Related papers: On the microscopic foundation of dissipative parti…
Tissue dynamics and collective cell motion are crucial biological processes. Their biological machinery is mostly known, and simulation models such as the "active vertex model" (AVM) exist and yield reasonable agreement with experimental…
Microflows are intensively used for investigating and controlling the dynamics of particles, including soft particles such as biological cells and capsules. A classic result is the tank-treading motion of elliptically deformed soft…
The aim of this work is the description of the chain formation phenomena observed in colloidal suspensions of superparamagnetic nanoparticles under high magnetic fields. We propose a new methodology based on an on-the-fly Coarse-Grain (CG)…
Functional connectivity estimates are highly sensitive to analysis choices and can be dominated by noise when the number of sampled time points is small relative to network dimensionality. This issue is particularly acute in fMRI, where…
An important class of fluid-structure problems involve the dynamics of ordered arrays of immersed, flexible fibers. While specialized numerical methods have been developed to study fluid-fiber systems, they become infeasible when there are…
Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a…
Coarse graining techniques offer a promising alternative to large-scale simulations of complex dynamical systems, as long as the coarse-grained system is truly representative of the initial one. Here, we investigate how the dynamical…
The construction of coarse-grained descriptions of a system's kinetics is well established in biophysics. One prominent example is Markov state models in protein folding dynamics. In this paper, we develop a coarse-grained, discrete state…
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…
Viscosity is a fundamental property of liquids and determines the diffusivity of suspended particles. A gradient in viscosity leads to a gradient in diffusivity, yet it is unknown whether such a gradient can lead to directed transport of…
Coarsening of bicontinuous microstructures is observed in a variety of systems, such as nanoporous metals and mixtures that have undergone spinodal decomposition. To better understand the morphological evolution of these structures during…
In this paper, we examine how to build coarse-grain transport models consistently from the kinetic to fluid regimes. The internal energy of the gas particles is described through a state-to-state approach. A kinetic equation allows us to…
The growth of amorphous TiO2 and anisotropic-polycrystalline ZnO thin-films is studied by means of coarse-grained three-dimensional kinetic Montecarlo simulations under conditions typically encountered in Plasma Enhanced Chemical Vapor…
In a recent letter (Denkov et al., Phys. Rev. Lett., vol. 100 (2008) p. 138301) we calculated theoretically the macroscopic viscous stress of steadily sheared foam/emulsion from the energy dissipated inside the transient planar films,…
Coarse-grained models are widely used to explain the effective behavior of partially observable physical systems with hidden degrees of freedom. Reduction procedures in state space typically disrupt Markovianity and a fluctuation relation…
Significant efforts have been devoted in the last decade towards improving the predictivity of coarse-grained models in molecular dynamics simulations and providing a rigorous justification of their use, through a combination of theoretical…
The dynamics of viscous thin-film particle-laden flows down inclined surfaces are commonly modeled with one of two approaches: a diffusive flux model or a suspension balance model. The diffusive flux model assumes that the particles migrate…
It is well known that energy dissipation and finite size can deeply affect the dynamics of granular matter, often making usual hydrodynamic approaches problematic. Here we report on the experi-mental investigation of a small model system,…
We investigate the segregation of a dense binary mixture of granular particles that only differ in their restitution coefficient. The mixture is vertically vibrated in the presence of gravity. We find a partial segregation of the species,…
Using Brownian dynamics (BD) simulations and an analytical approach we investigate the shear-induced, nonequilibrium dynamics of dense colloidal suspensions confined to a narrow slit-pore. Focusing on situations where the colloids arrange…