Related papers: Adaptive Resolution Molecular Dynamics Technique: …
Using molecular dynamics simulations and integral equations (Rogers-Young, Percus-Yevick and hypernetted chain closures) we investigate the thermodynamic of particles interacting with continuous core-softened intermolecular potential.…
Computational magnetohydrodynamics (MHD) for space physics has become an essential area in understanding the multiscale dynamics of geophysical and astrophysical plasma processes, partially motivated by the lack of space data. Full MHD…
Dynamic Mode Decomposition (DMD) is a powerful data-driven method used to extract spatio-temporal coherent structures that dictate a given dynamical system. The method consists of stacking collected temporal snapshots into a matrix and…
The paper sets forth comprehensive basics of Discrete Thermodynamics of Chemical Equilibria (DTD), developed by the author during the last decade and spread over series of publications. Based on the linear equations of irreversible…
Warm dense matter (WMD) describes an intermediate phase, between condensed matter and classical plasmas, found in natural and man-made systems. In a laboratory setting, WDM needs to be created dynamically. It is typically laser or…
Multiresolution topology optimization (MTO) methods involve decoupling of the design and analysis discretizations, such that a high-resolution design can be obtained at relatively low analysis costs. Recent studies have shown that the MTO…
A novel Douglas alternating direction implicit (ADI) method is proposed in this work to solve a two-dimensional (2D) heat equation with interfaces. The ADI scheme is a powerful finite difference method for solving parabolic equations, due…
Many thermodynamic instabilities in one dimension (e.g. DNA thermal denaturation, wetting of interfaces) can be described in terms of simple models involving harmonic coupling between nearest neighbors and an asymmetric on-site potential…
Magnetohydrodynamic (MHD) turbulence is a ubiquitous dynamical state of astrophysical plasmas and a primary agent in the redistribution, dissipation, and conversion of energy into particle populations. Yet turbulence is still most often…
Using conservation of energy - a fundamental property of closed classical and quantum mechanical systems - we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a…
We employ a fast and accurate algorithm to treat dielectric interfaces within molecular dynamics simulations and demonstrate the importance of dielectric boundary forces (DBFs) in two systems of interests in soft-condensed matter science.…
Dissipative particle dynamics (DPD) does not conserve energy and this precludes its use in the study of thermal processes in complex fluids. We present here a generalization of DPD that incorporates an internal energy and a temperature…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
A molecular dynamics simulation is performed for a supercooled liquid of rigid diatomic molecules. The time-dependent self and collective density correlators of the molecular centers of mass are determined and compared with the predictions…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
Fully adaptive computations of the resistive magnetohydrodynamic (MHD) equations are presented in two and three space dimensions using a finite volume discretization on locally refined dyadic grids. Divergence cleaning is used to control…
We present a fully adaptive multiresolution scheme for spatially two-dimensional, possibly degenerate reaction-diffusion systems, focusing on combustion models and models of pattern formation and chemotaxis in mathematical biology.…
We demonstrate the application of the Dynamic Mode Decomposition (DMD) for the diagnostic analysis of the nonlinear dynamics of a magnetized plasma in resistive magnetohydrodynamics. The DMD method is an ideal spatio-temporal matrix…
Molecular Dynamics (MD) simulations are vital for exploring complex systems in computational physics and chemistry. While machine learning methods dramatically reduce computational costs relative to ab initio methods, their accuracy in…
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…