Related papers: Multiscale models and approximation algorithms for…
The boundary conditions at the deformable interface between two contacting fluids are derived for the general case of the large-amplitude perturbations. The interface is modeled as perturbed free boundary that evolves in time, and the…
In this paper we propose a nonlinear elasticity model of macromolecular conformational change (deformation) induced by electrostatic forces generated by an implicit solvation model. The Poisson-Boltzmann equation for the electrostatic…
An accurate force calculation with the Poisson-Boltzmann equation is challenging, as it requires the electric field on the molecular surface. Here, we present a calculation of the electric field on the solute-solvent interface that is exact…
In this thesis, we develop multiscale models for particle simulations in population dynamics. These models are characterised by prescribing particle motion on two spatial scales: microscopic and macroscopic. At the microscopic level, each…
The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular…
The complexity of biomolecular interactions necessitates advanced methodologies to accurately capture their behavior in solution. In this work, we focus on monoclonal antibodies and adopt a multi-scale coarse-graining strategy for their…
Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…
Electronic nearsightedness is one of the fundamental principles governing the behavior of condensed matter and supporting its description in terms of local entities such as chemical bonds. Locality also underlies the tremendous success of…
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)…
We study the simulation of charged systems in the presence of general boundary conditions in a local Monte Carlo algorithm based on a constrained electric field. We firstly show how to implement constant-potential, Dirichlet, boundary…
The macroscopic properties of materials that we observe and exploit in engineering application result from complex interactions between physics at multiple length and time scales: electronic, atomistic, defects, domains etc. Multiscale…
Lubricated friction is a multiscale problem where molecular processes dictate the macroscopic response of the system. Traditional lubrication models rely on semi-empirical constitutive relations, which become unreliable under extreme…
The immersed boundary method is a mathematical formulation and numerical method for solving fluid-structure interaction problems. For many biological problems, such as models that include the cell membrane, the immersed structure is a…
Biological membranes constitute boundaries of cells and cell organelles. Physico-chemical mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…
Modeling biological processes is a highly demanding task because not all processes are fully understood. Mathematical models allow us to test hypotheses about possible mechanisms of biological processes. The mathematical mechanisms…
The inclusion of long-range electrostatics in atomistic machine learning (ML) is receiving increasing attention for achieving quantum-mechanical accuracy in predicting a wide range of molecular and material properties. However, there is…
A thermodynamically consistent particle-based model for fluid dynamics with continuous velocities and a non-ideal equation of state is presented. Excluded volume interactions are modeled by means of biased stochastic multiparticle…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…