@article{zhang_bykhovski_brown_2022, title={Investigation of THz Absorptive Signatures in Opioids}, volume={12}, ISSN={["2076-3417"]}, DOI={10.3390/app12010061}, abstractNote={We investigate the possibility of sensing opioid drugs, such as fentanyl, by their THz electromagnetic signatures. The methods include both computer modeling and experiments. Molecular dynamics simulations predict that fentanyl should display THz resonances, with several of them occurring below 1.0 THz; the lowest one is at around 0.337 THz (337 GHz). Spectroscopy measurements were conducted on oxycodone, which was used as a surrogate for fentanyl. They display vibrational absorption resonances between ∼1.4 and 1.6 THz.}, number={1}, journal={APPLIED SCIENCES-BASEL}, author={Zhang, Weidong and Bykhovski, Alexei and Brown, Elliott R.}, year={2022}, month={Jan} }
 @article{zhang_bykhovski_himed_yan_brown_2020, title={An investigation of THz label-free opioid sensing}, ISSN={["2162-2027"]}, DOI={10.1109/IRMMW-THZ46771.2020.9370421}, abstractNote={We present numerical modeling and experiments on the THz electromagnetic signatures of various opioid powders.}, journal={2020 45TH INTERNATIONAL CONFERENCE ON INFRARED, MILLIMETER, AND TERAHERTZ WAVES (IRMMW-THZ)}, author={Zhang, W-D and Bykhovski, A. and Himed, L. and Yan, Z-G and Brown, E. R.}, year={2020} }
 @article{zhang_bykhovski_deibel_brown_2017, title={Experimental and Theoretical Study of Strong Low-Terahertz Absorption of Thymine}, volume={38}, ISSN={["1866-6906"]}, DOI={10.1007/s10762-017-0420-z}, number={12}, journal={JOURNAL OF INFRARED MILLIMETER AND TERAHERTZ WAVES}, author={Zhang, W. -D. and Bykhovski, A. and Deibel, J. A. and Brown, E. R.}, year={2017}, month={Dec}, pages={1521–1529} }
 @article{bykhovski_zhang_jensen_woolard_2013, title={Analysis of Electronic Structure, Binding, and Vibrations in Biotin-Streptavidin Complexes Based on Density Functional Theory and Molecular Mechanics}, volume={117}, ISSN={["1520-6106"]}, DOI={10.1021/jp3075833}, abstractNote={In this work, the biotin-streptavidin complex was studied with density functional theory (DFT), molecular mechanical methods (MM), and a hybrid DFT/MM approach in order to obtain the theoretical predictions for electronic structures, binding, optical transitions, harmonic vibrations, and absorption spectra. It was demonstrated that biotin solvation in water can reduce the binding strength to streptavidin by more than half. All studied properties, including the biotin binding and the UV absorption of the biotin-streptavidin complex, are predicted to be protonation state dependent. The absorption edge of the complex calculated with TDDFT/MM was found to be virtually insensitive to the choice of the MM force field and strongly dependent on the type of embedding of the DFT partition. Both UV and terahertz light absorption spectra are predicted to be sensitive to the presence of biotin in the streptavidin tetramer.}, number={1}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Bykhovski, Alexei and Zhang, Weidong and Jensen, James and Woolard, Dwight}, year={2013}, month={Jan}, pages={25–37} }
 @article{bykhovski_woolard_2013, title={Terahertz Spectra of Biotin Based on First Principle, Molecular Mechanical, and Hybrid Simulations}, volume={3}, ISSN={["2156-342X"]}, DOI={10.1109/tthz.2013.2267413}, abstractNote={Terahertz (THz) absorption of biotin was simulated using the first principle and the density functional theory (DFT) both in the harmonic approximation and with corrections for the anharmonicity. Anharmonicity corrections were calculated using two different approaches. First, the perturbation theory-based first principle calculations were performed to include third- and fourth-order anharmonicity corrections in atomic displacements to harmonic vibrational states. Second, the atom-centered density matrix propagation molecular dynamics model that provides a good energy conservation was used to calculate the atomic trajectories, velocities, and a dipole moment time history of biotin at low and room temperatures. Predicted low-THz lines agree well with the experimental spectra. The influence of the polyethylene (PE) matrix embedment on the THz spectra of biotin at the nanoscale was studied using the developed hybrid DFT/molecular mechanical approach. While PE is almost transparent at THz frequencies, additional low-THz lines are predicted in the biotin/PE system, which reflects a dynamic interaction between biotin and a surrounding PE cavity.}, number={4}, journal={IEEE TRANSACTIONS ON TERAHERTZ SCIENCE AND TECHNOLOGY}, author={Bykhovski, Alexei and Woolard, Dwight}, year={2013}, month={Jul}, pages={357–362} }
