... Descriptors : *ENERGETIC PROPERTIES, QUANTUM ... MOLECULAR DYNAMICS, CHEMICAL REACTIONS ... THRUST, QUANTUM CHEMISTRY ...

One dimensional molecular dynamics simulations of the onset of detonation have been performed using three-body potentials which accurately reproduce the effects of endothermic bond breaking and exothermic bond recombinations. A stable detonation wave of r...

The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativist...

A quantum dynamics approach, called Gaussian molecular dynamics, is introduced. As in the centroid molecular dynamics, the N-body quantum system is mapped to an N-body classical system with an effective Hamiltonian arising within the variational Gaussian wave-packet approximation. The approach ...

To accurately predict the fate of contaminants in the environment and to make sound decisions about environmental remediation, we must accurately understand sorption mechanisms and surface reactivity of environmental particles. Sorption of selected pesticides on kaolinite surface...

We argue that the dynamic extended molecular orbital (DEMO) method may be less accurate than expected because the motion of the centre of mass was not properly removed prior to the SCF calculation. Under such conditions the virial theorem is a misleading indication of the accuracy of the wavefunction.

Signaling complexes typically consist of highly dynamic molecular ensembles that are challenging to study and to describe accurately. Conventional mechanical descriptions misrepresent this reality and can be actively counterproductive by misdirecting us away from investigating critical issues.

Many contemporary problems in science ranging from the spread of hazardous chemical or nuclear plumes to protein folding in molecular dynamics to scale up of small scale effects in nanotechnology, to making accurate predictions of the coupled atmosphere-o...

Quasiharmonic-lattice-dynamics and molecular-dynamics calculations were performed on metallic sodium from the low-temperature region to above melting at several different volumes. A pseudopotential model was used that consisted of a large volume-dependent potential plus a small effective two-body potential. From the molecular-dynamics ...

A method to measure the phonon dispersion of a crystal based on molecular dynamics simulation is proposed and implemented as an extension to an open source classical molecular dynamics simulation code LAMMPS. In the proposed method, the dynamical matrix is constructed by observing the ...

... Title : A METHOD OF ACCURATELY MEASURING DYNAMIC STABILITY DERRIVATIVES IN TRANSONIC AND SUPERSONIC WIND TUNNELS,. ...

The authors have reported the calculation of the kinematic viscosity index of squalane from nonequilibrium molecular dynamics simulations. This represents the first accurate quantitative prediction of this measure of lubricant performance by molecular simulation. Using the same general alkane potential model, this ...

Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual trajectories computed in molecular ...

A method for on-line accurate monitoring and precise control of molecular beam epitaxial growth of Groups III-III-V or Groups III-V-V layers in an advanced semiconductor device incorporates reflection mass spectrometry. The reflection mass spectrometry is responsive to intentional perturbations in molecular fluxes incident on a ...

This invention is comprised of a method for on-line accurate monitoring and precise control of molecular beam epitaxial growth of Groups III-III-V or Groups III-V-V layers in an advanced semiconductor device incorporates reflection mass spectrometry. The reflection mass spectrometry is responsive to intentional perturbations in ...

A method for on-line accurate monitoring and precise control of molecular beam epitaxial growth of Groups III-III-V or Groups III-V-V layers in an advanced semiconductor device incorporates reflection mass spectrometry. The reflection mass spectrometry is responsive to intentional perturbations in molecular fluxes incident on a ...

... Title : Molecular Dynamics and Protein Structure. ... a Workship on Molecular Dynamics of Proteins. ... Dynamics and Structure Refinement; Simulation ...

The observed flow enhancement in highly confining geometries is believed to be caused by fluid velocity slip at the solid wall surface. Here we present a simple and highly accurate method to predict this slip using equilibrium molecular dynamics. Unlike previous equilibrium molecular dynamics ...

A new approach for the calculation of nonlinear quantum time correlation functions within the path-integral centroid dynamics formalism is presented. This approach combines information on the real-time dynamics obtained from centroid molecular dynamics with classical operators with information on the corresponding ...

The development in the 1950's and 60's of crossed molecular beam methods for studying chemical reactions at the single-collision molecular level stimulated the need and desire for theoretical methods to describe these and other dynamical processes in molecular systems. Chemical ...

Decomposition of energetic molecules such as pentaerythritol tetranitrate is accompanied by extensive changes in their electronic configuration and thus is challenging for ab initio Born-Oppenheimer molecular dynamics simulations. The performance of single-determinant methods (in particular, density-functional theory) is validated on electronic structure ...

