biological Sciences (BIO) [1556359] Funding Source: National Science Foundation; Div Of Biological InfrastructureNational Science Foundation (NSF)NSF - Directorate for Biological Sciences (BIO) [1556359] Funding Source: National Science Foundation
National Science Foundation (NSF) (DBI2959989); University at Buffalo (UB) (Holm Fund 1126960-1-68255); Los Alamos National Laboratory (LANL) (Molecular Crystal Studies 1125895-1-71842).
6

26
Optical soc amer
Washington}, month = {Jun}, pages = {A1-A8}, type = {Article}, abstract = {

Intramolecular vibrations of large macromolecules reside in the terahertz range. In particular, protein vibrations are closely spaced in frequency, resulting in a nearly continuous vibrational density of states. This density of vibrations interferes with the identification of specific absorption lines and their subsequent association with specific functional motions. This challenge is compounded with the absorption being dominated by the solvent and local relaxational motions. A strategy for removing the isotropic relaxational loss and isolating specific vibrations is to use aligned samples and polarization-sensitive measurements. Here, we demonstrate a technique to rapidly attain the anisotropic resonant absorbance using terahertz time domain spectroscopy and a spinning sample. The technique, modulated orientation-sensitive terahertz spectroscopy (MOSTS), has a nonzero signal only for anisotropic samples, as demonstrated by a comparison between a silicon wafer and a wire grid polarizer. For sucrose and oxalic acid molecular crystals, the MOSTS response is in agreement with modeled results for the intermolecular vibrations. Further, we demonstrate that, even in the presence of a large relaxational background, MOSTS isolates underlying vibrational resonances. (C) 2016 Chinese Laser Press

}, keywords = {absorption-spectroscopy, dynamics, enzyme catalysis, low-frequency modes, lysozyme, neutron-scattering, Optics, perspective, polarization modulation, proteins, water}, isbn = {2327-9125}, doi = {https://doi.org/10.1364/PRJ.4.0000A1}, author = {Singh, R. and George, D. K. and Bae, C. J. and Niessen, K. A. and Markelz, A. G.} } @conference {547, title = { The Role of Dynamical Transition in Protein Function: Coupling of Protein Collective Vibrations and Water Dynamics}, booktitle = {30th Anniversary Symposium of The Protein Society}, year = {2016}, address = {Baltimore, MD}, abstract = {

Computational simulations have revealed protein collective vibrations prompt structural rearrangements to accomplish biological function. However, the biological importance of collective vibrations has not been experimentally demonstrated. The attempts have been hampered by the inability to distinguish localized water or side-chain relaxational motions from protein long-range vibrations using conventional techniques. The dynamical transition (DT), extensively observed using X-ray, neutron scattering, NMR and terahertz techniques [1,2], describes a rapid increase in the temperature-dependent dynamics of critically hydrated proteins above \~{}220 K, and has been attributed to thermally activated solvent motions. While some proteins lose function below the specific temperature, others do not. We suggest the difference arises from the nature of the required motions for function. Specifically, functional motions enabled by long-range vibrations will be vulnerable to DT, which require surrounding solvent to be sufficiently mobile. We explored the coupling of protein vibrations to solvent dynamics by applying a recently developed technique, anisotropy terahertz microscopy [3], to directly measure the collective vibrations for lysozyme and investigate the temperature dependence in 150-300 K range. We find long-range intramolecular vibrations occur at 220K and rapidly increase in strength with increasing temperature, consistent with enhanced access above the DT. The results suggest collective vibrations are slaved to DT, and those proteins with function reliant on these motions will cease function below DT.

1. Doster,W., et al. Phys.Rev.Lett., 2010.104(9):098101.

2. Niessen,K., et al. Biophys.Rev., 2015.7,201.

3. Acbas,G., et al. Nat.Commun., 2014.5,3076.

}, doi = {10.1002/pro.3026}, url = {https://onlinelibrary.wiley.com/doi/10.1002/pro.3026}, author = {Xu, Mengyang and Niessen, Katherine and Deng, Yanting and Michki, Nigel and Snell, Edward and Markelz, Andrea} } @article {255, title = {Terahertz optical measurements of correlated motions with possible allosteric function}, journal = {Biophysical Reviews}, volume = {7}, number = {2}, year = {2015}, note = {19}, month = {2015-Jun}, pages = {201-216}, abstract = {

A suggested mechanism for allosteric response is the distortion of the energy landscape with agonist binding changing the protein structure{\textquoteright}s access to functional configurations. Intramolecular vibrations are indicative of the energy landscape and may have trajectories that enable functional conformational change. Here, we discuss the development of an optical method to measure the intramolecular vibrations in proteins, namely, crystal anisotropy terahertz microscopy, and the various approaches which can be used to identify the spectral data with specific structural motions.

}, isbn = {1867-2450}, doi = {https://dx.doi.org/10.1007\%2Fs12551-015-0168-4}, author = {Niessen, Katherine A. and Xu, Mengyang and Markelz, A. G.} } @article {290, title = {Terahertz Optical Measurements of Correlated Motions with Possible Allosteric Function}, journal = {Biophysical Journal}, volume = {7}, year = {2015}, month = {04/2015}, pages = {201{\textendash}216}, doi = {10.1007/s12551-015-0168-4}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5425745/}, author = {Niessen, K. A. and Xu, M. and Markelz, A. G.} } @proceedings {240, title = {Measurements and Calculations of Protein Intramolecular Vibrations in the THz Range}, year = {2014}, note = {ISI Document Delivery No.: BF0IL
Times Cited: 0
Cited Reference Count: 13
Cited References:
Acbas G, 2014, NAT COMMUN, V5, DOI 10.1038/ncomms4076
Balog E, 2004, PHYS REV LETT, V93, DOI 10.1103/PhysRevLett.93.028103
Best RB, 2012, J CHEM THEORY COMPUT, V8, P3257, DOI 10.1021/ct300400x
BROOKS BR, 1983, J COMPUT CHEM, V4, P187, DOI 10.1002/jcc.540040211
BRUCCOLERI RE, 1986, BIOPOLYMERS, V25, P1767, DOI 10.1002/bip.360250916
CHEETHAM JC, 1992, J MOL BIOL, V224, P613, DOI 10.1016/0022-2836(92)90548-X
Dong J, 1999, ACTA CRYSTALLOGR D, V55, P745, DOI 10.1107/S0907444998016047
Guo JN, 2014, BIOCHEMISTRY-US, V53, P2855, DOI 10.1021/bi500238q
Hammes-Schiffer S, 2006, ANNU REV BIOCHEM, V75, P519, DOI 10.1146/annurev.biochem.75.103004.142800
Henzler-Wildman KA, 2007, NATURE, V450, P838, DOI 10.1038/nature06410
Jo S, 2008, J COMPUT CHEM, V29, P1859, DOI 10.1002/jcc.20945
PERUTZ MF, 1970, NATURE, V228, P726, DOI 10.1038/228726a0
TEETER MM, 1990, J PHYS CHEM-US, V94, P8091, DOI 10.1021/j100384a021
Niessen, Katherine A. Snell, Edward Markelz, A. G.
Irmmw-thz
Proceedings Paper
39th International Conference on Infrared, Millimeter, and Terahertz waves (IRMMW-THz)
Sep 14-19, 2014
Tucson, AZ
THORLABS, Tydex, TOPTICA Photon, Bruker, Gentec EO, Lake Shore Cryotron, Ekspla, Zomega, TeraSense, Insight Product, Emcore, QMC Instruments, TeraView, NeaSpec, Advantest, MenloSystems, Traycer, Microtech Instruments Inc, LongWave Photon, Virginia Diodes Inc, ASU, MTT S, Journal Infrared Millimeter \& Tera Hertz Waves, Tera Hertz Sci \& Technol, Army Res Off
Snell, Edward/G-2055-2018
Snell, Edward/0000-0001-8714-3191
345 e 47th st, new york, ny 10017 usa
2162-2027}, publisher = {Ieee}, address = {New York}, abstract = {

We report the calculations and measurements of intramolecular vibrational modes and their dependence on inhibitor binding in the THz range. We see an increase in anisotropic THz absorption at low frequency with inhibitor binding in both the measurements and calculations. This surprising result suggests an increase in flexibility with binding. We will discuss the possible reasons for this discrepancy.

}, keywords = {charmm}, isbn = {978-1-4799-3877-3}, doi = {10.1109/IRMMW-THz.2014.6956080}, author = {Niessen, K. A. and Snell, E. and Markelz, A. G.} } @article {219, title = {Optical measurements of long-range protein vibrations}, journal = {Nature Communications}, volume = {5}, year = {2014}, note = {ISI Document Delivery No.: AA4RQ
Times Cited: 101
Cited Reference Count: 48
Cited References:
AUSTIN RH, 1989, PHYS REV LETT, V62, P1912, DOI 10.1103/PhysRevLett.62.1912
Bahar I, 2005, CURR OPIN STRUC BIOL, V15, P586, DOI 10.1016/j.sbi.2005.08.007
Balabin IA, 2000, SCIENCE, V290, P114, DOI 10.1126/science.290.5489.114
Balog E, 2004, PHYS REV LETT, V93, DOI 10.1103/PhysRevLett.93.028103
Barth A, 2002, Q REV BIOPHYS, V35, P369, DOI 10.1017/S0033583502003815
Benkovic SJ, 2003, SCIENCE, V301, P1196, DOI 10.1126/science.1085515
Brooks BR, 2009, J COMPUT CHEM, V30, P1545, DOI 10.1002/jcc.21287
BROOKS BR, 1983, J COMPUT CHEM, V4, P187, DOI 10.1002/jcc.540040211
Brooks CL, 1988, PROTEINS THEORETICAL
Chen JY, 2007, APPL PHYS LETT, V90, DOI 10.1063/1.2748852
Chen JY, 2005, PHYS REV E, V72, DOI 10.1103/PhysRevE.72.040901
Ding T, 2012, VIB SPECTROSC, V61, P144, DOI 10.1016/j.vibspec.2012.02.020
GENZEL L, 1976, BIOPOLYMERS, V15, P219, DOI 10.1002/bip.1976.360150115
George DK, 2013, IEEE T THZ SCI TECHN, V3, P288, DOI 10.1109/TTHZ.2013.2256233
GRISCHKOWSKY D, 1990, J OPT SOC AM B, V7, P2006, DOI 10.1364/JOSAB.7.002006
Hafner J, 2011, J CHEM PHYS, V135, DOI 10.1063/1.3646312
Hammes GG, 2002, BIOCHEMISTRY-US, V41, P8221, DOI 10.1021/bi0260839
He YF, 2011, BIOPHYS J, V100, P1058, DOI 10.1016/j.bpj.2010.12.3731
KACHALOVA GS, 1991, FEBS LETT, V284, P91, DOI 10.1016/0014-5793(91)80769-Y
Karplus M, 2005, P NATL ACAD SCI USA, V102, P6679, DOI 10.1073/pnas.0408930102
Knab J, 2006, BIOPHYS J, V90, P2576, DOI 10.1529/biophysj.105.069088
Knab JR, 2010, APPL PHYS LETT, V97, DOI 10.1063/1.3467192
LEVY RM, 1984, J PHYS CHEM-US, V88, P4233, DOI 10.1021/j150663a009
Lipps F, 2012, PHYS CHEM CHEM PHYS, V14, P6375, DOI 10.1039/c2cp23760a
Liu D, 2008, PHYS REV LETT, V101, DOI 10.1103/PhysRevLett.101.135501
MacKerell AD, 1998, J PHYS CHEM B, V102, P3586, DOI 10.1021/jp973084f
Markelz AG, 2008, IEEE J SEL TOP QUANT, V14, P180, DOI 10.1109/JSTQE.2007.913424
Meinhold L, 2007, PHYS REV LETT, V99, DOI 10.1103/PhysRevLett.99.138101
Meinhold L, 2007, PROTEINS, V66, P941, DOI 10.1002/prot.21246
Mittleman D.M., 2003, SENSING TERAHERTZ RA
MOELLER KD, 1992, BIOPHYS J, V61, P276, DOI 10.1016/S0006-3495(92)81834-9
Perutz MF, 1998, ANNU REV BIOPH BIOM, V27, P1, DOI 10.1146/annurev.biophys.27.1.1
Planken PCM, 2011, J INFRARED MILLIM TE, V32, P975, DOI 10.1007/s10762-011-9824-3
Rheinstadter MC, 2009, PHYS REV LETT, V103, DOI 10.1103/PhysRevLett.103.128104
Sakai K., 2005, TERAHERTZ OPTOELECTR
Schumacher M, 2002, NATURE, V417, P501, DOI 10.1038/417501a
Siegrist K, 2006, J AM CHEM SOC, V128, P5764, DOI 10.1021/ja058176u
Singh R, 2012, J PHYS CHEM A, V116, P10359, DOI 10.1021/jp307288r
SMITH J, 1990, J CHEM PHYS, V93, P2974, DOI 10.1063/1.458885
SMITH JC, 1991, Q REV BIOPHYS, V24, P227, DOI 10.1017/S0033583500003723
TEETER MM, 1990, J PHYS CHEM-US, V94, P8091, DOI 10.1021/j100384a021
TIDOR B, 1994, J MOL BIOL, V238, P405, DOI 10.1006/jmbi.1994.1300
Tych KM, 2011, J APPL CRYSTALLOGR, V44, P129, DOI 10.1107/S0021889810043372
Urabe H, 1998, BIOPHYS J, V74, P1533, DOI 10.1016/S0006-3495(98)77865-8
Walther M, 2003, CHEM PHYS, V288, P261, DOI 10.1016/S0301-0104(03)00031-4
WU Q, 1995, APPL PHYS LETT, V67, P3523, DOI 10.1063/1.114909
Xie AH, 2002, PHYS REV LETT, V88, DOI 10.1103/PhysRevLett.88.018102
Xu J, 2006, J PHYS CHEM B, V110, P24255, DOI 10.1021/jp064830w
Acbas, Gheorghe Niessen, Katherine A. Snell, Edward H. Markelz, A. G.
Snell, Edward/G-2055-2018
Snell, Edward/0000-0001-8714-3191; Markelz, Andrea/0000-0003-0443-4319
National Science Foundation MRIboolean AND2 grant [DBI2959989]
We thank Yunfen He and Benjamin Keen for their assistance with calculations. All calculations performed using facilities provided by The Center for Computational Research, SUNY, Buffalo. We thank the National Science Foundation MRI boolean AND 2 grant DBI2959989 for support.
101
4
108
Nature publishing group
London}, month = {Jan}, pages = {7}, type = {Article}, abstract = {

Protein biological function depends on structural flexibility and change. From cellular communication through membrane ion channels to oxygen uptake and delivery by haemoglobin, structural changes are critical. It has been suggested that vibrations that extend through the protein play a crucial role in controlling these structural changes. While nature may utilize such long-range vibrations for optimization of biological processes, bench-top characterization of these extended structural motions for engineered biochemistry has been elusive. Here we show the first optical observation of long-range protein vibrational modes. This is achieved by orientation-sensitive terahertz near-field microscopy measurements of chicken egg white lysozyme single crystals. Underdamped modes are found to exist for frequencies \>10 cm(-1). The existence of these persisting motions indicates that damping and intermode coupling are weaker than previously assumed. The methodology developed permits protein engineering based on dynamical network optimization.

}, keywords = {absorption, crystals, dynamics, frequency raman-spectra, hydration, lysozyme, motions, Science \& Technology - Other Topics, sensitivity, simulations, spectroscopy}, isbn = {2041-1723}, doi = {https://doi.org/10.1038/ncomms4076}, author = {Acbas, G. and Niessen, K. A. and Snell, E. H. and Markelz, A. G.} } @proceedings {245, title = {Probing the Stability of Fluorescent Proteins by Terahertz Spectroscopy}, year = {2014}, note = {ISI Document Delivery No.: BF0IL
Times Cited: 0
Cited Reference Count: 7
Cited References:
Dean KM, 2011, BIOPHYS J, V101, P961, DOI 10.1016/j.bpj.2011.06.055
He YF, 2011, BIOPHYS J, V100, P1058, DOI 10.1016/j.bpj.2010.12.3731
Helms V, 2007, CHEMPHYSCHEM, V8, P23, DOI 10.1002/cphc.200600298
Leu BM, 2008, BIOPHYS J, V95, P5874, DOI 10.1529/biophysj.108.138198
Markelz AG, 2007, CHEM PHYS LETT, V442, P413, DOI 10.1016/j.cplett.2007.05.080
Nagy A, 2004, THERMOCHIM ACTA, V410, P161, DOI 10.1016/S0040-6031(03)00397-6
Zaccai G, 2000, SCIENCE, V288, P1604, DOI 10.1126/science.288.5471.1604
Xu, Mengyang George, D. K. Jimenez, R. Markelz, A. G.
Irmmw-thz
Proceedings Paper
39th International Conference on Infrared, Millimeter, and Terahertz waves (IRMMW-THz)
Sep 14-19, 2014
Tucson, AZ
THORLABS, Tydex, TOPTICA Photon, Bruker, Gentec EO, Lake Shore Cryotron, Ekspla, Zomega, TeraSense, Insight Product, Emcore, QMC Instruments, TeraView, NeaSpec, Advantest, MenloSystems, Traycer, Microtech Instruments Inc, LongWave Photon, Virginia Diodes Inc, ASU, MTT S, Journal Infrared Millimeter \& Tera Hertz Waves, Tera Hertz Sci \& Technol, Army Res Off
George, Deepu/J-9882-2014
George, Deepu/0000-0003-0021-0705
345 e 47th st, new york, ny 10017 usa
2162-2027}, publisher = {Ieee}, address = {New York}, abstract = {

The higher transmission through tissues of long wavelength light motivates the development of fluorescent proteins with excitation shifted to the red. However red fluorescent proteins (RFPs) are more susceptible to photobleaching than their shorter wavelength counterparts. In particular RFPs are more susceptible to photobleaching [1]. A possible reason for this is a decrease in the structural stability of the beta barrel. Measurements of structural stability include atomic root mean squared displacement \<x(2)\> measured by the X-ray B-factor and neutron quasi elastic scattering. To date, X-ray measurements of RFP{\textquoteright}s do not indicate a structural stability change and systematic scattering studies have not been performed. Using THz dielectric response we examine if the picosecond structural flexibility decreases with increasing FP stability.

