Related papers: SiMPLISTIC: A Novel Pairwise Potential for Implici…
Molecular dynamics (MD) simulations are widely used to study biological systems, where water molecules often play a critical role in protein-ligand interactions. In conventional MD preparation protocols, water molecules are typically added…
Efficient, accurate, and adaptable implicit solvent models remain a significant challenge in the field of molecular simulation. A recent implicit solvent model, IS-SPA, based on approximating the mean solvent force using the superposition…
Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…
We propose a new algorithm to learn the network of the interactions of pairwise Ising models. The algorithm is based on the pseudo-likelihood method (PLM), that has already been proven to efficiently solve the problem in a large variety of…
Chemical potential of species in solution is essential for understanding various chemical processes at interfaces. Molecular dynamics (MD) simulations, constrained by fixed compositions, cannot satisfy a constant chemical potential…
Hybrid particle-field methods are computationally efficient approaches for modelling soft matter systems. So far applications of these methodologies have been limited to constant volume conditions. Here, we reformulate particle-field…
We establish a biophysical model for the dynamics of lipid vesicles exposed to surfactants. The solubilization of the lipid membrane due to the insertion of surfactant molecules induces a reduction of membrane surface area at almost…
We present a methodology for simulating dilute suspensions of particles settling under gravity, with the main purpose of overcoming limitations of triply periodic configurations, mainly the strong vertical correlation that hinders the study…
This article presents a multi-physics methodology for the numerical simulation of physical systems that involve the non-linear interaction of multi-phase reactive fluids and elastoplastic solids, inducing high strain-rates and high…
Hydrophobic thickness mismatch between integral membrane proteins and the surrounding lipid bilayer can produce lipid bilayer thickness deformations. Experiment and theory have shown that protein-induced lipid bilayer thickness deformations…
We present a multi-level elastodynamics timestep solver for accelerating incremental potential contact (IPC) simulations. Our method retains the robustness of gold standard IPC in the face of intricate geometry, complex heterogeneous…
Knowledge of the underlying mechanisms of multiphase flow dynamics in porous media is crucial for optimizing subsurface engineering applications like geological carbon sequestration. However, studying the micro-mechanisms of multiphase…
In experimental systems, colloidal particles are virtually always at least somewhat polydisperse, which can have profound effects on their ability to crystallize. Unfortunately, accurately predicting the effects of polydispersity on phase…
Elastin-like polypeptides (ELPs) undergo a sharp solubility transition from low temperature solvated phases to coacervates at elevated temperatures, driven by the increased strength of hydrophobic interactions at higher temperatures. The…
Particle-In-Cell (PIC) methods are frequently used for kinetic, high-fidelity simulations of plasmas. Implicit formulations of PIC algorithms feature strong conservation properties, up to numerical round-off errors, and are not subject to…
A two-state-model consisting of hexagonally connected lipids being either in the ordered or disordered state is used to set up a Monte Carlo Simulation for lipid monolayers. The connection of the lipids is realized by Newtonian springs…
The hydrodynamic interactions of a suspension of self-propelled particles are studied using a direct numerical simulation method which simultaneously solves for the host fluid and the swimming particles. A modified version of the "Smoothed…
We present a quasi-static finite element simulator for human face animation. We model the face as an actuated soft body, which can be efficiently simulated using Projective Dynamics (PD). We adopt Incremental Potential Contact (IPC) to…
A novel numerical technique designed for interface flow simulations using the Volume of Fluid (VOF) method on arbitrary unstructured meshes has been introduced. The method is called SimPLIC, which seamlessly integrates Piecewise Linear…
Previously, we have proposed a direct simulation scheme for colloidal dispersions in a Newtonian solvent [Phys.Rev.E 71,036707 (2005)]. An improved formulation called the ``Smoothed Profile (SP) method'' is presented here in which…