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Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
Model reduction plays a critical role in system control, with established methods such as balanced truncation widely used for linear systems. However, extending these methods to nonlinear settings, particularly polynomial dynamical systems…
This paper proposes and validates two new particle regularization techniques for the Smoothed Particle Hydrodynamics (SPH) numerical method to improve its stability and accuracy for free surface flow simulations. We introduce a general form…
Some recent work pointed out the usefulness of taking a large-deviation perspective when trying to extract anything resembling a macroscopic order parameter from a computer simulation. In this paper we note that the end-to-end distance of…
Using a recently developed bead-spring model for semiflexible polymers that takes into account their natural extensibility, we report an efficient algorithm to simulate the dynamics for polymers like double-stranded DNA (dsDNA) in the…
Many-body dissipative particle dynamics (MDPD) is a mesoscale method capable of reproducing liquid-vapour coexistence in a single simulation. Despite having been introduced more than a decade ago, this method remains broadly unexplored and,…
The stochastic differential equations for a model of dissipative particle dynamics, with both total energy and total momentum conservation at every time-step, are presented. The algorithm satisfies detailed balance as well as the…
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…
Ultrasound-guided drug and gene delivery (usdg) enables controlled and spatially precise delivery of drugs and macromolecules, encapsulated in microbubbles (embs) and submicron gas vesicles (gvs), to target areas such as cancer tumors. It…
We derive a mesoscopic modeling and simulation technique that is very close to the technique known as dissipative particle dynamics. The model is derived from molecular dynamics by means of a systematic coarse-graining procedure. Thus the…
This work presents the mathematical and computational aspects of a smooth dissipative particle dynamics with dynamic virtual particle allocation method (SDPD-DV) for modeling and simulation of mesoscopic fluids in wall-bounded domains. The…
Dynamical systems describe the changes in processes that arise naturally from their underlying physical principles, such as the laws of motion or the conservation of mass, energy or momentum. These models facilitate a causal explanation for…
This study proposes an acceleration technique for the computational challenges in extending the variational deterministic-particle-based scheme (VDS) [Bao et al., Journal of Computational Physics 522 (2025) 113589] to 3D complex fluid…
We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of lipid membranes. Our CG model is a two-dimensional representation of the membrane,…
We examine the phase transition of polymer adsorption as well as the underlying kinetics of polymer binding from dilute solutions on a structureless solid surface. The emphasis is put on the properties of regular multiblock copolymers,…
We present new linear energy-stable numerical schemes for numerical simulation of complex polymer-solvent mixtures. The mathematical model proposed by Zhou, Zhang and E (Physical Review E 73, 2006) consists of the Cahn-Hilliard equation…
In this article we show in details the derivation of an integration scheme for the dissipative particle dynamic model (DPD) using the stochastic Trotter formula [De Fabritiis et al., Physica A, 361, 429 (2006)]. We explain some subtleties…
We present a promising coarse-graining strategy for linking micro- and mesoscales of soft matter systems. The approach is based on effective pairwise interaction potentials obtained from detailed atomistic molecular dynamics (MD)…
Using molecular dynamics simulations we examine the dynamics of a family of model polymers with varying chain length and torsional potential barriers. We focus on features of the dynamics of polymers that are seen experimentally but absent…
This study focuses on comparing the individual polymer chain dynamics in an entangled polymeric liquid under different shear and extension rates. Polymer chains under various shear rates and extension rates were simulated using a…