Related papers: Pairwise adaptive thermostats for improved accurac…
An exact and efficient new method to simulate dynamics in dissipative quantum systems is presented. A stochastic Liouville equation, deduced from Feynman and Vernon's path-integral expression of the reduced density matrix, is used to…
In this paper we develop a dual-support smoothed particle hydrodynamics (DS-SPH) that naturally satisfies the conservation of momentum, angular momentum and energy when the varying smoothing length is utilized. The DS-SPH is based on the…
A proper treatment of electrostatic interactions is crucial for the accurate calculation of forces in computer simulations. Electrostatic interactions are typically modeled using Ewald based methods, which have become one of the…
We present a systematic, top-down, thermodynamic parametrization scheme for dissipative particle dynamics (DPD) using water-octanol partition coefficients, supplemented by water-octanol phase equilibria and pure liquid phase density data.…
We present a method, based on a non-Markovian Langevin equation, to include quantum corrections to the classical dynamics of ions in a quasi-harmonic system. By properly fitting the correlation function of the noise, one can vary the…
In this paper we introduce adaptive time step control for simulation of evolution of ice sheets. The discretization error in the approximations is estimated using "Milne's device" by comparing the result from two different methods in a…
In this paper, we present an efficient numerical method to address a thermodynamically consistent gas flow model in porous media involving compressible gas and deformable rock. The accurate modeling of gas flow in porous media often poses…
Simulations of nano- to micro-meter scale fluidic systems under thermal gradients require consistent mesoscopic methods accounting for both hydrodynamic interactions and proper transport of energy. One such method is dissipative particle…
Thermophoresis is an effective method to drive the motion of nanoparticles in fluids. The transport of nanoparticles in polymer networks has significant fundamental and applied importance in biology and medicine, and can be described as…
Coarse-grain Lagrangian methods, such as Dissipative Particle Dynamics ( Hoogerbrugge et al., EPL, 1992), are suitable for describing mesoscopic fluid systems that include thermal fluctuations. However, the realistic simulation of liquids…
Two of the most successful methods that are presently available for simulating the quantum dynamics of condensed phase systems are centroid molecular dynamics (CMD) and ring polymer molecular dynamics (RPMD). Despite their conceptual…
The selective frequency damping (SFD) method is an alternative to classical Newton's method to obtain unstable steady-state solutions of dynamical systems. However this method has two main limitations: it does not converge for arbitrary…
Accurate and efficient plasma models are essential to understand and control experimental devices. Existing magnetohydrodynamic or kinetic models are nonlinear, computationally intensive, and can be difficult to interpret, while often only…
A new configurational temperature thermostat suitable for molecules with holonomic constraints is derived. This thermostat has a simple set of motion equations, can generate the canonical ensemble in both position and momentum space, acts…
We present a novel approach of mapping dissipative particle dynamics (DPD) into classical molecular dynamics. By introducing the invariant volume element representing the swarm of atoms we show that the interactions between the emerging…
The stochastic thermodynamics of a dilute, well-stirred mixture of chemically-reacting species is built on the stochastic trajectories of reaction events obtained from the Chemical Master Equation. However, when the molecular populations…
The standard {\em system-plus-reservoir} approach used in the study of dissipative systems can be meaningfully generalized to a dissipative coupling involving the momentum, instead of the coordinate: the corresponding equation of motion…
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…
The Langevin equation accounts for unresolved bath degrees of freedom driving the system toward the bath temperature. Because of this, numerical solutions of the Langevin equation have a long history. Here, we recapitulate, combine, and…
We study the Langevin dynamics of a dipole diffusing in a random electrical field E derived from a quenched Gaussian potential. We show that in a suitable adiabatic limit (where the dynamics of the dipole moment is much faster than the…