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We present an algorithm to simulate the many-body depletion interaction between anisotropic colloids in an implicit way, integrating out the degrees of freedom of the depletants, which we treat as an ideal gas. Because the depletant…
The cell membrane is inherently asymmetric and heterogeneous in its composition, a feature that is crucial for its function. Using atomistic molecular dynamics simulations, the physical properties of a 3-component asymmetric mixed lipid…
Ionic liquids (ILs) are an exciting class of electrolytes finding applications in many areas from energy storage to solvents, where they have been touted as ``designer solvents'' as they can be mixed to precisely tailor the physiochemical…
The present work proposes an approach for fluid-solid and contact interaction problems including thermo-mechanical coupling and reversible phase transitions. The solid field is assumed to consist of several arbitrarily-shaped, undeformable…
The membrane curvature of cells and intracellular compartments continuously adapts to enable cells to perform vital functions, from cell division to signal trafficking. Understanding how membrane geometry affects these processes in vivo is…
We consider a multiscale approach based on immersed methods for the efficient computational modeling of tissues composed of an elastic matrix (in two or three-dimensions) and a thin vascular structure (treated as a co-dimension two…
Solvent-free coarse grained models represent one of the most promising approaches for molecular simulations of mesoscopically large membranes. In these models, the size of the simulated membrane is limited by the slow relaxation time of…
Contrastive language-image pretraining (CLIP) has demonstrated remarkable success in various image tasks. However, how to extend CLIP with effective temporal modeling is still an open and crucial problem. Existing factorized or joint…
A new approach is developed to integrate numerically the equations of motion for systems of interacting rigid polyatomic molecules. With the aid of a leapfrog framework, we directly involve principal angular velocities into the integration,…
Recent applications (e.g. active gels and self-assembly of elastic sheets) motivate the need to efficiently simulate the dynamics of thin elastic sheets. We present semi-implicit time stepping algorithms to improve the time step constraints…
We present a novel Relativistic Semi-Implicit Method (RelSIM) for particle-in-cell (PIC) simulations of astrophysical plasmas, implemented in a code framework ready for production runs. While explicit PIC methods have gained widespread…
Complex fluids exhibit structure on a wide range of length and time scales, and hierarchical approaches are necessary to investigate all facets of their often unusual properties. The study of idealized coarse-grained models at different…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
Soft pair potentials predict a reentrant liquid phase for high concentrations, a behavior not observed experimentally. Here, very soft microgels confined at an oil-water interface are used as a model system of particles interacting via a…
We propose a very simple but realistic enough model which allows to include a large number of molecules in molecular dynamics MD simulations of these bilayers, but nevertheless taking into account molecular charge distributions, flexible…
An analytically solvable model of unsaturated lipid bilayer is derived by introducing finite bending angle of the unsaturated bond relative to straight part of the lipid chain considered previously in our model of semi-flexible strings. It…
Implicit integration of the viscous term can significantly improve performance in computational fluid dynamics for highly viscous fluids such as lava. We show improvements over our previous proposal for semi-implicit viscous integration in…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
Laboratory plasmas in open magnetic geometries can be found in many different applications such as (1) Scrape-Of-Layer (SOL) and divertor regions in toroidal confinement fusion devices (\approx1-10^2\hspace{1mm}\mathrm{eV}), (2) linear…
Robotic manipulation with deformable objects represents a data-intensive regime in embodied learning, where shape, contact, and topology co-evolve in ways that far exceed the variability of rigids. Although simulation promises relief from…