Related papers: Bayesian selection for coarse-grained models of li…
A gaussian distribution of binding energies, but conditioned to exploit generally available information on packing in liquids, provides a statistical-thermodynamic theory of liquid water that is structurally non-committal, molecularly…
Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and…
In this work, we review previously developed coarse-grained (CG) particle models for biological membrane and red blood cells (RBCs) and discuss the advantages of the CG particle method over the continuum and atomic simulations on modeling…
The complexity of biomolecular interactions necessitates advanced methodologies to accurately capture their behavior in solution. In this work, we focus on monoclonal antibodies and adopt a multi-scale coarse-graining strategy for their…
Geochemical processes in subsurface reservoirs affected by microbial activity change the material properties of porous media. This is a complex biogeochemical process in subsurface reservoirs that currently contains strong conceptual…
Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and drastically accelerates simulation. However, such CG procedure induces information losses, which makes…
Coarse-grained (CG) modeling enables molecular simulations to reach time and length scales inaccessible to fully atomistic methods. For classical CG models, the choice of mapping, that is, how atoms are grouped into CG sites, is a major…
We introduce a general framework for constructing coarse-grained potential models without ad hoc approximations such as limiting the potential to two- and/or three-body contributions. The scheme, called Deep Coarse-Grained Potential…
The data-based discovery of effective, coarse-grained (CG) models of high-dimensional dynamical systems presents a unique challenge in computational physics and particularly in the context of multiscale problems. The present paper offers a…
In the present article, novel Coarse-Graining (CG) algorithms for the Eulerian-Lagrangian (EL) simulation of particle-laden flows are proposed. These include different variants of Reproducing Kernel Particle Methods (RKPM) and an extended…
Bayesian filtering is a key tool in many problems that involve the online processing of data, including data assimilation, optimal control, nonlinear tracking and others. Unfortunately, the implementation of filters for nonlinear, possibly…
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…
Developing effective coarse grained (CG) approach is a promising way for studying dynamics on large size networks. In the present work, we have proposed a strength-based CG (\sCG) method to study critical phenomena of the Potts model on…
Sampling equilibrium molecular configurations from the Boltzmann distribution is a longstanding challenge. Boltzmann Generators (BGs) address this by combining exact-likelihood generative models with importance sampling, but practical…
The first paper of this series [J. Chem. Phys. 158, 034103 (2023)] demonstrated that excess entropy scaling holds for both fine-grained and corresponding coarse-grained (CG) systems. Despite its universality, a more exact determination of…
In this paper, we test various models of wastewater infrastructure for risk analysis and compare their performance. While many representations are available, existing studies do not consider selection of the appropriate model for risk…
Water is a notoriously difficult substance to model both accurately and efficiently. Here, we focus on descriptions with a single coarse-grained particle per molecule using the so-called Approximate Non-Conformal (ANC) and generalized…
Assessing the magnitude of fuel consumption of marine traffic is a challenging task. The consumption can be reduced by the ways the vessels are operated, to achieve both improved cost efficiency and reduced CO2 emissions. Mathematical…
A high level of physical detail in a molecular model improves its ability to perform high accuracy simulations, but can also significantly affect its complexity and computational cost. In some situations, it is worthwhile to add additional…
Cellular regulatory dynamics is driven by large and intricate networks of interactions at the molecular scale, whose sheer size obfuscates understanding. In light of limited experimental data, many parameters of such dynamics are unknown,…