Related papers: Many-Body Coarse-Grained Interactions using Gaussi…
Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used.…
This paper deals with the complex problem of how to simulate multiparticle contacts. The collision process is responsible for the transfer and dissipation of energy in granular media. A novel model of the interaction force between particles…
Coarse-grained (CG) force field methods for molecular systems are a crucial tool to simulate large biological macromolecules and are therefore essential for characterisations of biomolecular systems. While state-of-the-art deep learning…
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ…
Dimensionality reduction represents a crucial step in extracting meaningful insights from Molecular Dynamics (MD) simulations. Conventional approaches, including linear methods such as principal component analysis as well as various…
Hybrid particle-field molecular dynamics is a molecular simulation strategy wherein particles couple to a density field instead of through ordinary pair potentials. Traditionally considered a mean-field theory, a momentum and…
We develop a Gaussian process framework for learning interaction kernels in multi-species interacting particle systems from trajectory data. Such systems provide a canonical setting for multiscale modeling, where simple microscopic…
After discussing the significance of interactions to understand complex multiscale stochastic systems (CMSS), we turn our attention to the construction of a Generalised Theory of Interactions (GToI). We define interactions as discrete,…
We develop coarse-graining schemes for stochastic many-particle microscopic models with competing short- and long-range interactions on a d-dimensional lattice. We focus on the coarse-graining of equilibrium Gibbs states and using cluster…
The approach to the theory of many-particle interacting systems from a unified standpoint, based on the variational principle for free energy is reviewed. A systematic discussion is given of the approximate free energies of complex…
The conformational behavior of a coarse-grained finite polymer chain near an attractive spherical surface was investigated by means of multicanonical Monte Carlo computer simulations. In a detailed analysis of canonical equilibrium data…
Ab-initio predictions of nuclei with masses up to A~100 or more is becoming possible thanks to novel advances in computations and in the formalism of many-body physics. Some of the most fundamental issues include how to deal with…
Total energies of crystal structures can be calculated to high precision using quantum-based density functional theory (DFT) methods, but the calculations can be time consuming and scale badly with system size. Cluster expansions of total…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such…
In the framework of the polymer reference interaction site model (PRISM) extended to incorporate the centers of mass (CM) of the groups of monomers constitutive of the macromolecules as auxiliary sites, a general relationship between the…
Simple models for spherical particles with a soft shell have been shown to self-assemble into numerous crystal phases and even quasicrystals. However, most of these models rely on a simple pairwise interaction, which is usually a valid…
The field theory approach to the statistical mechanics of a system of N polymer rings linked together is generalized to the case of links that have a fixed number $2s$ of maxima and minima. Such kind of links are called plats and appear for…
In biomimetic and biological systems, interactions between surfaces are often mediated by adhesive molecules, nanoparticles, or colloids dispersed in the surrounding solution. We present here a general, statistical-mechanical model for two…