Related papers: A Concurrent Multiscale Micromorphic Molecular Dyn…
A fundamental objective of materials modeling is identifying atomic structures that align with experimental observables. Conventional approaches for disordered materials involve sampling from thermodynamic ensembles and hoping for an…
In molecular dynamics (MD), systems are molecules made up of atoms, and the aim is to determine their evolution over time. MD is based on a numerical resolution algorithm, whose role is to apply the forces generated by the various…
Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…
We present a data-driven method for separating complex, multiscale systems into their constituent time-scale components using a recursive implementation of dynamic mode decomposition (DMD). Local linear models are built from windowed…
Molecular dynamics (MD) is a powerful and popular tool for understanding the dynamical evolution of materials at the nano and mesoscopic scales. There are various flavors of MD ranging from the high fidelity albeit computationally expensive…
We introduce mapping-variable ring polymer molecular dynamics (MV-RPMD), a model dynamics for the direct simulation of multi-electron processes. An extension of the RPMD idea, this method is based on an exact, imaginary time path-integral…
Molecular dynamics is based on solving Newton's equations for many-particle systems that evolve along complex, highly fluctuating trajectories. The orbital instability and short-time complexity of Newtonian orbits is in sharp contrast to…
We introduce a new micro-macro Markov chain Monte Carlo method (mM-MCMC) to sample invariant distributions of molecular dynamics systems that exhibit a time-scale separation between the microscopic (fast) dynamics, and the macroscopic…
The fluid-mechanics community is currently divided in assessing the boundaries of applicability of the macroscopic approach to fluid mechanical problems. Can the dynamics of nano-droplets be described by the same macroscopic equations as…
Soft materials (e.g., enveloped viruses, liposomes, membranes and supercooled liquids) simultaneously deform or display collective behaviors, while undergoing atomic scale vibrations and collisions. While the multiple space-time character…
A new methodology is developed to integrate numerically the equations of motion for classical many-body systems in molecular dynamics simulations. Its distinguishable feature is the possibility to preserve, independently on the size of the…
Quantum mechanics based ab-initio molecular dynamics (MD) simulation schemes offer an accurate and direct means to monitor the time-evolution of materials. Nevertheless, the expensive and repetitive energy and force computations required in…
In this article, a few problems related to multiscale modelling of magnetic materials at finite temperatures and possible ways of solving these problems are discussed. The discussion is mainly centred around two established multiscale…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
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 provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…
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,…
Understanding the deep connection of microscopic dynamics and statistical regularity yields insights into the foundation of statistical mechanics. In this work, based on the classical three-body system under the Lennard-Jones potential upon…
We study a ferromagnetic suspension or a suspension of magnetic nanoparticles in an anisotropic nematic medium, in three different one-dimensional variational settings, ordered in terms of increasing complexity. The three models are…
We demonstrate that the integration of the recently developed dynamic mode decomposition (DMD) with a multi-resolution analysis allows for a decomposition method capable of robustly separating complex systems into a hierarchy of…