@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{zhao_woolard_2010, title={Vibrational characteristics of genetic codons: 5 '-GGX-3 ' and 5 '-XGG-3 ' (X = A C, and T)}, volume={10}, number={3}, journal={IEEE Sensors Journal}, author={Zhao, P. J. and Woolard, B. N.}, year={2010}, pages={630–638} }
 @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{zhao_woolard_2008, title={Influence of base-pair interaction on vibrational spectrum of a poly-dG molecule bonded to Si substrates}, volume={8}, ISSN={["1558-1748"]}, DOI={10.1109/JSEN.2008.923178}, abstractNote={A theoretical investigation is presented that characterizes the interaction dynamics of a double deoxyguanonsine molecular system, where two guanine bases are coupled via a sugar-phosphate backbone that is bound to the surface of silicon. Molecular dynamical simulations show that the influence of the coupling between the guanine bases (i.e., as compared with individual deoxyguanonsine molecules) leads to a significant increase of the absorption intensity from microwave to infrared (IR) frequencies. Furthermore, these results show that the strong coupling between the guanine bases leads to a much larger number of distinguishable vibrational modes at frequency below the IR at ~ 1350 cm-1. These effects also produce double-peak features in the Far-IR absorption intensity, which represent a splitting of the individual peaks associated with a single deoxyguanonsine molecule. Guanine base coupling also leads to a general shifting of all the absorption peaks towards the terahertz frequency regime (i.e., ~10 THz and below), which is also accompanied by a reduction of the absorption intensity as one progresses to longer wavelengths. Most importantly, this interaction phenomenon creates additional spectral features, which may be useful in a long-wavelength optics-based technique for DNA sequencing.}, number={5-6}, journal={IEEE SENSORS JOURNAL}, author={Zhao, Peiji and Woolard, Brandee}, year={2008}, pages={998–1003} }
 @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} }
 @article{zhao_woolard_2007, title={Suppression of electron-phonon scattering in double-quantum-dot based-quantum gates}, volume={90}, number={9}, 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} }
 @article{lasater_kelley_salinger_woolard_zhao_2006, title={Parallel parameter study of the Wigner-Poisson equations for RTDs}, volume={51}, ISSN={["1873-7668"]}, DOI={10.1016/j.camwa.2006.05.006}, abstractNote={We will discuss a parametric study of the solution of the Wigner-Poisson equations for resonant tunneling diodes. These structures exhibit self-sustaining oscillations in certain operating regimes. We will describe the engineering consequences of our study and how it is a significant advance from some previous work, which used much coarser grids. We use LOCA and other packages in the Trilinos framework from Sandia National Laboratory to enable efficient parallelization of the solution methods and to perform bifurcation analysis of this model. We report on the parallel efficiency and scalability of our implementation.}, number={11}, journal={COMPUTERS & MATHEMATICS WITH APPLICATIONS}, author={Lasater, M. S. and Kelley, C. T. and Salinger, A. G. and Woolard, D. L. and Zhao, P.}, year={2006}, month={Jun}, pages={1677–1688} }
 @article{zhao_woolard_2005, title={Wigner-Poisson model based nano-electronic engineering modeling and design}, volume={2}, journal={Dynamics of Continuous, Discrete & Impulsive Systems. Series B, Applications & Algorithms}, author={Zhao, P. J. and Woolard, D.}, year={2005}, pages={854–859} }
 @article{unlu_rosen_cui_zhao_2004, title={Multi-band Wigner function formulation of quantum transport}, volume={327}, ISSN={["1873-2429"]}, DOI={10.1016/j.physleta.2004.05.022}, abstractNote={A Wigner function representation of multi-band quantum transport theory is developed in this paper. The equations are derived using non-equilibrium Green's function formulation with the generalized Kadanoff-Baym ansatz and the multi-band $\bf{k.p}$ Hamiltonian including spin. The results are applied to a two-band resonant inter-band tunneling structure.}, number={2-3}, journal={PHYSICS LETTERS A}, author={Unlu, MB and Rosen, B and Cui, HL and Zhao, PJ}, year={2004}, month={Jun}, pages={230–240} }
