An attempt at the computer-aided management of HIV infection

AbstractThe immune system is a complex and diverse system in the human body and HIV virus disrupts and destroys it through extremely complicated but surprisingly logical process. The purpose of this paper is to make an attempt to present a method for the computer-aided management of HIV infection process by means of a mathematical model describing the dynamics of the host pathogen interaction with HIV-1. Treatments for the AIDS disease must be changed to more efficient ones in accordance with the disease progression and the status of the immune system. The level of progression and the status are represented by parameters which are governed by our mathematical model. It is then exhibited that our model is numerically stable and uniquely solvable. With this knowledge, our mathematical model for HIV disease progression is formulated and physiological interpretations are provided. The results of our numerical simulations are visualized, and it is seen that our results agree with medical aspects from the point of view of antiretroviral therapy. It is then expected that our approach will take to address practical clinical issues and will be applied to the computer-aided management of antiretroviral therapies

Experimentally Constrained Molecular Relaxation: The Case of Glassy GeSe2

An ideal atomistic model of a disordered material should contradict no experiments,and should also be consistent with accurate force fields (either {\it ab initio}or empirical). We make significant progress toward jointly satisfying {\it both} of these criteria using a hybrid reverse Monte Carlo approach in conjunction with approximate first principles molecular dynamics. We illustrate the method by studying the complex binary glassy material g-GeSe$_2$. By constraining the model to agree with partial structure factors and {\it ab initio} simulation, we obtain a 647-atom model in close agreement with experiment, including the first sharp diffraction peak in the static structure factor. We compute the electronic state densities and compare to photoelectron spectroscopies. The approach is general and flexible.Comment: 6 pages, 4 figure

Approximate ab initio calculation of vibrational properties of hydrogenated amorphous silicon with inner voids

We have performed an approximate ab initio calculation of vibrational properties of hydrogenated amorphous silicon (a-Si:H) using a molecular dynamics method. A 216 atom model for pure amorphous silicon (a-Si) has been employed as a starting point for our a-Si:H models with voids that were made by removing a cluster of silicon atoms out of the bulk and terminating the resulting dangling bonds with hydrogens. Our calculation shows that the presence of voids leads to localized low energy (30-50 cm^{-1}) states in the vibrational spectrum of the system. The nature and localization properties of these states are analyzed by various visualization techniques.Comment: 15 pages with 6 PS figures, to appear in PRB in December 199

Inclusion of Experimental Information in First Principles Modeling of Materials

We propose a novel approach to model amorphous materials using a first principles density functional method while simultaneously enforcing agreement with selected experimental data. We illustrate our method with applications to amorphous silicon and glassy GeSe$_2$. The structural, vibrational and electronic properties of the models are found to be in agreement with experimental results. The method is general and can be extended to other complex materials.Comment: 11 pages, 8 PostScript figures, submitted to J. Phys.: Condens. Matter in honor of Mike Thorpe's 60th birthda

Time-Resolved Spin Torque Switching and Enhanced Damping in Py/Cu/Py Spin-Valve Nanopillars

We report time-resolved measurements of current-induced reversal of a free magnetic layer in Py/Cu/Py elliptical nanopillars at temperatures T = 4.2 K to 160 K. Comparison of the data to Landau-Lifshitz-Gilbert macrospin simulations of the free layer switching yields numerical values for the spin torque and the Gilbert damping parameters as functions of T. The damping is strongly T-dependent, which we attribute to the antiferromagnetic pinning behavior of a thin permalloy oxide layer around the perimeter of the free layer. This adventitious antiferromagnetic pinning layer can have a major impact on spin torque phenomena.Comment: 5 pages, 4 figure

Strong and Tunable Nonlinear Optomechanical Coupling in a Low-Loss System

A major goal in optomechanics is to observe and control quantum behavior in a system consisting of a mechanical resonator coupled to an optical cavity. Work towards this goal has focused on increasing the strength of the coupling between the mechanical and optical degrees of freedom; however, the form of this coupling is crucial in determining which phenomena can be observed in such a system. Here we demonstrate that avoided crossings in the spectrum of an optical cavity containing a flexible dielectric membrane allow us to realize several different forms of the optomechanical coupling. These include cavity detunings that are (to lowest order) linear, quadratic, or quartic in the membrane's displacement, and a cavity finesse that is linear in (or independent of) the membrane's displacement. All these couplings are realized in a single device with extremely low optical loss and can be tuned over a wide range in situ; in particular, we find that the quadratic coupling can be increased three orders of magnitude beyond previous devices. As a result of these advances, the device presented here should be capable of demonstrating the quantization of the membrane's mechanical energy.Comment: 12 pages, 4 figures, 1 tabl

Energetics of crystalline silicon dioxide-silicon (SiO2/Si) interfaces

We consider the interface between a (100) silicon surface and several naturally occurring crystalline silicon dioxide (SiO{sub 2}-silica) polymorphs: {alpha}-quartz, {beta}-cristobalite, tridymite, and keatite. Using a classical empirical potential, we compute the strain energy required for epitaxy for each silica structure. Tridymite is the least energetically favorable epitaxial phase, followed by {alpha}-quartz, then {beta}-cristobalite, while the most energetically favorable phase is keatite. We discuss the implications of this for epitaxial growth, and the crystalline to amorphous transition within atomically thin silica layers

Fast algorithm for calculating two-photon absorption spectra

We report a numerical calculation of the two-photon absorption coefficient of electrons in a binding potential using the real-time real-space higher-order difference method. By introducing random vector averaging for the intermediate state, the task of evaluating the two-dimensional time integral is reduced to calculating two one-dimensional integrals. This allows the reduction of the computation load down to the same order as that for the linear response function. The relative advantage of the method compared to the straightforward multi-dimensional time integration is greater for the calculation of non-linear response functions of higher order at higher energy resolution.Comment: 4 pages, 2 figures. It will be published in Phys. Rev. E on 1, March, 199

Magnetic vortex oscillator driven by dc spin-polarized current

Transfer of angular momentum from a spin-polarized current to a ferromagnet provides an efficient means to control the dynamics of nanomagnets. A peculiar consequence of this spin-torque, the ability to induce persistent oscillations of a nanomagnet by applying a dc current, has previously been reported only for spatially uniform nanomagnets. Here we demonstrate that a quintessentially nonuniform magnetic structure, a magnetic vortex, isolated within a nanoscale spin valve structure, can be excited into persistent microwave-frequency oscillations by a spin-polarized dc current. Comparison to micromagnetic simulations leads to identification of the oscillations with a precession of the vortex core. The oscillations, which can be obtained in essentially zero magnetic field, exhibit linewidths that can be narrower than 300 kHz, making these highly compact spin-torque vortex oscillator devices potential candidates for microwave signal-processing applications, and a powerful new tool for fundamental studies of vortex dynamics in magnetic nanostructures.Comment: 14 pages, 4 figure

Strong linewidth variation for spin-torque nano-oscillators as a function of in-plane magnetic field angle

We measure the microwave signals produced by spin-torque-driven magnetization dynamics in patterned magnetic multilayer devices at room temperature, as a function of the angle of a magnetic field applied in the sample plane. We find strong variations in the frequency linewidth of the signals, with a decrease by more than a factor of 20 as the field is rotated from the magnetic easy axis to the in-plane hard axis. Based on micromagnetic simulations, we identify these variations as due to a transition from spatially incoherent to coherent precession.Comment: 15 pages, 5 figure