Related papers: Understanding Molecular Dynamics with Stochastic P…
Stochasticity plays a fundamental role in various biochemical processes, such as cell regulatory networks and enzyme cascades. Isothermal, well-mixed systems can be modelled as Markov processes, typically simulated using the Gillespie…
We consider the modeling of the dynamics of the chemostat at its very source. The chemostat is classically represented as a system of ordinary differential equations. Our goal is to establish a stochastic model that is valid at the scale…
Metastable condensed matter typically fluctuates about local energy minima at the femtosecond time scale before transitioning between local minima after nanoseconds or microseconds. This vast scale separation limits the applicability of…
In most cases the ultrafast dynamics of resonantly excited molecules are considered, and almost always computed in the molecular frame, while experiments are carried out in the laboratory frame. Here we provide a formalism in terms of a lab…
The developing field of stochastic thermodynamics extends concepts of macroscopic thermodynamics such as entropy production and work to the microscopic level of individual trajectories taken by a system through phase space. The scheme…
In these lecture notes, the basic principles of stochastic thermodynamics are developed starting with a closed system in contact with a heat bath. A trajectory undergoes Markovian transitions between observable meso-states that correspond…
Markedly increased computational power and data acquisition have led to growing interest in data-driven inverse dynamics problems. These seek to answer a fundamental question: What can we learn from time series measurements of a complex…
We prove that for a combined system of classical and quantum particles, it is possible to write a dynamics for the classical particles that incorporates in a natural way the Boltzmann equilibrium population for the quantum subsystem. In…
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…
Andersen dynamics is a standard method for molecular simulations, and a precursor of the Hamiltonian Monte Carlo algorithm used in MCMC inference. The stochastic process corresponding to Andersen dynamics is a PDMP (piecewise deterministic…
Thermodynamics with internal variables is a common approach in continuum mechanics to model inelastic (i.e., non-equilibrium) material behavior. While this approach is computationally and theoretically attractive, it currently lacks a…
This article proposes a novel thermostat applicable to any particle-based dynamic simulation. Each pair of particles is thermostated either (with probability P) with a pairwise Lowe-Andersen thermostat, or (with probability 1-P) with a…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
This is our current research perspective on models providing insight into statistical mechanics. It is necessarily personal, emphasizing our own interest in simulation as it developed from the National Laboratories' work to the worldwide…
Small systems in a thermodynamic medium --- like colloids in a suspension or the molecular machinery in living cells --- are strongly affected by the thermal fluctuations of their environment. Physicists model such systems by means of…
Numerical simulation of stochastic dynamics of vortex filaments under action of random (Langevin) force is fulfilled. Calculations are performed on base of the full Biot--Savart law for different intensities of the Langevin force. A new…
Many coarse-grained models have been developed for equilibrium studies of lipid bilayer membranes. To achieve in simulations access to length-scales and time-scales difficult to attain in fully atomistic molecular dynamics, these…
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and…
Sampling from flat energy or density distributions has proven useful in equilibrating complex systems with large energy barriers. Several thermostats and barostats are presented to sample these flat distributions by molecular dynamics.…
We present a numerical method to produce stochastic dynamics according to the generalized Langevin equation with a non-stationary memory kernel. This type of dynamics occurs when a microscopic system with an explicitly time-dependent…