Related papers: A concise introduction to molecular dynamics simul…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
Novel technological applications often involve fluid flows in the Knudsen regime in which the mean free path is comparable to the system size. We use molecular dynamics simulations to study the transition between the dilute gas and the…
Molecular dynamics (MD) simulations are a crucial computational tool for researchers to understand and engineer molecular structure and function in areas such as drug discovery, protein engineering, and material design. Despite their…
This paper gives a systematic method for constructing an N-body potential, approximating the true potential, that accurately captures meso-scale behavior of the chemical or biological system using pairwise potentials coming from…
We discuss classical and quantum computations in terms of corresponding Hamiltonian dynamics. This allows us to introduce quantum computations which involve parallel processing of both: the data and programme instructions. Using mixed…
Theoretical and experimental investigations of water vapor interaction with porous materials are very needful for various fields of science and technology. Not only studies of the interaction of water vapor and porous material as a…
Vulcanian explosive eruption, which is a nonlinear and nonequilibrium abrupt dynamics of magma-gas mixture, is modeled by a two-component Lennard-Jones particle system. Molecular-dynamics simulation of a shock-tube experiment gives…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
Molecular dynamics (MD) provides insights into atomic-scale processes by integrating over time the equations that describe the motion of atoms under the action of interatomic forces. Machine learning models have substantially accelerated MD…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
Acid-base reactions are ubiquitous in nature. Understanding their mechanisms is crucial in many fields, from biochemistry to industrial catalysis. Unfortunately, experiments only give limited information without much insight into the…
Simulating the molecular dynamics (MD) using classical or semi-classical trajectories provides important details for the understanding of many chemical reactions, protein folding, drug design, and solvation effects. MD simulations using…
Molecular dynamics (MD) simulation with modified Brenner's reactive empirical bond order (REBO) potential is a powerful tool to investigate plasma wall interaction on divertor plates in a nuclear fusion device. However, MD simulation box's…
Development of computer technology in chemistry, bring many application of chemistry. Not only the application to visualize the structure of molecule but also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an example…
Multi-scale computer simulations combine the computationally efficient classical algorithms with more expensive but also more accurate ab-initio quantum mechanical algorithms. This work describes one implementation of multi-scale…
Molecular dynamics (MD) simulations are essential tools in computational chemistry and drug discovery, offering crucial insights into dynamic molecular behavior. However, their utility is significantly limited by substantial computational…
This paper invites the reader to experiment with an easy-to-use MATLAB implementation of Metropolis integrators for Molecular Dynamics (MD) simulation. These integrators are analysis-based, in the sense that they can rigorously simulate…
In a first course to classical mechanics elementary physical processes like elastic two-body collisions, the mass-spring model, or the gravitational two-body problem are discussed in detail. The continuation to many-body systems, however,…
Understanding and prediction of the chemical reactions are fundamental demanding in the study of many complex chemical systems. Reactive molecular dynamics (MD) simulation has been widely used for this purpose as it can offer atomic details…
Molecular dynamics (MD) simulations have become popular in materials science, biochemistry, biophysics and several other fields. Improvements in computational resources, in quality of force field parameters and algorithms have yielded…