Related papers: Molecular Dynamics for Low Temperature Plasma-Surf…
As molecular scientists have made progress in their ability to engineer nano-scale molecular structure, we are facing new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs…
We discuss techniques to engineer effective long-range interactions between polar molecules using external static electric and microwave fields. We consider a setup where molecules are trapped in a two-dimensional pancake geometry by a…
Studies of the long-range interactions between cold atoms and surfaces are now of vital interest. The interest is partly driven by nanotechnology applications, partly by the exploding interest in the encompassing superfield of Casimir…
The behavior of nuclear matter is studied at low densities and temperatures using classical molecular dynamics with three different sets of potentials with different compressibility. Nuclear matter is found to arrange in crystalline…
Molecular dynamics (MD) simulations involving reactive potentials can be used to model material failure. The empirical potentials which are used in such simulations are able to adapt to the atomic environment, at the expense of a…
Molecular dynamics simulations at a constant electric potential are an essential tool to study electrochemical processes, providing microscopic information on the structural, thermodynamic, and dynamical properties. Despite the numerous…
Modeling plasmas in terms of atoms or ions is theoretically appealing for several reasons. When it is relevant, the notion of atom or ion in a plasma provides us with an interpretation scheme of the plasma's microscopic structure. From the…
LAMMPS is a widely popular classical Molecular Dynamics package. It was designed for materials modeling but it is well prepared for simulations in Soft Matter. The use packages like LAMMPS has advantages and disadvantages. The main…
Chemical potential of species in solution is essential for understanding various chemical processes at interfaces. Molecular dynamics (MD) simulations, constrained by fixed compositions, cannot satisfy a constant chemical potential…
A molecular dynamics (MD) simulation is used to quantitatively analyze the induced membrane potential for an applied external field varied between 0.4 V/nm to 2.0 V/nm. The change in the electrostatic potential in the DPPC is directly…
In this review we discuss the recent progress in the simulation of soft active matter systems and in particular the hydrodynamics of microswimmers using the method of multiparticle collision dynamics, which solves the hydrodynamic flows…
This article reviews the current state of the art in the field of cold and ultracold molecules and demonstrates that chemical reactions, inelastic collisions and dissociation of molecules at subKelvin temperatures can be manipulated with…
Ring-polymer molecular dynamics (RPMD) has become a popular method for describing chemical reactions due to its ability to simultaneously capture tunneling, zero-point energy, anharmonicity and recrossing. Here we highlight that despite its…
In this paper, a hybrid quasi-static atomistic simulation method at finite temperature is developed, which combines the advantages of MD for thermal equilibrium and atomic-scale finite element method (AFEM) for efficient equilibration. Some…
In this article, microscopic understanding of the surface tension are provided, which needs basic knowledge of thermodynamics, statistical mechanics as well as continuum mechanics. By introducing the intermolecular interaction potential and…
Time-resolved investigations of ultrafast electronic and molecular dynamics were not possible until recently. The typical time scale of these processes is in the picosecond to attosecond realm. The tremendous technological progress in…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
We describe a hybrid molecular dynamics approach for the description of ultracold neutral plasmas, based on an adiabatic treatment of the electron gas and a full molecular dynamics simulation of the ions, which allows us to follow the…
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…
We present methods for exploratory studies of molecular dynamics using MATLAB. Such methods are not suitable for large scale applications, but they can be used for developement and testing of new types of interactions and other aspects of…