@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} }
 @inproceedings{chen_park_chen_wang_bethea_martini_woolard_2013, title={Ultra-broadband wavelength conversion sensor using thermochromic liquid crystals}, volume={8624}, booktitle={Terahertz, rf, millimeter, and submillimeter-wave technology and applications vi}, author={Chen, I. A. and Park, S. W. and Chen, G. and Wang, C. and Bethea, C. and Martini, R. and Woolard, D.}, year={2013} }
 @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{zhao_woolard_2008, title={Electron-longitudinal-acoustic-phonon scattering in double-quantum-dot based quantum gates}, volume={372}, number={10}, journal={Physics Letters. A}, author={Zhao, P. and Woolard, D. L.}, year={2008}, pages={1666–1670} }
 @article{zhang_woolard_2008, title={Magneto-transport physics in superlattices with staggered-bandgap structure}, volume={8}, ISSN={["1530-437X"]}, DOI={10.1109/JSEN.2008.922722}, abstractNote={Physical models are presented to describe magneto-transports within double-barrier structure with staggered-band lineups. Here, a special case, where the magnetic field is perpendicular to the heterolayers, is considered and the conduction-band electron current is calculated. In addition, the spatial charge transfer due to the heavyhole (HH) interband tunneling is also studied. The interband tunneling probability is related to the Landau index number, which characterizes the quantization of in-plane electron motions. As a consequence, the inversion of hole populations between Landau levels is shown to occur which is a new phenomenon that has relevance for millimeterwave amplification.}, number={5-6}, journal={IEEE SENSORS JOURNAL}, author={Zhang, Weidong and Woolard, Dwight L.}, year={2008}, pages={914–921} }
 @article{woolard_trew_polla_stroscio_varshney_jensen_jensen_lugli_aono_2008, title={Nanosensors for defense and security}, volume={8}, ISSN={["1530-437X"]}, DOI={10.1109/jsen.2008.924436}, abstractNote={The 59 articles in this special issue focus on nanosensors for defense and security.}, number={5-6}, journal={IEEE SENSORS JOURNAL}, author={Woolard, Dwight L. and Trew, Robert J. and Polla, Dennis L. and Stroscio, Michael A. and Varshney, Usha and Jensen, Janet and Jensen, James O. and Lugli, Paolo O. and Aono, Masakazu}, year={2008}, pages={641–646} }
 @inproceedings{zhang_woolard_zhao_2007, title={A Spin-Polarized interband-current source based upon staggered-bandgap heterostructures}, ISBN={978-1-4244-0607-4}, booktitle={2007 7TH IEEE CONFERENCE ON NANOTECHNOLOGY}, publisher={[Piscataway, NJ]: IEEE}, author={Zhang, W. D. and Woolard, D. and Zhao, P.}, year={2007}, pages={214–219} }
 @article{zhao_woolard_2007, title={Electrostatic characteristics of tether atoms in connecting organic molecules to the surface of silicon}, volume={91}, number={6}, journal={Applied Physics Letters}, author={Zhao, P. and Woolard, D. L.}, year={2007} }
 @inproceedings{woolard_zhao_2007, title={THz detection cell for sub-wavelength bio-molecular sensing}, ISBN={978-1-4244-0607-4}, booktitle={2007 7TH IEEE CONFERENCE ON NANOTECHNOLOGY}, publisher={[Piscataway, NJ]: IEEE}, author={Woolard, D. L. and Zhao, P.}, year={2007}, pages={320–325} }