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We present a powerful and easy-to-implement iterative algorithm for solving large-scale optimization problems that involve $L_1$/total-variation (TV) regularization. The method is based on combining the Alternating Directions Method of…
We present a flexible discretization technique for computational models of thin tubular networks embedded in a bulk domain, for example a porous medium. These systems occur in the simulation of fluid flow in vascularized biological tissue,…
We introduce a general framework for constructing coarse-grained potential models without ad hoc approximations such as limiting the potential to two- and/or three-body contributions. The scheme, called Deep Coarse-Grained Potential…
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…
A kinetic model for the Boltzmann equation is proposed and explored as a practical means to investigate the properties of a dilute granular gas. It is shown that all spatially homogeneous initial distributions approach a universal…
The Martini 3 force field is a full re-parametrization of the Martini coarse-grained model for biomolecular simulations. Due to the improved interaction balance it allows for more accurate description of condensed phase systems. In the…
Computer simulations can provide mechanistic insight into ionic liquids (ILs) and predict the properties of experimentally unrealized ion combinations. However, ILs suffer from a particularly large disparity in the time scales of atomistic…
Lipid membranes have complex compositions and modeling the thermodynamic properties of multi-component lipid systems remains a remote goal. In this work we attempt to describe the thermodynamics of binary lipid mixtures by mapping…
An improved numerical solver for the unified solution of compressible and incompressible fluids involving interfaces is proposed. The present method is based on the CIP-CUP (Cubic Interpolated Propagation / Combined, Unified Procedure)…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
One of the biggest challenges for simulating the Boltzmann equation is the evaluation of fivefold collision integral. Given the recent successes of deep learning and the availability of efficient tools, it is an obvious idea to try to…
A sparse octree based parallel implementation of the lattice Boltzmann method for non-uniform meshes is presented in this paper. To couple grids of different resolutions, a second order accurate compact interpolation is employed and further…
We propose a new regularisation strategy for the classical ensemble Kalman inversion (EKI) framework. The strategy consists of: (i) an adaptive choice for the regularisation parameter in the update formula in EKI, and (ii) criteria for the…
The necessity for accurate and computationally efficient representations of water in atomistic simulations that can span biologically relevant timescales has born the necessity of coarse-grained (CG) modeling. Despite numerous advances, CG…
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…
In this paper, a novel isogeometric method for Biot's consolidation model is constructed and analyzed, using a four-field formulation where the unknown variables are the solid displacement, solid pressure, fluid flux, and fluid pressure.…
We present a fully-integrated lattice Boltzmann (LB) method for fluid--structure interaction (FSI) simulations that efficiently models deformable solids in complex suspensions and active systems. Our Eulerian method (LBRMT) couples…
A discrete unified gas kinetic scheme (DUGKS) coupled with the immersed boundary (IB) method is developed to perform interface-resolved simulation of particle-laden flows. The present method (IB-DUGKS) preserves the respective advantages of…
We introduce a new procedure for iterative selection of determinant spaces capable of describing highly correlated systems. This adaptive configuration interaction (ACI) determines an optimal basis by an iterative procedure in which the…
A general lattice Boltzmann method for simulation of fluids with tailored transport coefficients is presented. It is based on the recently introduced quasi-equilibrium kinetic models, and a general lattice Boltzmann implementation is…