A combination of electronic structure calculations, classical molecular dynamics simulations and metadynamics is proposed to study the phase behavior of complex crystals. While the former provide accurate energetics for thermodynamic properties, molecular dynamics and metadynamics simulations ...

Decomposition of energetic molecules such as pentaerythritol tetranitrate is accompanied by extensive changes in their electronic configuration and thus is challenging for ab initio Born-Oppenheimer molecular dynamics simulations. The performance of single-determinant methods (in particular, density-functional theory) is validated on electronic structure ...

A biased potential molecular dynamics simulation approach, accelerated molecular dynamics (AMD), has been implemented in the framework of ab initio molecular dynamics for the study of chemical reactions. Using two examples, the double proton transfer reaction in formic acid ...

A biased potential molecular dynamics simulation approach, accelerated molecular dynamics (AMD), has been implemented in the framework of ab initio molecular dynamics for the study of chemical reactions. Using two examples, the double proton transfer reaction in formic acid ...

An outstanding problem in the computer-based microscopic description of Group IV materials, is the need for an accurate transferable model of the energetic and electronic properties of semiconductor structures. The three complementary approaches have been the ab-initio method including Car-Parinello simulations, the classical molecular ...

A dynamical model for the structure of the human immunodeficiency virus 1 (HIV-1) protease dimer in aqueous solution has been developed on the basis of molecular dynamics simulation. The model provides an accurate account of the crystal geometry and also a prediction of the structural reorganization expected to ...

dynamics of molecular species on the millisecond to femtosecond time scales, 2) photochemistry and relaxation dynamics of molecular species in gases, heterogeneous and...

Linear response theory coupled to molecular dynamics simulations with an explicit solvent representation is used to derive fractional contributions of amino acid residues to the solvation of proteins. The new fractional methods developed here are compared with standard approaches based on empirical 1D and 3D statistical potentials, as well as with ...

... Title : Light Scattering Studies of Molecular Dynamics in Molecular Crystals, Liquid Crystals and Polymers for Applications in Chemical Defense. ...

For a laser driven molecule, we show that the ionization and the dissociation channels can be separated by preparing the molecule in a specific vibrational state. Specifically, we investigate the dynamics of the hydrogen molecular ion under a femtosecond infrared laser field aligned with the molecular axis. We find dissociation ...

Quantum molecular dynamics simulations of pure samples and of mixtures of various species yield important structural, dynamical, and electronic properties that characterize matter at high compressions and moderate temperatures. A fully quantum mechanical treatment of the electrons, contained in a periodically replicated reference cell ...

The dynamics of sodium is investigated using the coulomb and Born-Mayer interaction augmented by a model pseudopotential to represent the electron interactions including screening, exchange, and correlation. The model parameters were previously determined and have been shown to accurately reproduce experimental equation-of-state, lattice vibration, and ...

The dynamic behavior of the oxidation reaction of the Cu surface during the Cu chemical-mechanical polishing (CMP) process was investigated by a novel tight-binding quantum chemical molecular dynamics method. We confirmed that our tight-binding quantum chemical molecular dynamics method with ...

The role of protein dynamics in enzyme catalysis is one of the most active and controversial areas in enzymology today. Some researchers claim that protein dynamics are at the heart of enzyme catalytic efficiency, while others state that dynamics make no significant contribution to catalysis. What is the biochemist - or student - to ...

Simulation of the motion of particles in large molecular chains is computationally complex, generally involving the solution of large systems of differential equations employing iterative techniques. Generating solutions for even very short time intervals can require significant amounts of computational effort. Though the particle trajectories are significant, further insight ...

Neural networks are used to study intramolecular energy flow in molecular systems (tetratomics to macromolecules), developing new techniques for efficient analysis of data obtained from molecular-dynamics and quantum mechanics calculations. Neural networks can map phase space points to intramolecular vibrational energies along a classical trajectory ...

We introduce a new method of solution for the Fredholm integral equations of the second kind. The method would be useful when the direct iterative approach leads to a divergent perturbation series solution. By using the method, we obtain an accurate expression of the propagator for diffusive dynamics of a pair of particles interacting via an arbitrary ...

We introduce a new method of solution for the Fredholm integral equations of the second kind. The method would be useful when the direct iterative approach leads to a divergent perturbation series solution. By using the method, we obtain an accurate expression of the propagator for diffusive dynamics of a pair of particles interacting via an arbitrary ...

