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Efficient molecular dynamics (MD) simulation is vital for understanding atomic-scale processes in materials science and biophysics. Traditional density functional theory (DFT) methods are computationally expensive, which limits the…
Polymer-related materials exhibit rich glassy behaviors at different length scales due to their various molecular structures and topological constraints. Recent studies have identified transient interpenetration of the long-chain rings…
We report a novel multi-scale simulation methodology to quantitatively predict the thermodynamic behaviour of polymer mixtures, that exhibit phases with broken orientational symmetry. Our system consists of a binary mixture of oligomers and…
We have presented some practical consequences on the molecular-dynamics simulations arising from the numerical algorithm published recently in paper Int. J. Mod. Phys. C 16, 413 (2005). The algorithm is not a finite-difference method and…
Molecular Dynamics (MD) simulations are essential for accurately predicting the physical and chemical properties of large molecular systems across various pressure and temperature ensembles. However, the high computational costs associated…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
We present a study of single-mode Rayleigh-Taylor instabilities (smRTI) with a modified Direct Simulation Monte Carlo (mDSMC) code in two dimensions. The mDSMC code is aimed to capture the dynamics of matter for a large range of Knudsen…
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…
Nonadiabatic ring-polymer molecular dynamics employs the mapping approach to describe nonadiabatic effects within the ring-polymer ansatz. In this paper, it is generalized to allow for the nuclear and electronic degrees of freedom to be…
Path integral molecular dynamics (PIMD) has been successfully applied to perform simulations of large bosonic systems in a recent work (Hirshberg et al., PNAS, 116, 21445 (2019)). In this work we extend PIMD techniques to study Green's…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
Path integrals are a central tool when it comes to describing quantum or thermal fluctuations of particles or fields. Their success dates back to Feynman who showed how to use them within the framework of quantum mechanics. Since then, path…
Simulations of biophysical systems inevitably include steps that correspond to time integrations of ordinary differential equations. These equations are often related to enzyme action in the synthesis and destruction of molecular species,…
A new method is proposed to numerically integrate a dynamical system on a manifold such that the trajectory stably remains on the manifold and preserves first integrals of the system. The idea is that given an initial point in the manifold…
Rayleigh-Taylor instability (RTI) as a multi-scale, strongly nonlinear physical phenomenon which plays an important role in the engineering applications and scientific research. In this paper, the mesoscopic lattice Boltzmann method is used…
We propose a modification of the embedded-atom method-type potential aiming at reconciling simulated melting and ground-state properties of metals by means of classical molecular dynamics. Considering titanium, magnesium, gold, and platinum…
We consider the geometric numerical integration of Hamiltonian systems subject to both equality and "hard" inequality constraints. As in the standard geometric integration setting, we target long-term structure preservation. We…
We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three…
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…
Nuclear quantum effects (NQEs) play an essential role in many atomistic systems, yet their explicit inclusion in molecular simulations remains challenging. Path-integral molecular dynamics (PIMD) provides a rigorous framework for…