}, keywords = {dynamics}, isbn = {978-1-4799-3877-3}, doi = {https://doi.org/10.1109/IRMMW-THz.2014.6956442}, author = {Xu, M. Y. and George, D. K. and Jimenez, R. and Markelz, A. G.} } @inbook {300, title = {Protein Dielectric Response at Terahertz Frequencies: Correlated and Diffusive Contributions}, booktitle = {Terahertz Biomedical Science and Technology}, volume = {edited by Joo Huik Son }, year = {2014}, publisher = {Taylor and Francis }, organization = {Taylor and Francis }, chapter = {11}, doi = {10.1201/b17060 }, author = {George, D. K. and Markelz, A. G.} } @proceedings {218, title = {Measuring phonons in protein crystals}, volume = {8623}, year = {2013}, note = {ISI Document Delivery No.: BGG42
Times Cited: 0
Cited Reference Count: 5
Cited References:
Bahar I, 2005, CURR OPIN STRUC BIOL, V15, P586, DOI 10.1016/j.sbi.2005.08.007
BROOKS B, 1985, P NATL ACAD SCI USA, V82, P4995, DOI 10.1073/pnas.82.15.4995
BROOKS BR, 1983, J COMPUT CHEM, V4, P187, DOI 10.1002/jcc.540040211
Karplus M, 2005, P NATL ACAD SCI USA, V102, P6679, DOI 10.1073/pnas.0408930102
Planken PCM, 2011, J INFRARED MILLIM TE, V32, P975, DOI 10.1007/s10762-011-9824-3
Acbas, Gheorghe Niessen, Katherine A. George, Deepu K. Snell, Edward Markelz, A. G.
Proceedings Paper
Conference on Ultrafast Phenomena and Nanophotonics XVII
Feb 03-06, 2013
San Francisco, CA
SPIE, Femtolasers Inc
Snell, Edward/G-2055-2018; George, Deepu/J-9882-2014
Snell, Edward/0000-0001-8714-3191; George, Deepu/0000-0003-0021-0705; Markelz, Andrea/0000-0003-0443-4319
National Science Foundation MRI2 [DBI2959989]
We thank the National Science Foundation MRI2 grant DBI2959989 for support.
1000 20th st, po box 10, bellingham, wa 98227-0010 usa
0277-786x
862305}, publisher = {Spie-Int Soc Optical Engineering}, address = {Bellingham}, abstract = {

Using Terahertz near field microscopy we find orientation dependent narrow band absorption features for lysozyme crystals. Here we discuss identification of protein collective modes associated with the observed features. Using normal mode calculations we find good agreement with several of the measured features, suggesting that the modes arise from internal molecular motions and not crystal phonons. Such internal modes have been associated with protein function.

}, keywords = {correlated motions, dynamics, mode, molecular crystals, molecular vibrations, normal modes, phonons, protein dynamics, spectroscopy, Terahertz}, isbn = {978-0-8194-9392-7}, doi = {https://doi.org/10.1117/12.2006275}, author = {Acbas, G. and Niessen, K. A. and George, D. K. and Snell, E. and Markelz, A. G.}, editor = {Betz, M. and Elezzabi, A. Y. and Song, J. J. and Tsen, K. T.} } @article {184, title = {Photoactive yellow protein terahertz response: hydration, heating and intermediate states}, journal = {IEEE Transactions on Terahertz Science and Technology}, volume = {3}, number = {3}, year = {2013}, pages = {288-294}, isbn = {2156-342X}, doi = {https://doi.org/10.1109/TTHZ.2013.2256233}, author = {George, Deepu K and Knab, Joseph R and He, Yunfen and Kumauchi, Masato and Birge, Robert R and Hoff, Wouter D and Markelz, Andrea G} } @inbook {301, title = {Terahertz Spectroscopy of Liquids and Biomolecules}, booktitle = {Terahertz Spectroscopy and Imaging}, year = {2013}, pages = {229-250}, publisher = {Springer-Verlag}, organization = {Springer-Verlag}, chapter = {9}, address = {Berlin-Heidelberg}, doi = {10.1007/978-3-642-29564-5_9}, author = {George, D. K. and Markelz, A. G.} } @article {291, title = {Functional State Dependence of Picosecond Protein Dynamics}, journal = {arXiv:1105.4425}, year = {2012}, url = {http://arxiv.org/0054394}, author = {Chen, J. Y. and George, D. K. and He, Y. and Knab, J. R. and Markelz, A.G.} } @article {233, title = {Hydration and temperature interdependence of protein picosecond dynamics}, journal = {Physical Chemistry Chemical Physics}, volume = {14}, number = {18}, year = {2012}, note = {ISI Document Delivery No.: 928AI
Times Cited: 25
Cited Reference Count: 39
Cited References:
Bonvicini D, 1998, IEEE T DIELECT EL IN, V5, P33, DOI 10.1109/94.660757
BROOKS BR, 1983, J COMPUT CHEM, V4, P187, DOI 10.1002/jcc.540040211
Brovchenko I, 2008, CHEMPHYSCHEM, V9, P2695, DOI 10.1002/cphc.200800662
Chen G, 2008, PHILOS MAG, V88, P3877, DOI 10.1080/14786430802585117
Chen JY, 2005, PHYS REV E, V72, DOI 10.1103/PhysRevE.72.040901
Chen SH, 2006, P NATL ACAD SCI USA, V103, P9012, DOI 10.1073/pnas.0602474103
Ding T, 2011, J PHYS CHEM A, V115, P11559, DOI 10.1021/jp200553d
Doster W, 2010, PHYS REV LETT, V104, DOI 10.1103/PhysRevLett.104.098101
DOSTER W, 1989, NATURE, V337, P754, DOI 10.1038/337754a0
Doster W, 2010, BBA-PROTEINS PROTEOM, V1804, P3, DOI 10.1016/j.bbapap.2009.06.019
Ebbinghaus S, 2007, P NATL ACAD SCI USA, V104, P20749, DOI 10.1073/pnas.0709207104
Frauenfelder H, 2003, P NATL ACAD SCI USA, V100, P8615, DOI 10.1073/pnas.1633688100
GASCOYNE PRC, 1977, J CHEM SOC FARAD T 1, V73, P171, DOI 10.1039/f19777300171
GRISCHKOWSKY D, 1990, J OPT SOC AM B, V7, P2006, DOI 10.1364/JOSAB.7.002006
HARVEY SC, 1972, J PHYS CHEM-US, V76, P2987, DOI 10.1021/j100665a011
He YF, 2008, PHYS REV LETT, V101, DOI 10.1103/PhysRevLett.101.178103
Kauzmann W, 1942, REV MOD PHYS, V14, P0012, DOI 10.1103/RevModPhys.14.12
Khodadadi S, 2010, BBA-PROTEINS PROTEOM, V1804, P15, DOI 10.1016/j.bbapap.2009.05.006
Knab J, 2006, BIOPHYS J, V90, P2576, DOI 10.1529/biophysj.105.069088
Makarov VA, 2000, BIOPHYS J, V79, P2966, DOI 10.1016/S0006-3495(00)76533-7
Markelz AG, 2008, IEEE J SEL TOP QUANT, V14, P180, DOI 10.1109/JSTQE.2007.913424
Markelz AG, 2007, CHEM PHYS LETT, V442, P413, DOI 10.1016/j.cplett.2007.05.080
Oleinikova A, 2005, PHYS REV LETT, V95, DOI 10.1103/PhysRevLett.95.247802
Oleinikova A, 2005, J PHYS CHEM B, V109, P1988, DOI 10.1021/jp045903j
Oleinikova A, 2006, MOL PHYS, V104, P3841, DOI 10.1080/00268970601108229
Paciaroni A, 2008, PHILOS MAG, V88, P4071, DOI 10.1080/14786430802464263
Parak FG, 2003, CURR OPIN STRUC BIOL, V13, P552, DOI 10.1016/j.sbi.2003.09.004
Pawlus S, 2008, PHYS REV LETT, V100, DOI 10.1103/PhysRevLett.100.108103
Roh JH, 2006, BIOPHYS J, V91, P2573, DOI 10.1529/biophysj.106.082214
Roh JH, 2009, BIOPHYS J, V96, P2755, DOI 10.1016/j.bpj.2008.12.3895
Roh JH, 2005, PHYS REV LETT, V95, DOI 10.1103/PhysRevLett.95.038101
RUPLEY JA, 1991, ADV PROTEIN CHEM, V41, P37
Schiro G, 2011, J PHYS CHEM LETT, V2, P2275, DOI 10.1021/jz200797g
Shen YC, 2003, APPL PHYS LETT, V82, P2350, DOI 10.1063/1.1565680
Soderholm S, 2000, J RAMAN SPECTROSC, V31, P995, DOI 10.1002/1097-4555(200011)31:11<995::AID-JRS634>3.0.CO;2-L
Whitmire SE, 2003, BIOPHYS J, V85, P1269, DOI 10.1016/S0006-3495(03)74562-7
WU Q, 1995, APPL PHYS LETT, V67, P3523, DOI 10.1063/1.114909
Zaccai G, 2000, SCIENCE, V288, P1604, DOI 10.1126/science.288.5471.1604
Zhang CF, 2006, J PHYS CHEM B, V110, P23607, DOI 10.1021/jp063545+
Lipps, Ferdinand Levy, Seth Markelz, A. G.
Markelz, Andrea/0000-0003-0443-4319
26

66
Royal soc chemistry
Cambridge
1463-9084}, pages = {6375-6381}, type = {Article}, abstract = {

We investigate the nature of the solvent motions giving rise to the rapid temperature dependence of protein picoseconds motions at 220 K, often referred to as the protein dynamical transition. The interdependence of picoseconds dynamics on hydration and temperature is examined using terahertz time domain spectroscopy to measure the complex permittivity in the 0.2-2.0 THz range for myoglobin. Both the real and imaginary parts of the permittivity over the frequency range measured have a strong temperature dependence at \>0.27 h (g water per g protein), however the permittivity change is strongest for frequencies \<1 THz. The temperature dependence of the real part of the permittivity is not consistent with the relaxational response of the bound water, and may reflect the low frequency protein structural vibrations slaved to the solvent excitations. The hydration necessary to observe the dynamical transition is found to be frequency dependent, with a critical hydration of 0.19 h for frequencies \>1 THz, and 0.27 h for frequencies \<1 THz. The data are consistent with the dynamical transition solvent fluctuations requiring only clusters of similar to 5 water molecules, whereas the enhancement of lowest frequency motions requires a fully spanning water network.

}, keywords = {Chemistry, dielectric-relaxation, fluctuations, inelastic neutron-scattering, lysozyme, myoglobin, percolation, Physics, spectra, spectroscopy, terahertz beams, transition, water}, isbn = {1463-9076}, doi = {https://doi.org/10.1039/C2CP23760A}, author = {Lipps, F. and Levy, S. and Markelz, A. G.} } @article {202, title = {Improved mode assignment for molecular crystals through anisotropic terahertz spectroscopy}, journal = {The Journal of Physical Chemistry A}, volume = {116}, number = {42}, year = {2012}, pages = {10359-10364}, isbn = {1089-5639}, doi = {https://doi.org/10.1021/jp307288r}, author = {Singh, Rohit and George, Deepu Koshy and Benedict, Jason B and Korter, Timothy M and Markelz, Andrea G} } @proceedings {307, title = {Multi-component response in multilayer graphene revealed through terahertz and infrared magneto-spectroscopy}, year = {2012}, month = {9/2012}, address = {Wollongong, Australia}, doi = {10.1109/IRMMW-THz.2012.6380102}, author = {Ellis, C. T. and Stier, A. V. and George, D. K. and Tischler, J. G. and Glaser, E. R. and Myers-Ward, R. L. and Tedesco, J. L. and Eddy, C. R. and Gaskill, D. K. and Markelz, A. G. and Cerne, J.} } @proceedings {220, title = {Orientation Sensitive Terahertz Resonances Observed in Protein Crystals}, year = {2012}, note = {ISI Document Delivery No.: BJT74
Times Cited: 1
Cited Reference Count: 15
Cited References:
Arora K, 2007, P NATL ACAD SCI USA, V104, P18496, DOI 10.1073/pnas.0706443104
Bahar I, 2005, CURR OPIN STRUC BIOL, V15, P586, DOI 10.1016/j.sbi.2005.08.007
Balu R, 2008, BIOPHYS J, V94, P3217, DOI 10.1529/biophysj.107.105163
BROOKS B, 1985, P NATL ACAD SCI USA, V82, P4995, DOI 10.1073/pnas.82.15.4995
Goodey NM, 2008, NAT CHEM BIOL, V4, P474, DOI 10.1038/nchembio.98
Hammes-Schiffer S, 2006, ANNU REV BIOCHEM, V75, P519, DOI 10.1146/annurev.biochem.75.103004.142800
Jarymowycz VA, 2006, CHEM REV, V106, P1624, DOI 10.1021/cr040421p
Karplus M, 2005, P NATL ACAD SCI USA, V102, P6679, DOI 10.1073/pnas.0408930102
Knab JR, 2010, APPL PHYS LETT, V97, DOI 10.1063/1.3467192
Lange OF, 2008, SCIENCE, V320, P1471, DOI 10.1126/science.1157092
Liu D, 2008, PHYS REV LETT, V101, DOI 10.1103/PhysRevLett.101.135501
Mellinger JS, 2007, J PHYS CHEM A, V111, P10977, DOI 10.1021/jp074975i
Planken PCM, 2011, J INFRARED MILLIM TE, V32, P975, DOI 10.1007/s10762-011-9824-3
Rheinstadter MC, 2009, PHYS REV LETT, V103, DOI 10.1103/PhysRevLett.103.128104
Tych KM, 2011, J APPL CRYSTALLOGR, V44, P129, DOI 10.1107/S0021889810043372
Acbas, Gheorghe Snell, Edward Markelz, A. G.
Irmmw-thz
Proceedings Paper
37th International Conference on Infrared, Millimeter, and Terahertz Waves (IRMMW-THz)
Sep 23-28, 2012
Univ Wollongong, Wollongong, AUSTRALIA
IEEE, USN, Off Naval Res Sci \& Technol, ETRI, UOW, Sch Engn Phys, Ctr Ultrahigh Bandwidth Devices Opt Syst, Victoria Suntech Adv Solar Facil, Swinburne, Ctr Micro Photon, Edinburgh Photon, Tydex, TRAS Inc, Inst Photon \& Opt Sci, LakeShore, Australian Synchrotron, CSIRO, Univ Wollongong, Inst Superconducting \& Elect Mat, Ctr Med Radiat Phys, Univ Sydney, IEEE Microwave Theory \& Tech Soc
Snell, Edward/G-2055-2018
Snell, Edward/0000-0001-8714-3191
345 e 47th st, new york, ny 10017 usa
2162-2027}, publisher = {Ieee}, address = {New York}, abstract = {

A method is presented for measuring anisotropic THz response for small crystals, Crystal Anisotropy Terahertz Microscopy (CATM). Sucrose CATM measurements find the expected anisotropic phonon resonances. CATM measurements of protein crystals find the expected broadband water absorption is suppressed and strong orientation and hydration dependent resonant features.

