Related papers: Multicanonical molecular dynamics by variable-temp…
A rigorous two-thermostat formulation for ab-initio molecular dynamics using the fictitious Lagrangian approach is presented. It integrates the concepts of mass renormalization and temperature control for the wave functions. The new…
A holonomic constraint is used to enforce a constant instantaneous configurational temperature on an equilibrium system. Three sets of equations of motion are obtained, differing according to the way in which the holonomic constraint is…
Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed…
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…
We present a method for performing multithermal-multibaric molecular dynamics simulations that sample entire regions of the temperature-pressure (TP) phase diagram. The method uses a variational principle [Valsson and Parrinello, Phys. Rev.…
The thermodynamic properties of systems with long-range interactions is still an ongoing challenge, both from the point of view of theory as well as computer simulation. In this work we study a model system, a Coulomb gas confined inside a…
In order to increase the efficiency of the computer simulation of biological molecules, it is very common to impose holonomic constraints on the fastest degrees of freedom; normally bond lengths, but also possibly bond angles. However, as…
Nonequilibrium molecular dynamics simulations often use mechanisms called thermostats to regulate the temperature. A Hamiltonian is presented for the case of the isoenergetic (constant internal energy) thermostat corresponding to a tunable…
We study the 38-atom Lennard-Jones cluster with parallel tempering Monte Carlo methods in the microcanonical and molecular dynamics ensembles. A new Monte Carlo algorithm is presented that samples rigorously the molecular dynamics ensemble…
We applied a multicanonical algorithm (entropic sampling) to a two-dimensional and a three-dimensional Lennard-Jones system with quasicrystalline and glassy ground states. Focusing on the ability of the algorithm to locate low lying energy…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is parallel replica dynamics, which relies on the rapid convergence of the underlying…
We study thermodynamical formalism of a discrete nonautonomous dynamical system determined by a sequence of continuous self-maps of a compact metric space. Using the methods of Convex Analysis we get variational principles for pressure…
The model quantum system of fermions in a one dimensional harmonic oscillator potential is investigated by a molecular dynamics method at constant temperature. Although in quantum mechanics the equipartition theorem cannot be used like in…
A generalized multibaker map with periodic boundary conditions is shown to model boundary-driven transport, when the driving is applied by a ``perturbation'' of the dynamics localised in a macroscopically small region. In this case there…
Molecular simulations in an open environment, involving ion exchange, are necessary to study various systems, from biosystems to confined electrolytes. However, grand-canonical simulations are often computationally demanding in condensed…
Many-body systems relaxing to equilibrium can exhibit complex dynamics even if their steady state is trivial. At low temperatures or high densities their evolution is often dominated by steric hindrances affecting particle motion [1,2,3].…
We consider dynamical systems evolving near an equilibrium statistical state where the interest is in modelling long term behavior that is consistent with thermodynamic constraints. We adjust the distribution using an entropy-optimizing…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
We show how thermodynamic properties of molecular models can be computed over a large, multidimensional parameter space by combining multistate reweighting analysis with a linear basis function approach. This approach reduces the…