Related papers: Validity of Molecular Dynamics Simulations for Sof…
Molecular Dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size…
Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous…
We consider several multiscale-in-time kinetic Monte Carlo models, in which some variables evolve on a fast time scale, while the others evolve on a slow time scale. In the first two models we consider, a particle evolves in a…
A molecular dynamics (MD) simulation is used to quantitatively analyze the induced membrane potential for an applied external field varied between 0.4 V/nm to 2.0 V/nm. The change in the electrostatic potential in the DPPC is directly…
Molecular-dynamics algorithms for systems of particles interacting through discrete or "hard" potentials are fundamentally different to the methods for continuous or "soft" potential systems. Although many software packages have been…
The present work is an example of the application of the dynamical system analysis in the context of cosmology. Here cosmic evolution is considered in the background of homogeneous and isotropic flat Friedmann-Lema\^{i}tre-Robertson-Walker…
The equilibrium shape of liquid drops on elastic substrates is determined by minimising elastic and capillary free energies, focusing on thick incompressible substrates. The problem is governed by three length scales: the size of the drop…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
Shadow molecular dynamics provide an efficient and stable atomistic simulation framework for flexible charge models with long-range electrostatic interactions. While previous implementations have been limited to atomic monopole charge…
We perform molecular dynamics simulation of a small number of particles in a box with periodic boundary conditions from a view point of chaotic dynamical systems. There is a transition at a critical energy E_c that each particle is confined…
A permanent electric dipole moment (EDM) of a particle or system is a separation of charge along its angular-momentum axis and is a direct signal of T-violation and, assuming CPT symmetry, CP violation. For over sixty years EDMs have been…
The use of energy functionals based on density as the basic variable is advocated for ab initio molecular dynamics. It is demonstrated that the constraint of positivity of density can be incorporated easily by using square root density for…
The physical foundations of the dissipation of energy and the associated heating in weakly collisional plasmas are poorly understood. Here, we compare and contrast several measures that have been used to characterize energy dissipation and…
Metals are traditionally considered hard matter. However, it is well known that their atomic lattices may become dynamic and undergo reconfigurations even well-below the melting temperature. The innate atomic dynamics of metals is directly…
Molecular dynamics simulations of interacting soft disks confined in a heterogeneous quenched matrix of soft obstacles show dynamics which is fundamentally different from that of hard disks. The interactions between the disks can enhance…
The glass transition of a hard sphere system is investigated within the framework of the density functional theory (DFT). Molecular dynamics (MD) simulations are performed to study dynamical behavior of the system on the one hand and to…
Elastic models of the glass transition relate the relaxation dynamics and the elastic properties of structural glasses. They are based on the assumption that the relaxation dynamics occurs through activated events in the energy landscape…
The absolute stability of a dark matter (DM) particle is not a binding requirement. Here we suggest a few scenarios where the DM particle is liable to decay via extremely feeble interactions. This can happen via inexplicably small Yukawa…
In recent years, certain molecular crystals have been reported to possess surprising flexibility by undergoing significant elastic or plastic deformation in response to mechanical loads. However, despite this experimental evidence, there…
Energy landscape mappings are performed for two different molecular systems under mechanical loads. Barrier heights are observed to scale as $\Delta U\sim\delta^{3/2}$, where $\delta$ is a residual load. Catastrophe theory predicts that…