}, keywords = {dynamics, mode}, isbn = {978-1-4673-1597-5}, doi = {https://doi.org/10.1109/IRMMW-THz.2012.6380168}, author = {Acbas, G. and Snell, E. and Markelz, A. G.} } @inbook {302, title = {Terahertz / Far Infrared Spectroscopy: Protein Dynamics}, booktitle = {Encyclopedia of Biophysics}, volume = {ed. Gordon C. K. Roberts}, year = {2012}, publisher = {Springer}, organization = {Springer}, author = {Markelz, A. G.} } @article {186, title = {Terahertz magneto-optical polarization modulation spectroscopy}, journal = {JOSA BJOSA B}, volume = {29}, number = {6}, year = {2012}, pages = {1406-1412}, isbn = {1520-8540}, doi = {https://doi.org/10.1364/JOSAB.29.001406}, author = {George, Deepu K and Stier, Andreas V and Ellis, Chase T and McCombe, Bruce D and {\v C}erne, John and Markelz, Andrea G} } @article {221, title = {Terahertz Response and Colossal Kerr Rotation from the Surface States of the Topological Insulator Bi2Se3}, journal = {Physical Review Letters}, volume = {108}, number = {8}, year = {2012}, note = {ISI Document Delivery No.: 896NY
Times Cited: 164
Cited Reference Count: 35
Cited References:
Akhmerov AR, 2009, PHYS REV LETT, V102, DOI 10.1103/PhysRevLett.102.216404
Alpichshev Z, 2010, PHYS REV LETT, V104, DOI 10.1103/PhysRevLett.104.016401
Analytis JG, 2010, PHYS REV B, V81, DOI 10.1103/PhysRevB.81.205407
Bansal N., ARXIV11045709
Benia HM, 2011, PHYS REV LETT, V107, DOI 10.1103/PhysRevLett.107.177602
Bianchi M, 2010, NAT COMMUN, V1, DOI 10.1038/ncomms1131
Butch NP, 2010, PHYS REV B, V81, DOI 10.1103/PhysRevB.81.241301
Chen J, 2011, PHYS REV B, V83, DOI 10.1103/PhysRevB.83.241304
Chen YL, 2009, SCIENCE, V325, P178, DOI 10.1126/science.1173034
Essin AM, 2009, PHYS REV LETT, V102, DOI 10.1103/PhysRevLett.102.146805
Eto K, 2010, PHYS REV B, V81, DOI 10.1103/PhysRevB.81.195309
Fu L, 2007, PHYS REV B, V76, DOI 10.1103/PhysRevB.76.045302
Fu L, 2008, PHYS REV LETT, V100, DOI 10.1103/PhysRevLett.100.096407
Hsieh D, 2008, NATURE, V452, P970, DOI 10.1038/nature06843
Hsieh D, 2009, NATURE, V460, P1101, DOI 10.1038/nature08234
Jenkins GS, 2010, PHYS REV B, V82, DOI 10.1103/PhysRevB.82.125120
King PDC, 2011, PHYS REV LETT, V107, DOI 10.1103/PhysRevLett.107.096802
LaForge AD, 2010, PHYS REV B, V81, DOI 10.1103/PhysRevB.81.125120
Lan YP, 2011, PHYS REV B, V83, DOI 10.1103/PhysRevB.83.205109
Maciejko J, 2010, PHYS REV LETT, V105, DOI 10.1103/PhysRevLett.105.166803
Moore JE, 2007, PHYS REV B, V75, DOI 10.1103/PhysRevB.75.121306
Qi XL, 2008, PHYS REV B, V78, DOI 10.1103/PhysRevB.78.195424
Qu DX, 2010, SCIENCE, V329, P821, DOI 10.1126/science.1189792
Roushan P, 2009, NATURE, V460, P1106, DOI 10.1038/nature08308
Roy R, 2009, PHYS REV B, V79, DOI 10.1103/PhysRevB.79.195322
Steinberg H, 2011, PHYS REV B, V84, DOI 10.1103/PhysRevB.84.233101
Sushkov AB, 2010, PHYS REV B, V82, DOI 10.1103/PhysRevB.82.125110
THOULESS DJ, 1982, PHYS REV LETT, V49, P405, DOI 10.1103/PhysRevLett.49.405
Tkachov G, 2011, PHYS REV B, V84, DOI 10.1103/PhysRevB.84.035405
Tse WK, 2010, PHYS REV B, V82, DOI 10.1103/PhysRevB.82.161104
Tse WK, 2010, PHYS REV LETT, V105, DOI 10.1103/PhysRevLett.105.057401
VONKLITZING K, 1980, PHYS REV LETT, V45, P494, DOI 10.1103/physrevlett.45.494
Xia Y, 2009, NAT PHYS, V5, P398, DOI 10.1038/NPHYS1274
Xiong J., PHYSICA A E IN PRESS
Zhang XA, 2010, PHYS REV B, V82, DOI 10.1103/PhysRevB.82.245107
Aguilar, R. Valdes Stier, A. V. Liu, W. Bilbro, L. S. George, D. K. Bansal, N. Wu, L. Cerne, J. Markelz, A. G. Oh, S. Armitage, N. P.
George, Deepu/J-9882-2014; Aguilar, Rolando Valdes/A-6637-2012; Liu, Wei/H-5999-2012; Wu, Liang/C-8715-2015
George, Deepu/0000-0003-0021-0705; Aguilar, Rolando Valdes/0000-0002-4321-4792; Wu, Liang/0000-0003-1696-7809; Markelz, Andrea/0000-0003-0443-4319
"Institute for Quantum Matter" DOE [DE-FG02-08ER46544]; Gordon and Betty Moore FoundationGordon and Betty Moore Foundation; NSFNational Science Foundation (NSF) [MRI-R2 0959989, DMR-1006078, DMR-0845464]; IAMDN of Rutgers University; ONROffice of Naval Research [N000140910749]; Division Of Materials ResearchNational Science Foundation (NSF)NSF - Directorate for Mathematical \& Physical Sciences (MPS) [0845464] Funding Source: National Science Foundation
The authors would like to thank H. D. Drew, J. Hancock, Z. Hao, G. S. Jenkins, A. Kuzmenko, A. MacDonald, N. A. Mecholsky, A. J. Pearson, O. Tchernyshyov, W-K. Tse, and Y. Wan for helpful discussions and/or correspondences. Support for the measurements at JHU was provided under the auspices of the "Institute for Quantum Matter" DOE DE-FG02-08ER46544 and the Gordon and Betty Moore Foundation. The work at UB was supported by NSF MRI-R2 0959989 and NSF DMR-1006078. The work at Rutgers was supported by IAMDN of Rutgers University, NSF DMR-0845464 and ONR N000140910749.
166
3
157
Amer physical soc
College pk}, month = {Feb}, pages = {5}, type = {Article}, abstract = {

We report the THz response of thin films of the topological insulator Bi2Se3. At low frequencies, transport is essentially thickness independent showing the dominant contribution of the surface electrons. Despite their extended exposure to ambient conditions, these surfaces exhibit robust properties including narrow, almost thickness-independent Drude peaks, and an unprecedentedly large polarization rotation of linearly polarized light reflected in an applied magnetic field. This Kerr rotation can be as large as 65 degrees and can be explained by a cyclotron resonance effect of the surface states.

}, keywords = {bi2te3, Physics}, isbn = {0031-9007}, doi = {https://doi.org/10.1103/physrevlett.108.087403}, author = {Aguilar, R. V. and Stier, A. V. and Liu, W. and Bilbro, L. S. and George, D. K. and Bansal, N. and Wu, L. and Cerne, J. and Markelz, A. G. and Oh, S. and Armitage, N. P.} } @article {183, title = {Terahertz spectroscopic analysis of peptides and proteins}, journal = {Journal of Infrared, Millimeter, and Terahertz Waves}, volume = {33}, number = {10}, year = {2012}, pages = {973-988}, isbn = {1866-6892}, doi = {https://doi.org/10.1007/s10762-012-9915-9}, author = {Falconer, Robert J and Markelz, Andrea G} } @article {187, title = {Evidence of protein collective motions on the picosecond timescale}, journal = {Biophysical Journal}, volume = {100}, number = {4}, year = {2011}, pages = {1058-1065}, isbn = {0006-3495}, doi = {https://dx.doi.org/10.1016\%2Fj.bpj.2010.12.3731}, author = {He, Yunfen and Chen, J-Y and Knab, Joseph R and Zheng, Wenjun and Markelz, Andrea G} } @proceedings {244, title = {Magneto Optical Polarization Measurements using THz Polarization Modulation Spectroscopy}, year = {2011}, note = {ISI Document Delivery No.: BJT73
Times Cited: 0
Cited Reference Count: 3
Cited References:
Cerne J, 2000, PHYS REV B, V61, P8133, DOI 10.1103/PhysRevB.61.8133
Crassee I, 2011, NAT PHYS, V7, P48, DOI 10.1038/NPHYS1816
Tse WK, 2010, PHYS REV LETT, V105, DOI 10.1103/PhysRevLett.105.057401
Stier, A. V. George, D. Markelz, A. G. Cerne, J.
Irmmw-thz
Proceedings Paper
36th International Conference on Infrared, Millimeter, and Terahertz Waves (IRMMW-THz)
Oct 02-07, 2011
Houston, TX
Rice Univ, IEEE Microwave Theory \& Tech Soc, NASA, California Inst Technol, Jet Prop Lab, Univ Wollongong
George, Deepu/J-9882-2014
George, Deepu/0000-0003-0021-0705
345 e 47th st, new york, ny 10017 usa
2162-2027}, publisher = {Ieee}, address = {New York}, abstract = {

We report a new broad band technique for rapidly measuring the complex Faraday and Kerr rotations in materials such as topological insulators and graphene, combining the distinct advantages of THz time domain spectroscopy and polarization modulation techniques. The performance of the system is demonstrated using GaAs two dimensional electron gas in a magnetic field.

}, isbn = {978-1-4577-0509-0}, doi = {10.1364/JOSAB.29.001406}, author = {Stier, A. V. and George, D. and Markelz, A. G. and Cerne, J.}, editor = {Koch, M.} } @conference {330, title = { Characterization of Phonons in Molecular Crystals }, booktitle = {Frontiers in Optics 2010}, year = {2010}, month = {10/2010}, address = {Rochester}, abstract = {

We demonstrate a new technique for characterizing the phonons in molecular crystals, Modulated Orientation Sensitive Terahertz Spectroscopy (MOSTS). The technique suppresses crystal defects and solvent contributions, and enhances contributions due to molecular structure and anisotropy.

}, doi = {10.1364/FIO.2010.JWA19}, author = {Singh, R. and George, D. and Markelz, A. G.} } @article {274, title = {Hydration Effects on Energy Relaxation of Ferric Cytochrome C Films after Soret-Band Photoexcitation}, journal = {Journal of Physical Chemistry B}, volume = {114}, number = {46}, year = {2010}, note = {ISI Document Delivery No.: 681CT
Times Cited: 3
Cited Reference Count: 87
Cited References:
Bagchi B, 2005, CHEM REV, V105, P3197, DOI 10.1021/cr020661+
BAI YW, 1995, SCIENCE, V269, P192, DOI 10.1126/science.7618079
Bertini I, 2000, J MAGN RESON, V147, P1, DOI 10.1006/jmre.2000.2131
Bizzarri AR, 2002, J PHYS CHEM B, V106, P6617, DOI 10.1021/jp020100m
BONE S, 1985, J MOL BIOL, V181, P323, DOI 10.1016/0022-2836(85)90096-8
Bone S, 2008, J PHYS CHEM B, V112, P10071, DOI 10.1021/jp8009782
BULL HB, 1968, ARCH BIOCHEM BIOPHYS, V128, P488, DOI 10.1016/0003-9861(68)90055-6
BULL HB, 1970, ARCH BIOCHEM BIOPHYS, V137, P299, DOI 10.1016/0003-9861(70)90443-1
CHAMPION PM, 1981, J CHEM PHYS, V75, P490, DOI 10.1063/1.441846
Chen EF, 1999, J AM CHEM SOC, V121, P3811, DOI 10.1021/ja983169+
Chen JY, 2005, PHYS REV E, V72, DOI 10.1103/PhysRevE.72.040901
Cianetti S, 2004, J AM CHEM SOC, V126, P13932, DOI 10.1021/ja046442i
Dragomir I, 2007, BIOPHYS J, V92, P989, DOI 10.1529/biophysj.106.095976
Eaton W A, 1981, Methods Enzymol, V76, P175
EATON WA, 1967, J CHEM PHYS, V46, P2533, DOI 10.1063/1.1841081
EATON WA, 1968, J CHEM PHYS, V49, P985, DOI 10.1063/1.1670263
Ehrler OT, 2009, ACCOUNTS CHEM RES, V42, P769, DOI 10.1021/ar800263z
FERRAND M, 1993, P NATL ACAD SCI USA, V90, P9668, DOI 10.1073/pnas.90.20.9668
GASCOYNE PRC, 1977, J CHEM SOC FARAD T 1, V73, P171, DOI 10.1039/f19777300171
GIBSON QH, 1957, NATURE, V180, P1416, DOI 10.1038/1801416b0
Gregory R.B., 1995, PROTEIN SOLVENT INTE
HALLE B, 1981, J AM CHEM SOC, V103, P500, DOI 10.1021/ja00393a004
Halle B, 2004, PHILOS T R SOC B, V359, P1207, DOI 10.1098/rstb.2004.1499
Henchman RH, 2002, PROTEIN SCI, V11, P2080, DOI 10.1110/ps.0214002
Hertel IV, 2006, REP PROG PHYS, V69, P1897, DOI 10.1088/0034-4885/69/6/R06
Jayaram B, 2004, ANNU REV BIOPH BIOM, V33, P343, DOI 10.1146/annurev.biophys.33.110502.140414
Jimenez R, 2002, J PHYS CHEM B, V106, P9172, DOI 10.1021/jp0209648
JONES CM, 1993, P NATL ACAD SCI USA, V90, P11860, DOI 10.1073/pnas.90.24.11860
Joti Y, 2008, BIOPHYS J, V94, P4435, DOI 10.1529/biophysj.107.118042
Jougeward K. A., 1988, J BIOL CHEM, V263, P6027
Kamal JKA, 2004, P NATL ACAD SCI USA, V101, P13411, DOI 10.1073/pnas.0405724101
Kamei T, 2002, BIOPHYS J, V82, P418, DOI 10.1016/S0006-3495(02)75406-4
Kholodenko Y, 2000, CHEM PHYS, V259, P71, DOI 10.1016/S0301-0104(00)00182-8
Kubinec M. G., 1992, CURR OPIN STRUC BIOL, V2, P828
Kumar ATN, 2001, J PHYS CHEM B, V105, P7847, DOI 10.1021/jp0101209
Levy Y, 2004, P NATL ACAD SCI USA, V101, P3325, DOI 10.1073/pnas.0400157101
Levy Y, 2006, ANNU REV BIOPH BIOM, V35, P389, DOI 10.1146/annurev.biophys.35.040405.102134
LI P, 1992, J CHEM PHYS, V97, P3214, DOI 10.1063/1.463008
Lim MH, 1996, J PHYS CHEM-US, V100, P12043, DOI 10.1021/jp9536458
Lowenich D, 2008, PHOTOCHEM PHOTOBIOL, V84, P193, DOI 10.1111/j.1751-1097.2007.00219.x
Makinen M. W., 1983, IRON PORPHYRINS, P41
Manas ES, 1999, J PHYS CHEM B, V103, P6334, DOI 10.1021/jp9908552
MARGOLIASH E., 1966, ADVANCE PROTEIN CHEM, V21, P113, DOI 10.1016/S0065-3233(08)60128-X
MARTIN JL, 1994, METHOD ENZYMOL, V232, P416
MARTIN JL, 1992, ANNU REV BIOPH BIOM, V21, P199, DOI 10.1146/annurev.biophys.21.1.199
MARTIN JL, 1983, P NATL ACAD SCI-BIOL, V80, P173, DOI 10.1073/pnas.80.1.173
Mitra RK, 2007, LANGMUIR, V23, P10224, DOI 10.1021/la7014447
MOORE GR, 1990, CYTOCHROMES EVOLUTIO
Negrerie M, 2006, J PHYS CHEM B, V110, P12766, DOI 10.1021/jp0559377
Nibbering ETJ, 2005, ANNU REV PHYS CHEM, V56, P337, DOI 10.1146/annurev.physchem.56.092503.141314
Oleinikova A, 2007, BIOPHYS J, V93, P2986, DOI 10.1529/biophysj.107.108753
OTTING G, 1989, J AM CHEM SOC, V111, P1871, DOI 10.1021/ja00187a050
Pal SK, 2004, CHEM REV, V104, P2099, DOI 10.1021/cr020689l
Pascher T, 1996, SCIENCE, V271, P1558, DOI 10.1126/science.271.5255.1558
Qiu WH, 2006, P NATL ACAD SCI USA, V103, P13979, DOI 10.1073/pnas.0606235103
Qiu WH, 2005, J PHYS CHEM B, V109, P16901, DOI 10.1021/jp0511754
Raschke TM, 2006, CURR OPIN STRUC BIOL, V16, P152, DOI 10.1016/j.sbi.2006.03.002
Reddy CK, 2001, J MOL BIOL, V314, P619, DOI 10.1006/jmbi.2001.5154
RODRIGUEZ J, 1991, J CHEM PHYS, V94, P6020, DOI 10.1063/1.460439
RUPLEY JA, 1991, ADV PROTEIN CHEM, V41, P37
SCHEJTER A, 1964, BIOCHEMISTRY-US, V3, P1045, DOI 10.1021/bi00896a006
SCHEJTER A, 1984, BIOCHEMISTRY-US, V23, P1081, DOI 10.1021/bi00301a007
SHECHTER E, 1967, BIOPOLYMERS, V5, P788, DOI 10.1002/bip.1967.360050812
Smith JC, 2002, J MOL LIQ, V101, P27, DOI 10.1016/S0167-7322(02)00100-9
Stolow A, 2004, CHEM REV, V104, P1719, DOI 10.1021/cr020683w
Stolow A, 2003, ANNU REV PHYS CHEM, V54, P89, DOI 10.1146/annurev.physchem.54.011002.103809
SUBRAMANIAN S, 1972, BIOPOLYMERS, V11, P1305, DOI 10.1002/bip.1972.360110614
SUTHERLAND JC, 1972, J CHEM PHYS, V57, P76, DOI 10.1063/1.1678020
TAKANO T, 1981, J MOL BIOL, V153, P95, DOI 10.1016/0022-2836(81)90529-5
TAKANO T, 1981, J MOL BIOL, V153, P79, DOI 10.1016/0022-2836(81)90528-3
TALER G, 1995, BIOCHEMISTRY-US, V34, P14209, DOI 10.1021/bi00043a027
TEETER MM, 1991, ANNU REV BIOPHYS BIO, V20, P577, DOI 10.1146/annurev.biophys.20.1.577
Vos MH, 1999, BBA-BIOENERGETICS, V1411, P1, DOI 10.1016/S0005-2728(99)00035-3
Wang W, 2000, J PHYS CHEM B, V104, P10789, DOI 10.1021/jp0008602
WEI YZ, 1994, J PHYS CHEM-US, V98, P6644, DOI 10.1021/j100077a034
Werner JH, 2006, P NATL ACAD SCI USA, V103, P11130, DOI 10.1073/pnas.0604712103
Wilson M. T, 1996, CYTOCHROME C MULTIDI, P611
Ye MP, 2007, BIOPHYS J, V93, P2756, DOI 10.1529/biophysj.107.106799
Ye S, 2007, AIP CONF PROC, V893, P1307, DOI 10.1063/1.2730382
Ye X, 2002, J AM CHEM SOC, V124, P5914, DOI 10.1021/ja017359n
Ye XO, 2003, J PHYS CHEM A, V107, P8156, DOI 10.1021/jp0276799
Yeh SR, 1998, ACCOUNTS CHEM RES, V31, P727, DOI 10.1021/ar970084p
Yokoyama K, 2001, J PHYS CHEM B, V105, P12622, DOI 10.1021/jp011217y
Zang C, 2009, J AM CHEM SOC, V131, P2846, DOI 10.1021/ja8057293
Zelent B, 2004, J PHYS CHEM B, V108, P10317, DOI 10.1021/jp037664q
Zhang LY, 2007, P NATL ACAD SCI USA, V104, P18461, DOI 10.1073/pnas.0707647104
Zhou HX, 2001, BIOPHYS CHEM, V93, P171, DOI 10.1016/S0301-4622(01)00219-8
Ye, Shuji Markelz, Andrea
Ye, Shuji/B-4479-2010
Markelz, Andrea/0000-0003-0443-4319
NSFNational Science Foundation (NSF) [PHY-0349256, DBI-2959989]; University of Science and Technology of China; Fundamental Research Funds for the Central UniversitiesFundamental Research Funds for the Central Universities; National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [21073175]; National Basic Research Program of ChinaNational Basic Research Program of China [2010CB923300]
This work was supported by NSF CAREER Grant PHY-0349256 and NSF MRI-R2 Grant DBI-2959989, the start-up funding from University of Science and Technology of China, the Fundamental Research Funds for the Central Universities, National Natural Science Foundation of China (Grant 21073175), and National Basic Research Program of China (Grant 2010CB923300).
3
2
20
Amer chemical soc
Washington}, month = {Nov}, pages = {15151-15157}, type = {Article}, abstract = {

Protein hydration plays a critical role in protein dynamics and biological processes. Pump-probe transmission measurement has been applied to investigate the hydration effects on the energy relaxation of a heme protein ferric Cytochrome c (Cyt c) film after soret-band photoexcitation. Transient dynamics study indicates that the energy internal conversion time of similar to 300 fs is independent of hydration. The vibrationally excited electronic ground-state recovery rates show two transitions at the hydration level of h = 12.4-16.5\% and 21.7-23.5\%. The first transition occurs at the hydration level for the onset of an increasing ferric Cyt c flexibility while the second transition occurs at the saturated hydration level. The hydration dependence of steady-state electronic absorption spectrum results shows that the Q-band peak is nearly constant in center wavelength, but the line width surprisingly narrows with increasing hydration. For the similar to 695 nm absorbance associated with the MET80-Fe bond, the intensity increases with increasing hydration and slightly blue shifts. The 695 nm peak grows rapidly at h = 12.4\% and then plateaus at h = 21.7\%. This research shows that similar to 695 nm absorbance and ground-state recovery rates are sensitive to the hydration of the protein. This study will aid in understanding how hydration modulates the activity of the protein dynamics at a local level.

