Related papers: The 3D coarse-graining formulation of interacting …
Soft, slender structures are ubiquitous in natural and engineered systems, with broad application potential from biomimetic materials to soft robotics. However, there is a notable lack of computational tools that simultaneously preserve…
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…
3D Gaussian Splatting (3DGS) enables high-fidelity real-time rendering, a key requirement for immersive applications. However, the extension of 3DGS to dynamic scenes remains limitations on the substantial data volume of dense Gaussians and…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
Many coarse-grained models have been developed for equilibrium studies of lipid bilayer membranes. To achieve in simulations access to length-scales and time-scales difficult to attain in fully atomistic molecular dynamics, these…
Coarse-grained descriptions of dislocation motion in crystalline metals inherently represent a loss of information regarding dislocation-dislocation interactions. In the present work, we consider a coarse-graining framework capable of…
Simulations of macromolecular diffusion and adsorption in confined environments can offer valuable mechanistic insights into numerous biophysical processes. In order to model solutes at atomic detail on relevant time scales, Brownian…
We describe in detail how to implement a coarse-grained hybrid Molecular Dynamics and Stochastic Rotation Dynamics simulation technique that captures the combined effects of Brownian and hydrodynamic forces in colloidal suspensions. The…
We introduce Coarse-Grained Nonlinear Dynamics, an efficient and universal parameterization of nonlinear system dynamics based on the Volterra series expansion. These models require a number of parameters only quasilinear in the system's…
Active semiflexible filaments are crucial in various biophysical processes, yet insights into their single-filament behavior have predominantly relied on theory and simulations, owing to the scarcity of controllable synthetic systems. Here,…
We present a novel platform for the large-scale simulation of fibrous structures immersed in a Stokesian fluid and evolving under confinement or in free-space. One of the main motivations for this work is to study the dynamics of fiber…
We propose a highly coarse-grained simulation model for crystalline polymer solids with crystalline lamellar structures. The mechanical properties of a crystalline polymer solid are mainly determined by the crystalline lamellar structures.…
Two-dimensional covalent organic frameworks (2D COFs) are an interesting class of 2D materials since their reticular synthesis allows the tailored design of structures and functionalities. For many of their applications the mechanical…
The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the…
The dynamics of energetic particle (EP) species, born from fusion reactions or plasma heating schemes, are critical for predicting the behavior of magnetic confinement fusion experiments and future fusion reactors. Because energetic…
Coarse-grained (CG) modeling has gained significant attention in recent years due to its wide applicability in enhancing the spatiotemporal scales of molecular simulations. While CG simulations, often performed with Hamiltonian mechanics,…
Sand production is an important issue for many hydrocarbon recovery applications in unconsolidated reservoirs. The model using the Computational Fluid Dynamics coupled with Discrete Element Method (CFD-DEM) can capture micro-scale features…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
The elastohydrodynamics of slender bodies in a viscous fluid have long been the source of theoretical investigation, being pertinent to the microscale world of ciliates and flagellates as well as to biological and engineered active matter…
In soft matter systems the local displacement field can be accessed directly by video microscopy enabling one to compute local strain fields and hence the elastic moduli using a coarse-graining procedure. We study this process for a simple…