@article {282, title = {Is the Protein Dynamical Transition useful?}, journal = {Biophysical Journal}, volume = {118}, year = {2020}, chapter = {521a}, doi = {10.1016/j.bpj.2019.11.2866}, author = {Sharma, A. and George, D. K. and Crossen, K. and McKinney, J. and Kerfeld, C. and Markelz, A.} } @proceedings {544, title = {Stabilization of Terahertz Vibrational Modes in Illuminated Orange Carotenoid Protein Crystals}, year = {2020}, address = {Buffalo, NY}, abstract = {

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

}, doi = {10.1109/IRMMW-THz46771.2020.9370827}, author = {McKinney, J. and Sharma, A. and Deng, Y. and George, D. and Lechno-Yossef, S. and Kerfeld, C. and Markelz, A.} } @proceedings {612, title = {THz Transmission through Submillimeter Apertures}, year = {2020}, month = {11/2020}, address = {Buffalo NY}, abstract = {
Terahertz near-field microspectroscopy is emerging as an essential tool for characterization of novel materials and biomolecules. It is important to ensure the near field geometry used does not introduce spectral artifacts. For example, many scanning techniques can be strongly influenced by the interaction between the scattering tip and the sample. Here we examine the spectroscopic effects of a 200 μm diameter aperture for THz near-field measurements. We use HFSS to model free-space transmission through samples with resonant absorbance as a function of sample thickness, lateral sample width, and aperture diameter. We examine the transmitted power and spectral fidelity for coupling of transmitted THz light onto a detector. These studies inform corrective post-measurement analysis algorithms and design of near-field detection systems.
}, doi = {10.1109/IRMMW-THz46771.2020.9370923}, url = {https://ieeexplore.ieee.org/document/9370923}, author = {LaFave, T. and Lee, A. and Kao, T.-Y. and Markelz, A.} } @article {248, title = {Deuteration and Inhibitor Binding Dependence of Protein Collective Vibrations}, journal = {Biophysical Journal}, volume = {116}, number = {3}, year = {2019}, note = {ISI Document Delivery No.: HO2XG
Times Cited: 0
Cited Reference Count: 2
Cited References:
Mahajan S, 2015, ARCH BIOCHEM BIOPHYS, V567, P59, DOI 10.1016/j.abb.2014.12.020
Niessen KA, 2017, BIOPHYS J, V112, P933, DOI 10.1016/j.bpj.2016.12.049
Deng, Yanting Mckinney, Jeffrey Markelz, Andrea
63rd Annual Meeting of the Biophysical-Society
Mar 02-06, 2019
Baltimore, MD
Biophys Soc

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

8
Cell press
Cambridge
1542-0086
1}, month = {Feb}, pages = {489A-489A}, type = {Meeting Abstract}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2018.11.2638}, author = {McKinney, J. A. and Deng, Y. T. and George, D. and Markelz, A.} } @article {249, title = {Spectral Assignment of Lysozyme Collective Vibrations}, journal = {Biophysical Journal}, volume = {116}, number = {3}, year = {2019}, note = {ISI Document Delivery No.: HO2XG
Times Cited: 0
Cited Reference Count: 1
Cited References:
Niessen KA, 2017, BIOPHYS J, V112, P933, DOI 10.1016/j.bpj.2016.12.049
Deng, Yanting Mckinney, Jeffrey Romo, Tod Grossfield, Alan Markelz, Andrea
63rd Annual Meeting of the Biophysical-Society
Mar 02-06, 2019
Baltimore, MD
Biophys Soc