}, keywords = {Chemistry, circular-dichroism, conformation change, dynamics, ferricytochrome-c, protein hydration, resolved resonance raman, spectroscopy, unfolded states, vibrational-relaxation, water-molecules}, isbn = {1520-6106}, doi = {10.1021/jp104217j}, author = {Ye, S. J. and Markelz, A.} } @article {292, title = {Why is THz Sensitive to Protein Functional States? Oxidation State of Cytochrome C}, journal = {Terahertz Science and Technology}, volume = {3}, year = {2010}, chapter = {149-162}, abstract = {

We investigate the presence of structural collective motions on a picosecond time scale for the heme protein, cytochrome c, as a function of oxidation and hydration, using terahertz (THz) time-domain spectroscopy and molecular dynamics simulations. Structural collective mode frequencies have been calculated to lie in this frequency range, and the density of states can be considered a measure of flexibility. A dramatic increase in the THz response occurs with oxidation, with the largest increase for lowest hydrations and highest frequencies. For both oxidation states the measured THz response rapidly increases with hydration saturating above ~25\% (g H2O/g protein), in contrast to the rapid turn-on in dynamics observed at this hydration level for other proteins. Quasi-harmonic collective vibrational modes and dipole-dipole correlation functions are calculated from the molecular dynamics trajectories. The collective mode density of states alone reproduces the measured hydration dependence providing strong evidence of the existence of these collective motions. The large oxidation dependence is reproduced only by the dipole-dipole correlation function, indicating the contrast arises from diffusive motions consistent with structural changes occurring in the vicinity of a buried internal water molecule.

}, doi = {10.11906/TST.149-162.2010.12.15}, url = {http://www.tstnetwork.org/10.11906/TST.149-162.2010.12.15/}, author = {He,Y. and Chen, J.-Y. and Knab, J. R. and Zheng, W. and Markelz, A.G.} } @proceedings {232, title = {The role of the protein surface on the local biological water dynamics}, volume = {7397}, year = {2009}, note = {ISI Document Delivery No.: BVQ85
Times Cited: 0
Cited Reference Count: 12
Cited References:
Balu R, 2008, BIOPHYS J, V94, P3217, DOI 10.1529/biophysj.107.105163
Bergner A, 2005, REV SCI INSTRUM, V76, DOI 10.1063/1.1928427
Born B, 2009, J AM CHEM SOC, V131, P3752, DOI 10.1021/ja808997y
Chen JY, 2007, APPL PHYS LETT, V90, DOI 10.1063/1.2748852
He YF, 2008, PHYS REV LETT, V101, DOI 10.1103/PhysRevLett.101.178103
Heugen U, 2006, P NATL ACAD SCI USA, V103, P12301, DOI 10.1073/pnas.0604897103
Jepsen PU, 2007, OPT EXPRESS, V15, P14717, DOI 10.1364/OE.15.014717
Kindt JT, 1996, J PHYS CHEM-US, V100, P10373, DOI 10.1021/jp960141g
Knab J, 2006, BIOPHYS J, V90, P2576, DOI 10.1529/biophysj.105.069088
THRANE L, 1995, CHEM PHYS LETT, V240, P330, DOI 10.1016/0009-2614(95)00543-D
Xu J, 2006, J CHEM PHYS, V124, DOI 10.1063/1.2151267
Yada H, 2008, CHEM PHYS LETT, V464, P166, DOI 10.1016/j.cplett.2008.09.015
Liang, Wei He, Yunfen George, Deepu Markelz, A. G.
Proceedings Paper
Conference on Biosensing II
Aug 04-06, 2009
San Diego, CA
Spie
George, Deepu/J-9882-2014
George, Deepu/0000-0003-0021-0705; Markelz, Andrea/0000-0003-0443-4319
1000 20th st, po box 10, bellingham, wa 98227-0010 usa
0277-786x
73970t}, publisher = {Spie-Int Soc Optical Engineering}, address = {Bellingham}, abstract = {

Protein function is reliant on structural flexibility and this flexibility is slaved to the surrounding solvent. Here we discuss how the exposed surface of the protein influences the solvent dynamics and thereby influences the protein{\textquoteright}s own structural dynamics. We discuss measurements of the THz absorption of water in the presence of hydrophilic and hydrophobic surfaces.

}, keywords = {alanine, dynamics, hydration, lysine, lysozyme, proteins, relaxation, spectroscopy, Terahertz, thz}, isbn = {978-0-8194-7687-6}, doi = {https://doi.org/10.1117/12.828697}, author = {Liang, W. and He, Y. F. and George, D. and Markelz, A. G.}, editor = {Razeghi, M. and Mohseni, H.} } @proceedings {188, title = {The role of structure in the protein dynamical transition}, year = {2008}, pages = {1-3}, publisher = {IEEE}, isbn = {1424421195}, doi = {https://doi.org/10.1109/ICIMW.2008.4665800}, author = {He, Yunfen and Markelz, Andrea G} } @article {195, title = {Terahertz dielectric sensitivity to biomolecular structure and function}, journal = {IEEE Journal of Selected Topics in Quantum Electronics}, volume = {14}, number = {1}, year = {2008}, pages = {180-190}, isbn = {1077-260X}, doi = {https://doi.org/10.1109/JSTQE.2007.913424}, author = {Markelz, Andrea G} } @article {243, title = {Terahertz response of quantum point contacts}, journal = {Applied Physics LettersApplied Physics LettersApplied Physics Letters}, volume = {92}, number = {22}, year = {2008}, note = {ISI Document Delivery No.: 310KL
Times Cited: 25
Cited Reference Count: 21
Cited References:
Aizin GR, 2007, APPL PHYS LETT, V91, DOI 10.1063/1.2800369
ARNONE DD, 1995, APPL PHYS LETT, V66, P3149, DOI 10.1063/1.113705
FENG SC, 1993, PHYS REV B, V48, P5354, DOI 10.1103/PhysRevB.48.5354
Hashiba H, 2004, APPL PHYS LETT, V85, P6036, DOI 10.1063/1.1834716
HU Q, 1993, APPL PHYS LETT, V62, P837, DOI 10.1063/1.108567
Hu Q, 1996, SEMICOND SCI TECH, V11, P1888, DOI 10.1088/0268-1242/11/12/021
JANSSEN TJBM, 1994, J PHYS-CONDENS MAT, V6, pL163, DOI 10.1088/0953-8984/6/13/002
Kabir NA, 2006, APPL PHYS LETT, V89, DOI 10.1063/1.2357605
KARADI C, 1994, J OPT SOC AM B, V11, P2566, DOI 10.1364/JOSAB.11.002566
Knap W, 2002, APPL PHYS LETT, V81, P4637, DOI 10.1063/1.1525851
Knap W, 2002, APPL PHYS LETT, V80, P3433, DOI 10.1063/1.1473685
Lee M, 2005, APPL PHYS LETT, V86, DOI 10.1063/1.1851606
MITTLEMAN D, 2002, SPRINGER SERIES OPTI
Peralta XG, 2002, APPL PHYS LETT, V81, P1627, DOI 10.1063/1.1497433
Ryzhii V, 2006, JPN J APPL PHYS 2, V45, pL1118, DOI 10.1143/JJAP.45.L1118
Shaner EA, 2007, APPL PHYS LETT, V90, DOI 10.1063/1.2735943
Shaner EA, 2005, APPL PHYS LETT, V87, DOI 10.1063/1.2128057
Teppe F, 2005, APPL PHYS LETT, V87, DOI 10.1063/1.2005394
VANHOUTEN H, 1992, SEMICONDUCT SEMIMET, P9
WYSS RA, 1993, APPL PHYS LETT, V63, P1522, DOI 10.1063/1.110736
WYSS RA, 1995, APPL PHYS LETT, V66, P1144, DOI 10.1063/1.113840
Song, J. W. Kabir, N. A. Kawano, Y. Ishibashi, K. Aizin, G. R. Mourokh, L. Reno, J. L. Markelz, A. G. Bird, J. P.
Ishibashi, Koji/G-7065-2012; Bird, Jonathan P/G-4068-2010
Ishibashi, Koji/0000-0001-8131-9969; Bird, Jonathan P/0000-0002-6966-9007; Markelz, Andrea/0000-0003-0443-4319
27

6
Amer inst physics
Melville
1077-3118}, month = {Jun}, pages = {3}, type = {Article}, abstract = {

We measure a clear terahertz response in the low-temperature conductance of a quantum point contact at 1.4 and 2.5 THz. We show that this photoresponse does not arise from a heating effect, but that it is instead excellently described by a classical model of terahertz-induced gate-voltage rectification. This effect is distinct from the rectification mechanisms that have been studied previously, being determined by the phase-dependent interference of the source drain and gate voltage modulations induced by the terahertz field. (C) 2008 American Institute of Physics.

}, keywords = {detector, devices, field-effect transistors, Physics, plasma-waves, radiation, resonant detection, subterahertz, transport}, isbn = {0003-6951}, doi = {https://doi.org/10.1063/1.2938416}, author = {Song, J. W. and Kabir, N. A. and Kawano, Y. and Ishibashi, K. and Aizin, G. R. and Mourokh, L. and Reno, J. L. and Markelz, A. G. and Bird, J. P.} } @article {222, title = {Terahertz spectroscopy of bacteriorhodopsin and rhodopsin: Similarities and differences}, journal = {Biophysical Journal}, volume = {94}, number = {8}, year = {2008}, note = {ISI Document Delivery No.: 280IP
Times Cited: 50
Cited Reference Count: 72
Cited References:
Abdulaev NG, 1998, P NATL ACAD SCI USA, V95, P12854, DOI 10.1073/pnas.95.22.12854
Alexandrov V, 2005, PROTEIN SCI, V14, P633, DOI 10.1110/ps.04882105
Alexiev U, 2003, J MOL BIOL, V328, P705, DOI 10.1016/S0022-2836(03)00326-7
Altenbach C, 2001, BIOCHEMISTRY-US, V40, P15493, DOI 10.1021/bi011545o
AMADEI A, 1993, PROTEINS, V17, P412, DOI 10.1002/prot.340170408
Balog E, 2004, PHYS REV LETT, V93, DOI 10.1103/PhysRevLett.93.028103
Beck M, 1998, BIOCHEMISTRY-US, V37, P7630, DOI 10.1021/bi9801560
Bizzarri AR, 2001, EUR BIOPHYS J BIOPHY, V30, P443, DOI 10.1007/s002490100167
BROOKS B, 1983, P NATL ACAD SCI-BIOL, V80, P6571, DOI 10.1073/pnas.80.21.6571
BROOKS BR, 1995, J COMPUT CHEM, V16, P1522, DOI 10.1002/jcc.540161209
Bu ZM, 2000, J MOL BIOL, V301, P525, DOI 10.1006/jmbi.2000.3978
Chen JY, 2005, PHYS REV E, V72, DOI 10.1103/PhysRevE.72.040901
Chen Q, 2001, J OPT SOC AM B, V18, P823, DOI 10.1364/JOSAB.18.000823
Chung HS, 2005, P NATL ACAD SCI USA, V102, P612, DOI 10.1073/pnas.0408646102
Crozier PS, 2003, J MOL BIOL, V333, P493, DOI 10.1016/j.jmb.2003.08.045
Farrens DL, 1996, SCIENCE, V274, P768, DOI 10.1126/science.274.5288.768
Filippovich S. Y., 2004, PHOTOCHEM PHOTOBIOL, V3, P1
Fotiadis D, 2006, CURR OPIN STRUC BIOL, V16, P252, DOI 10.1016/j.sbi.2006.03.013
Gabel F, 2005, BIOPHYS J, V89, P3303, DOI 10.1529/biophysj.105.061028
Gabel F, 2002, Q REV BIOPHYS, V35, P327, DOI 10.1017/S0033583502003840
Getmanova E, 2004, BIOCHEMISTRY-US, V43, P1126, DOI 10.1021/bi030120u
Giraud G, 2003, BIOPHYS J, V85, P1903, DOI 10.1016/S0006-3495(03)74618-9
GRISCHKOWSKY D, 1991, FEMTOSECOND PULSES T
Groma GI, 2001, BIOPHYS J, V81, P3432, DOI 10.1016/S0006-3495(01)75975-9
Hendler RW, 2003, EUR J BIOCHEM, V270, P1920, DOI 10.1046/j.1432-1033.2003.03547.x
Hu KS, 2000, J PHOTOCH PHOTOBIO B, V58, P163, DOI 10.1016/S1011-1344(00)00125-1
Humphrey W, 1996, J MOL GRAPH MODEL, V14, P33, DOI 10.1016/0263-7855(96)00018-5
ICHIYE T, 1991, PROTEINS, V11, P205, DOI 10.1002/prot.340110305
Jaaskelainen S, 1998, PROTEIN SCI, V7, P1359
Joti Y, 2004, PHYSICA B, V350, pE627, DOI 10.1016/j.physb.2004.03.167
Kamikubo H, 1997, BIOCHEMISTRY-US, V36, P12282, DOI 10.1021/bi9712302
Kataoka M, 2000, BBA-BIOENERGETICS, V1460, P166, DOI 10.1016/S0005-2728(00)00137-7
Keskin O, 2000, BIOPHYS J, V78, P2093, DOI 10.1016/S0006-3495(00)76756-7
Kim JE, 2003, BIOCHEMISTRY-US, V42, P5169, DOI 10.1021/bi030026d
Kim JE, 2002, J PHYS CHEM A, V106, P8508, DOI 10.1021/jp021069r
Knab J, 2006, BIOPHYS J, V90, P2576, DOI 10.1529/biophysj.105.069088
KONIG B, 1989, P NATL ACAD SCI USA, V86, P6878, DOI 10.1073/pnas.86.18.6878
Korter TM, 2006, CHEM PHYS LETT, V418, P65, DOI 10.1016/j.cplett.2005.10.097
Koutsopoulos S, 2005, PROTEINS, V61, P377, DOI 10.1002/prot.20606
Langen R, 1999, BIOCHEMISTRY-US, V38, P7918, DOI 10.1021/bi990010g
Lee AG, 2004, BBA-BIOMEMBRANES, V1666, P62, DOI 10.1016/j.bbamem.2004.05.012
Li J, 2004, J MOL BIOL, V343, P1409, DOI 10.1016/j.jmb.2004.08.090
Liang Y, 2003, J BIOL CHEM, V278, P21655, DOI 10.1074/jbc.M302536200
MacKerell AD, 2001, BIOPOLYMERS, V56, P257
Markelz A, 2002, PHYS MED BIOL, V47, P3797, DOI 10.1088/0031-9155/47/21/318
Markelz AG, 2000, CHEM PHYS LETT, V320, P42, DOI 10.1016/S0009-2614(00)00227-X
McCamant DW, 2005, J PHYS CHEM B, V109, P10449, DOI 10.1021/jp050095x
Niv MY, 2006, J COMPUT AID MOL DES, V20, P437, DOI 10.1007/s10822-006-9061-3
Oesterhelt D, 1974, Methods Enzymol, V31, P667
Okada T, 2001, CURR OPIN STRUC BIOL, V11, P420, DOI 10.1016/S0959-440X(00)00227-X
Pitman MC, 2005, J AM CHEM SOC, V127, P4576, DOI 10.1021/ja042715y
Rader AJ, 2004, P NATL ACAD SCI USA, V101, P7246, DOI 10.1073/pnas.0401429101
Ridge KD, 2003, TRENDS BIOCHEM SCI, V28, P479, DOI 10.1016/S0968-0004(03)00172-5
Ruprecht JJ, 2004, EMBO J, V23, P3609, DOI 10.1038/sj.emboj.7600374
Saam J, 2002, BIOPHYS J, V83, P3097, DOI 10.1016/S0006-3495(02)75314-9
Sass HJ, 2000, NATURE, V406, P649, DOI 10.1038/35020607
Schmuttenmaer CA, 2004, CHEM REV, V104, P1759, DOI 10.1021/cr020685g
Siegel PH, 2004, IEEE T MICROW THEORY, V52, P2438, DOI 10.1109/TMTT.2004.835916
Siegrist K, 2006, J AM CHEM SOC, V128, P5764, DOI 10.1021/ja058176u
Subramaniam S, 2000, BBA-BIOENERGETICS, V1460, P157, DOI 10.1016/S0005-2728(00)00136-5
Tajkhorshid E, 2000, BIOPHYS J, V78, P683, DOI 10.1016/S0006-3495(00)76626-4
Tama F, 2000, PROTEINS, V41, P1
Tama F, 2002, J MOL BIOL, V321, P297, DOI 10.1016/S0022-2836(02)00627-7
Tama F, 2001, PROTEIN ENG, V14, P1, DOI 10.1093/protein/14.1.1
Teller DC, 2001, BIOCHEMISTRY-US, V40, P7761, DOI 10.1021/bi0155091
Thomas A, 1999, PROTEINS, V34, P96, DOI 10.1002/(SICI)1097-0134(19990101)34:1<96::AID-PROT8>3.0.CO;2-0
Ujj L, 1998, BIOPHYS J, V74, P1492, DOI 10.1016/S0006-3495(98)77861-0
Vogel R, 2004, J MOL BIOL, V338, P597, DOI 10.1016/j.jmb.2004.03.006
Vogel R, 2003, BIOPOLYMERS, V72, P133, DOI 10.1002/bip.10407
Whitmire SE, 2003, BIOPHYS J, V85, P1269, DOI 10.1016/S0006-3495(03)74562-7
Yan ECY, 2004, BIOCHEMISTRY-US, V43, P10867, DOI 10.1021/bi0400148
Zhang J, 2006, PROTEIN PEPTIDE LETT, V13, P33, DOI 10.2174/092986606774502027
Balu, R. Zhang, H. Zukowski, E. Chen, J. -Y. Markelz, A. G. Gregurick, S. K.
Zhang, Hailiang/F-8325-2010
Markelz, Andrea/0000-0003-0443-4319
52

27
Cell press
Cambridge
1542-0086}, month = {Apr}, pages = {3217-3226}, type = {Article}, abstract = {

We studied the low-frequency terahertz spectroscopy of two photoactive protein systems, rhodopsin and bacteriorhodopsin, as a means to characterize collective low-frequency motions in helical transmembrane proteins. From this work, we found that the nature of the vibrational motions activated by terahertz radiation is surprisingly similar between these two structurally similar proteins. Specifically, at the lowest frequencies probed, the cytoplasmic loop regions of the proteins are highly active; and at the higher terahertz frequencies studied, the extracellular loop regions of the protein systems become vibrationally activated. In the case of bacteriorhodopsin, the calculated terahertz spectra are compared with the experimental terahertz signature. This work illustrates the importance of terahertz spectroscopy to identify vibrational degrees of freedom which correlate to known conformational changes in these proteins.