A new protocol combining classical MD simulations and DFT calculations is presented to accurately estimate the (1)H NMR chemical shifts of highly mobile guest-host systems and their thermal dependence. This strategy has been successfully applied for the hydrogen molecule trapped into C(60) fullerene, an unresolved and challenging prototypical case for which experimental values ...

Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice, the largest outer time step possible is limited not by the physical forces but by resonances between the fast and slow modes. In this paper we show that this problem can be alleviated by using a simple ...

Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice, the largest outer time step possible is limited not by the physical forces but by resonances between the fast and slow modes. In this paper we show that this problem can be alleviated by using a simple ...

A new Quantum Dynamics approach, called Gaussian Molecular Dynamics (GMD), is introduced. As in the Centroid Molecular Dynamics (CMD), the N-body quantum system is mapped to an N-body classical system with an effective Hamiltonian arising within the Variational Gaussian Wave-packet ...

We present a software module which allows one to efficiently perform molecular dynamics and local minimization calculations in internal coordinates when incorporated into a molecular dynamics package. We have implemented a reference interface to the NIH version of the X-PLOR structure refinement package and we show ...

The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated by using forces computed "on the fly" from electronic structure calculations, has had a profound influence in modern theoretical research. Ab initio molecular dynamics allows ...

The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated by using forces computed �on the fly� from electronic structure calculations, has had a profound influence in modern theoretical research. Ab initio molecular dynamics allows ...

-Parrinello molecular dynamics (CPMD) with density functional the- ory within the local density approximation (DFT; the Jastrow factor is from the RPA pseudopotential, including the one-body (electron-proton) term [12 with conclusions from CPMD DFT-LDA. Accurate RQMC (solid lines) simulations find a reversible crossover. 0 0.5 1 1

The confinement of the metalloenzyme organophosphorous hydrolase in functionalized mesoporous silica (FMS) enhances the stability and increases catalytic specific activity by 200% compared to the enzyme in solution. The mechanism by which these processes take place is not well understood. We have developed two coarse-grain models of confinement to provide insights into how the nanocage environment ...

The response of beryllium to dynamic loading has been extensively studied, both experimentally and theoretically, due to its importance in several technological areas. Compared to other metals, it is quite challenging to accurately represent the various anomalous behaviors of beryllium using classical interatomic potentials. A new parameterization of the ...

We present results for several structural and dynamical properties of the liquid Li1-xNax alloy. The study has been carried out by means of the orbital-free ab initio molecular dynamics method, combined with local ionic pseudopotentials constructed within the same framework. We obtain good agreement with the available experimental ...

... DYNAMIC RESPONSE, ENERGY TRANSFER, MOLECULAR STRUCTURE, OSCILLATION, VIBRATIONAL SPECTRA, MORSE POTENTIAL. ...

... hydrogen and obtain solid plasmas. ... HYDROGEN, *DYNAMICS, *MOLECULAR PROPERTIES, *SOLIDS, MEASUREMENT, GAMMA ...

The results of molecular dynamics calculations on the equilibrium interface between liquid water and

... Descriptors : *ALUMINUM, *MOLECULAR DYNAMICS, *NICKEL, *NANOPARTICLES, SINTERING, INTERMETALLIC COMPOUNDS ...

The present recursive algorithm for solving molecular systems' dynamical equations of motion employs

... A VALIDATION OF A MOLECULAR DYNAMICS SIMULATION IN DETERMINING THE THERMAL CONDUCTIVITY OF A LA-ZR PYROCHLORE ...

... Title : A Molecular Dynamics Investigation of the Structural Characteristics of Amorphous and Annealed Poly (Vinylidene Fluoride) and Vinylidene ...

A method is presented to treat electrons within the many-body quantum Monte Carlo (QMC) approach ``on-the-fly'' throughout a molecular dynamics (MD) simulation. Our approach leverages the large (10--100) ratio of QMC electron to MD ion motion to couple the stochastic, imaginary-time electronic and real-time ionic trajectories. This continuous evolution of ...

An efficient numerical technique to produce accurate solutions to the equations of fluid dynamics is

We discuss the application of a recently proposed thermodynamically self-consistent integral equation, the variational modified hypernetted chain (VMHNC) approximation, to the study of the structural properties of liquid metals. We show a comparison between the structure of the liquid alkali metals, as obtained within the VMHNC, and molecular dynamics ...

