Related papers: A Concurrent Multiscale Micromorphic Molecular Dyn…
A multiscale theory of interacting continuum mechanics and thermodynamics of mixtures of fluids, electrodynamics, polarization and magnetization is proposed. The mechanical (reversible) part of the theory is constructed in a purely…
A novel approach to simulate simple protein-ligand systems at large time- and length-scales is to couple Markov state models (MSMs) of molecular kinetics with particle-based reaction-diffusion (RD) simulations, MSM/RD. Currently, MSM/RD…
Developments in dynamical systems theory provides new support for the macroscale modelling of pdes and other microscale systems such as Lattice Boltzmann, Monte Carlo or Molecular Dynamics simulators. By systematically resolving subgrid…
Mesoscale phenomena -- involving a level of description between the finest atomistic scale and the macroscopic continuum -- can be studied by a variation on the usual atomistic-level molecular dynamics (MD) simulation technique. In…
Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular…
Computer simulation methods, such as Monte Carlo or Molecular Dynamics, are very powerful computational techniques that provide detailed and essentially exact information on classical many-body problems. With the advent of ab-initio…
Multiscale thermodynamics is a theory of relations among levels of investigation of complex systems. It includes the classical equilibrium thermodynamics as a special case but it is applicable to both static and time evolving processes in…
Classical molecular dynamics (MD) is a well established and powerful tool in various fields of science, e.g. chemistry, plasma physics, cluster physics and condensed matter physics. Objects of investigation are few-body systems and…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
In this paper, we develop a multiscale hierarchy framework for objective molecular dynamics (OMD), a reduced order molecular dynamics with a certain symmetry, that connects it to the statistical kinetic equation, and the macroscopic…
Dynamical systems theory provides powerful methods to extract effective macroscopic dynamics from complex systems with slow modes and fast modes. Here we derive and theoretically support a macroscopic, spatially discrete, model for a class…
Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible…
Despite its widespread use in materials science, conventional molecular dynamics (MD) simulations are severely constrained by timescale limitations. To address this shortcoming, we propose an empirical formulation of accelerated MD method,…
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…
Many scientific and engineering systems exhibit intrinsically multimodal behavior arising from latent regime switching and non-unique physical mechanisms. In such settings, learning the full conditional distribution of admissible outcomes…
We propose a general multiscale approach for the mechanical behavior of three-dimensional networks of macromolecules undergoing strain-induced unfolding. Starting from a (statistically based) energetic analysis of the macromolecule…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
Consider the macroscale modelling of microscale spatiotemporal dynamics. Here we develop a new approach to ensure coarse scale discrete models preserve important self-adjoint properties of the fine scale dynamics. The first part explores…
Molecular dynamics (MD) has served as a powerful tool for designing materials with reduced reliance on laboratory testing. However, the use of MD directly to treat the deformation and failure of materials at the mesoscale is still largely…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…