}, keywords = {Biophysics, bovine rhodopsin, conformational-changes, elastic, frequency normal-modes, light activation, molecular-dynamics simulation, neutron-scattering, protein-coupled receptors, transmembrane helices, vibrational-modes, wild-type}, isbn = {0006-3495}, doi = {10.1529/biophysj.107.105163}, author = {Balu, R. and Zhang, H. and Zukowski, E. and Chen, J. Y. and Markelz, A. G. and Gregurick, S. K.} } @inbook {303, title = {Development of Tagless Biosensors for Detecting the Presence of Pathogens}, booktitle = {Terahertz Frequency Detection and Identification of Materials and Objects}, volume = {ed X.-C. Zhang, R. E. Miles, H. Eisele and A. Krotkus}, year = {2007}, pages = {123-134}, publisher = {Springer}, organization = {Springer}, chapter = {9}, address = {Dordrecht, The Netherlands}, author = {Markelz, A. G. and Chen, J.-Y. and Knab, J. R. and He, Y. and Ye, S.} } @article {293, title = {Protein dynamical transition in terahertz dielectric response}, journal = {Chemical Physics Letters}, volume = {442}, year = {2007}, pages = {413 - 417}, abstract = {

The 200K protein dynamical transition is observed for the first time in the terahertz dielectric response. The complex dielectric permittivity ε=ε'+iε" is determined in the 0.2{\textendash}2.0THz and 80{\textendash}294K ranges. ε" has a linear temperature dependence up to 200K then sharply increases. The low temperature linear dependence in ε" suggests anharmonicity for temperatures 80K\<t\<180k, challenging="" the="" assumed="" harmonicity="" below="" 200k.="" temperature="" dependence="" is="" consistent="" with="" thermally="" activated="" sidechain="" motions="" and="" shows="" involved="" in="" dynamical="" transition="" extend="" to="" subpicosecond="" time="" scales.\<="" div=""\>

}, isbn = {0009-2614}, doi = {10.1016/j.cplett.2007.05.080}, url = {https://www.sciencedirect.com/science/article/pii/S000926140700680X}, author = {Markelz, Andrea G. and Knab, Joseph R. and Chen, Jing Yin and He, Yunfen} } @article {223, title = {Terahertz dielectric assay of solution phase protein binding}, journal = {Applied Physics Letters}, volume = {90}, number = {24}, year = {2007}, note = {ISI Document Delivery No.: 179QR
Times Cited: 51
Cited Reference Count: 9
Cited References:
Balog E, 2004, PHYS REV LETT, V93, DOI 10.1103/PhysRevLett.93.028103
Brucherseifer M, 2000, APPL PHYS LETT, V77, P4049, DOI 10.1063/1.1332415
Chen JY, 2005, PHYS REV E, V72, DOI 10.1103/PhysRevE.72.040901
Fear G, 2007, PHARMACOL THERAPEUT, V113, P354, DOI 10.1016/j.pharmthera.2006.09.001
Heugen U, 2006, P NATL ACAD SCI USA, V103, P12301, DOI 10.1073/pnas.0604897103
Knab J, 2006, BIOPHYS J, V90, P2576, DOI 10.1529/biophysj.105.069088
LEHRER SS, 1967, J BIOL CHEM, V242, P4644
Menikh A, 2004, BIOSENS BIOELECTRON, V20, P658, DOI 10.1016/j.bios.2004.03.006
Xu J, 2006, PROTEIN SCI, V15, P1175, DOI 10.1110/ps.062073506
Chen, Jing-Yin Knab, J. R. Ye, Shuji He, Yunfen Markelz, A. G.
Ye, Shuji/B-4479-2010
Markelz, Andrea/0000-0003-0443-4319
53
1
42
Amer inst physics
Melville
1077-3118}, month = {Jun}, pages = {3}, type = {Article}, abstract = {

The authors demonstrate a method for rapid determination of protein-ligand binding on solution phase samples using terahertz dielectric spectroscopy. Measurements were performed using terahertz time domain spectroscopy on aqueous solutions below the liquid-solid transition for water. Small ligand binding sensitivity was demonstrated using triacetylglucosamine and hen egg white lysozyme with a decrease in dielectric response with binding. The magnitude of the change increases with frequency. (c) 2007 American Institute of Physics.

}, keywords = {dynamics, lysozyme, Physics, spectroscopy, water}, isbn = {0003-6951}, doi = {10.1063/1.2748852}, author = {Chen, J. Y. and Knab, J. R. and Ye, S. J. and He, Y. F. and Markelz, A. G.} } @article {191, title = {Terahertz measurements of protein relaxational dynamics}, journal = {Proceedings of the IEEE}, volume = {95}, number = {8}, year = {2007}, pages = {1605-1610}, isbn = {0018-9219}, doi = {10.1109/JPROC.2007.898906}, author = {Knab, Joseph R and Chen, Jing-Yin and He, Yunfen and Markelz, Andrea G} } @article {189, title = {Hydration dependence of conformational dielectric relaxation of lysozyme}, journal = {Biophysical Journal}, volume = {90}, number = {7}, year = {2006}, pages = {2576-2581}, isbn = {0006-3495}, doi = {10.1529/biophysj.105.069088}, author = {Knab, Joseph and Chen, Jing-Yin and Markelz, Andrea} } @proceedings {192, title = {Protein conformational dynamics measured with terahertz time domain spectroscopy}, year = {2006}, pages = {183-183}, publisher = {IEEE}, isbn = {1424403995}, doi = {https://doi.org/10.1088/0031-9155/47/21/318}, author = {Knab, Joseph R and Chen, Jing-Yin and Ye, Shuji and He, Yunfen and Markelz, Andrea G} } @article {229, title = {Terahertz transmission characteristics of high-mobility GaAs and InAs two-dimensional-electron-gas systems}, journal = {Applied Physics Letters}, volume = {89}, number = {13}, year = {2006}, note = {ISI Document Delivery No.: 089JE
Times Cited: 18
Cited Reference Count: 16
Cited References:
ANDO T, 1982, REV MOD PHYS, V54, P437, DOI 10.1103/RevModPhys.54.437
ANDO T, 1989, HIGH MAGNETIC FIELDS, V2, P164
Ashcroft NW, 1976, SOLID STATE PHYS, P1
Beard MC, 2000, PHYS REV B, V62, P15764, DOI 10.1103/PhysRevB.62.15764
Cerne J, 2000, PHYS REV B, V61, P8133, DOI 10.1103/PhysRevB.61.8133
COLERIDGE PT, 1991, PHYS REV B, V44, P3793, DOI 10.1103/PhysRevB.44.3793
Dorozhkin PS, 2005, APPL PHYS LETT, V87, DOI 10.1063/1.2035883
Knap W, 2002, APPL PHYS LETT, V81, P4637, DOI 10.1063/1.1525851
Knap W, 2002, APPL PHYS LETT, V80, P3433, DOI 10.1063/1.1473685
Kukushkin IV, 2005, APPL PHYS LETT, V86, DOI 10.1063/1.1856143
MADELUNG O, 1996, SEMICONDUCTORS BASIC, P109
MCKNIGHT SW, 1987, INFRARED PHYS, V27, P327, DOI 10.1016/0020-0891(87)90074-1
Peralta XG, 2002, APPL PHYS LETT, V81, P1627, DOI 10.1063/1.1497433
Sadofyev YG, 2002, APPL PHYS LETT, V81, P1833, DOI 10.1063/1.1504882
Shaner EA, 2005, APPL PHYS LETT, V87, DOI 10.1063/1.2128057
ZAWADZKI W, 1974, ADV PHYS, V23, P435, DOI 10.1080/00018737400101371
Kabir, N. A. Yoon, Y. Knab, J. R. Chen, J. -Y. Markelz, A. G. Reno, J. L. Sadofyev, Y. Johnson, S. Zhang, Y. -H. Bird, J. P.
Bird, Jonathan P/G-4068-2010
Bird, Jonathan P/0000-0002-6966-9007; Markelz, Andrea/0000-0003-0443-4319
18

15
Amer inst physics
Melville}, month = {Sep}, pages = {3}, type = {Article}, abstract = {

Frequency-dependent complex conductivity of high-mobility GaAs and InAs two-dimensional-electron-gas (2DEG) systems is studied by terahertz time domain spectroscopy. Determining the momentum relaxation time from a Drude model, the authors find a lower value than that from dc measurements, particularly at high frequencies/low temperatures. These deviations are consistent with the ratio tau(t)/tau(q,) where tau(q) is the full scattering time. This suggests that small-angle scattering leads to weaker heating of 2DEGs at low temperatures than expected from dc mobilit9y. (c) 2006 American Institute of Physics.

}, keywords = {field-effect transistors, photoconductivity, Physics, plasma-waves, radiation, resonant detection, subterahertz}, isbn = {0003-6951}, doi = {10.1063/1.2357605}, author = {Kabir, N. A. and Yoon, Y. and Knab, J. R. and Chen, J. Y. and Markelz, A. G. and Reno, J. L. and Sadofyev, Y. and Johnson, S. and Zhang, Y. H. and Bird, J. P.} } @proceedings {308, title = {Ultrafast Carriers Dynamics in GaSb/Mn Random Alloys}, year = {2006}, address = {Vienna Austria}, doi = {10.1063/1.2730382}, author = {Ye, S. and Knab, J. and Chen, J.-Y. and Wang, S. and Cheon, M. and Luo, H. and Markelz, A. G.} } @proceedings {309, title = {Using terahertz spectroscopy as a protein binding assay}, volume = {Proc SPIE 6080,}, year = {2006}, month = {02/2006}, pages = {35-42}, address = { San Jose, California, United States}, abstract = {

The vibrational modes corresponding to protein tertiary structural motion lay in the far infrared or terahertz frequency range. These collective large scale motions depend on global structure and thus will necessarily be perturbed by ligand binding events. We discuss the use of terahertz dielectric spectroscopy to measure these vibrational modes and the sensitivity of the technique to changes in protein conformation, oxidation state and environment. A challenge of applying this sensitivity as a spectroscopic assay for ligand binding is the sensitivity of the technique to both bulk water and water bound to the protein. This sensitivity can entirely obscure the signal from the protein or protein-ligand complex itself, thus necessitating sophisticated sample preparation making the technique impractical for industrial applications. We discuss methods to overcome this background and demonstrate how terahertz spectroscopy can be used to quickly assay protein binding for proteomics and pharmaceutical research.

}, doi = {10.1117/12.664098}, author = {Chen, J.-Y. and Knab, J. R. and Ye, S. and He, Y. and Markelz, A. G.} } @proceedings {190, title = {Critical hydration and temperature effects on terahertz biomolecular sensing}, volume = {5995}, year = {2005}, pages = {59950P}, publisher = {International Society for Optics and Photonics}, doi = {10.1117/12.630854}, author = {Knab, Joseph and Shah, Binni and Chen, Jing-Yin and Markelz, Andrea} } @article {263, title = {Large oxidation dependence observed in terahertz dielectric response for cytochrome c}, journal = {Physical Review E}, volume = {72}, number = {4}, year = {2005}, note = {ISI Document Delivery No.: 979GO
Times Cited: 51
Cited Reference Count: 29
Cited References:
BERGHUIS AM, 1992, J MOL BIOL, V223, P959, DOI 10.1016/0022-2836(92)90255-I
BONE S, 1985, J MOL BIOL, V181, P323, DOI 10.1016/0022-2836(85)90096-8
BONE S, 1982, J MOL BIOL, V157, P571, DOI 10.1016/0022-2836(82)90477-6
BROOKS B, 1985, P NATL ACAD SCI USA, V82, P4995, DOI 10.1073/pnas.82.15.4995
Brucherseifer M, 2000, APPL PHYS LETT, V77, P4049, DOI 10.1063/1.1332415
Carlson HA, 2002, CURR OPIN CHEM BIOL, V6, P447, DOI 10.1016/S1367-5931(02)00341-1
CHEN JY, IN PRESS BIOPHYS J
CUSACK S, 1986, PHYSICA B \& C, V136, P256, DOI 10.1016/S0378-4363(86)80069-9
EDEN D, 1982, P NATL ACAD SCI-BIOL, V79, P815, DOI 10.1073/pnas.79.3.815
FROHWIRT EM, 1959, BIOPHYS J, V71, P570
Jackson J.D., 1975, CLASSICAL ELECTRODYN
KOPPENOL WH, 1982, J BIOL CHEM, V257, P4426
Kutteruf MR, 2003, CHEM PHYS LETT, V375, P337, DOI 10.1016/S0009-2614(03)00856-X
Markelz A, 2002, PHYS MED BIOL, V47, P3797, DOI 10.1088/0031-9155/47/21/318
Markelz AG, 2000, CHEM PHYS LETT, V320, P42, DOI 10.1016/S0009-2614(00)00227-X
Menikh A, 2004, BIOSENS BIOELECTRON, V20, P658, DOI 10.1016/j.bios.2004.03.006
Nagel M, 2002, APPL PHYS LETT, V80, P154, DOI 10.1063/1.1428619
PETHIG R, 1979, DIELECTRIC ELECTRONI
Qi PXR, 1996, BIOCHEMISTRY-US, V35, P12275, DOI 10.1021/bi961042w
RINGE D, 1985, PROG BIOPHYS MOL BIO, V45, P197, DOI 10.1016/0079-6107(85)90002-1
SHECHTER E, 1967, BIOPOLYMERS, V5, P788, DOI 10.1002/bip.1967.360050812
SIMONSON T, 1995, P NATL ACAD SCI USA, V92, P1082, DOI 10.1073/pnas.92.4.1082
SREENATHAN BR, 1971, BIOCHEM BIOPH RES CO, V42, P1122, DOI 10.1016/0006-291X(71)90021-0
Takano T., 1984, Methods and Applications in Crystallographic Computing. International Summer School on Crystallographic Computing, P262
TAKANO T, 1980, P NATL ACAD SCI-BIOL, V77, P6371, DOI 10.1073/pnas.77.11.6371
Whitmire SE, 2003, BIOPHYS J, V85, P1269, DOI 10.1016/S0006-3495(03)74562-7
WHITMIRE SE, 2003, SENSING SCI ELECT TE, V2
Yamamoto K, 2002, B CHEM SOC JPN, V75, P1083, DOI 10.1246/bcsj.75.1083
Zhang CF, 2004, J PHYS CHEM B, V108, P10077, DOI 10.1021/jp049933y
Chen, JY Knab, JR Cerne, J Markelz, AG
Markelz, Andrea/0000-0003-0443-4319
52

22
Amer physical soc
College pk
1550-2376
1}, month = {Oct}, pages = {4}, type = {Article}, abstract = {

Far infrared dielectric response is used to characterize the collective mode density of states for cytochrome c as a function of oxidation state and hydration using terahertz time domain spectroscopy. A strong absorbance and refractive index increase was observed with the oxidation. A simple phenomenological fitting using a continuous distribution of oscillators reproduces the frequency dependence of the complex dielectric response as well as demonstrates quantitative agreement with a uniform increase in either mode density or polarizability with oxidation in the 5-80 cm(-1) frequency range. Hydration dependence measurements find that a difference in the equilibrium water content for ferri and ferro cytochrome c is not sufficient to account for the large change in terahertz response. The large dielectric increase at terahertz frequencies with oxidation suggests either a significant global softening of the potential and/or a significant increase in polarizability with oxidation.