Accurate molecular dynamics calculations have been made for the thermodynamic properties of the square-well potential in the solid phase. Hard-sphere perturbation terms for fcc and hcp phases have been computed over the solid range, and a phase diagram including solid--solid and solid--liquid phase boundaries has been constructed. The ...

Multiscale analysis to characterize the size effect of silica nanoparticles on the mechanical properties of nanoparticle/polymer nanocomposites is developed and verified through a molecular dynamics simulation and continuum micromechanics model. In the micromechanics model, the particle-matrix interface mechanical property is incorporated, and the ...

The equation of state (EOS) of the solar interior is accurately and smoothly determined from ab initio simulations named quantum Langevin molecular dynamics in the pressure range of 58 Mbar {<=}P {<=} 4.6 x 10{sup 5} Mbar at the temperature range of 1 eV {<=}T {<=} 1500 eV. The central pressure is calculated ...

We propose a real-space finite differences approach for accurate and unbiased O(N) Density Functional Theory molecular dynamics simulations based on a localized orbitals representation of the electronic structure. The discretization error can be reduced systematically by adapting the mesh spacing, while the orbitals truncation error ...

The multiple signal classification method (MUSIC) for frequency estimation is used to compute the frequency dispersion curves of a diatomic chain from the time-dependent structure factor. In this paper, the authors demonstrate that MUSIC can accurately determine the frequencies from very short time trajectories. MUSIC is also used to show how the frequencies can vary in time, ...

The dynamics of two molecular glass formers are monitored at microsecond scales via muon spin relaxation. Measurements in transverse magnetic fields display unambiguous signatures of critical behavior at temperatures somewhat above those signaling the thermodynamic glass transition, namely at the onset of stochastic molecular motions. ...

Violation of energy conservation in Poisson-Boltzmann molecular dynamics, due to the limited accuracy and precision of numerical methods, is a major bottleneck preventing its wide adoption in biomolecular simulations. We explored the ideas of enforcing interface conditions by the immerse interface method and of removing charge singularity to improve the ...

The sheer vastness of the number of computations required to simulate a biological molecule puts incredible pressure on algorithms to be efficient while maintaining sufficient accuracy. This dissertation summarizes various projects whose purposes address the large span of types of problems in molecular dynamics simulations of biological systems including: ...

... Molecular dynamics is used to model the structurc and dynamics of electric double laycr� ... Page 5. Molecular Dynamics Modeling of Electric ...

In our quest for accurate linear scaling first-principles molecular dynamics methods for pseudopotential DFT calculations, we investigate the accuracy of real-space grid approaches, with finite differences and spherical localization regions. We examine how the positions of the localization centers affect the accuracy and the ...

ABSTRACT : Atomistic Molecular Dynamics provides powerful and flexible tools for the prediction and analysis of molecular and macromolecular systems. Specifically, it provides a means by which we can measure theoretically that which cannot be measured experimentally: the dynamic time-evolution of complex systems ...

Atomistic Molecular Dynamics provides powerful and flexible tools for the prediction and analysis of molecular and macromolecular systems. Specifically, it provides a means by which we can measure theoretically that which cannot be measured experimentally: the dynamic time-evolution of complex systems comprising ...

The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies indicate that ...

Remarkable agreement between molecular dynamics simulations and experimental measurements has been obtained for methane for a large range of intensive variables, including those corresponding to liquid/vapor coexistence. Using a simple Lennard-Jones potential the simulations not only predict the PVT properties up to 2000�C and 20,000 bar with errors ...

We report here a direct ab initio molecular dynamics study of the p-/o-H2+HOC+ reaction on the basis of the accurate SAC-MP2 potential energy surface. The quasi-classical trajectory method was employed. This work largely focuses on the study of reaction mechanisms. A roaming mechanism was identified for this ...

This report provides a study of gases in microporous solids using molecular modeling. The theory of gas transport in porous materials as well as the molecular modeling literature is briefly reviewed. Work complete is described and analyzed with retard to the prevailing theory. The work covers two simple subjects, construction of porous solid models and ...

A new method, here called thermal Gaussian molecular dynamics (TGMD), for simulating the dynamics of quantum many-body systems has recently been introduced [I. Georgescu and V. A. Mandelshtam, Phys. Rev. B 82, 094305 (2010)]. As in the centroid molecular dynamics (CMD), in TGMD the N-body ...

A new method, here called thermal Gaussian molecular dynamics (TGMD), for simulating the dynamics of quantum many-body systems has recently been introduced [I. Georgescu and V. A. Mandelshtam, Phys. Rev. B 82, 094305 (2010)]. As in the centroid molecular dynamics (CMD), in TGMD the N-body ...