 @article{zhao_woolard_gelmont_cui_2003, title={Creation and quenching of interference-induced emitter-quantum wells within double-barrier tunneling structures}, volume={94}, ISSN={["0021-8979"]}, DOI={10.1063/1.1587003}, abstractNote={The initial creation and subsequent quenching of the emitter quantum well within double-barrier resonant tunneling structures (RTSs) is the key process that explains the origin of the hysteresis and plateau-like structure of the I–V characteristics. This fundamental process, which evolves out of quantum-mechanical interference, defines the basic mechanism that can lead to intrinsic high-frequency oscillations. This article presents numerical results, derived from a coupled Wigner–Poisson model, that illustrate the underlying mechanisms responsible for the creation and disappearance of the emitter-quantum well. Additional theoretical results are also given that demonstrates how subband state coupling, between the emitter-quantum well (EQW) and the main-quantum well (MQW) defined by the double-barrier heterostructure, leads to the hysteresis and instability behavior. This article will reveal how the quantum interference that develops between the incident and reflected electron wave function (i.e., from the first barrier) leads to the formation of an emitter-quantum well. An analysis is also performed to define the effects of EQW–MQW subband coupling on the current–density verses voltage (I–V) characteristics and the overall I–V dependence on the initial charging states of the individual wells. In particular, this analysis is used to show how the EQW is formed and quenched and how it influences the time-dependent behavior of the structure when it is subject to forward- and backward-bias sweeps of the applied bias voltages. This article provides fundamental quantum-mechanical explanations for the complicated time-dependent processes within double-barrier RTSs and provides insight into the hysteresis and intrinsic oscillation behavior.}, number={3}, journal={JOURNAL OF APPLIED PHYSICS}, author={Zhao, PJ and Woolard, DL and Gelmont, BL and Cui, HL}, year={2003}, month={Aug}, pages={1833–1849} }
 @article{zhao_woolard_cui_2003, title={Multisubband theory for the origination of intrinsic oscillations within double-barrier quantum well systems}, volume={67}, number={8}, journal={Physical Review. B, Condensed Matter and Materials Physics}, author={Zhao, P. J. and Woolard, D. L. and Cui, H. L.}, year={2003}, pages={085312–1} }
 @article{zhao_horing_woolard_cui_2003, title={Nonequilibrium Green's function formulation of quantum transport theory for multi-band semiconductors}, volume={310}, ISSN={["0375-9601"]}, DOI={10.1016/S0375-9601(03)00286-X}, abstractNote={Abstract We present a nonequilibrium Green's function formulation of many-body quantum transport theory for multi-band semiconductor systems with a phonon bath. The equations are expressed exactly in terms of single particle nonequilibrium Green's functions and self-energies, treating the open electron–hole system in weak interaction with the bath. A decoupling technique is employed to separate the individual band Green's function equations of motion from one another, with the band–band interaction effects embedded in “cross-band” self-energies. This nonequilibrium Green's function formulation of quantum transport theory is amenable to solution by parallel computing because of its formal decoupling with respect to inter-band interactions. Moreover, this formulation also permits coding the simulator of an n-band semiconductor in terms of that for an (n−1)-band system, in step with the current tendency and development of programming technology. Finally, the focus of these equations on individual bands provides a relatively direct route for the determination of carrier motion in energy bands, and to delineate the influence of intra- and inter-band interactions. A detailed description is provided for three-band semiconductor systems.}, number={4}, journal={PHYSICS LETTERS A}, author={Zhao, P and Horing, NJM and Woolard, DL and Cui, HL}, year={2003}, month={Apr}, pages={258–264} }
