Related papers: Expressions for forces and torques in molecular si…
Computer simulations of inhomogeneous soft matter systems often require accurate methods for computing the local pressure. We present a simple derivation, based on the virial relation, of two equivalent expressions for the local (atomistic)…
We present general first principles derivation of expression for current-induced forces. The expression is applicable in non-equilibrium molecular systems with arbitrary intra-molecular interactions and for any electron-nuclei coupling. It…
Embedding rigid inclusions into elastic matrix materials is a procedure of high practical relevance, for instance for the fabrication of elastic composite materials. We theoretically analyze the following situation. Rigid spherical…
We derive expressions for determination of the stress and the elastic constants in systems composed of particles interacting via non-central two-body potentials as thermal averages of products of first and second partial derivatives of the…
Torque is ubiquitous in many molecular systems, including collisions, chemical reactions, vibrations, electronic excitations and especially rotor molecules. We present a straightforward theoretical method based on forces acting on atoms and…
A general framework for performing event-driven simulations of systems with semi-flexible or rigid bodies interacting under impulsive torques and forces is outlined. Two different approaches are presented. In the first, the dynamics and…
The dynamics of anisotropic particles are dictated by forces and torques that can be challenging to mathematically represent in computer simulations. Several data-driven approaches have been developed to approximate these interactions, but…
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…
Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the…
Microscopic stress fields are widely used in molecular simulations to understand mechanical behavior. Recently, decomposition methods of multibody forces to central force pairs between the interacting particles have been proposed. Here, we…
Complex plasmas are low-temperature plasmas that contain micrometer-size particles in addition to the neutral gas particles and the ions and electrons that make up the plasma. The microparticles interact strongly and display a wealth of…
We derive exact expressions for the forces and torques between biaxial molecules interacting via the RE-squared potential, a recent variant of the Gay-Berne potential. Moreover, efficient routines have been provided for rigid body MD…
We present several closed-form expressions of useful mass distributions. These include the potentials and accelerations of circular rings and arcs, the potentials of uniform density rings and arcs at arbitrary eccentricities, and the…
We describe an educational simulation of some effects within the gas of hard spheres. The focus of the presented simulation is on the comprehension of random character of the velocity of molecules in the gas and of the energy at fixed…
We extend the insertion approach for calculating depletion potentials to the case of non-spherical solutes. Instead of a brute-force calculation we suggest to employ the recently developed curvature expansion of density profiles close to…
In this article, formulas for the calculation of force and torque between two circular filaments arbitrarily oriented in space were derived by using Kalantarov-Zeitlin's method. Formulas are presented in an analytical form through integral…
Molecular dynamics simulations provide a mechanistic description of molecules by relying on empirical potentials. The quality and transferability of such potentials can be improved leveraging data-driven models derived with machine learning…
At first, pressure formulas for the electrons under the external potential produced by fixed nuclei are derived both in the surface integral and volume integral forms concerning an arbitrary volume chosen in the system; the surface integral…
An overview of computational methods to describe high-dimensional potential energy surfaces suitable for atomistic simulations is given. Particular emphasis is put on accuracy, computability, transferability and extensibility of the methods…
In Molecular Dynamics (MD), the forces applied to atoms derive from potentials which describe the energy of bonds, valence angles, torsion angles, and Lennard-Jones interactions of which molecules are made. These de finitions are classic;…