Functionally relevant slow conformational motions of proteins are, at present, in most cases inaccessible to molecular dynamics (MD) simulations. The main reason is that the major part of the computational effort is spend for the accurate description of a huge number of high frequency motions of the protein and the surrounding solvent. ...

A combined classical mechanical and quantum mechanical study of zeolites is presented. An accurate and transferrable classical mechanical force field for zeolites is derived. The utility of this force field is demonstrated by comparing the results of energy minimization, molecular dynamics, and normal mode analysis studies of silica ...

One of the functions of microvilli in the microvessel endothelial glycocalyx is molecular filtering. The microvillus behaves as a mechanosensory system which may sense the fluid shear and drag forces. The permeability of small particles in microvessel is crucial for drug design and drug delivery. Therefore a better understanding of flow field around microvillus is important to ...

Dynamics Research Interests Chemical Physics: Molecular dynamics, spectroscopy, photochemistry and kinetics. Applications of high resolution spectroscopy to molecular dynamics;...

dynamics of molecular species on the millisecond to femtosecond time scales and photochemistry and relaxation dynamics of molecular species in gases, heterogeneous and...

We use a combination of molecular dynamics (MD) and first-principles techniques to study the structure and energies of twin boundaries in hcp zirconium. The empirical many-body potential of Zr is used to test the stability of various possible twin structures, but the final relaxed positions are accurately determined using fully ...

Coarse-grained models decrease the number of force sites and thus reduce computational requirements for molecular simulation. While these models are successful in describing structural properties, dynamic evolution is faster than the corresponding atomistic simulations or experiments. We consider coarse-grained models for four polymers and one polymer ...

The diffusion of an adatom on a substrate submitted to a standing surface acoustic wave is theoretically studied. By performing large scale molecular dynamic simulations, we show that the wave dynamically structures the substrate by encouraging the presence of the adatom in the vicinity of the maximum displacements of the substrate. ...

... 2. Measurement Techniques for Experimental Modal Analysis. ... will yield accurate dynamic properties of ... limitations, these dynamics properties can ...

Molecular dynamics simulations were performed using a modified amoeba force field to determine hydration and dynamical properties of the divalent cations Ca2+ and Mg2+. The extension of amoeba to divalent cations required the introduction of a cation specific parametrization. To accomplish this, the Thole polarization damping model ...

Molecular dynamics simulations were performed using a modified amoeba force field to determine hydration and dynamical properties of the divalent cations Ca2+ and Mg2+. The extension of amoeba to divalent cations required the introduction of a cation specific parametrization. To accomplish this, the Thol� polarization damping model ...

A method is presented to treat electrons within the many-body quantum Monte Carlo (QMC) approach �on-the-fly� throughout a molecular dynamics (MD) simulation. Our approach leverages the large (10 100) ratio of the QMC electron to MD ion motion to couple the stochastic, imaginary-time electronic and real-time ionic trajectories. This continuous ...

Lithium-ion batteries have the potential to revolutionize the transportation industry, as they did for wireless communication. A judicious choice of the liquid electrolytes used in these systems is required to achieve a good balance among high-energy storage, long cycle life and stability, and fast charging. Ethylene-carbonate (EC) and propylene-carbonate (PC) are popular electrolytes. However, to ...

We have cooled ensembles of the molecular hydrogen ions H{sub 2}{sup +}, H{sub 3}{sup +}, and all their deuterated variants to temperatures of a few mK in a radio frequency trap, by sympathetic cooling with laser-cooled beryllium ions. The molecular ions are embedded in the central regions of Coulomb crystals. Mass spectroscopy and ...

The importance of quantum effects as well as the accuracy of the ab initio-based polarizable TTM2.1-F force field in describing liquid water are quantitatively assessed by a detailed analysis of the temperature dependence of several thermodynamic and dynamical properties computed using the path-integral molecular dynamics and centroid ...

There is a pressing need for accurate calculations of finite temperature ground and excited state properties of nanoscale systems relevant to structural biology, hydrogen economy, environmental and material science problems. To address this challenging task we have designed a multiscale dynamical approach that combines the accuracy and computational ...

The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations ...

The local field at large distances from a charged or dipolar impurity in a nonpolar polarizable fluid is related to the dielectric constant of the medium. The predicted local field agrees accurately with molecular dynamics results. In contrast, the usual continuum theory prediction is only accurate to first order ...