}, keywords = {absorption, binding, conformation, dna, dynamics, heart ferricytochrome-c, modes, Physics, protein flexibility, spectroscopy, state}, isbn = {1539-3755}, doi = {10.1103/PhysRevE.72.040901}, author = {Chen, J. Y. and Knab, J. R. and Cerne, J. and Markelz, A. G.} } @article {234, title = {Protein dynamics studies using terahertz dielectric response}, journal = {Abstracts of Papers of the American Chemical Society}, volume = {230}, year = {2005}, note = {ISI Document Delivery No.: 032TJ
Times Cited: 0
Cited Reference Count: 0
Markelz, A. G. Knab, J. R. Chen, J. -Y.
230th National Meeting of the American-Chemical-Society
Aug 28-sep 01, 2005
Washington, DC
Amer Chem Soc

2
Amer chemical soc
Washington}, month = {Aug}, pages = {U347-U348}, type = {Meeting Abstract}, keywords = {Chemistry}, isbn = {0065-7727}, doi = {10.1016/j.cplett.2007.05.080}, author = {Markelz, A. G. and Knab, J. R. and Chen, J. Y.} } @proceedings {311, title = {Measuring Protein Flexibility with Terahertz Spectroscopy: Basic Research and Applications}, year = {2004}, month = {06/2004}, address = {San Diego, CA}, doi = {10.1109/LEOSST.2004.1338649}, author = {Markelz, A. G. and Chen, J.-Y. and Knab, J. R. and Maeder, M.} } @proceedings {196, title = {Tagless and universal biosensor for point detection of pathogens}, volume = {5411}, year = {2004}, pages = {182-186}, publisher = {International Society for Optics and Photonics}, doi = {https://doi.org/10.1117/12.563613}, author = {Markelz, Andrea G and Knab, Joseph R and Chen, Jing-Yin and {\v C}erne, John and Cox, William A} } @proceedings {310, title = {Terahertz measurements of the Photoactive Protein Bacteriorhodopsin mutant D96N: M and P states}, volume = {826}, year = {2004}, pages = {pages261{\textendash}267}, address = {Warrendale, PA}, abstract = {

We use terahertz (THz) spectroscopy as a biomaterials characterization tool. Previously we have shown a strong contrast between the THz dielectric response for wild type (WT) and D96N mutant of bacteriorhodopsin. In those studies we observed a large increase in the THz absorbance of WT with excitation to thermally captured photo-intermediates whereas no such increase in absorbance was observed for the mutant D96N. These results suggest that the THz response is sensitive to structural changes and relative flexibility of biomolecules. However the photo-intermediate populations of the WT and D96N samples were not equivalent in those measurements. While the WT samples had relaxed (bR), M and P state intermediates present, the D96N samples had only bR and M states. Here we present terahertz absorbance measurements of D96N as a function of M and P state populations at room temperature. The THz response is constant for intermediate states populations up to 23\% M state and up to 30\% P state. These results verify that there is a fundamental difference in the conformational dynamics as measured by THz dielectric response for a single residue mutation.

}, doi = {10.1557/PROC-826-V2.6}, author = {Chen, C.-Y. and Knab, J. R. and Cerne, J. and Hillebrecht, J. R. and Birge, R. R. and Markelz, A. G.} } @proceedings {312, title = {Thz Dielectric Response As A Function Of Protein Hydration: Intramolecular Coupling Contribution}, year = {2004}, month = {10/2004}, address = {Philadelphia, PA}, author = {Markelz, A. G. and Chen, J.-Y. and Knab, J. R. and Maeder, M.} } @proceedings {313, title = {Biosensing with Terahertz Spectroscopy: Ligand Binding Effects}, year = {2003}, address = {Santa Barbara, CA}, author = {Chen, J.-Y. and Cerne, J. and Markelz, A. G.} } @article {294, title = {Direct measurements of optical phonons in SrTiO3 nanosystems}, journal = {Physica E: Low-dimensional Systems and Nanostructures}, volume = {19}, year = {2003}, month = {2003/07/01/}, pages = {236 - 239}, abstract = {

We use terahertz time domain spectroscopy to examine finite size effects on the optical phonon modes in SrTiO3 thin films. In temperature-dependent measurements we find a near absence of mode softening in the TO1 phonon frequency. Furthermore we see an increase in the soft mode frequency with reduced thickness. Both of these results correlate well with the reduced dielectric response observed for nanoscale ferroelectric systems.

}, keywords = {Ferroelectrics, Finite size, Mode softening, phonons, Strontium titanate, Terahertz}, isbn = {1386-9477}, doi = {10.1016/S1386-9477(03)00305-9}, url = {https://www.sciencedirect.com/science/article/pii/S1386947703003059}, author = {Wolpert, D and Korolev, K and Sachs, S and Knab, J and Cox, W and Cerne, J and Markelz, A.G and Zhao, T and Ramesh, R and Moeckly, B.H} } @proceedings {275, title = {Finite size effects in ferroelectric nanosystems: Absence of mode softening}, volume = {2}, year = {2003}, note = {cited By 0}, month = {02/2003}, pages = {76-81}, address = {San Francisco, CA}, abstract = {

We present measurements of the mode softening behavior for PbZr 0.5Ti0.5O3 (PZT(50)) thin films using terahertz time domain spectroscopy (TTDS). The films were grown using pulsed laser deposition (PLD) techniques on silicon substrates to study how reduced size affects the mode softening behavior. At room temperature two modes are observed at 1.1 THz (37 cm-1) and at 2.3 THz (77 cm-1). As the temperature is increased toward Tc we do not see strong mode softening, but rather a spectral weight transfer from the high frequency mode to the low frequency mode. This absence of mode softening is more dramatic than that reported by other investigators[1]. We will discuss the possible sources for this discrepancy. These results suggest a change in lattice dynamics for nanoscale ferroelectric films that may be highly dependent on the sample preparation technique.

}, keywords = {Ferroelectric materials, Fourier Transform Infrared Spectroscopy, Frequency ranges, Lead compounds, Mode softening, nanostructured materials, Natural frequencies, Optical modes, Permittivity, phase transitions, phonons, Routers, Thermal effects}, isbn = {0972842209}, author = {D. Wolpert and W. Cox and J. Cerne and A. Markelz and T. Zhao and R. Ramesh}, editor = {Romanowicz M.} } @article {273, title = {Protein flexibility and conformational state: A comparison of collective vibrational modes of wild-type and D96N bacteriorhodopsin}, journal = {Biophysical Journal}, volume = {85}, number = {2}, year = {2003}, note = {ISI Document Delivery No.: 705ZZ
Times Cited: 117
Cited Reference Count: 55
Cited References:
AUSTIN RH, 1975, BIOCHEMISTRY-US, V14, P5355, DOI 10.1021/bi00695a021
Birge RR, 1996, J PHYS CHEM-US, V100, P9990, DOI 10.1021/jp953669e
BOUSCHE O, 1992, PHOTOCHEM PHOTOBIOL, V56, P1085, DOI 10.1111/j.1751-1097.1992.tb09732.x
BROOKS BR, 1983, J COMPUT CHEM, V4, P187, DOI 10.1002/jcc.540040211
BROOKS BR, 1995, J COMPUT CHEM, V16, P1522, DOI 10.1002/jcc.540161209
Brooks CL, 1988, PROTEINS THEORETICAL
Brucherseifer M, 2000, APPL PHYS LETT, V77, P4049, DOI 10.1063/1.1332415
Chen Q, 2001, J OPT SOC AM B, V18, P823, DOI 10.1364/JOSAB.18.000823
DENCHER NA, 1989, P NATL ACAD SCI USA, V86, P7876, DOI 10.1073/pnas.86.20.7876
Der A, 2001, BIOCHEMISTRY-MOSCOW+, V66, P1234, DOI 10.1023/A:1013179101782
Diehl M, 1997, BIOPHYS J, V73, P2726, DOI 10.1016/S0006-3495(97)78301-2
DOSTER W, 1989, NATURE, V337, P754, DOI 10.1038/337754a0
FERRAND M, 1993, P NATL ACAD SCI USA, V90, P9668, DOI 10.1073/pnas.90.20.9668
GENZEL L, 1984, SPECTROSCOPY BIOL MO, P609
GRISCHKOWSKY D, 1991, OSA PROC, V9, P9
Guilbert C, 1996, CHEM PHYS, V204, P327, DOI 10.1016/0301-0104(95)00293-6
Han PY, 2000, OPT LETT, V25, P242, DOI 10.1364/OL.25.000242
Hinsen K, 1998, PROTEINS, V33, P417, DOI 10.1002/(SICI)1097-0134(19981115)33:3<417::AID-PROT10>3.0.CO;2-8
JANEZIC D, 1995, J COMPUT CHEM, V16, P1543, DOI 10.1002/jcc.540161210
Kusnetzow A, 1999, BIOPHYS J, V76, P2370, DOI 10.1016/S0006-3495(99)77394-7
Lanyi JK, 1999, INT REV CYTOL, V187, P161, DOI 10.1016/S0074-7696(08)62418-3
Lanyi JK, 2001, TRENDS BIOTECHNOL, V19, P140, DOI 10.1016/S0167-7799(01)01576-1
LINDSAY SM, 1988, BIOPOLYMERS, V27, P1015, DOI 10.1002/bip.360270610
Lisy V, 1997, J BIOMOL STRUCT DYN, V14, P517, DOI 10.1080/07391102.1997.10508150
LONGBOTTOM C, 2002, POTENTIAL USES TERAH
Luecke H, 1999, SCIENCE, V286, P255, DOI 10.1126/science.286.5438.255
Luecke H, 1999, J MOL BIOL, V291, P899, DOI 10.1006/jmbi.1999.3027
MacKerell AD, 1998, J PHYS CHEM B, V102, P3586, DOI 10.1021/jp973084f
Markelz AG, 2000, CHEM PHYS LETT, V320, P42, DOI 10.1016/S0009-2614(00)00227-X
MCINTOSH AR, 1991, BIOPHYS J, V60, P1, DOI 10.1016/S0006-3495(91)82025-2
MOUAWAD L, 1993, BIOPOLYMERS, V33, P599, DOI 10.1002/bip.360330409
Mouawad L, 1996, J MOL BIOL, V258, P393, DOI 10.1006/jmbi.1996.0257
Nagel M, 2002, APPL PHYS LETT, V80, P154, DOI 10.1063/1.1428619
Oesterhelt D, 1974, Methods Enzymol, V31, P667
Palmo K, 1998, J COMPUT CHEM, V19, P754, DOI 10.1002/(SICI)1096-987X(199805)19:7<754::AID-JCC6>3.0.CO;2-P
PERAHIA D, 1995, COMPUT CHEM, V19, P241, DOI 10.1016/0097-8485(95)00011-G
Person W.B., 1982, VIBRATIONAL INTENSIT
Polavarapu P. L., 1998, VIBRATIONAL SPECTRA
POWELL JW, 1991, J MOL STRUCT, V247, P107, DOI 10.1016/0022-2860(91)87067-R
POWELL JW, 1987, PHYS REV A, V35, P3929, DOI 10.1103/PhysRevA.35.3929
Ren L, 2001, BIOCHEMISTRY-US, V40, P13906, DOI 10.1021/bi0116487
ROITBERG A, 1995, SCIENCE, V268, P1319, DOI 10.1126/science.7539156
Sass HJ, 1997, EMBO J, V16, P1484, DOI 10.1093/emboj/16.7.1484
Stuart JA, 1996, BIOMEMBR A\&B, V2, P33
Urabe H, 1998, BIOPHYS J, V74, P1533, DOI 10.1016/S0006-3495(98)77865-8
VARO G, 1983, BIOPHYS J, V43, P47, DOI 10.1016/S0006-3495(83)84322-7
Walther M, 2000, CHEM PHYS LETT, V332, P389, DOI 10.1016/S0009-2614(00)01271-9
WEIDLICH T, 1990, BIOPOLYMERS, V30, P477, DOI 10.1002/bip.360300324
WEIDLICH T, 1990, J BIOMOL STRUCT DYN, V8, P139, DOI 10.1080/07391102.1990.10507795
WEIDLICH T, 1987, BIOPOLYMERS, V26, P439, DOI 10.1002/bip.360260310
WEIDLICH T, 1988, J PHYS CHEM-US, V92, P6475
WITTLIN A, 1986, PHYS REV A, V34, P493, DOI 10.1103/PhysRevA.34.493
Woolard DL, 1997, J APPL TOXICOL, V17, P243, DOI 10.1002/(SICI)1099-1263(199707)17:4<243::AID-JAT436>3.0.CO;2-6
Xie AH, 2002, PHYS REV LETT, V88, DOI 10.1103/PhysRevLett.88.018102
Zaccai G, 2000, SCIENCE, V288, P1604, DOI 10.1126/science.288.5471.1604
Whitmire, SE Wolpert, D Markelz, AG Hillebrecht, JR Galan, J Birge, RR
Markelz, Andrea/0000-0003-0443-4319
NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCESUnited States Department of Health \& Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of General Medical Sciences (NIGMS) [R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548, R01GM034548] Funding Source: NIH RePORTER; NIGMS NIH HHSUnited States Department of Health \& Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of General Medical Sciences (NIGMS) [R01 GM034548, R01 GM034548-15] Funding Source: Medline
122
3
31
Cell press
Cambridge
1542-0086}, month = {Aug}, pages = {1269-1277}, type = {Article}, abstract = {

Far infrared ( FIR) spectral measurements of wild-type (WT) and D96N mutant bacteriorhodopsin thin films have been carried out using terahertz time domain spectroscopy as a function of hydration, temperature, and conformational state. The results are compared to calculated spectra generated via normal mode analyses using CHARMM. We find that the FIR absorbance is slowly increasing with frequency and without strong narrow features over the range of 2-60 cm(-1) and up to a resolution of 0.17 cm(-1). The broad absorption shifts in frequency with decreasing temperature as expected with a strongly anharmonic potential and in agreement with neutron inelastic scattering results. Decreasing hydration shifts the absorption to higher frequencies, possibly resulting from decreased coupling mediated by the interior water molecules. Ground-state FIR absorbances have nearly identical frequency dependence, with the mutant having less optical density than the WT. In the M state, the FIR absorbance of the WT increases whereas there is no change for D96N. These results represent the first measurement of FIR absorbance change as a function of conformational state.

}, keywords = {angstrom resolution, Biophysics, dna, films, frequency, harmonic-analysis, inelastic neutron-scattering, large systems, mixed basis, normal-modes, purple membranes, structural-changes, transform infrared-spectroscopy}, isbn = {0006-3495}, doi = {10.1016/S0006-3495(03)74562-7}, author = {Whitmire, S. E. and Wolpert, D. and Markelz, A. G. and Hillebrecht, J. R. and Galan, J. and Birge, R. R.} } @article {295, title = {Terahertz Applications to Biomolecular Sensing}, journal = { International Journal of High Speed Electronics and Systems}, volume = {13}, year = {2003}, chapter = {951-967}, doi = {10.1142/S0129156403002101}, url = {https://www.worldscientific.com/doi/abs/10.1142/S0129156403002101}, author = {Markelz, A. G. and Whitmire, S. E.} } @article {198, title = {Terahertz applications to biomolecular sensing}, journal = {International Journal of High Speed Electronics and Systems}, volume = {13}, number = {04}, year = {2003}, pages = {951-967}, isbn = {0129-1564}, doi = {https://doi.org/10.1142/S0129156403002101}, author = {Markelz, Andrea G and Whitmire, Scott E} } @proceedings {314, title = {Terahertz Biosensors based on Xerogel Substrates}, year = {2003}, address = {Santa Barbara, CA}, author = {Chen, J.-Y. and Cox, W. and Bright, F. V. and Cerne, J. and Markelz, A. G.} } @proceedings {315, title = {Ultrafast THz spectroscopy of photoactive biomolecules}, year = {2003}, month = {01/2003}, pages = {146-153}, address = {San Jose, California}, author = {Chen, J.-Y. and Whitmire, S. E. and Markelz, A. G. and Hillebrecht, J. R. and Birge, R. R.} } @article {194, title = {THz time domain spectroscopy of biomolecular conformational modes}, journal = {Physics in Medicine \& Biology}, volume = {47}, number = {21}, year = {2002}, pages = {3797}, isbn = {0031-9155}, doi = {https://doi.org/10.1088/0031-9155/47/21/318}, author = {Markelz, Andrea and Whitmire, Scott and Hillebrecht, Jay and Birge, Robert} } @proceedings {316, title = {Terahertz Time domain spectroscopy of the M intermediate state of Bacteriorhodopsin}, year = {2001}, month = {09/2001}, pages = {345-348}, address = {Toulouse, France}, author = {Whitmire, S. and Markelz, A. G. and Hillebrecht, J. R. and Birge, R. R.} } @proceedings {296, title = {High field pulsed terahertz measurements of nonlinear conductivity}, volume = {46}, year = {2000}, month = {2000}, pages = {105 - 106}, edition = {Postconference}, address = {Kaua{\textquoteright}i-Lihue, HI, USA}, abstract = {

High field pulsed terahertz spectroscopy is used to measure the inplane nonlinear conductivity response of two dimensional electron gases. Results are compared to FEL measurements suggesting LO phonon bottleneck weakening at 0.5 THz.

