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Dynamic facilitation theory assumes short-ranged dynamic constraints to be the essential feature of supercooled liquids and draws much of its conclusions from the study of kinetically constrained models. While deceptively simple, these…
In this work, we explore the dynamics of active entangled chains using molecular dynamics simulations of a modified Kremer-Grest model. The active chains are diluted in a mesh of very long passive linear chains, to avoid constraint release…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
The dynamic behavior of a partially wetting polymer droplet driven over a nanostructured interface is studied using molecular dynamics simulations. We consider the bead-spring model to represent a polymeric liquid that partially wets a…
Sampling from discrete distributions with multiple modes and energy barriers is fundamental to machine learning and computational physics. Recent discrete neural samplers like MDNS suffer from mode collapse and fail to sample high-energy…
Ensuring a satisfactory statistical convergence of anharmonic thermodynamic properties requires sampling of many atomic configurations, however the methods to obtain those necessarily produce correlated samples, thereby reducing the…
We present a method for determining the free energy dependence on a selected number of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting…
The interplay of electronic and nuclear degrees of freedom presents an outstanding problem in condensed matter physics and chemistry. Computational challenges arise especially for large systems, long time scales, in nonequilibrium, or in…
In this pedagogical work we reviewed the mathematical formalism and the physical interpretation, based on statistical mechanics, of the meta-heuristics called simulated annealing. Moreover, we presented the mathematical formulation of the…
In reverse quantum annealing, the initial state is an eigenstate of the final problem Hamiltonian and the transverse field is cycled rather than strictly decreased as in standard (forward) quantum annealing. We present a numerical study of…
As with many parts of the natural sciences, machine learning interatomic potentials (MLIPs) are revolutionizing the modeling of molecular crystals. However, challenges remain for the accurate and efficient calculation of sublimation…
First-principles molecular dynamics simulation based on a plane wave/pseudopotential implementation of density functional theory is adopted to investigate atomic scale energy transport for semiconductors (silicon and germanium). By imposing…
The simulation of rare events is one of the key problems in atomistic simulations. Towards its solution a plethora of methods have been proposed. Here we combine two such methods metadynamics and inte-grated tempering sampling. In…
Coarse grain (CG) molecular dynamics (MD) can simulate systems inaccessible to fine grain (FG) MD simulations. A CG simulation decreases the degrees of freedom by mapping atoms from an FG representation into agglomerate CG particles. The FG…
The intratumor heterogeneity has been recognized to characterize cancer cells impairing the efficacy of cancer treatments. We here propose an extension of constraint-based modeling approach in order to simulate metabolism of cell…
To evaluate electrostatics interactions, Molecular dynamics (MD) simulations rely on Particle Mesh Ewald (PME), an O(Nlog(N)) algorithm that uses Fast Fourier Transforms (FFTs) or, alternatively, on O(N) Fast Multipole Methods (FMM)…
The problem of metastability for a stochastic dynamics with a parallel updating rule is addressed in the Freidlin--Wentzel regime, namely, finite volume, small magnetic field, and small temperature. The model is characterized by the…
Structural, dynamical, bonding, and electronic properties of water molecules around a soluted methane molecule are studied from first principles. The results are compatible with experiments and qualitatively support the conclusions of…
Semi-empirical molecular dynamics is used to simulate several gaseous atomic hydrogen interactions with hydrocarbon grains in space: recoil, adsorption, diffusion, chemisorption and recombination into molecular hydrogen. Their probabilities…
The kinetic damping mechanism of low frequency transverse perturbations propagating parallel to the magnetic field in a magnetized warm electron plasma is simulated by means of electromagnetic (EM) Vlasov simulations. The short-time-scale…