Related papers: Introduction to molecular dynamics simulations
We review the recent literature on the simulation of the structure and deformation of amorphous glasses, including oxide and metallic glasses. We consider simulations at different length and time scales. At the nanometer scale, we review…
The study of molecular dynamics simulations is largely facilitated by analysis and visualization toolsets. However, these toolsets are often designed for specific use cases and those only, while scripting extensions to such toolsets is…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
In most cases the ultrafast dynamics of resonantly excited molecules are considered, and almost always computed in the molecular frame, while experiments are carried out in the laboratory frame. Here we provide a formalism in terms of a lab…
We present a general molecular-dynamics simulation scheme, based on the Nose' thermostat, for sampling according to arbitrary phase space distributions. We formulate numerical methods based on both Nose'-Hoover and Nose'-Poincare'…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
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…
This paper presents an overview of several modeling tools for analyzing molecular line observations at submillimeter wavelengths. These tools are already proving to be very valuable for the interpretation of data from current telescopes,…
Quantum computing has the potential to reduce the computational cost required for quantum dynamics simulations. However, existing quantum algorithms for coupled electron-nuclear dynamics simulation either require fault-tolerant devices, or…
We propose a local, O(N) molecular dynamics algorithm for the simulation of charged systems. The long ranged Coulomb potential is generated by a propagating electric field that obeys modified Maxwell equations. On coupling the…
In the context of the recently developed "equation-free" approach to the computer-assisted analysis of complex systems, we illustrate the computation of coarsely self-similar solutions. Dynamic renormalization and fixed point algorithms for…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
QwaveMPS is an open-source Python library for simulating one-dimensional quantum many-body waveguide systems using matrix product states (MPS). It provides a user-friendly interface for constructing, evolving, and analyzing quantum states…
In order to understand the physics phenomea on the fundamental aspects, the software simulations are a good exercise to succed in this way. Some work of heat transport and molecular physics laboratory are studied in a comparative mode…
We present Molecular Dynamics simulations of the thermal glass transition in a dense model polymer liquid. We performed a comparative study of both constant volume and constant pressure cooling of the polymer melt. Great emphasis was laid…
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…
We have investigated by molecular dynamics method the influence of a finite number of particles used in computer simulations on fluctuations of thermodynamic properties. As a case study, we used the two-dimensional Lennard-Jones system. 2D…
We provide a self-contained introduction to random matrices. While some applications are mentioned, our main emphasis is on three different approaches to random matrix models: the Coulomb gas method and its interpretation in terms of…