}, keywords = {0.5 THz, 2D electron gases, Conductivity measurement, electrical conductivity measurement, Electron emission, FEL measurements, Finite impulse response filter, high field pulsed terahertz measurements, high field pulsed terahertz spectroscopy, high-speed optical techniques, inplane nonlinear conductivity response, LO phonon bottleneck weakening, nonlinear conductivity, nonlinear optics, phonons, Power measurement, Pulse measurements, Resonance, semiconductor quantum wells, spectroscopy, Submillimeter wave measurements, submillimetre wave spectroscopy, two dimensional electron gases, two-dimensional electron gas}, doi = {10.1109/NLO.2000.883591}, url = {https://ieeexplore.ieee.org/document/883591/authors$\#$authors}, author = {A. G. Markelz} } @article {271, title = {Pulsed terahertz spectroscopy of DNA, bovine serum albumin and collagen between 0.1 and 2.0 THz}, journal = {Chemical Physics Letters}, volume = {320}, number = {1-2}, year = {2000}, note = {ISI Document Delivery No.: 299RG
Times Cited: 561
Cited Reference Count: 24
Cited References:
Cai Y, 1998, APPL PHYS LETT, V73, P444, DOI 10.1063/1.121894
CARTER DC, 1994, ADV PROTEIN CHEM, V45, P153
Chen EF, 1998, BIOCHEMISTRY-US, V37, P5589, DOI 10.1021/bi972369f
CHEVILLE RA, 1995, OPT LETT, V20, P1646, DOI 10.1364/OL.20.001646
FENG Y, 1991, PHYS REV A, V43, P1049, DOI 10.1103/PhysRevA.43.1049
Fraser R.D.B., 1973, CONFORMATION FIBROUS
Frushour B., 1975, ADV INFRARED RAMAN S, V1
GENZEL L, 1984, SPECTROSCOPY BIOL MO, P609
GRIEBENOW K, 1995, P NATL ACAD SCI USA, V92, P10969, DOI 10.1073/pnas.92.24.10969
HAYWARD S, 1995, ANNU REV PHYS CHEM, V46, P223, DOI 10.1146/annurev.pc.46.100195.001255
KATZENELLENBOGE.N, 1992, ULTRA WIDEBAND SHORT
Kindt JT, 1996, J PHYS CHEM-US, V100, P10373, DOI 10.1021/jp960141g
LINDSAY SM, 1988, BIOPOLYMERS, V27, P1015, DOI 10.1002/bip.360270610
Lisy V, 1997, J BIOMOL STRUCT DYN, V14, P517, DOI 10.1080/07391102.1997.10508150
Markelz AG, 1998, APPL PHYS LETT, V72, P2229, DOI 10.1063/1.121329
Nossal R. J., 1991, MOL CELL BIOPHYSICS
POWELL JW, 1987, PHYS REV A, V35, P3929, DOI 10.1103/PhysRevA.35.3929
POWELL JW, 1991, J MOL STRUCT, V247, P119
ROITBERG A, 1995, SCIENCE, V268, P1319, DOI 10.1126/science.7539156
WEIDLICH T, 1990, BIOPOLYMERS, V30, P477, DOI 10.1002/bip.360300324
WEIDLICH T, 1990, J BIOMOL STRUCT DYN, V8, P139, DOI 10.1080/07391102.1990.10507795
WITTLIN A, 1986, PHYS REV A, V34, P493, DOI 10.1103/PhysRevA.34.493
YOUNG L, 1990, PHYS REV A, V41, P7020, DOI 10.1103/PhysRevA.41.7020
ZHUANG W, 1990, PHYS REV A, V41, P7033, DOI 10.1103/PhysRevA.41.7033
Markelz, AG Roitberg, A Heilweil, EJ
Roitberg, Adrian/A-2378-2009
Markelz, Andrea/0000-0003-0443-4319
598
7
235
Elsevier science bv
Amsterdam}, month = {Mar}, pages = {42-48}, type = {Article}, abstract = {

We report the first use of pulsed terahertz spectroscopy to examine low-frequency collective vibrational modes of biomolecules. Broadband absorption increasing with frequency was observed for lyophilized powder samples of calf thymus DNA, bovine serum albumin and collagen in the 0.06-2.00 THz (2-67 cm(-1)) frequency range, suggesting that a large number of the low-frequency collective modes for these systems are IR active. Transmission measurements at room temperature showed increasing FIR absorption with hydration and denaturing. (C) 2000 published by Elsevier Science B.V. All rights reserved.

}, keywords = {b-dna, Chemistry, films, modes, Physics, proteins}, isbn = {0009-2614}, doi = {10.1016/S0009-2614(00)00227-X}, author = {Markelz, A. G. and Roitberg, A. and Heilweil, E. J.} } @article {297, title = {Relaxation times in InAs/AlSb quantum wells }, journal = {Applied Physics Letters}, volume = {72}, year = {1998}, chapter = {2439}, doi = {10.1063/1.121377}, url = {https://aip.scitation.org/doi/abs/10.1063/1.121377}, author = {Markelz, A. G. and Asmar, N. G. and Gwinn, E. G.} } @article {270, title = {Temperature-dependent terahertz output from semi-insulating GaAs photoconductive switches}, journal = {Applied Physics Letters}, volume = {72}, number = {18}, year = {1998}, note = {ISI Document Delivery No.: ZK775
Times Cited: 22
Cited Reference Count: 21
Cited References:
Brener I, 1996, OPT LETT, V21, P1924, DOI 10.1364/OL.21.001924
BRORSON SD, 1994, APPL PHYS LETT, V64, P2385, DOI 10.1063/1.111622
CHEVILLE RA, 1995, OPT LETT, V20, P1646, DOI 10.1364/OL.20.001646
Flanders BN, 1996, J PHYS CHEM-US, V100, P11824, DOI 10.1021/jp960953c
Haran G, 1997, CHEM PHYS LETT, V274, P365, DOI 10.1016/S0009-2614(97)00705-7
HU BB, 1990, APPL PHYS LETT, V57, P2629, DOI 10.1063/1.103829
HU BB, 1995, PHYS REV LETT, V74, P1689, DOI 10.1103/PhysRevLett.74.1689
Jepsen PU, 1996, J OPT SOC AM B, V13, P2424, DOI 10.1364/JOSAB.13.002424
KATZENELLENBOGE.N, 1992, ULTRA WIDEBAND SHORT
Kindt JT, 1996, J PHYS CHEM-US, V100, P10373, DOI 10.1021/jp960141g
Nahata A, 1996, APPL PHYS LETT, V69, P2321, DOI 10.1063/1.117511
NUSS MC, 1987, PHYS REV LETT, V58, P2355, DOI 10.1103/PhysRevLett.58.2355
NUSS MC, 1991, PHYS REV LETT, V66, P3305, DOI 10.1103/PhysRevLett.66.3305
PARKS B, 1995, PHYS REV LETT, V74, P3265, DOI 10.1103/PhysRevLett.74.3265
RALPH SE, 1992, PHOTO INDUCED SPACE, V261
RODRIGUEZ G, 1994, OPT LETT, V19, P1194
SAETA PN, 1992, APPL PHYS LETT, V60, P1477, DOI 10.1063/1.107276
WANG HH, 1993, J ELECTRON MATER, V22, P1461, DOI 10.1007/BF02649999
Wang S, 1989, FUNDAMENTALS SEMICON
ZHANG XC, 1990, APPL PHYS LETT, V56, P1011, DOI 10.1063/1.102601
ZHANG XC, 1994, APPL PHYS LETT, V64, P622, DOI 10.1063/1.111069
Markelz, AG Heilweil, EJ
Markelz, Andrea/0000-0003-0443-4319
22

6
Amer inst physics
Woodbury}, month = {May}, pages = {2229-2231}, type = {Article}, abstract = {

The temperature dependence of the terahertz (THz) output power and spectra from biased photoconductive switches was measured for several antenna gap widths and applied biases. The spectrally integrated THz output had a nonmonotonic temperature dependence in all cases with the value increasing by a factor of 3 from room temperature to 150 K for low biases and 100 K at high biases. An abrupt decrease in output power occurs below 90 K, and the spectrum shifts to lower frequencies as the temperature is lowered. (C) 1998 American Institute of Physics.

}, keywords = {domain, generation, Physics, pulses, semiconductor surfaces, transmission spectroscopy}, isbn = {0003-6951}, doi = {10.1063/1.121329}, author = {Markelz, A. G. and Heilweil, E. J.} } @article {266, title = {Interband impact ionization by terahertz illumination of InAs heterostructures}, journal = {Applied Physics Letters}, volume = {69}, number = {26}, year = {1996}, note = {ISI Document Delivery No.: VY894
Times Cited: 91
Cited Reference Count: 17
Cited References:
ASMAR NG, 1995, PHYS REV B, V51, P18041, DOI 10.1103/PhysRevB.51.18041
Asmar NG, 1996, APPL PHYS LETT, V68, P829, DOI 10.1063/1.116547
BAIER HU, 1986, SOLID STATE COMMUN, V58, P327, DOI 10.1016/0038-1098(86)90094-3
BLOEMBER.N, 1974, IEEE J QUANTUM ELECT, VQE10, P375, DOI 10.1109/JQE.1974.1068132
BOLOGNESI CR, 1994, IEEE ELECTR DEVICE L, V15, P16, DOI 10.1109/55.289476
CERNE J, 1995, PHYS REV B, V51, P5253, DOI 10.1103/PhysRevB.51.5253
GANICHEV SD, 1986, ZH EKSP TEOR FIZ+, V90, P445
GAUER C, 1994, SEMICOND SCI TECH, V9, P1580, DOI 10.1088/0268-1242/9/9/002
Kochman B, 1996, APPL PHYS LETT, V68, P1936, DOI 10.1063/1.115631
MARKELZ AG, 1994, SOLID STATE ELECTRON, V37, P1243, DOI 10.1016/0038-1101(94)90399-9
MARKELZ AG, 1994, SEMICOND SCI TECH, V9, P634, DOI 10.1088/0268-1242/9/5S/063
NGUYEN C, 1993, J VAC SCI TECHNOL B, V11, P1706, DOI 10.1116/1.586509
NGUYEN C, 1993, J ELECTRON MATER, V22, P255, DOI 10.1007/BF02665035
TUTTLE G, 1990, J APPL PHYS, V67, P3032, DOI 10.1063/1.345426
Walpole J. N., 1971, Journal of Applied Physics, V42, P5609, DOI 10.1063/1.1659990
WHITE CRH, 1991, APPL PHYS LETT, V58, P1164, DOI 10.1063/1.104352
XIE H, 1994, J APPL PHYS, V76, P92, DOI 10.1063/1.357065
Markelz, AG Asmar, NG Brar, B Gwinn, EG
Markelz, Andrea/0000-0003-0443-4319
92

6
Amer inst physics
Melville
1077-3118}, month = {Dec}, pages = {3975-3977}, type = {Article}, abstract = {

Experimental studies of InAs heterostructures illuminated by far-infrared (FIR) radiation reveal an abrupt increase in the charge density for FIR intensities above a threshold value that rises with increasing frequency. We attribute this charge density rise to interband impact ionization in a regime in which omega tau(m) similar to 1, where tau(m) is the momentum relaxation time, and f=omega/2 pi is the FIR frequency. The dependence of the density rise on the FIR field strength supports this interpretation, and gives threshold fields of 3.7-8.9 kV/cm for the frequency range 0.3-0.66 THz. (C) 1996 American Institute of Physics.

}, keywords = {energy, far-infrared excitation, inas/alsb quantum-wells, inplane, modulation, Physics}, isbn = {0003-6951}, doi = {10.1063/1.117842}, author = {Markelz, A. G. and Asmar, N. G. and Brar, B. and Gwinn, E. G.} } @article {268, title = {Nonlinear response of quantum-confined electrons in nonparabolic subbands}, journal = {Journal of Applied Physics}, volume = {80}, number = {4}, year = {1996}, note = {7}, month = {Aug 15}, pages = {2533-2535}, abstract = {

We show that quantum confinement can dramatically alter the density-dependence of the third-order susceptibility, chi(NP)((3)) that arises from band nonparabolicity. Our results predict an oscillatory dependence of the efficiencies for third-harmonic generation and four-wave mixing on the subband occupation of quantum wells, and for narrow wells with high charge densities predict an enhancement over the bulk susceptibility. We also make a simple estimate of the fields required to saturate this nonparabolicity contribution to chi((3)). We discuss these results in light of recent experiments on third-harmonic generation from narrow-gap quantum wells at frequencies of similar to 1 THz, and show that nonparabolicity may not be the only nonlinearity contributing to the large chi((3)) observed. (C) 1996 American Institute of Physics.

}, isbn = {0021-8979}, doi = {10.1063/1.363040}, author = {Markelz, A. G. and Gwinn, E. G.} } @article {258, title = {Temperature of quasi-two-dimensional electron gases under steady-state terahertz drive}, journal = {Applied Physics Letters}, volume = {68}, number = {6}, year = {1996}, note = {ISI Document Delivery No.: TT663
Times Cited: 59
Cited Reference Count: 12
Cited References:
ASMAR NG, 1995, PHYS REV B, V51, P18041, DOI 10.1103/PhysRevB.51.18041
BETHUNE DS, 1989, J OPT SOC AM B, V6, P910, DOI 10.1364/JOSAB.6.000910
CERNE J, 1995, PHYS REV B, V51, P5253, DOI 10.1103/PhysRevB.51.5253
CONWELL E, 1967, SOLID STATE PHYS S, V9
GUPTA R, 1992, PHYS REV B, V46, P7745, DOI 10.1103/PhysRevB.46.7745
HEYMAN JN, 1994, PHYS REV LETT, V72, P2183, DOI 10.1103/PhysRevLett.72.2183
KOMIYAMA S, 1985, PHYS REV B, V32, P5532, DOI 10.1103/PhysRevB.32.5532
MARKELZ AG, 1994, SOLID STATE ELECTRON, V37, P1243, DOI 10.1016/0038-1101(94)90399-9
MARKELZ AG, 1995, THESIS U CALIFORNIA
SHAH J, 1984, APPL PHYS LETT, V44, P322, DOI 10.1063/1.94739
SHAH J, 1978, SOLID STATE ELECTRON, V21, P43, DOI 10.1016/0038-1101(78)90113-2
YANG CH, 1985, PHYS REV LETT, V55, P2359, DOI 10.1103/PhysRevLett.55.2359
Asmar, NG Cerne, J Markelz, AG Gwinn, EG Sherwin, MS Campman, KL Gossard, AC
Sherwin, Mark S/Q-4762-2017
Sherwin, Mark S/0000-0002-3869-1893; Markelz, Andrea/0000-0003-0443-4319
59

7
Amer inst physics
Woodbury}, month = {Feb}, pages = {829-831}, type = {Article}, abstract = {

We use photoluminescence to study the time-average energy distribution of electrons in the presence of strong steady-state drive at terahertz (THz) frequencies, in a modulation-doped 125 Angstrom AlGaAs/GaAs square well that is held at low lattice temperature TL. We find that the energy distribution can be characterized by an effective electron temperature, T-e(\>T-L), that agrees well with values estimated from the THz-illuminated, dc conductivity. This agreement indicates that under strong THz drive, LO phonon scattering dominates both energy and momentum relaxation; that the carrier distribution maintains a heated, thermal form; and that phonon drift effects are negligible. (C) 1996 American Institute of Physics.

}, keywords = {hot-electrons, Physics}, isbn = {0003-6951}, doi = {10.1063/1.116547}, author = {Asmar, N. G. and Cerne, J. and Markelz, A. G. and Gwinn, E. G. and Sherwin, M. S. and Campman, K. L. and Gossard, A. C.} } @inbook {304, title = {Third Harmonic Generation in a Gaas/Algaas Superlattice in the Bloch Oscillator Regime}, booktitle = {Hot Carriers in Semiconductors}, volume = {eds. Hess, Karl, Leburton, J.P., Ravaioli, U.}, year = {1996}, pages = {161-163}, publisher = {Plenum Press}, organization = {Plenum Press}, address = {New York, NY}, url = {https://www.springer.com/gp/book/9781461380351}, author = {Wanke, M. C. and Markelz, A. G. and Unterrainer, K. and Allen, S. J. and Bhatt, R.} } @article {265, title = {Undressing a collective intersubband excitation in a quantum well}, journal = {Physical Review Letters}, volume = {76}, number = {13}, year = {1996}, note = {Sherwin, Mark S/Q-4762-2017
Sherwin, Mark S/0000-0002-3869-1893; Markelz, Andrea/0000-0003-0443-4319
78}, month = {Mar 25}, pages = {2382-2385}, abstract = {

We have experimentally measured the 1-2 intersubband absorption in a single 40 nm wide modulation-doped Al0.3Ga0.7As/GaAs square quantum well as a function of frequency, intensity, and charge density. The low-intensity depolarization-shifted absorption occurs near 80 cm(-1) (10 meV or 2.4 THz), nearly 30\% higher than the intersubband spacing. At higher intensities, the absorption peak shifts to lower frequencies. Our data are in good agreement with a theory proposed by Zaluzny, which attributes the redshift to a reduction in the depolarization shift as the excited subband becomes populated.

}, isbn = {0031-9007}, doi = {10.1103/PhysRevLett.76.2382}, author = {Craig, K. and Galdrikian, B. and Heyman, J. N. and Markelz, A. G. and Williams, J. B. and Sherwin, M. S. and Campman, K. and Hopkins, P. F. and Gossard, A. C.} } @article {272, title = {NONLINEAR QUANTUM DYNAMICS IN SEMICONDUCTOR QUANTUM-WELLS}, journal = {Physica D-Nonlinear Phenomena}, volume = {83}, number = {1-3}, year = {1995}, note = {Sherwin, Mark S/Q-4762-2017
Sherwin, Mark S/0000-0002-3869-1893; Markelz, Andrea/0000-0003-0443-4319
14th Annual International Conference of the Center-for-Nonlinear-Studies - Quantum Complexity in Mesoscopic Systems
May 16-20, 1994
Los alamos, nm
Ctr nonlinear studies
34}, month = {May 15}, pages = {229-242}, abstract = {

We discuss recent measurements of the nonlinear response of electrons in wide quantum wells driven by intense electromagnetic radiation at terahertz frequencies. The theme is the interplay of quantum mechanics, strong periodic driving, the electron-electron interaction and dissipation. We discuss harmonic generation from an asymmetric double quantum well in which the effects of dynamic screening are important. Measurements and theory are found to be in good agreement. We also discuss intensity-dependent absorption in a 400 Angstrom square quantum well. A new nonlinear quantum effect occurs, in which the frequency at which electromagnetic radiation is absorbed shifts to the red with increasing intensity. The preliminary experimental results are in agreement with a theory by Zaluzny, in which the source of the nonlinearity is the self-consistent potential in the Hartree approximation for the electron dynamics.

