Related papers: Isothermal-isobaric molecular dynamics using stoch…
We show that a stochastic approach enables calculations of the optical properties of large 2-dimensional and nanotubular excitonic molecular aggregates. Previous studies of such systems relied on numerically diagonalizing the dense and…
Computational multi-scale methods capitalize on a large time-scale separation to efficiently simulate slow dynamics over long time intervals. For stochastic systems, one often aims at resolving the statistics of the slowest dynamics. This…
We propose in this work a second-order Langevin sampler for the isothermal-isobaric ensemble (the NPT ensemble), preserving a positive volume for the simulation box. We first derive the suitable equations of motion for particles to be…
The stochastic differential equations for a model of dissipative particle dynamics, with both total energy and total momentum conservation at every time-step, are presented. The algorithm satisfies detailed balance as well as the…
We present an accelerated algorithm that samples correctly the thermodynamic ensemble in complex systems where the dynamics is controlled by activation barriers. The efficiency of the thermodynamically-weighted activation-relaxation…
Time-irreversible stochastic processes are frequently used in natural sciences to explain non-equilibrium phenomena and to design efficient stochastic algorithms. Our main goal in this thesis is to analyse their dynamics by means of large…
We study the convergence to equilibrium of an underdamped Langevin equation that is controlled by a linear feedback force. Specifically, we are interested in sampling the possibly multimodal invariant probability distribution of a Langevin…
Determining the 3D structures of biological molecules is a key problem for both biology and medicine. Electron Cryomicroscopy (Cryo-EM) is a promising technique for structure estimation which relies heavily on computational methods to…
Adaptive Langevin dynamics is a method for sampling the Boltzmann-Gibbs distribution at prescribed temperature in cases where the potential gradient is subject to stochastic perturbation of unknown magnitude. The method replaces the…
We present how entropy estimates and logarithmic Sobolev inequalities on the one hand, and the notion of quasi-stationary distribution on the other hand, are useful tools to analyze metastable overdamped Langevin dynamics, in particular to…
Biased sampling of collective variables is widely used to accelerate rare events in molecular simulations and to explore free energy surfaces. However, computational efficiency of these methods decreases with increasing number of collective…
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…
Quantifying energy flows at nanometer scales promises to guide future research in a variety of disciplines, from microscopic control and manipulation, to autonomously operating molecular machines. A general understanding of the…
Thermodynamic properties can be in principle derived from the partition function, which, in many-atom systems, is hard to evaluate as it involves a sum on the accessible microscopic states. Recently, the partition function has been computed…
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 discuss several algorithms for sampling from unnormalized probability distributions in statistical physics, but using the language of statistics and machine learning. We provide a self-contained introduction to some key ideas and…
The viscosity and self-diffusion constant of a mesoscale hydrodynamic method, dissipative particle dynamics (DPD), are investigated. The viscosity of DPD with finite time step, including the Lowe-Anderson thermostat, is derived analytically…
New explicit velocity- and position-Verlet-like algorithms of the second order are proposed to integrate the equations of motion in many-body systems. The algorithms are derived on the basis of an extended decomposition scheme at the…
We present a mechanism for thermalizing a moving particle by microscopic deterministic scattering. As an example, we consider the periodic Lorentz gas. We modify the collision rules by including energy transfer between particle and…
Recent molecular dynamics simulations show that a dilute relativistic gas equilibrates to a Juettner velocity distribution if ensemble velocities are measured simultaneously in the observer frame. The analysis of relativistic Brownian…