The local field at large distances from a charged or dipolar impurity in a nonpolar polarizable fluid is related to the dielectric constant of the medium. The predicted local field agrees accurately with molecular dynamics results. In contrast, the usual continuum theory prediction is only accurate to first order ...

Liquid water is investigated theoretically using combined molecular dynamics (MD) simulations and accurate electronic structure methods. The statistical mechanically averaged molecular properties of liquid water are calculated using the combined coupled cluster/molecular mechanics (CC/MM) ...

The electronic absorption, circular dichroism and X-ray absorption spectroscopy of the red copper protein nitrosocyanin is simulated with classical molecular dynamics simulations in conjunction with time-dependent density functional theory (TDDFT) and multireference configuration interaction (MRCI) calculations on the active site, with the remainder of the ...

Stochastic dynamical systems governed by the chemical master equation find use in the modeling of biological phenomena in cells, where they provide more accurate representations than their deterministic counterparts, particularly when the levels of molecular population are small. The analysis of parametric sensitivity in such systems ...

We examined three united atom models in light of their description of polyolefin dynamics and investigated the relative influence of various potentials on the resulting dynamics. Results were compared with a collection of experimental data on polyethylene, poly(ethylene-alt-propylene), polypropylene, and head-to-head polypropylene, including quasielastic ...

The basic methodology of equilibrium molecular dynamics is described. Examples from the literature are used to illustrate how molecular dynamics has been used to resolve theoretical controversies, provide data to test theories, and occasionally to discove...

III II Ii? 6190-548A 9 August 1989 yin- MOLECULAR DYNAMICS OF LIPID BILAYERS DTIC ... Contract Title: Molecular Dynamics of Lipid Bilayers ...

Plasticity of metal wires in torsion: Molecular dynamics and dislocation dynamics simulations of single crystal wires under torsion using both molecular dynamics (MD) and dislocation dynamics (DD) simulations. This will provide insight into how the deformation changes as a ...

The unexpected higher intensity at low momentum region in (e,2e) ionization cross sections, as called turn-up effect, was observed recently. This work systemically investigated this effect for the highest occupied molecular orbital of oxygen at various impact energies of 400, 600, 800, 1200, 1800, and 2400 eV by electron momentum spectroscopy. This turn-up became higher as the ...

The accurate molecular simulation of many hydrated chemical systems, including clay minerals and other phyllosilicates and their interfaces with aqueous solutions, requires improved classical force field potentials to better describe structure and vibrational behavior. Classical and ab initio molecular dynamics ...

We study a response of a hydrogen molecular ion to the strong 2-cycle 800-nm laser pulse, using highly accurate numerical solution of the time-dependent Schrodinger equation in 4 spatial dimension. We use a computational approach which employs an adaptive, discontinuous spectral element basis as well as multiresolution analysis and separated ...

The molecular probe N-methyl-6-quinolone (MQ) gives experimental access to its local chemical environment, e.g. inside a biomolecule. Using ab initio molecular dynamics (MD), it is possible to simulate the time evolution of the Stokes shift as a function of the actual atomistic coupling to the surrounding hydrogen bond network and thus ...

The C6 coefficients of van der Waals interactions have been evaluated by the dynamic polarizabilities at imaginary frequencies computed by time-dependent density-functional theory using the optimized effective potentials. The C6 coefficients thus obtained agree accurately with those from the exact-exchange counterpart in ab initio ...

The two-particle contribution to the potential part of the stress tensor autocorrelation function of a dense hard sphere fluid is studied. It is shown that the long-time decay is given as the solution of a diffusion equation for the relative particle in a potential of mean force. The diffusion constant needed in order to accurately reproduce molecular ...

It is proposed that the equilibrium generalized mean spherical model of fluid structure may be extended to nonequilibrium states with equation of state information used in equilibrium replaced by an exact condition on the two-body distribution function. The model is applied to the homogeneous cooling state of granular fluids, and upon comparison to molecular-dynamics ...

It was the purpose of the project described here to carry out careful and detailed investigations of petroleum and coal asphaltene transport through model porous systems under a broad range of temperature conditions. The experimental studies were to be coupled with detailed, in-depth statistical and molecular dynamics models intended to provide a ...

We propose a method for including the fractional occupancy of electronic energy levels within a tight-binding density-matrix formalism. This method is based on successful techniques used in first-principles methods. Molecular-dynamics test simulations show that the density-matrix technique accurately reproduces the physics of a direct-diagonalization ...