 @article{zhao_woolard_cui_horing_2003, title={Origin of intrinsic oscillations in double-barrier quantum-well systems}, volume={311}, ISSN={["1873-2429"]}, DOI={10.1016/S0375-9601(03)00543-7}, abstractNote={We present a theory accounting for the origin of high-frequency current oscillations in a double barrier quantum-well system. The origin of such current oscillations is traced to the development of a dynamic emitter quantum-well and the concomitant coupling of the energy levels in the double barrier quantum-well system. The relationship between the oscillation frequency and the energy level structure of the system is expressed as ν=ΔE0/h: A self-consistent, time-dependent Wigner–Poisson numerical computer experiment is used to exhibit remarkable intrinsic, sustained current oscillations in the double-barrier quantum well at terahertz frequencies; and a procedure for calculating ΔE0, the energy difference at time t0 (defined such that the contribution to the energy difference from the potential oscillation is zero) is also presented. The simulated oscillation frequency determined using the Wigner–Poisson analysis is in very good agreement with that calculated using a Schrödinger equation with a self-consistent potential determined from the Poisson equation.}, number={4-5}, journal={PHYSICS LETTERS A}, author={Zhao, PJ and Woolard, DL and Cui, HL and Horing, NJM}, year={2003}, month={May}, pages={432–437} }
 @article{woolard_zhao_cui_2002, title={THz-frequency intrinsic oscillations in double-barrier quantum well systems}, volume={314}, ISSN={["1873-2135"]}, DOI={10.1016/S0921-4526(01)01372-2}, abstractNote={Traditional implementations of double-barrier quantum well structures (DBQWSs) have not been successful as oscillator sources at THz frequencies because they are utilized in an extrinsic (i.e., external charge exchange) manner. Indeed, the true failing of a “traditional” DBQWS-based oscillator is tied directly to the physical principles associated with its implementation. In this paper, greater insight into the physics of instabilities within nanoscale tunneling structures is revealed. Here, self-consistent, time-dependent Wigner–Poisson simulations demonstrate sustained THz-frequency current-oscillations in a DBQWS that arise without the benefit of external charging processes. More importantly, dependencies between the emitter-boundary structure and the DBQWS are identified that strongly influence the internal instability phenomenon. These new results offer potential methodologies for inducing and controlling intrinsic oscillations in DBQWSs.}, number={1-4}, journal={PHYSICA B-CONDENSED MATTER}, author={Woolard, D and Zhao, P and Cui, HL}, year={2002}, month={Mar}, pages={108–112} }
 @article{zhao_cui_woolard_jensen_buot_2001, title={Equivalent circuit parameters of resonant tunneling diodes extracted from self-consistent Wigner-Poisson simulation}, volume={48}, ISSN={["1557-9646"]}, DOI={10.1109/16.915658}, abstractNote={The equivalent circuit parameters of resonant tunneling diodes (RTD) are extracted from numerical simulation results for RTDs. The RTD models used in this paper are double barrier structures. The influence of the resonant tunneling structure (RTS) parameters, such as the height of barriers, the width of the quantum well, the width of the spacers, and the width of the barriers, on the device parameters are systematically discussed. The effects of device temperature on device parameters are also discussed. Scattering between electrons and phonons greatly affects device parameters and thereby the function of the RTDs. Physical explanations about how the structure parameters and device temperature influence the device parameters are provided. Based on the analysis results, a general way to get an RTD oscillator with a higher maximum frequency is suggested.}, number={4}, journal={IEEE TRANSACTIONS ON ELECTRON DEVICES}, author={Zhao, PJ and Cui, HL and Woolard, DL and Jensen, KL and Buot, FA}, year={2001}, month={Apr}, pages={614–627} }
 @article{zhao_cui_woolard_buot_2001, title={Operation principle of resonant tunneling THz oscillator at fixed bias voltages}, volume={13}, number={1-4}, journal={VLSI Design (Yverdon, Switzerland)}, author={Zhao, P. and Cui, H. L. and Woolard, D. and Buot, F.}, year={2001}, pages={413–417} }