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This note provides an introduction to molecular dynamics, the computational implementation of the theory of statistical physics. The discussion is focused on the properties of Langevin dynamics, a degenerate stochastic differential equation…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
We consider the convergence of kinetic Langevin dynamics to its ergodic invariant measure, which is Gibbs distribution. Instead of the standard setup where the friction coefficient is a constant scalar, we investigate position-dependent…
Microstructural changes in solids, driven by energy flows, do not develop in a static continuous space, such as the space considered in conventional plasticity models. The applied forces create an evolving internal energy landscape, which…
Investigating processes in complex molecular systems, which are characterized by many variables, is a crucial problem in computational physics. These systems can be reduced to a few meaningful degrees of freedom known as collective…
We study time-changed Markov processes to speed up the convergence of Markov chain Monte Carlo (MCMC) algorithms. The time-changed process is defined by adjusting the speed of time of a base process via a user-chosen, state-dependent…
Present-day atomistic simulations generate long trajectories of ever more complex systems. Analyzing these data, discovering metastable states, and uncovering their nature is becoming increasingly challenging. In this paper, we first use…
Accurate prediction of energy and forces for 3D molecular systems is one of fundamental challenges at the core of AI for Science applications. Many powerful and data-efficient neural networks predict molecular energies and forces from…
Particle MCMC is a class of algorithms that can be used to analyse state-space models. They use MCMC moves to update the parameters of the models, and particle filters to propose values for the path of the state-space model. Currently the…
The time-evolving precision matrix of a piecewise-constant Gaussian graphical model encodes the dynamic conditional dependency structure of a multivariate time-series. Traditionally, graphical models are estimated under the assumption that…
The properties of polymer liquids on hard and soft substrates are investigated by molecular dynamics simulation of a coarse-grained bead-spring model and dynamic single-chain-in-mean-field (SCMF) simulations of a soft, coarse-grained…
Machine-learned (ML) coarse-grained (CG) models are a promising tool for significantly enhancing the efficiency of molecular simulations by systematically removing degrees of freedom while retaining fidelity to the underlying fine-grained…
The generalized Langevin equation is used as a model for various coarse-grained physical processes, e.g., the time evolution of the velocity of a given larger particle in an implicitly represented solvent, when the relevant time scales of…
In this paper, we show how kernel-based models for the Koopman generator -- the gEDMD method -- can be used to identify coarse-grained dynamics on reduced variables, which retain the slowest transition timescales of the original dynamics.…
In computational materials science, coarse-graining approaches often lack a priori uncertainty quantification (UQ) tools that estimate the accuracy of a reduced-order model before it is calibrated or deployed. This is especially the case in…
To evaluate shear viscosity of ethylene glycol oligomers (EGO)/water binary mixture by means of coarse-grained molecular dynamics (CG-MD) simulations, we proposed the self-diffusion-coefficient-based parameterization of non-bonded…
This paper introduces a new structural phase field crystal (PFC) type model that expands the PFC methodology to a wider class of structurally complex crystal structures than previously possible. Specifically, our new approach allows for…
We address the problem of the so-called ``granular gases'', i.e. gases of massive particles in rapid movement undergoing inelastic collisions. We introduce a class of models of driven granular gases for which the stationary state is the…
The efforts associated with parametrization of continuum-based models for crystal plasticity are a significant obstacle for the routine use of these models in materials science and engineering. While phenomenological constitutive…
State-space models (SSMs) are a powerful statistical tool for modelling time-varying systems via a latent state. In these models, the latent state is never directly observed. Instead, a sequence of observations related to the state is…