 @article{bykhovski_woolard_2013, title={Terahertz Spectra of Biotin Based on First Principle, Molecular Mechanical, and Hybrid Simulations}, volume={17}, ISSN={["2168-2194"]}, DOI={10.1109/jbhi.2013.2253786}, abstractNote={Terahertz (THz) absorption of biotin was simulated using the first principle and the density functional theory (DFT) both in the harmonic approximation and with corrections for the anharmonicity. Anharmonicity corrections were calculated using two different approaches. First, the perturbation theory-based first principle calculations were performed to include third- and fourth-order anharmonicity corrections in atomic displacements to harmonic vibrational states. Second, the atom-centered density matrix propagation molecular dynamics model that provides a good energy conservation was used to calculate the atomic trajectories, velocities, and a dipole moment time history of biotin at low and room temperatures. Predicted low-THz lines agree well with the experimental spectra. The influence of the polyethylene (PE) matrix embedment on the THz spectra of biotin at the nanoscale was studied using the developed hybrid DFT/molecular mechanical approach. While PE is almost transparent at THz frequencies, additional low-THz lines are predicted in the biotin/PE system, which reflects a dynamic interaction between biotin and a surrounding PE cavity.}, number={4}, journal={IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS}, author={Bykhovski, Alexei and Woolard, Dwight}, year={2013}, month={Jul}, pages={768–773} }
 @article{mokrauer_kelley_bykhovski_2011, title={Efficient Parallel Computation of Molecular Potential Energy Surfaces for the Study of Light-Induced Transition Dynamics in Multiple Coordinates}, volume={10}, ISSN={["1941-0085"]}, DOI={10.1109/tnano.2010.2058862}, abstractNote={The conformational dynamics of molecules that arise due to light-induced transitions are critically important in many biochemical reactions, and therefore dictate the functionality of many types of biological sensors. Therefore, researchers of biological science and biological-inspired technology often need to prescribe the molecular geometry of the stable states and the associated transition trajectories that occur as a result of external excitation, e.g., light-induced transitions from the ground state to the excited states. The traditional approach to study this type of phenomenology is to limit the number of varying molecular coordinates to one or a few due to the considerable computational expense of the required physically modeling required for generating an accurate physical model for analysis. While the conformational dynamics for some types of simple molecules (e.g., retinal) are known to be adequately described by one or few numbers of molecular coordinates, light-induced transitions in arbitrarily complex molecules can be expected to involve the influence of multiple coordinates, and their influence can be expected to vary as a function of time. The research reported here will address the development of parallel computational algorithms that allow for the highly efficient study of molecular conformational dynamics over multiple numbers of multidimensional energy surfaces. Here, the goal is the development of a simulation tool that is capable of: constructing physically accurate multidimensional potential energy surfaces (i.e., from first-principle physical modeling codes); deriving the natural trajectories to local minima within individual surfaces; and that allows for dynamics human interfacing for specifying the transition between energy surfaces and the number of coordinates to be used for the optimization within a particular energy surface. As will be illustrated, this type of physics-based simulation tool will allow researchers to efficiently explore the light-induced conformation dynamics associated with complex biomolecules, and therefore, be a useful tool for the design of biological-sensing processes in the future.}, number={1}, journal={IEEE TRANSACTIONS ON NANOTECHNOLOGY}, author={Mokrauer, David and Kelley, C. T. and Bykhovski, Alexei}, year={2011}, month={Jan}, pages={70–74} }
 @article{bykhovski_zhao_woolard_2010, title={First Principle Study of the Terahertz and Far-Infrared Spectral Signatures in DNA Bonded to Silicon Nanodots}, volume={10}, ISSN={["1530-437X"]}, DOI={10.1109/jsen.2009.2038442}, abstractNote={The first principle study of hydrogen-terminated silicon (111) with deoxyguanosine (dG) residues chemically bonded to a silicon surface via carbon linkers is performed to reveal new insights into the spectral signatures of constrained DNA chains. Silicon surface structure models are generated to accommodate one or two dG residues. In particular, structural models for two dG residues bonded onto silicon nanodots and that formed a single strand of DNA in the lateral direction (along the surface) were developed. First principle simulations with