@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 {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.} } @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} } @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
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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 {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 {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} } @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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Sy S, 2010, PHYS MED BIOL, V55, P7587, DOI 10.1088/0031-9155/55/24/013
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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.} } @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} } @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:
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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
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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
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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
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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
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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
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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
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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 {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.} } @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 {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 {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.} } @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.} }