Related papers: A simple time coarse graining method for molecular…
State-space smoothing has found many applications in science and engineering. Under linear and Gaussian assumptions, smoothed estimates can be obtained using efficient recursions, for example Rauch-Tung-Striebel and Mayne-Fraser algorithms.…
Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds…
We propose a novel computational strategy to study the glass transition of molecular fluids. Our approach combines the construction of simple yet realistic models with the development of Monte Carlo algorithms to accelerate equilibration…
We present simulations of causal dynamical collapse models of field theories on a 1+1 null lattice. We use our simulations to compare and contrast two possible interpretations of the models, one in which the field values are real and the…
We study coarse-graining methods for stochastic differential equations. In particular we consider averaging and a type of projection operator method, sometimes referred to as effective dynamic via conditional expectations. The projection…
Coarse-grained (CG) molecular dynamics enables simulations of atomic systems such as biomolecules at timescales inaccessible to all-atom (AA) methods, but existing CG neural potentials trained via force matching capture only the gradient of…
We use computer simulations to test a simple idea for mapping between long-time self diffusivities obtained from molecular and Brownian dynamics. The strategy we explore is motivated by the behavior of fluids comprising particles that…
We present general results on fluctuations and spatial correlations of the coarse-grained empirical density and current of Markovian diffusion in equilibrium or non-equilibrium steady states on all time scales. We unravel a deep connection…
Molecular dynamics algorithms are subject to some amount of error dependent on the size of the time step that is used. This error can be corrected by periodically updating the system with a Metropolis criteria, where the integration step is…
We derive a coarse-grained description of the dynamics of a nanoparticle immersed in an isothermal simple fluid by performing a systematic coarse graining of the underlying microscopic dynamics. As coarse-grained or relevant variables we…
A simple stochastic model of solute drag by moving grain boundaries (GBs) is presented. Using a small number of parameters, the model describes solute interactions with GBs and captures nonlinear GB dynamics, solute saturation in the…
In typical single-molecule force spectroscopy experiments the mechanical unfolding of molecular complexes or biomolecules is studied applying a force ramp to one end of the system while the other end is kept fixed in space. The…
Normalizing flows are a promising tool for modeling probability distributions in physical systems. While state-of-the-art flows accurately approximate distributions and energies, applications in physics additionally require smooth energies…
We show that the coarse-grained dynamics model with the time-dependent and fluctuating potential (transient potential) can be derived from the microscopic Hamiltonian dynamics. The concept of the transient potential was first introduced…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…
We explore a computational approach to coarse graining the evolution of the large-scale features of a randomly forced Burgers equation in one spatial dimension. The long term evolution of the solution energy spectrum appears self-similar in…
We apply the functional Renormalisation Group (fRG) to study relaxation in a stochastic process governed by an overdamped Langevin equation with one degree of freedom, exploiting the connection with supersymmetric quantum mechanics in…
We present a detailed derivation and testing of our approach to rescale the dynamics of mesoscale simulations of coarse-grained polymer melts (I. Y. Lyubimov et al. J. Chem. Phys. \textbf{132}, 11876, 2010). Starting from the…
Molecular dynamics simulations are typically constrained to have a fixed number of particles, which limits our capability to simulate chemical and physical processes where the composition of the system changes during the simulation time.…
We derive a microscopic theory for the structural dynamics in the vicinity of the glass transition for a liquid exposed to a one-dimensional periodic potential. The periodic potential breaks translational invariance, in particular, the…