Related papers: Multiscale perturbative approach to active matter …
A first step towards implementing a notion of coarse graining in an intrinsically Lorentzian, discrete quantum- gravity approach, namely causal set quantum gravity is taken. It makes use of an abstract notion of scale, based on counting the…
The paper constructs a coarse-grained model to investigate dry sliding friction of the body-centered-cubic Fe micron-scale system by smoothed particle hydrodynamics simulations and examines influences of the spring force on the characters…
In order to understand the physical processes of nanopore experiments at the molecular level, microscopic information from molecular dynamics is greatly needed. Coarse-grained models are a good alternative to classical all-atom models since…
Using the orbital-free density functional theory as a model theory, we present an analysis of the field theoretic approach to quasi-continuum method. In particular, by perturbation method and multiple scale analysis, we provide a formal…
The theoretical understanding of pattern formation in active systems remains a central problem of interest. Heterogeneous flocks made up of multiple species can exhibit a remarkable diversity of collective states that cannot be obtained…
Non-cohesive granular media exhibit complex responses to sudden impact that often differ from those of ordinary solids and liquids. We investigate how this response is mediated by the presence of interstitial gas between the grains. Using…
This work presents a systematic methodology for describing the transient dynamics of coarse-grained molecular systems inferred from all-atom simulated data. We suggest Langevin-type dynamics where the coarse-grained interaction potential…
We study a minimal model involving two species of particles interacting via quorum-sensing rules. Combining simulations of the microscopic model and linear stability analysis of the associated coarse-grained field theory, we identify a…
A coarse-grained molecular model, which consists of a spherical particle and an orientation vector, is proposed to simulate lipid membrane on a large length scale. The solvent is implicitly represented by an effective attractive interaction…
The prediction of the equation of state and the phase behavior of simple fluids (noble gases, carbon dioxide, benzene, methane, short alkane chains) and their mixtures by Monte Carlo computer simulation and analytic approximations based on…
Brute-force simulations for dynamics on very large networks are quite expensive. While phenomenological treatments may capture some macroscopic properties, they often ignore important microscopic details. Fortunately, one may be only…
We develop a rigid multiblob method for numerically solving the mobility problem for suspensions of passive and active rigid particles of complex shape in Stokes flow in unconfined, partially confined, and fully confined geometries. As in a…
A coarse-grained model is developed to allow large-scale molecular dynamics (MD) simulations of a branched polyetherimide derived from two backbone monomers [4,4'-bisphenol A dianhydride (BPADA) and m-phenylenediamine (MPD)], a chain…
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…
We investigate coarse-grained models of suspended self-thermophoretic microswimmers. Upon heating, the Janus spheres, with hemispheres made of different materials, induce a heterogeneous local solvent temperature that causes the…
Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries, reaction fluxes (rate laws), and…
Mathematical approaches from dynamical systems theory are used in a range of fields. This includes biology where they are used to describe processes such as protein-protein interaction and gene regulatory networks. As such networks increase…
We develop a model-independent approach to lagrangian perturbation theory for the large scale structure of the universe. We focus on the displacement field for dark matter particles, and derive its most general structure without assuming a…
Granular systems confined in a shallow box and driven by vertical vibration provide a simple geometry to study fluidized granular media. Grains gain kinetic energy vertically through collisions with the walls and redistribute it…
We present a novel linear solver that works well for large systems obtained from discretizing PDEs. It is robust and, for the examples we studied, the computational effort scales linearly with the number of equations. The algorithm is based…