Related papers: Coarse-graining two-dimensional turbulence via dyn…
We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and…
Using a Coarse-grained Molecular Dynamics (CMD) approach we study the apparent nonlinear dynamics of water molecules filling/emptying carbon nanotubes as a function of system parameters. Different levels of the pore hydrophobicity give rise…
We present a proof-of-principle implementation of the first fully covariant filtering scheme applied to relativistic fluid turbulence. The filtering is performed with respect to special observers, identified dynamically as moving with the…
To study materials phenomena simultaneously at various length scales, descriptions in which matter can be coarse grained to arbitrary levels, are necessary. Attempts to do this in the static regime (i.e. zero temperature) have already been…
Conjugated organic molecules play a central role in a wide range of optoelectronic devices, including organic light-emitting diodes, organic field-effect transistors, and organic solar cells. A major bottleneck in the computational design…
Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently limited by the molecular mechanics force field employed.…
We introduce Coarse-Grained Nonlinear Dynamics, an efficient and universal parameterization of nonlinear system dynamics based on the Volterra series expansion. These models require a number of parameters only quasilinear in the system's…
We address an iterative procedure that can be used to detect coarse-grained hyperbolic unstable equilibria (saddle points) of microscopic simulators when no equations at the macroscopic level are available. The scheme is based on the…
We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered…
This article introduces, and reviews recent work using, a simple optimisation technique for analysing the nonlinear stability of a state in a dynamical system. The technique can be used to identify the most efficient way to disturb a system…
This article provides non-trivial technical ingredients for the article "The quantitative hydrodynamic limit of the Kawasaki dynamics" by the same authors. In that work a quantitative version of the hydrodynamic limit is deduced using a…
The issue of the parameterization of small scale (``subgrid'') turbulence is addressed in the context of passive scalar transport. We focus on the Kraichnan advection model which lends itself to the analytical investigation of the closure…
Dissipative particle dynamics (DPD) is now a well-established method for simulating soft matter systems. However, its applicability was recently questioned because some investigations showed an upper coarse-graining limit that would prevent…
The present works is focused on studying bifurcating solutions in compressible fluid dynamics. On one side, the physics of the problem is thoroughly investigated using high-fidelity simulations of the compressible Navier-Stokes equations…
We develop coarse-grained particle approaches for studying the elastic mechanics of vesicles with heterogeneous membranes having phase-separated domains. We perform simulations both of passive shape fluctuations and of active systems where…
Recent developments in multiscale computation allow the solution of ``coarse equations'' for the expected macroscopic behavior of microscopically/stochastically evolving particle distributions without ever obtaining these coarse equations…
Two-scale models pose a promising approach in simulating reactive flow and transport in evolving porous media. Classically, homogenized flow and transport equations are solved on the macroscopic scale, while effective parameters are…
We parameterize sub-grid scale (SGS) fluxes in sinusoidally forced two-dimensional turbulence on the $\beta$-plane at high Reynolds numbers (Re$\sim$25000) using simple 2-layer Convolutional Neural Networks (CNN) having only…
In this article we expand and develop the authors' recent proposed methodology for efficient stochastic superparameterization (SP) algorithms for geophysical turbulence. Geophysical turbulence is characterized by significant intermittent…
By analogy with the kinetic theory of gases, most turbulence modeling strate- gies rely on an eddy viscosity to model the unresolved turbulent fluctuations. How- ever, the ratio of unresolved to resolved scales - very much like a degree of…