Related papers: The 3D coarse-graining formulation of interacting …
In this paper, we present a coarse-grained model of DNA based on the soft ellipsoid contact potential (ECP) to evaluate the base pairing interaction properly. We extend the ellipsoid contact like potential model (ECP), suitably modified and…
This chapter summarizes several approaches combining theory, simulation and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane mediated…
This paper proposes a systematic and novel component level co-rotational (CR) framework, for upgrading existing 3D continuum finite elements to flexible multibody analysis. Without using any model reduction techniques, the high efficiency…
Reconstructing and simulating elastic objects from visual observations is crucial for applications in computer vision and robotics. Existing methods, such as 3D Gaussians, model 3D appearance and geometry, but lack the ability to estimate…
Using a fixed Eulerian mesh, the phase-field method has been successfully utilized for a broad range of moving boundary problems involving multiphase fluids and single-phase fluid-structure interaction. Nevertheless, multiphase fluids…
We use Brownian dynamics simulations and theory to study the over-damped spatiotemporal dynamics and pattern formation in a fluid-permeated array of equally spaced, active, elastic filaments that are pinned at one end and free at the other.…
We derive and introduce anisotropic effective pair potentials to coarse-grain solutions of semiflexible rings polymers of various lengths. The system has been recently investigated by means of full monomer-resolved computer simulations,…
In this work, we present a computational formulation based on continuum mechanics to study the interaction of fluid membranes embedded with semiflexible filaments. This is motivated by systems in membrane biology, such as cytoskeletal…
Developing physics-based models for molecular simulation requires fitting many unknown parameters to diverse experimental datasets. Traditionally, this process is piecemeal and difficult to reproduce, leading to a fragmented landscape of…
We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered…
We describe simulations of a microscopic elastic filament immersed in a fluid and subject to a uniform external force. Our method accounts for the hydrodynamic coupling between the flow generated by the filament and the friction force it…
Semiflexible slender filaments are ubiquitous in nature and cell biology, including in the cytoskeleton, where reorganization of actin filaments allows the cell to move and divide. Most methods for simulating semiflexible inextensible…
In analogy with classic rigidity problems of networks and frames, the elastic properties of hydrogels made of DNA nanostars (DNAns) are expected to strongly depend on the precise geometry of their building blocks. However, it is currently…
We experimentally measure a three-dimensional (3D) granular system's reversibility under cyclic compression. We image the grains using a refractive-index-matched fluid, then analyze the images using the artificial intelligence of…
Peritrichous bacteria swim in viscous fluids by rotating multiple helical flagellar filaments. As the bacterium swims forward, all its flagella rotate in synchrony behind the cell in a helical bundle. When the bacterium changes its…
The linear-frictional contact model is the most commonly used contact mechanism for discrete element (DEM) simulations of granular materials. Linear springs with a frictional slider are used for modeling interactions in directions normal…
Molecular dynamics (MD) is a crucial technique for simulating biological systems, enabling the exploration of their dynamic nature and fostering an understanding of their functions and properties. To address exploration inefficiency,…
We propose a numerical methodology for the numerical simulation of distinct, interacting physical processes described by a combination of compressible, inert and reactive forms of the Euler equations, multiphase equations and elastoplastic…
We coarse-grain a model of closely-packed ellipses that can vary their aspect ratio to derive continuum equations for materials comprising confluent deformable particles such as epithelial cell layers. We show that contractile nearest…
Natural filaments, such as proteins, plant tendrils, octopus tentacles, and elephant trunks, can transform into arbitrary three-dimensional shapes that carry out vital functions. Their shape-morphing behavior arises from intricate…