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