Related papers: Expressions for forces and torques in molecular si…
This document attempts to clarify potential confusion regarding electrostatics calculations, specifically in the context of biomolecular structure and specifically as regards the units typically used to contour/visualize isopotential…
Torques on interfaces can be described by a divergence-free tensor which is fully encoded in the geometry. This tensor consists of two terms, one originating in the couple of the stress, the other capturing an intrinsic contribution due to…
This paper presents a novel particle method to compute strongly coupled incompressible fluid and rigid bodies. The method adopts a velocity-based formulation and utilizes the linear complementarity problem for the incompressibility…
Interatomic potentials approximate the potential energy of atoms as a function of their coordinates. Their main application is the effective simulation of many-atom systems. Here, we review empirical interatomic potentials designed to…
Assessing the structural properties of large proteins is important to gain an understanding of their function in, e.g., biological systems or biomedical applications. We propose a method to examine the mechanical properties of proteins…
The system of particles interacting via multibody interatomic potential of general form is considered. Possible variants of partition of the total force acting on a single particle into pair contributions are discussed. Two definitions for…
A new model for computer simulation of solids, composed of bonded rigid body particles, is proposed. Vectors rigidly connected with particles are used for description of deformation of a single bond. The expression for potential energy of…
The static friction between crystalline surfaces separated by a molecularly thin layer of adsorbed molecules is calculated using molecular dynamics simulations. These molecules naturally lead to a finite static friction that is consistent…
The quality of biomolecular simulations critically depends on the accuracy of the force field used to calculate the potential energy of the molecular configurations. Currently, most simulations employ non-polarisable force fields, which…
In this article we give our perspective on the successes and promise of various molecular and coarse-grained simulation approaches to probing the effect of mechanical forces in the actin cytoskeleton.
A theoretical model is proposed for low temperature friction between two smooth rigid solid surfaces separated by lubricant molecules, admitting their deformations and rotations. Appearance of different modes of energy dissipation (by…
Most computer simulations of molecular dynamics take place under equilibrium conditions--in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are…
Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…
An analytical description of polymer melts and their mixtures as liquids of interacting soft colloidal particles is obtained from liquid-state theory. The derived center-of-mass pair correlation functions with no adjustable parameters…
Simulations at the atomic scale provide a direct and effective way to understand the mechanical properties of materials. In the regime of classical mechanics, simulations for the thermodynamic properties of metals and alloys can be done by…
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…
Molecular Dynamics simulations are becoming a powerful tool for examining and predicting atomic and molecular processes in various environment. The present review shows how, in the fields of plasma physics, chemistry and interactions with…
We derive an expression for the mutual gravitational force and torque of two bodies having arbitrary shapes and mass distributions, as an expansion in power series of their products of inertia and of the relative coordinates of their…
An accurate prediction of the translational and rotational motion of particles suspended in a fluid is only possible if a complete set of correlations for the force coefficients of fluid-particle interaction is known. The present study is…
We consider mechanically generated molecular braids composed of two molecules where long range interactions between them can be considered to be very weak. We describe a model that takes account of the thermal fluctuations of the braid,…