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We apply a hybrid Molecular Dynamics and mesoscopic simulation technique to study the steady-state sedimentation of hard sphere particles for Peclet numbers (Pe) ranging from 0.08 to 12. Hydrodynamic back-flow causes a reduction of the…
We propose a mathematical derivation of stochastic compressible Navier-Stokes equation. We consider many-particle systems with a Hamiltonian dynamics supplemented by a friction term and environmental noise. Both the interaction potential…
The purpose of this paper is to establish a well-posedness theory for conservative stochastic partial differential equations on the whole space. This class of stochastic PDEs arises in fluctuating hydrodynamics, and includes the…
We present Monte Carlo simulations of liquid-crystalline material confined to a nanoscopic slit-pore. The simulations are carried out under isothermal conditions in a specialized isostress ensemble in which N fluid molecules are exposed to…
We analyze the dynamics of a Brownian gas in contact with a heat bath in which large temperature fluctuations occur. There are two distinct time scales present, one describes the decay of the fluctuations in the temperature and the other…
We develop stochastic mixed finite element methods for spatially adaptive simulations of fluid-structure interactions when subject to thermal fluctuations. To account for thermal fluctuations, we introduce a discrete fluctuation-dissipation…
Starting at the mesoscopic level with a general formulation of stochastic thermodynamics in terms of Markov jump processes, we identify the scaling conditions that ensure the emergence of a (typically nonlinear) deterministic dynamics and…
We extend the analysis of the thermodynamics of the climate system by investigating the role played by processes taking place at various spatial and temporal scales through a procedure of coarse graining. The coarser is the graining of the…
The transport coefficients of a dilute gas of inelastic hard spheres immersed in a molecular gas are determined. We assume that the number density of the granular gas is much smaller than that of the surrounding molecular gas, so that the…
Coarse-grained (CG) modeling has gained significant attention in recent years due to its wide applicability in enhancing the spatiotemporal scales of molecular simulations. While CG simulations, often performed with Hamiltonian mechanics,…
In recent years, extracellular vesicles such have become promising carriers as the next-generation drug delivery platforms. Effective loading of exogenous cargos without compromising the extracellular vesicle membrane is a major challenge.…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
A lubrication model can be used to describe the dynamics of a weakly volatile viscous fluid layer on a hydrophobic substrate. Thin layers of the fluid are unstable to perturbations and break up into slowly evolving interacting droplets. A…
Using an interpolant form for the gradient of a function of position, we write an integral version of the conservation equations for a fluid. In the appropriate limit, these become the usual conservation laws of mass, momentum and energy.…
We present a microscopic derivation of the nonlinear fluctuating hydrodynamic equation for the homogeneous crystalline solid from the Hamiltonian description of a many-particle system. We propose a microscopic expression of the displacement…
The laws of thermodynamics apply to biophysical systems on the nanoscale as described by the framework of stochastic thermodynamics. This theory provides universal, exact relations for quantities like work, which have been verified in…
The Weak-form Sparse Identification of Nonlinear Dynamics algorithm (WSINDy) has been demonstrated to offer coarse-graining capabilities in the context of interacting particle systems (https://doi.org/10.1016/j.physd.2022.133406). In this…
At the nanoscale, random effects govern not only the dynamics of a physical system but may also affect its observation. This work introduces a novel paradigm for coarse graining that eschews the assignment of a unique coarse-grained…
The stochastic response of nanoscale oscillators of arbitrary geometry immersed in a viscous fluid is studied. Using the fluctuation-dissipation theorem it is shown that deterministic calculations of the governing fluid and solid equations…
Coupled length and time scales determine the dynamic behavior of polymers and underlie their unique viscoelastic properties. To resolve the long-time dynamics it is imperative to determine which time and length scales must be correctly…