Clustering and annihilation of atomic-scale bond defects dominate nucleation and evolution of submicron-scale extended interstitial defects in irradiated silicon. Molecular dynamics simulations reveal the role of the bond defect in the thermal evolution of extended defects and identify the atomistic evolution paths. Accurate density ...

In this paper, we introduce a symmetry-adapted quantum nuclear propagation technique that utilizes distributed approximating functionals for quantum wavepacket dynamics in extended condensed-phase systems. The approach is developed with a goal for implementation in quantum-classical methods such as the recently developed quantum wavepacket ab intio ...

A fitting scheme is proposed to obtain effective potentials from Car-Parrinello molecular-dynamics (CPMD) simulations. It is used to parameterize a new pair potential for silica. MD simulations with this new potential are done to determine structural and dynamic properties and to compare these properties to those obtained from CPMD and a MD simulation ...

A recently introduced computational algorithm to extend time scales of atomically detailed simulations is illustrated. The algorithm, milestoning, is based on partitioning the dynamics to a sequence of trajectories between "milestones" and constructing a non-Markovian model for the motion along a reaction coordinate. The kinetics of a conformational transition in a blocked ...

The physicochemical properties of two molten salts, namely, KCl and NaCl, have been studied with a molecular-dynamics approach using a density-functional-based tight-binding (DFTB) model. The obtained results have been compared with a number of previously reported simulations, carried out on smaller systems and using classical force-field techniques. A good agreement has been ...

We review concurrent multiscale simulations of dynamic and temperature-dependent processes found in nanomechanical systems coupled to larger scale surroundings. We focus on the behavior of sub-micron Micro-Electro-Mechanical Systems (MEMS), especially microresonators. These systems are often called NEMS, for Nano-Electro-Mechanical Systems. The coupling of length scales ...

The quantum nature of nuclei plays an important role in the accurate modelling of light atoms such as hydrogen, but it is often neglected in simulations due to the high computational overhead involved. It has recently been shown that zero-point energy effects can be included comparatively cheaply in simulations of harmonic and quasiharmonic systems by augmenting classical ...

The quantum nature of nuclei plays an important role in the accurate modelling of light atoms such as hydrogen, but it is often neglected in simulations due to the high computational overhead involved. It has recently been shown that zero-point energy effects can be included comparatively cheaply in simulations of harmonic and quasiharmonic systems by augmenting classical ...

The recently introduced approximate many-body quantum simulation method, ring polymer molecular dynamics (RPMD), is compared to the centroid molecular dynamics method (CMD). Comparisons of simulation results for liquid para-hydrogen at two state points and liquid ortho-deuterium at one state point are presented. ...

In this work, we present an efficient algorithmic implementation of the energy and analytical forces of the recent density functional based van der Waals (vdW) correction proposed by Tkatchenko and Scheffler (PRL 102, 073005 (2009)) within the framework of plane-wave based ab initio molecular dynamics. The algorithm presented herein is a highly ...

Phenomena of many spherical particles in aqueous phase are ubiquitous in a plethora of natural and engineered processes. Brownian dynamics (BD), as originated from molecular dynamics (MD), is inherently limited to point-particles governed by the Oseen diffusion tensor. Stokesian dynamics (SD) incorporates ...

We propose an approximate method for evaluating the importance of non-Born-Oppenheimer effects on the quantum dynamics of nuclei. The method uses a generalization of the dephasing representation (DR) of quantum fidelity to several diabatic potential energy surfaces and its computational cost is the cost of dynamics of a classical phase space distribution. ...

Recent molecular dynamics simulation methods have enabled thermal conductivity of bulk materials to be estimated. In these simulations, periodic boundary conditions are used to extend the system dimensions to the thermodynamic limit. Such a strategy cannot be used for nanostructures with finite dimensions which are typically much larger than it is possible ...

We present a novel first principles molecular dynamics scheme, called Liouville-von Neumann molecular dynamics, based on Liouville-von Neumann equation for density matrices propagation and Magnus expansion of the time-evolution operator. The scheme combines formally accurate quantum propagation ...

We present a novel first principles molecular dynamics scheme, called Liouville-von Neumann molecular dynamics, based on Liouville-von Neumann equation for density matrices propagation and Magnus expansion of the time-evolution operator. The scheme combines formally accurate quantum propagation ...

We have used finite temperature ab initio molecular dynamics simulations in conjunction with computation of critical quantum nuclear effects to probe the differences between single-photon argon tagged action spectral results and infrared multiple-photon dissociation experiments for a proton bound molecular ion system. We find that the ...

