Related papers: Control-volume representation of molecular dynamic…
This paper presents a formulation of Lagrangian dynamics of constrained mechanical systems in terms of reduced quasi-velocities and quasi-forces that can be used for simulation, analysis, and control purposes. In this formulation, Cholesky…
We propose in this paper a discretization of the momentum convection operator for fluid flow simulations on quadrangular or hexahedral meshes. The space discretization is performed by the loworder nonconforming Rannacher-Turek finite…
Understanding what happens inside the rippling and dancing surface of a liquid remains one of the great challenges of fluid dynamics. Using molecular dynamics (MD) we can pick apart the interface structure and understand surface tension. In…
Particle-based methods are a practical tool in computational fluid dynamics, and novel types of methods have been proposed. However, widely developed Lagrangian-type formulations suffer from the nonuniform distribution of particles, which…
The fluid flow transport and hydrodynamic problems often take the form of hyperbolic systems of conservation laws. In this work we will present a new scheme of finite volume methods for solving these evolution equations. It is a family of…
Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in…
We study compressible fluid flow in narrow two-dimensional channels using a novel molecular dynamics simulation method. In the simulation area, an upstream source is maintained at constant density and temperature while a downstream…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
This paper presents a novel high-order cell-centered Lagrangian scheme for 2D compressible hydrodynamics by bridging the multi-moment constrained finite volume method (MCV) [16, 51, 52] with a nodal Riemann solver. This scheme (denoted by…
Molecular dynamics (MD) simulations are powerful tools for elucidating the macroscopic physical properties of materials from microscopic atomic behaviors. However, the massive, high-dimensional datasets generated by MD simulations pose a…
The method of Lagrangians with covariant derivative (MLCD) is applied to a special type of Lagrangian density depending on scalar and vector fields as well as on their first covariant derivatives. The corresponding Euler-Lagrange's…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
We present and discuss a novel approach to deal with conservation properties for the simulation of nonlinear complex porous media flows in the presence of: 1) multiscale heterogeneity structures appearing in the elliptic-pressure-velocity…
Extended Lagrangian molecular dynamics (XLMD) is a general method for performing molecular dynamics simulations using quantum and classical many-body potentials. Recently several new XLMD schemes have been proposed and tested on several…
We present a solution to the conservation form (Eulerian form) of the quantum hydrodynamic equations which arise in chemical dynamics by implementing a mixed/discontinuous Galerkin (MDG) finite element numerical scheme. We show that this…
Molecular dynamics simulations of myoglobin and aspartate aminotransferase, with explicit solvent, are shown to accurately reproduce the experimentally measured molar volumes. Single amino-acid substitution at VAL39 of aspartate…
Molecular Dynamic (MD) approach is applied to study the converging cylindrical shock waves in a dense Lennard-Jones (LJ) fluid. MD method is based on tracking of the atom motions and hence it has an fundamental advantages over hydrodynamic…
We use a novel non-equilibrium algorithm to simulate steady-state fluid transport through a two-dimensional (2D) membrane due to a concentration gradient by molecular dynamics (MD) for the first time. We confirm that, as required by the…
Molecular Dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size…
The internal dynamics of macro-molecular systems is characterized by widely separated time scales, ranging from fraction of ps to ns. In ordinary molecular dynamics simulations, the elementary time step dt used to integrate the equation of…