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The breakdown of dynamical scaling for a dilute polymer solution in 2D has been suggested by Shannon and Choy [Phys. Rev. Lett. {\bf 79}, 1455 (1997)]. However, we show here both numerically and analytically that dynamical scaling holds…
In the coarse grained Brownian Dynamics simulation method the many solvent molecules are replaced by random thermal kicks and an effective friction acting on the particles of interest. For Brownian Dynamics the friction has to be so strong…
Traditional approaches to optical matter often involve complex illumination fields with costly and unstable setups, requiring strong gradient forces, high-intensity laser spots that could harm samples, and substrate support. For binding,…
Multiparticle collision dynamics (MPCD) is a flexible and robust mesoscale computational technique for simulating solvent-mediated hydrodynamic interactions in soft materials. Here, we provide a critical overview of the MPCD method and…
Solutions of interacting linear polymers are mapped onto a system of ``soft'' spherical particles interacting via an effective pair potential. This coarse-graining reduces the individual monomer-level description to a problem involving only…
The phoretic Brownian dynamics method is shown here to be an effective approach to simulate the properties of colloidal chemophoretic based systems. The method is then optimized to allow for the comparison with results from multiparticle…
Modeling contact mechanics with high contrast coefficients presents significant mathematical and computational challenges, especially in achieving strongly symmetric stress approximations for mixed formulations. Due to the inherent…
We study relaxational behavior from a highly excited state for a composite system in partial contact with a heat bath, motivated by an experimental report of long-term energy storage in protein molecules. The system consists of two coupled…
In this article we formulate and solve the problem of molecular beam diffraction when each molecule consists of two interacting bodies. Then, using our results, we present the diffraction patterns for various molecular sizes employing the…
A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the…
We develop a computational method based on Dissipative Particle Dynamics (DPD) that introduces solvent hydrodynamic interactions to coarse-grained models of solutes, such as ions, molecules, or polymers. DPD-solvent (DPDS) is a fully…
This article presents a comparison of various implementations of the Lattice Discrete Particle Model (LDPM) for the numerical simulation of concrete and other heterogeneous quasibrittle materials. The comparison involves the use of…
This article presents a multi-physics methodology for the numerical simulation of physical systems that involve the non-linear interaction of multi-phase reactive fluids and elastoplastic solids, inducing high strain-rates and high…
The unavoidable interaction between thermal environments and quantum systems typically leads to the degradation of quantum coherence, which can be fought against by reservoir engineering. We propose the realization of a special mixture of…
This article presents a comprehensive review of the Hydrodynamic Scaling Model for the dynamics of polymers in dilute and nondilute solutions. The Hydrodynamic Scaling Model differs from some other treatments of non-dilute polymer solutions…
We address the response of a random heteropolymer to preferential solvation of certain monomer types at the globule-solvent interface. For each set of monomers that can comprise the molecule's surface, we represent the ensemble of allowed…
Bead spring models for polymers in solution are nonlinear if either the finite extensibility of the polymer, excluded volume effects or hydrodynamic interactions between polymer segments are taken into account. For such models we use a…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
We present an extension of the multiparticle collision dynamics method for flows with complex interfaces, including supramolecular near-contact interactions mimicking the effect of surfactants. The new method is demonstrated for the case of…