8
Cell press
Cambridge
1542-0086
1}, month = {Feb}, pages = {564A-564A}, type = {Meeting Abstract}, abstract = {
Global structural vibrations at terahertz (THz) frequencies have been associated with protein function and allosteric control. A chief obstacle to utilizing this control mechanism has been measurement of specific motions. Recently it was shown that while the vibrational density of states, and isotropic absorption spectra are broad and featureless, collective vibrations can be isolated based on their directionality using aligned samples (realized with protein crystals) and anisotropic THz microscopy [1]. However the assignment of resonant bands to specific structural motions was complicated by the high symmetry of the tetragonal crystals used, and the slow experimental method. To structurally map the vibrations of the chicken egg white lysozyme (CEWL) we measure anisotropic absorption of triclinic crystals using our new technique: ideal polarization varying anisotropic THz microscopy (IPV-ATM). The low symmetry triclinic crystals provide absolute protein orientation, and the near field IPV-ATM rapidly measures broadband terahertz linear dichroism of the microcrystals. All measurements were performed at room temperature under 100\% humidity conditions. The unit cell parameters of triclinic lysozyme nitrate crystals, α = 28.5A{\textdegree}, b = 32.7A{\textdegree}, c = 35.1A{\textdegree}, α = 88.2{\textdegree}, β = 108.9{\textdegree}, γ = 111.9{\textdegree}, belonging to the P1 space group, were determined by X-ray diffraction before and after THz measurements. The intramolecular vibrational absorbance of the triclinic crystals has a more complex polarization dependence than the higher symmetry tetragonal crystals, as expected. While the tetragonal crystals have two strong bands at 45cm-1 and 55cm-1, the triclinic crystals have a series of narrow bands between 40 and 60cm-1 and a prominent band at 30cm-1. We compare the measured spectra to normal mode ensemble averaged calculations to assign the observed resonances, and isolating which collective motions impact the catalytic site.
}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2018.11.3032}, author = {Deng, Y. T. and McKinney, J. and Romo, T. and Grossfield, A. and Markelz, A.} } @conference {286, title = {Investigation of the Isotope Shift in Protein Collective Vibrations}, booktitle = {APS 2018}, volume = {A50.013}, year = {2018}, url = {http://meetings.aps.org/link/BAPS.2018.MAR.A50.13}, author = {Luck, C. and Xu, M. and Markelz, A.} } @conference {284, title = {Measuring Protein Intramolecular Dynamics with Terahertz Light: Functional Changes and Relevance to Biology}, booktitle = {APS 2018}, volume = {H50.001}, year = {2018}, url = {http://meetings.aps.org/link/BAPS.2018.MAR.H50.1}, author = {Xu, M. and Deng, Y. and Luck, C. and Sharma, A. and Markelz, A.} } @conference {285, title = {Rapid Terahertz Dichroism Near Field Microscopy for Biomolecular Intramolecular Vibrational Spectroscopy}, booktitle = {APS 2018}, volume = {A50.008}, year = {2018}, url = {http://meetings.aps.org/link/BAPS.2018.MAR.A50.8}, author = {Deng, Y. and Niessen, K. and Markelz, A.} } @conference {288, title = {Global Picosecond Structural Dynamics of Orange Carotenoid Protein in Photo/Chemical Activated Signaling States}, booktitle = {APS 2017 S4.002}, year = {2017}, month = {03/2017}, url = {http://meetings.aps.org/link/BAPS.2017.MAR.S4.2}, author = {Deng, Y. and Xu, M. and Liu, H. and Blankenship, R. and Markelz, A.} } @conference {287, title = {Temperature dependence of phonons in photosynthesis proteins}, booktitle = {APS 2017 S4.003}, year = {2017}, url = {http://meetings.aps.org/link/BAPS.2017.MAR.S4.3}, author = {Xu, M. and Myles, D. and Blankenship, R. and Markelz, A.} } @article {274, title = {Hydration Effects on Energy Relaxation of Ferric Cytochrome C Films after Soret-Band Photoexcitation}, journal = {Journal of Physical Chemistry B}, volume = {114}, number = {46}, year = {2010}, note = {ISI Document Delivery No.: 681CT
Times Cited: 3
Cited Reference Count: 87
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Ye, Shuji Markelz, Andrea
Ye, Shuji/B-4479-2010
Markelz, Andrea/0000-0003-0443-4319
NSFNational Science Foundation (NSF) [PHY-0349256, DBI-2959989]; University of Science and Technology of China; Fundamental Research Funds for the Central UniversitiesFundamental Research Funds for the Central Universities; National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [21073175]; National Basic Research Program of ChinaNational Basic Research Program of China [2010CB923300]
This work was supported by NSF CAREER Grant PHY-0349256 and NSF MRI-R2 Grant DBI-2959989, the start-up funding from University of Science and Technology of China, the Fundamental Research Funds for the Central Universities, National Natural Science Foundation of China (Grant 21073175), and National Basic Research Program of China (Grant 2010CB923300).
3
2
20
Amer chemical soc
Washington}, month = {Nov}, pages = {15151-15157}, type = {Article}, abstract = {

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

}, keywords = {Chemistry, circular-dichroism, conformation change, dynamics, ferricytochrome-c, protein hydration, resolved resonance raman, spectroscopy, unfolded states, vibrational-relaxation, water-molecules}, isbn = {1520-6106}, doi = {10.1021/jp104217j}, author = {Ye, S. J. and Markelz, A.} } @article {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.} }