Related papers: Tunneling-splittings from path-integral molecular …
We develop a path-integral dynamics method for water that resembles centroid molecular dynamics (CMD), except that the centroids are averages of curvilinear, rather than cartesian, bead coordinates. The curvilinear coordinates are used…
We discuss the design of state-of-the-art numerical methods for molecular dynamics, focusing on the demands of soft matter simulation, where the purposes include sampling and dynamics calculations both in and out of equilibrium. We discuss…
Particle-in-Cell (PIC) methods are widely used computational tools for fluid and kinetic plasma modeling. While both the fluid and kinetic PIC approaches have been successfully used to target either kinetic or fluid simulations, little was…
This paper is devoted to the study of quantum dissipation in cluster decay phenomena in the frame of the Lindblad approach to quantum open systems. The tunneling of a metastable state across a piecewise quadratic potential is envisaged for…
We frame the issue of pedestrian dynamics modeling in terms of path-integrals, a formalism originally introduced in quantum mechanics to account for the behavior of quantum particles, later extended to quantum field theories and to…
The method to calculate the grand partition function of a particle system, in which constituents interact with each other via potential, that include repulsive and attractive components, is proposed. The cell model, which was introduced to…
This paper focuses on the temporal discretization of the Langevin dynamics, and on different resulting numerical integration schemes. Using a method based on the exponentiation of time dependent operators, we carefully derive a numerical…
Two first-principles simulation techniques, path integral Monte Carlo (PIMC) and density functional molecular dynamics (DFT-MD), are applied to study hot, dense helium in the density-temperature range of 0.387 - 5.35 g/cc and 500 K -…
The calculation of thermal conductivity in insulating solids at temperatures below the Debye temperature is problematic, due to the breakdown of classical and semi-classical approaches. In this work, we present a fully quantum methodology…
A new Langevin-Verlet thermostat that preserves the fluctuation-dissipation relationship for discrete time steps, is applied to molecular modeling and tested against several popular suites (AMBER, GROMACS, LAMMPS) using a small molecule as…
In this article we show in details the derivation of an integration scheme for the dissipative particle dynamic model (DPD) using the stochastic Trotter formula [De Fabritiis et al., Physica A, 361, 429 (2006)]. We explain some subtleties…
Generalized Langevin Equation (GLE) thermostats have been used very effectively as a tool to manipulate and optimize the sampling of thermodynamic ensembles and the associated static properties. Here we show that a similar, exquisite level…
Information about the nature of the low-temperature anomalies and in particular the properties of the tunneling systems in silica and lithium silica glasses are revealed via computer simulations. The potential energy landscape of these…
Coarse graining (CG) is an important task for efficient modeling and simulation of complex multi-scale systems, such as the conformational dynamics of biomolecules. This work presents a projection-based coarse-graining formalism for general…
The quantum harmonic oscillator is the fundamental building block to compute thermal properties of virtually any dielectric crystal at low temperatures in terms of phonons, extended further to cases with anharmonic couplings, or even…
We proposed a new technique to accelerate sampling methods for solving difficult optimization problems. Our method investigates the intrinsic connection between posterior distribution sampling and optimization with Langevin dynamics, and…
Warm dense matter (WDM) is an active field of research, with applications ranging from astrophysics to inertial confinement fusion. Ionization degree and continuum lowering are important quantities to understand how materials behave under…
Operator splitting methods tailored to coupled linear port-Hamiltonian systems are developed. We present algorithms that are able to exploit scalar coupling, as well as multirate potential of these coupled systems. The obtained algorithms…
The particle proper orthogonal decomposition (PPOD) is demonstrated on cases of particle flows in decaying homogeneous isotropic turbulence. Data is generated through one-way coupled simulations, where particle positions and velocities are…
Dissipative particle dynamics (DPD) is a novel particle method for mesoscale modeling of complex fluids. DPD particles are often thought to represent packets of real atoms, and the physical scale probed in DPD models are determined by the…