Related papers: Understanding three-body contributions to coarse-g…
We study the motion of an overdamped particle connected to a thermal heat bath in the presence of an external periodic potential in one dimension. When we coarse-grain, i.e., bin the particle positions using bin sizes that are larger than…
We develop an innovative numerical technique to describe few-body systems. Correlated Gaussian basis functions are used to expand the channel functions in the hyperspherical representation. The method is proven to be robust and efficient…
We introduce a machine-learning framework termed coarse-grained all-atom force field (CGAA-FF), which incorporates coarse-grained message passing within an all-atom force field using equivariant nature of graph models. The CGAA-FF model…
Magnus expansion is used to identify effective Hamiltonians describing the coarse-grained dynamics of more complex problems. Here, we apply this method to a two-level system driven by an and AC field. We derive Stark and Bloch-Siegert shifs…
We present a detailed derivation and testing of our approach to rescale the dynamics of mesoscale simulations of coarse-grained polymer melts (I. Y. Lyubimov et al. J. Chem. Phys. \textbf{132}, 11876, 2010). Starting from the…
We present a novel learning framework that consistently embeds underlying physics while bypassing a significant drawback of most modern, data-driven coarse-grained approaches in the context of molecular dynamics (MD), i.e., the availability…
Electrostatic interactions between macroions largely govern the equilibrium thermodynamic and dynamical properties of charge-stabilized colloidal suspensions and polyelectrolyte solutions. Predicting the properties of such complex,…
In unresolved flow CFD-DEM simulations, the porosity values for each CFD cell are determined using a coarse-graining algorithm. While this approach enables coupled simulations of representative numbers of particles, the influence of the…
We present a data-driven machine-learning approach for modeling space-time socioeconomic dynamics. Through coarse-graining fine-scale observations, our modeling framework simplifies these complex systems to a set of tractable mechanistic…
We show that cluster expansions (CE), previously used to model solid-state materials with binary or ternary configurational disorder, can be extended to the protein design problem. We present a generalized CE framework, in which properties…
Developing physics-based models for molecular simulation requires fitting many unknown parameters to diverse experimental datasets. Traditionally, this process is piecemeal and difficult to reproduce, leading to a fragmented landscape of…
Granular gases as dilute ensembles of particles in random motion are not only at the basis of elementary structure-forming processes in the universe and involved in many industrial and natural phenomena, but also excellent models to study…
A coarse-grained simulation model eliminates microscopic degrees of freedom and represents a polymer by a simplified structure. A priori, two classes of coarse-grained models may be distinguished: those which are designed for a specific…
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…
We describe in detail how to implement a coarse-grained hybrid Molecular Dynamics and Stochastic Rotation Dynamics simulation technique that captures the combined effects of Brownian and hydrodynamic forces in colloidal suspensions. The…
Multiscale systems are ubiquitous in science and technology, but are notoriously challenging to simulate as short spatiotemporal scales must be appropriately linked to emergent bulk physics. When expensive high-dimensional dynamical systems…
Interparticle cohesion is prevalent in stored powders, geological formations, and infrastructure engineering, yet a comprehensive understanding of the effects of its micro-mechanics on bulk properties has not been established…
The structure of polyelectrolytes is highly sensitive to small changes in the interactions between its monomers. In particular, interactions mediated by counterions play a significant role, and are affected by both specific molecular…
The rich and diverse dynamics of particle-based systems ultimately originates from the coupling of their degrees of freedom via internal interactions. To arrive at a tractable approximation of such many-body problems, coarse-graining is…
Semi-analytical methods, based on Eulerian perturbation theory, are a promising tool to follow the time evolution of cosmological perturbations at small redshifts and at mildly nonlinear scales. All these schemes are based on two…