Related papers: A consistency study of coarse-grained dynamical ch…
A fundamental objective of materials modeling is identifying atomic structures that align with experimental observables. Conventional approaches for disordered materials involve sampling from thermodynamic ensembles and hoping for an…
Molecular dynamics simulation is now a widespread approach for understanding complex systems on the atomistic scale. It finds applications from physics and chemistry to engineering, life and medical science. In the last decade, the approach…
Mathematical modelling of biological population dynamics often involves proposing high fidelity discrete agent-based models that capture stochasticity and individual-level processes. These models are often considered in conjunction with an…
We present a coarse-graining method applicable to dry scalar active matter with motility regulation. Our approach, based on a multiscale perturbative expansion of the backward Kolmogorov equation, does not rely on any specific microscopic…
Studying the conformations involved in the dimerization of cadherins is highly relevant to understand the development of tissue and its failure, which is associated with tumors and metastases. Experimental techniques, like X-ray…
We present a promising coarse-graining strategy for linking micro- and mesoscales of soft matter systems. The approach is based on effective pairwise interaction potentials obtained from detailed atomistic molecular dynamics (MD)…
Molecular Dynamics (MD) simulation is a powerful tool for understanding the dynamics and structure of matter. Since the resolution of MD is atomic-scale, achieving long time-scale simulations with femtosecond integration is very expensive.…
Increasing the efficiency of materials design and discovery remains a significant challenge, especially given the prohibitively large size of chemical compound space. The use of a chemically transferable coarse-grained model enables…
We study the closure problem for continuum balance equations that model mesoscale dynamics of large ODE systems. The underlying microscale model consists of classical Newton equations of particle dynamics. As a mesoscale model we use the…
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…
We propose a systematic coarse-grained representation of block copolymers, whereby each block is reduced to a single ``soft blob'' and effective intra- as well as intermolecular interactions act between centres of mass of the blocks. The…
Molecular Dynamics (MD) simulations are essential for accurately predicting the physical and chemical properties of large molecular systems across various pressure and temperature ensembles. However, the high computational costs associated…
Spatial multiscale methods have established themselves as useful tools for extending the length scales accessible by conventional statics (i.e., zero temperature molecular dynamics). Recently, extensions of these methods, such as the…
Dissipative particle dynamics (DPD) is a well-established mesoscale simulation method. However, there have been long-standing ambiguities regarding the dependence of its (purely repulsive) force field parameter on temperature as well as the…
The statistical mechanics of a linear non-interacting polymer chain with a large number of monomers is considered with fixed angular momentum. The radius of gyration for a linear polymer is derived exactly by functional integration. This…
Diffusive molecular dynamics is a novel model for materials with atomistic resolution that can reach diffusive time scales. The main ideas of diffusive molecular dynamics are to first minimize an approximate variational Gaussian free energy…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
Molecular dynamics (MD) simulations are powerful tools for elucidating the macroscopic physical properties of materials from microscopic atomic behaviors. However, the massive, high-dimensional datasets generated by MD simulations pose a…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
With the guidance offered by nonequilibrium statistical thermodynamics, simulation techniques are elevated from brute-force computer experiments to systematic tools for extracting complete, redundancy-free and consistent coarse grained…