Related papers: Metric tensor as the dynamical variable for variab…
An extended Hamiltonian approach to conduct isothermal-isobaric molecular dynamics simulations with full cell flexibility is presented. The components of the metric tensor are used as the fictitious degrees of freedom for the cell, thus…
We construct the molecular model and the tensor model for the dynamics of the nematic phases of bent-core molecules and star molecules in incompressible fluid. We start from the molecular interaction and the molecule--fluid friction, and…
We construct a tensor model for nematic phases of bent-core molecules from molecular theory. The form of free energy is determined by molecular symmetry, which includes the couplings and derivatives of a vector and two second-order tensors,…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
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…
The use of energy functionals based on density as the basic variable is advocated for ab initio molecular dynamics. It is demonstrated that the constraint of positivity of density can be incorporated easily by using square root density for…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
This paper develops a generative statistical model for representing, modeling, and comparing the morphological evolution of biological cells undergoing motility. It uses the elastic shape analysis to separate cell kinematics (overall…
In the mechanics of inviscid conservative fluids, it is classical to generate the equations of dynamics by formulating with adequate variables, that the pressure integral calculated in the time-space domain corresponding to the motion of…
The Cellular Automaton (CA) modeling and simulation of solid dynamics is a long-standing difficult problem. In this paper we present a new two-dimensional CA model for solid dynamics. In this model the solid body is represented by a set of…
Dynamic mode decomposition (DMD) is a data-driven method for estimating the dynamics of a discrete dynamical system. This paper proposes a tensor-based approach to DMD for applications in which the states can be viewed as tensors.…
This paper presents a novel approach to the description and understanding of two-dimensional binary cellular automata with the Moore neighborhood that preserve the number of active cells. Such dynamical systems are known to successfully…
The metric-affine gravity provides a useful framework for analyzing gravitational dynamics since it treats metric tensor and affine connection as fundamentally independent variables. In this work, we show that, a metric-affine gravity…
Matrix models have phase transitions in which distributions of variables change topologically like the Gross-Witten-Wadia transition. In a recent study, similar splitting-merging behavior of distributions of dynamical variables was observed…
Sampling from flat energy or density distributions has proven useful in equilibrating complex systems with large energy barriers. Several thermostats and barostats are presented to sample these flat distributions by molecular dynamics.…
We derive a mobility tensor for many cylindrical objects embedded in a viscous sheet. This tensor guarantees a positive dissipation rate for any configuration of particles and forces, analogously to the Rotne-Prager-Yamakawa tensor for…
Suspensions of swimming micro-organisms provide examples of coordinated active dynamics. That has stimulated the study of a phenomenological theory combining synchronization and polar order in active matter. Here, we consider another…
In this paper I present a first attempt for a possible description of fluids dynamics by mean of a cellular automata technique. With the use of simple and elementary rules, based on random behaviour either, the model permits to obtain the…
The variational discrete element method developed in [28] for dynamic elasto-plastic computations is adapted to compute the deformation of elastic Cosserat materials. In addition to cellwise displacement degrees of freedom (dofs), cellwise…
Molecular dynamics has been widely used to numerically solve equation of motion of classical many-particle system. It can be used to simulate many systems including biophysics, whose complexity level is determined by the involved elements.…