@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 {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
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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 {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.} } @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} } @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
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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 {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.} } @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.} } @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
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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 {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
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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.} } @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.} } @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
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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
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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:
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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
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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
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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.} } @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 {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
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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.} } @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} } @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 {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.} } @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.} }