We describe an efficient and accurate method to compute free energy changes in complex chemical systems that cannot be described through classical molecular dynamics simulations, examples of which are chemical and photochemical reactions in solution, enzymes, interfaces, etc. It is based on the use of dual-level Born-Oppenheimer ...

... Title : Microsatellite Alterations as Molecular Markers in Breast ... lack of early and accurate markers of disease. ... utility of a novel marker, the enzyme ...

... Title : Microsatellite Alterations as Molecular Markers in Breast ... lack of early and accurate markers of disease. ... utility of a novel marker, the enzyme ...

OAK 270 - Collaborative Research: Magma Rheology, Mixing of Rheological Fluids, Molecular Dynamics Simulation, and Lithospheric Dynamics

Biomolecular simulation derived properties of LPS membranes that impact the structural and internal dynamics of transmembrane proteins are shown to exhibit good agreement with available experimental data within the time scale simulated, chosen force field and simulation conditions. The molecular model used offers an accurate ...

We have developed a new protocol for using MolecularInversion Probes (MIP) to accurately and specifically measure allele copynumber (ACN). The new protocol provides for significant improvementsincluding the reduction of input DNA (from 2?g) by more than 25 fold (to75ng total genomic DNA), higher overall precision resulting in one orderof magnitude lower ...

In this paper the effect of bias and geometric symmetry breaking on the electronic spectrum of a model molecular system is studied. Geometric symmetry breaking can either enhance the dissipative effect of the bias, where spectral peaks are disabled, or enable new excitations that are absent under zero bias conditions. The spectral analysis is performed on a simple model system ...

Molecular dynamics (MD) simulation is the standard computational technique used to obtain information on the time evolution of the conformations of proteins and many other molecular systems. However, for most biological systems of interest, the time scale for slow conformational transitions is still inaccessible to standard MD ...

A novel combined Event-Driven/Time-Driven (ED/TD) algorithm to speed-up the Molecular Dynamics simulation of rarefied gases using realistic spherically symmetric soft potentials is presented. Due to the low density regime, the proposed method correctly identifies the time that must elapse before the next interaction occurs, similarly to Event-Driven ...

Computational models that reproduce and predict the detailed behavior of cellular systems form the Holy Grail of systems biology [1]. Molecular Dynamics represents the most accurate and fundamental approach to cell simulation, taking into account the fundamental physical rules at the atomic level. Due to the incredible high number of ...

A computational multiscale method is proposed to simulate coupled, nonequilibrium thermomechanical processes. This multiscale framework couples together thermomechanical equations at the coarse scale with nonequilibrium molecular dynamics at the fine scale. The novel concept of distributed coarse scale thermostats enables subsets of fine scale atoms to be ...

The quantum dynamics of the rotational quenching of the Mg24H+(X1?+) molecular cation interacting with He4(1S) as a buffer gas, at relative temperatures ranging from 1 K down to millikelvins, is described by accurate close coupling scattering calculations on an ab initio potential energy surface. The efficiency of the process is ...

Semiclassical methods that will allow much faster and more accurate three-dimensional atom/surface scattering calculations, both elastic and inelastic, are being developed. The scattering of He atoms from buckyballs is being investigated as a test problem. Somewhat more detail is given on studies of He atom scattering from defective Pt surfaces. Molecular ...

Simulation of the molecular dynamics of a small protein, bovine pancreatic trypsin inhibitor, was found to be more realistic when water molecules were included than when in vacuo: the time-averaged structure was much more like that observed in high-resolution x-ray studies, the amplitudes of atomic vibration in solution were smaller, and fewer incorrect ...

Multiple alignment of protein sequences helps to determine evolutionary linkage and to predict molecular structures. The factors to be considered while aligning multiple sequences are speed and accuracy of alignment. Although dynamic programming algorithms produce accurate alignments, they are computation intensive. In this paper we ...

Non-equilibrium molecular dynamics simulations are performed to calculate shear viscosities of 16 representative molecular liquids using the periodic perturbation method (PPM). A perturbation index is defined to measure the strength of the perturbation. It is identified that the predictions are systematically underestimated using PPM. ...

The question of coarse-graining is ubiquitous in molecular dynamics. In this paper, we are interested in deriving effective properties for the dynamics of a coarse-grained variable ?(x), where x describes the configuration of the system in a high-dimensional space \\mathbb{R}^n , and ? is a given smooth function with value in ...