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Mass-conserving reaction-diffusion (MCRD) systems are widely used to model phase separation and pattern formation in cell polarity, biomolecular condensates, and ecological systems. Numerical simulations and formal asymptotic analysis…
We develop a computational method based on Dissipative Particle Dynamics (DPD) that introduces solvent hydrodynamic interactions to coarse-grained models of solutes, such as ions, molecules, or polymers. DPD-solvent (DPDS) is a fully…
Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to…
Relevant information about the nature of the dynamics of ions in electrolytes can be obtained by studying the nonlinear dependence on an applied electric field. Here we use molecular dynamics (MD) simulations to study the field effects for…
The drag of turbulent flows can be drastically decreased by addition of small amounts of high molecular weight polymers. While drag reduction initially increases with polymer concentration, it eventually saturates to what is known as the…
We propose an experimental protocol for using cold atoms to create and probe quantum dimer models, thereby exploring the Pauling-Anderson vision of a macroscopic collection of resonating bonds. This process can allow the study of exotic…
Dynamic Hubbard models describe the fact that the wavefunction of an electron in an atomic orbital expands when a second electron occupies the orbital. These models give rise to superconductivity driven by lowering of kinetic energy when…
In this review article, we first briefly introduce the transport theory and quantum molecular dynamics model applied in the study of the heavy ion collisions from low to intermediate energies. The developments of improved quantum molecular…
The DMD (Dynamic Mode Decomposition) method has attracted widespread attention as a representative modal-decomposition method and can build a predictive model. However, the DMD may give predicted results that deviate from physical reality…
We study dynamics of clustering in systems containing active particles that are immersed in an explicit solvent. For this purpose we have adopted a hybrid simulation method, consisting of molecular dynamics and multi-particle collision…
Extended Lagrangian molecular dynamics (XLMD) is a general method for performing molecular dynamics simulations using quantum and classical many-body potentials. Recently several new XLMD schemes have been proposed and tested on several…
Using a hydrodynamic approach, we show that charge diffusion in two dimensional Coulomb interacting liquids with broken momentum conservation is intrinsically anomalous. The charge relaxation is governed by an overdamped, superdiffusive…
Electronic properties of quasi-two-dimensional molecular conductors $X$[Pd(dmit)$_2$]$_2$ are studied theoretically. We construct an effective model based on the fragment molecular orbital scheme developed recently, which can describe the…
We introduce a hybrid method for dielectric-metal composites that describes the dynamics of the metallic system classically whilst retaining a quantum description of the dielectric. The time-dependent dipole moment of the classical system…
Many astrophysical processes involving magnetic fields and quasi-stationary processes are well described when assuming the fluid as a perfect conductor. For these systems, the ideal-magnetohydrodynamics (MHD) description captures the…
Nonlocal models, including peridynamics, often use integral operators that embed lengthscales in their definition. However, the integrands in these operators are difficult to define from the data that are typically available for a given…
DL_POLY Quantum 2.1 is introduced here as a highly modular, sustainable, and scalable general-purpose molecular dynamics (MD) simulation software for large-scale long-time MD simulations of condensed phase and interfacial systems with the…
The primary distinction between solid and liquid phases is mechanical rigidity, with liquids having a disordered atomic structure that allows flow. While melting is a common phase transition, its microscopic mechanisms still remain unclear.…
This paper is the fourth in a series devoted to identifying and explaining the properties of strongly correlating liquids, i.e., liquids where virial and potential energy correlate better than 90% in their thermal equilibrium fluctuations…
Translational diffusion coefficients are routinely estimated from molecular dynamics simulations. Linear fits to mean squared displacement (MSD) curves have become the de facto standard, from simple liquids to complex biomacromolecules.…