}, isbn = {0167-2789}, doi = {10.1016/0167-2789(94)00266-S}, author = {Sherwin, M. S. and Craig, K. and Galdrikian, B. and Heyman, J. and Markelz, A. and Campman, K. and Fafard, S. and Hopkins, P. F. and Gossard, A.} } @article {262, title = {QUENCHING OF EXCITONIC QUANTUM-WELL PHOTOLUMINESCENCE BY INTENSE FAR-INFRARED RADIATION - FREE-CARRIER HEATING}, journal = {Physical Review B}, volume = {51}, number = {8}, year = {1995}, note = {Sherwin, Mark S/Q-4762-2017
Sherwin, Mark S/0000-0002-3869-1893; Markelz, Andrea/0000-0003-0443-4319
29}, month = {Feb 15}, pages = {5253-5262}, isbn = {0163-1829}, doi = {10.1103/PhysRevB.51.5253}, author = {Cerne, J. and Markelz, A. G. and Sherwin, M. S. and Allen, S. J. and Sundaram, M. and Gossard, A. C. and Vanson, P. C. and Bimberg, D.} } @article {259, title = {RESONANT-ENERGY RELAXATION OF TERAHERTZ-DRIVEN 2-DIMENSIONAL ELECTRON GASES}, journal = {Physical Review B}, volume = {51}, number = {24}, year = {1995}, note = {Sherwin, Mark S/Q-4762-2017
Sherwin, Mark S/0000-0002-3869-1893; Markelz, Andrea/0000-0003-0443-4319
119}, month = {Jun 15}, pages = {18041-18044}, isbn = {0163-1829}, doi = {10.1103/PhysRevB.51.18041}, author = {Asmar, N. G. and Markelz, A. G. and Gwinn, E. G. and Cerne, J. and Sherwin, M. S. and Campman, K. L. and Hopkins, P. F. and Gossard, A. C.} } @proceedings {181, title = {Terahertz grid frequency doublers}, year = {1995}, publisher = {Citeseer}, url = {https://www.nrao.edu/meetings/isstt/papers/1995/1995199206.pdf}, author = {Chiao, Jung-Chih and Markelz, Andrea and Li, Yongjun and Hacker, Jonathan and Crowe, Thomas and Allen, James and Rutledge, David} } @proceedings {317, title = {Third harmonic generation in a GaAs/AlGaAs Superlattice in the Bloch Oscillator Regime}, year = {1995}, month = {07/1995}, pages = {161-163}, address = {Chicago, IL}, author = {Wanke, M. C. and Markelz, A.G. and Unterrainer, K. and Allen, S. J. and Bhatt, R.} } @article {260, title = {DC TRANSPORT IN INTENSE, INPLANE TERAHERTZ ELECTRIC-FIELDS IN AL(X)GA(1-X)AS HETEROSTRUCTURES AT 300-K}, journal = {Solid-State Electronics}, volume = {37}, number = {4-6}, year = {1994}, note = {Markelz, Andrea/0000-0003-0443-4319
6th International Conference on Modulated Semiconductor Structures
Aug 23-27, 1993
Garmisch partenkir, germany
Tech univ munchen, walter schottky inst
1}, month = {Apr-Jun}, pages = {693-695}, abstract = {

We report 300 K studies of the dependence of the in-plane, d.c. conductivity, sigma(d.c.) (E(omega)), of a quasi 2D electron gas on the amplitude E(omega) and frequency of intense, far-infrared fields (omega/2pi = 0.24-3.5 THz). We measure sigma(d.c.) (E(omega) parallel-to E(d.c.)), where E(d.c.) is a small sensing field, and observe a monotonic decrease in sigma(d.c.) with increasing E(omega). Although a simple scaling ansatz collapses the measured sigma(d.c.) (E(omega)) data onto a single curve for frequencies from 0.25-3.45 THz (at low to moderate scaled fields), the decrease in conductivity is substantially more rapid than expected from comparison to similar data taken by Masselink et al. [Solid-St. Electron. 31, 337 (1988)] at 35 GHz. We tentatively attribute this difference to effects of a high-frequency modulation in the electron temperature.

}, isbn = {0038-1101}, doi = {10.1016/0038-1101(94)90278-X}, author = {Asmar, N. G. and Markelz, A. G. and Gwinn, E. G. and Hopkins, P. F. and Gossard, A. C.} } @article {261, title = {ENERGY RELAXATION AT THZ FREQUENCIES IN ALXGA1-XAS HETEROSTRUCTURES}, journal = {Semiconductor Science and Technology}, volume = {9}, number = {5}, year = {1994}, note = {Markelz, Andrea/0000-0003-0443-4319
S
8th International Conference on Hot Carriers in Semiconductors
Aug 16-20, 1993
Oxford univ, oxford, england
Sci \& engn res council; royal soc; brit council; oxford univ
2}, month = {May}, pages = {828-830}, abstract = {

We report 4.2 K studies of the dependence of the in-plane, DC conductivity of a quasi 2D electron gas on the amplitude E(omega) of applied fields with frequencies from 0.25 THz to 3.5 THz. We analyse the dependence of sigma(DC) on E(omega) assuming that electron-optical phonon scattering dominates energy relaxation, that the absorbed power has a Drude form and that the electron distribution is thermal. This simple analysis is self-consistent: Arrhenius plots of the estimated energy loss rate have a slope near -homega(LO)BAR/k(B) for all frequencies, as expected for energy loss by optical phonon emission. We find that the effective energy relaxation time tau(epsilon) varies with the frequency of the applied field, from tau(epsilon) approximately 4 ps at 0.34 THz to tau(epsilon) approximately 0.3 ps at 3.45 THz. This may indicate a frequency-dependent form for the hot-phonon distribution.

}, isbn = {0268-1242}, doi = {10.1088/0268-1242/9/5S/116}, author = {Asmar, N. G. and Markelz, A. G. and Gwinn, E. G. and Hopkins, P. F. and Gossard, A. C.} } @proceedings {319, title = {Far-infrared harmonic generation from semiconductor heterostructures}, volume = {1854}, year = {1994}, pages = {48-55}, author = {Markelz, A.G. and Gwinn, E. G. and Sherwin, M. S. and Heyman, J. N. and Nguyen, C. and Kroemer, H.} } @article {264, title = {FAR-INFRARED SATURATION SPECTROSCOPY OF A SINGLE SQUARE-WELL}, journal = {Semiconductor Science and Technology}, volume = {9}, number = {5}, year = {1994}, note = {Sherwin, Mark S/Q-4762-2017
Sherwin, Mark S/0000-0002-3869-1893; Markelz, Andrea/0000-0003-0443-4319
S
8th International Conference on Hot Carriers in Semiconductors
Aug 16-20, 1993
Oxford univ, oxford, england
Sci \& engn res council; royal soc; brit council; oxford univ
31}, month = {May}, pages = {627-629}, abstract = {

We have performed saturation spectroscopy measurements of the lowest intersubband transition in a single 400 angstrom GaAs/Al0.3Ga0.7As modulation-doped square quantum well. We couple intense tunable far-infrared radiation from the Santa Barbara free electron laser into our sample using an edge-coupling technique and measure absorption as a function of frequency and intensity. Saturation and frequency shifts in the absorption line are clearly observed. We attribute the frequency shifts to reductions in the many-body depolarization shift. From our preliminary measurements, we estimate the intersubband relaxation time to be 600 ps to within a factor of three.

}, isbn = {0268-1242}, doi = {10.1088/0268-1242/9/5S/061}, author = {Craig, K. and Felix, C. L. and Heyman, J. N. and Markelz, A. G. and Sherwin, M. S. and Campman, K. L. and Hopkins, P. F. and Gossard, A. C.} } @proceedings {318, title = {Frequency Dependence of the Third Order Susceptibility of InAs Quantum Wells at Terahertz Frequencies}, year = {1994}, month = {08/1994}, pages = {1193-1196}, author = {Markelz, A.G. and Cerne, J. and Gwinn, E. G. and Brar, B. and Kroemer, H.} } @article {269, title = {GIANT 3RD-ORDER NONLINEAR SUSCEPTIBILITIES FOR INPLANE FAR-INFRARED EXCITATION OF SINGLE INAS QUANTUM-WELLS}, journal = {Solid-State Electronics}, volume = {37}, number = {4-6}, year = {1994}, note = {Sherwin, Mark S/Q-4762-2017
Sherwin, Mark S/0000-0002-3869-1893; Markelz, Andrea/0000-0003-0443-4319
6th International Conference on Modulated Semiconductor Structures
Aug 23-27, 1993
Garmisch partenkir, germany
Tech univ munchen, walter schottky inst
9}, month = {Apr-Jun}, pages = {1243-1245}, abstract = {

Third-order, free-carrier nonlinear susceptibilities, chi(3), have been measured between 19 and 23 cm-1 for three InAs/AlSb quantum wells with sheet densities between 2.5 x 10(12) cm-2 and 8 x 10(12) cm-2. We find that these wells are strongly nonlinear at far-infrared frequencies: odd harmonics ninth order have been observed at high incident intensities, and the peak value of chi(3) reaches approximately 1 esu. This is several orders of magnitude larger than previously reported values for chi(3) in bulk n-GaAs (10(-4) esu)[1] and in polyacetylene (10(-7) esu)[2]. The large magnitude of chi(3) is attributed to the high carrier density in the InAs wells, and to the strong non-parabolicity of the conduction band in InAs. However, the free-carrier chi(3) for bulk InAs predicts a density-dependence different from that observed, and the measured decrease in chi(3) with increasing intensity indicates non-perturbative response. We find that the anisotropy of chi(3) displays the expected 4-fold symmetry.

}, isbn = {0038-1101}, doi = {10.1016/0038-1101(94)90399-9}, author = {Markelz, A. G. and Gwinn, E. G. and Sherwin, M. S. and Nguyen, C. and Kroemer, H.} } @article {257, title = {PROBING TERAHERTZ DYNAMICS IN SEMICONDUCTOR NANOSTRUCTURES WITH UCSB FREE-ELECTRON LASERS}, journal = {Journal of Luminescence}, volume = {60-1}, year = {1994}, note = {Sherwin, Mark S/Q-4762-2017; Guimaraes, Paulo Sergio Soares/B-6918-2012
Sherwin, Mark S/0000-0002-3869-1893; Guimaraes, Paulo Sergio Soares/0000-0002-0113-2641; Markelz, Andrea/0000-0003-0443-4319
1993 International Conference on Luminescence (ICL 93)
Aug 09-13, 1993
Univ connecticut, storrs, ct
Univ connecticut; opt soc amer; amer phys soc; ieee, laser \& electro opt soc; int union pure \& appl phys; int sci fdn; univ connecticut res fdn
3}, month = {Apr}, pages = {250-255}, abstract = {

The UCSB free-electron lasers provide kilowatts of continuously tunable radiation from 120 GHz to 4.8 THz. They have the most impact on terahertz science and technology that require a tunable, high power source to explore non-linear dynamics or that sacrifice incident power to recover the linear response of systems with very small cross-section. We describe three experiments that demonstrate the utility of these lasers in experiments on the terahertz dynamics of semiconductor nanostructures: (i) terahertz dynamics of resonant tunneling diodes, (ii) saturation spectroscopy of quantum wells and (iii) photon-assisted tunneling in superlattices.

}, isbn = {0022-2313}, doi = {10.1016/0022-2313(94)90142-2}, author = {Allen, S. J. and Craig, K. and Felix, C. L. and Guimaraes, P. and Heyman, J. N. and Kaminski, J. P. and Keay, B. J. and Markelz, A. G. and Ramian, G. and Scott, J. S. and Sherwin, M. S. and Campman, K. L. and Hopkins, P. F. and Gossard, A. C. and Chow, D. and Lui, M. and Liu, T. Y.} } @article {267, title = {SUBCUBIC POWER DEPENDENCE OF 3RD-HARMONIC GENERATION FOR INPLANE, FAR-INFRARED EXCITATION OF INAS QUANTUM-WELLS}, journal = {Semiconductor Science and Technology}, volume = {9}, number = {5}, year = {1994}, note = {Sherwin, Mark S/Q-4762-2017
Sherwin, Mark S/0000-0002-3869-1893; Markelz, Andrea/0000-0003-0443-4319
S
8th International Conference on Hot Carriers in Semiconductors
Aug 16-20, 1993
Oxford univ, oxford, england
Sci \& engn res council; royal soc; brit council; oxford univ
4}, month = {May}, pages = {634-637}, abstract = {

Large third-order, free-carrier nonlinear susceptibilities, chi(3) (to approximately 0.2 esu), and subcubic dependence of the third-harmonic power on the incident intensity, have been observed between 19 cm-1 and 23 cm-1 for InAs/AlSb quantum wells with electron sheet densities between 2.5 x 10(12) cm-2 and 8 X 10(12) cm-2. We find that the transmission of the fundamental, and the samples{\textquoteright} DC conductivity, decrease with increasing incident intensity, indicating a large rise in the scattering rate. Using the intensity-dependent transmission to account for absorption in the sample is not sufficient to recover a cubic power law for the third-harmonic intensity. In addition, given the increased scattering rate indicated by the conductivity data, the bulk free-carrier chi(3) due to non-parabolicity should decrease dramatically with increasing fundamental intensity, contrary to our results. Thus, non-parabolicity alone cannot account for the observed third-harmonic response.

}, isbn = {0268-1242}, doi = {https://doi.org/10.1088/0268-1242/9/5S/063}, author = {Markelz, A. G. and Asmar, N. G. and Gwinn, E. G. and Sherwin, M. S. and Nguyen, C. and Kroemer, H.} } @proceedings {320, title = {Far-infrared nonlinear response of electrons in semiconductor nanostructures}, volume = {1854}, year = {1993}, pages = {36-47}, author = {Sherwin, M. S. and Asmar, N. G. and Bewley, W. W. and Craig, K. and Felix, C. L. and Galdrikian, B. and Gwinn, E. G. and Markelz, A.G. and Gossard, A. C. and Hopkins, P. F. and Sundaram, M. and Birnir, B.} } @article {298, title = {Site-selective oxygen-isotope substitution in YBa2Cu3O7-δ}, journal = {Physical Review B}, volume = {44}, year = {1991}, chapter = {9556}, abstract = {

We report selective substitution of oxygen-18 and oxygen-16 isotopes into the inequivalent oxygen lattice sites in YBa2Cu3O7-δ. The technique involves gas-phase diffusion and exploits the site dependence of diffusion rates. The CuO2-plane [O(2),O(3)] sites of YBa2Cu3O7-δ can be filled with 18O while the apical [O(4)] and CuO-chain sites [O(1)] contain 16O (the opposite distribution can also be made). The site-selective isotope occupation has been confirmed by Raman spectroscopy. Our method will permit experiments to determine the contributions of the different oxygen sites to the isotope effect, in order to locate the pairing interaction within the unit cell.

}, doi = {10.1103/PhysRevB.44.9556}, url = {https://journals.aps.org/prb/abstract/10.1103/PhysRevB.44.9556}, author = {Morris, D. E. and Markelz, A. G. and Wei, J. Y. T. and Huitgren, C. T. and Nickel, J. H. and Hamilton, J. C. and McCarty, K. F.} } @proceedings {321, title = {Conversion of 124 and 123 + cupric oxide: microstructure and phase diagram}, volume = {169}, year = {1990}, pages = {245-248}, author = {Morris, D. E. and Nickel, J. H. and Markelz, A.G. and Gronksy, R. and Fendorf, M. and Burmester, C. P.} } @article {280, title = {CONVERSION OF 124 INTO 123+CUO AND 124, 123 AND 247 PHASE REGIONS IN THE Y-BA-CU-O SYSTEM}, journal = {Physica C}, volume = {168}, number = {1-2}, year = {1990}, note = {Markelz, Andrea/0000-0003-0443-4319
76}, month = {Jun 1}, pages = {153-160}, isbn = {0921-4534}, doi = {10.1016/0921-4534(90)90118-X}, author = {Morris, D. E. and Markelz, A. G. and Fayn, B. and Nickel, J. H.} } @article {281, title = {8 NEW HIGH-TEMPERATURE SUPERCONDUCTORS WITH THE 1-2-4 STRUCTURE}, journal = {Physical Review B}, volume = {39}, number = {10}, year = {1989}, note = {Scheven, Ulrich/D-7582-2013
Markelz, Andrea/0000-0003-0443-4319; Scheven, Ulrich/0000-0001-8111-0081
B
241}, month = {Apr 1}, pages = {7347-7350}, isbn = {0163-1829}, doi = {10.1103/physrevb.39.7347 }, author = {Morris, D. E. and Nickel, J. H. and Wei, J. Y. T. and Asmar, N. G. and Scott, J. S. and Scheven, U. M. and Hultgren, C. T. and Markelz, A. G. and Post, J. E. and Heaney, P. J. and Veblen, D. R. and Hazen, R. M.} } @article {278, title = {OXYGEN CONCENTRATION EFFECT ON TC OF THE BI-CA-SR-CU-O SUPERCONDUCTOR}, journal = {Physical Review B}, volume = {39}, number = {10}, year = {1989}, note = {A
155}, month = {Apr 1}, pages = {6612-6614}, isbn = {0163-1829}, doi = {https://doi.org/10.1103/physrevb.39.6612 }, author = {Morris, D. E. and Hultgren, C. T. and Markelz, A. M. and Wei, J. Y. T. and Asmar, N. G. and Nickel, J. H.} } @article {279, title = {SMALL OXYGEN ISOTOPE SHIFT IN YBA2CU3O7}, journal = {Physical Review B}, volume = {37}, number = {10}, year = {1988}, note = {Markelz, Andrea/0000-0003-0443-4319
B
74}, month = {Apr 1}, pages = {5936-5939}, isbn = {0163-1829}, doi = {10.1103/physrevb.37.5936}, author = {Morris, D. E. and Kuroda, R. M. and Markelz, A. G. and Nickel, J. H. and Wei, J. Y. T.} } @article {277, title = {SPECIFIC-HEAT MEASUREMENTS ON SUPERCONDUCTING BI-CA-SR-CU AND TL-CA-BA-CU OXIDES - ABSENCE OF A LINEAR TERM IN THE SPECIFIC-HEAT OF BI-CA-SR-CU OXIDES}, journal = {Physical Review B}, volume = {38}, number = {16}, year = {1988}, note = {Fisher, Robert Anthony/H-6779-2019
Markelz, Andrea/0000-0003-0443-4319
B
68}, month = {Dec 1}, pages = {11942-11945}, isbn = {0163-1829}, doi = {10.1103/PhysRevB.38.11942}, author = {Fisher, R. A. and Kim, S. and Lacy, S. E. and Phillips, N. E. and Morris, D. E. and Markelz, A. G. and Wei, J. Y. T. and Ginley, D. S.} }