valence electron basis and effective core potentials are conducted. These studies utilized all-atom geometric optimizations to determine the final conformations and normal mode analyses to derive the spectral absorption information. Stable dG conformations on silicon are obtained for varying types of DNA chain length and Nanodot size/shape. These results show that optically active modes lying within the terahertz spectrum typically arise out of joint coupling between the DNA's vibrational behavior and that of the substrate. However, the dominant absorption line below 6 THz is predicted to most strongly represent the DNA dynamics and effects of sodium, but it is only weakly influenced by the nanodot vibrations. In this study, the phonon-induced light absorption spectra of the DNA chains were analyzed in the context of nanodot influence (e.g., edge effects). These results suggest that DNA strands can be chemically bonded to arbitrary nanosized features on silicon surfaces without perturbing some of the key spectral signatures in the THz regime, and this suggests active THz illumination strategies for DNA identification and characterization.}, number={3}, journal={IEEE SENSORS JOURNAL}, author={Bykhovski, Alexei and Zhao, Peiji and Woolard, Dwight}, year={2010}, month={Mar}, pages={585–598} }
 @article{bykhovski_woolard_2010, title={Hybrid Ab Initio/Empirical Modeling of the Conformations and Light-Induced Transitions in Stilbene-Derivatives Bonded to DNA}, volume={9}, ISSN={["1536-125X"]}, DOI={10.1109/tnano.2010.2060349}, abstractNote={Modeling and simulation techniques are presented, which are both physically accurate and computationally efficient for treating complex organic structures that have relevance to sensing and characterization, including structures with covalent bonding to biological (i.e., DNA) molecules. The theoretical study of large and complex biological molecular systems is very challenging because ab initio quantum mechanical methods are usually too computationally demanding and alternative empirical approaches are often insufficient for describing the internal interactions and dynamics. The goal of this research is to provide detailed insight into the molecular interaction mechanisms (e.g., terahertz (THz) frequency spectral absorption), which can be used to define novel types of bioelectronic-sensing devices. Therefore, a mixed ab initio/molecular mechanical-modeling approach is implemented and applied to the study of stilbene-DNA conjugates that offer switchable spectral characteristics that may be useful for detection and identification purposes. In particular, results are generated for two conformations of a TGCGCA-DNA duplex with trimethoxystilbene carboxamide (TMS) end capping that are confirmed by experimental data. The model is also used to derive the influences of DNA sequence and/or TMS orientation on the conformation, electronic states, and atomic vibrations of single- and doubled-stranded variants of the TGCGCA-DNA duplex. These results, which include very distinct absorption spectra in the THz to UV range, demonstrate that hybrid methodologies can bridge the gap in understanding electronic and atomic structure, and light-induced interactions in complex bioorganic systems.}, number={5}, journal={IEEE TRANSACTIONS ON NANOTECHNOLOGY}, author={Bykhovski, Alexei D. and Woolard, Dwight L.}, year={2010}, month={Sep}, pages={565–574} }
 @article{bykhovski_gelmont_2010, title={Influence of Environment on Terahertz Spectra of Biological Molecules}, volume={114}, ISSN={["1520-5207"]}, DOI={10.1021/jp101510k}, abstractNote={The variability of molecular vibrations and low terahertz spectra of biological molecules depending on the three-dimensional structure of molecular clusters, chemical bonding, and molecular concentration in the surrounding media is studied using computer simulations. The resonant terahertz spectra of biological molecules and their associations are described within the framework of molecular mechanics using an all-atom molecular mechanical force field for proteins and nucleic acids. Both the absolute values of absorption coefficients and their spectral properties are considered for murein-lipoprotein and thioredoxin of E. coli and models of bacterial DNAs using energy minimization and molecular dynamics. The obtained results indicate that structural changes introduced by chemical reactions and molecule associations can strongly affect terahertz spectra, causing significant changes in absorption peak intensities and shifts in peak positions. Terahertz light absorption intensities of studied proteins are predicted to be strongly affected by solvents.}, number={38}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Bykhovski, Alexei and Gelmont, Boris}, year={2010}, month={Sep}, pages={12349–12357} }