Related papers: Constant pressure and temperature discrete-time La…
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…
The homogeneous state of a binary mixture of smooth inelastic hard disks or spheres is analyzed. The mixture is driven by a thermostat composed by two terms: a stochastic force and a drag force proportional to the particle velocity. The…
Dirac-Frenkel variational method with Davydov D2 trial wavefunction is extended by introducing a thermalization algorithm and applied to simulate dynamics of a general open quantum system. The algorithm allows to control temperature…
We introduce a new method to accurately and efficiently estimate the effective dynamics of collective variables in molecular simulations. Such reduced dynamics play an essential role in the study of a broad class of processes, ranging from…
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…
The ability to describe strongly interacting matter at finite temperature and baryon density provides the means to determine, for instance, the equation of state of QCD at non-zero baryon chemical potential. From a theoretical point of…
High-precision low-temperature thermometry is a challenge for experimental quantum physics and quantum sensing. Here we consider a thermometer modelled by a dynamically-controlled multilevel quantum probe in contact with a bath. Dynamical…
From the point of view of statistical mechanics, a full characterisation of a molecular system requires the experimental determination of its possible states, their populations and the respective interconversion rates. Well-established…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
In molecular dynamics, statistics of transitions, such as the mean transition time, are macroscopic observables which provide important dynamical information on the underlying microscopic stochastic process. A direct estimation using…
We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive…
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…
Understanding the realization of thermal equilibrium through the thermalization process in a many-body system is a fundamental and complex scientific question, bridging thermodynamics and classical dynamics and connecting to a host of…
We develop the stochastic approach to thermodynamics based on the stochastic dynamics, which can be discrete (master equation) continuous (Fokker-Planck equation), and on two assumptions concerning entropy. The first is the definition of…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
We investigate the influence of numerical discretization errors on computed averages in a molecular dynamics simulation of TIP4P liquid water at 300 K coupled to different deterministic (Nos\'e-Hoover and Nos\'e-Poincar\'e) and stochastic…
We present molecular dynamics simulations of the SPC/E model of water to probe the dynamic properties at temperatures from 350 K down to 190 K and pressures from 2.5GPa (25kbar) down to -300MPa (-3kbar). We compare our results with those…
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…
Suitable Langevin thermostats are introduced which are able to control both the temperature and the chemical potential of a one-dimensional lattice of nonlinear Schr\"odinger oscillators. The resulting non-equilibrium stationary states are…
We present a new method to sample conditioned trajectories of a system evolving under Langevin dynamics, based on Brownian bridges. The trajectories are conditioned to end at a certain point (or in a certain region) in space. The bridge…