Related papers: Variational formulations of transport phenomena on…
Motivated by the increased interest in pulsed-power magneto-inertial fusion devices in recent years, we present a method for implementing an arbitrarily shaped embedded boundary on a Cartesian mesh while solving the equations of…
A simple finite element formulation of the outlet gradient boundary condition is presented in the general context of convective-diffusive transport processes. Basically, the method is based on an upstream evaluation of the dependent…
The diffusion of molecules (penetrants) of variable size, shape, and chemistry through dense crosslinked polymer networks is a fundamental scientific problem that is broadly relevant in materials, polymer, physical and biological chemistry.…
We formulate an optimal transport problem for matrix-valued density functions. This is pertinent in the spectral analysis of multivariable time-series. The "mass" represents energy at various frequencies whereas, in addition to a usual…
One of the fundamental properties of semiconductors is their ability to support highly tunable electric currents in the presence of electric fields or carrier concentration gradients. These properties are described by transport coefficients…
In moving mesh methods, the underlying mesh is dynamically adapted without changing the connectivity of the mesh. We specifically consider the generation of meshes which are adapted to a scalar monitor function through equidistribution.…
Constructing physical models of living cells and tissues is an extremely challenging task because of the high complexities of both intra- and intercellular processes. In addition, the force that a single cell generates vanishes in total due…
This work presents a novel unfitted finite element framework to simulate coupled surface-bulk problems in time-dependent domains, focusing on fluid-fluid interactions in animal cells between the actomyosin cortex and the cytoplasm. The…
Understanding mechanisms of ion transport in bulk materials is central to designing next-generation ion conductors for energy storage devices, yet studies employing all-atom molecular dynamics (MD) have largely been limited to reporting…
Chemical kinetic models in terms of ordinary differential equations correspond to finite dimensional dissipative dynamical systems involving a multiple time scale structure. Most dimension reduction approaches aimed at a slow…
Active polymers are ubiquitous in nature, and often kicked by persistent noises that break detailed balance. In order to capture the out-of-equilibrium dynamics of such active polymers, we propose a simple yet reliable analytical framework…
The gas transport through non-volatile random porous media is investigated numerically. We extend our previous research of the transport of molecules inside the uppermost layer of a cometary surface (Skorov and Rickmann, 1995; Skorov et al.…
We construct numerical basis function sets on a lattice, whose spatial extension is scalable from single lattice sites to the continuum limit. They allow us to compute small and large bound states with comparable, moderate effort. Adopting…
Hamiltonian Monte Carlo (HMC) has emerged as a powerful Markov Chain Monte Carlo (MCMC) method to sample from complex continuous distributions. However, a fundamental limitation of HMC is that it can not be applied to distributions with…
This paper presents a framework based on matrices of monoids for the study of coupled cell networks. We formally prove within the proposed framework, that the set of results about invariant synchrony patterns for unweighted networks also…
We develop a mixture-based approach to robust density modeling and outlier detection for experimental multivariate data that includes measurement error information. Our model is designed to infer atypical measurements that are not due to…
In condensed matter physics, particularly in perovskite materials, the rotational motion of molecules and ions is associated with important issues such as ion conduction mechanism. Constrained Molecular Dynamics (MD) simulations offer a…
We discuss a theoretical model for bidirectional cargo transport in biological cells, which is driven by teams of molecular motors and subject to thermal fluctuations. The model describes explicitly the directed motion of the molecular…
The Convected Scheme (CS) is a `forward-trajectory' semi-Lagrangian method for solution of transport equations, which has been most often applied to the kinetic description of plasmas and rarefied neutral gases. In its simplest form, the CS…
We propose a method for multi-scale hybrid simulations of molecular dynamics (MD) and computational fluid dynamics (CFD). In the method, usual lattice-mesh based simulations are applied for CFD level, but each lattice is associated with a…