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We show that a mesoscopic coarse-grained dynamics model which incorporates the transient potential can be formally derived from an underlying microscopic dynamics model. As a microscopic dynamics model, we employ the overdamped Langevin…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…
High-dimensional recordings of dynamical processes are often characterized by a much smaller set of effective variables, evolving on low-dimensional manifolds. Identifying these latent dynamics requires solving two intertwined problems:…
Gravity-driven flows of granular matter are involved in a wide variety of situations, ranging from industrial processes to geophysical phenomena, such as avalanches or landslides. These flows are characterized by the coexistence of solid…
In recent papers, we have argued that kinetically constrained coarse grained models can be applied to understand dynamic properties of glass forming materials, and we have used this approach in various applications that appear to validate…
Granular fluids consist of collections of activated mesoscopic or macroscopic particles (e.g., powders or grains) whose flows often appear similar to those of normal fluids. To explore the qualitative and quantitative description of these…
Many biological systems can be described by finite Markov models. A general method for simplifying master equations is presented that is based on merging adjacent states. The approach preserves the steady-state probability distribution and…
Coarse-graining (CG) is a systematic reduction of the number of degrees of freedom (DOF) used to describe a system of interest. CG can be thought of as a projection on coarse-grained DOF and is therefore dependent on the functions used to…
Coarse-grained (CG) models facilitate an efficient exploration of complex systems by reducing the unnecessary degrees of freedom of the fine-grained (FG) system while recapitulating major structural correlations. Unlike structural…
A new definition of coarse-grained quantities describing the dust flow in General Relativity is proposed. It assigns the coarse--grained expansion, shear and vorticity to finite-size comoving domains of fluid in a covariant,…
Under many conditions, macroscopic grains flow like a fluid; kinetic theory pred icts continuum equations of motion for this granular fluid. In order to test the theory, we perform event driven molecular simulations of a two-dimensional gas…
In this paper we present a variational technique that handles coarse-graining and passing to a limit in a unified manner. The technique is based on a duality structure, which is present in many gradient flows and other variational…
In soft matter systems the local displacement field can be accessed directly by video microscopy enabling one to compute local strain fields and hence the elastic moduli using a coarse-graining procedure. We study this process for a simple…
Starting from a coarse-grained map of a quantum many-body system, we construct the inverse map that assigns a microscopic state to a coarse-grained state based on the maximum entropy principle. Assuming unitary evolution in the microscopic…
The coarse-graining approach to deriving the quantum Markovian master equation is revisited, with close attention given to the underlying approximations. It is further argued that the time interval over which the coarse-graining is…
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and…
We focus on finding a coarse grained description able to reproduce the thermodynamic behavior of a molecular system by using mesoparticles representing several molecules. Interactions between mesoparticles are modelled by an interparticle…
In this paper, we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular dynamics. The latter are ubiquitous in physicochemical and biological…
The compaction dynamics of a granular media subject to a sequence of vertical taps made of fluid pulses is investigated via Molecular Dynamics simulations. Our study focuses on three different levels: macroscopic (volume fraction),…
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…