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A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
A multigrid framework is described for multiphysics applications. The framework allows one to construct, adapt, and tailor a monolithic multigrid methodology to different linear systems coming from discretized partial differential…
Design, control, and estimation for dynamic systems require accurate and analytically tractable models. However, modern engineered systems contain components that are described with heterogeneous modeling paradigms, as well as subsystems…
We present a numerical method for simulating rarefied gases that interact with moving boundaries and rigid bodies. The gas is described by the BGK equation in Lagrangian form and solved using an Arbitrary Lagrangian-Eulerian method, in…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
The immersed boundary method is a numerical and mathematical formulation for solving fluid-structure interaction problems. It relies on solving fluid equations on an Eulerian fluid grid and interpolating the resulting velocity back onto…
Distribution grid operation faces new challenges caused by a rising share of renewable energy sources and the introduction of additional types of loads to the grid. With the increasing adoption of distributed generation and emerging…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
Elastic filaments are vital to biological, physical and engineering systems, from cilia driving fluid in the lungs to artificial swimmers and micro-robotics. Simulating slender structures requires intricate balance of elastic, body, active,…
A collision-based hybrid algorithm for the discrete ordinates approximation of the neutron transport equation is extended to the multigroup setting. The algorithm uses discrete energy and angle grids at two different resolutions and…
Polymorphs in molecular crystals are often very close in energy, yet they may possess markedly different physical and chemical properties. The understanding and prediction of polymorphism is of paramount importance for a variety of…
In this work, we develop a two-component coarse-grained molecular dynamics (CGMD) model for simulating the erythrocyte membrane. This proposed model possesses the key feature of combing the lipid bilayer and the erythrocyte cytoskeleton,…
Predicting the evolution of spatiotemporal physical systems from sparse and scattered observational data poses a significant challenge in various scientific domains. Traditional methods rely on dense grid-structured data, limiting their…
We utilize a multiscale modeling framework to study the effect of shape, size and ligand composition on the efficacy of binding of a ligand-coated-particle to a substrate functionalized with the target receptors. First, we show how…
We discuss the reliability of integral-equation methods based on several commonly used closure relations in determining the phase diagram of coarse-grained models of soft-matter systems characterized by mutually interacting soft and…
We develop a bonded-particle model for magneto-elastic rods that unifies large deformations, contact, and long-range magnetic interactions within a single discrete-element framework. The rod is discretized into orientable particles…
Numerical models of biomass particle pyrolysis focus on either the solid particle evolution or on the surrounding gas-phase dynamics, neglecting the coupled interactions between the two. This work addresses this limitation by proposing a…
Molecular modeling of thermally activated chemistry in condensed phases is essential to understand polymerization, depolymerization, and other processing steps of molecular materials. Current methods typically combine molecular dynamics…