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Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
Simple models for spherical particles with a soft shell have been shown to self-assemble into numerous crystal phases and even quasicrystals. However, most of these models rely on a simple pairwise interaction, which is usually a valid…
Many biological examples of fluid-structure interaction, including the transit of red blood cells through the narrow slits in the spleen and the intracellular trafficking of vesicles into dendritic spines, involve the near-contact of…
Algorithms based on gradient descent for computing the elastic shape registration of two simple surfaces in 3-dimensional space and therefore the elastic shape distance between them have been proposed by Kurtek, Jermyn, et al., and more…
The interplay of membrane proteins is vital for many biological processes, such as cellular transport, cell division, and signal transduction between nerve cells. Theoretical considerations have led to the idea that the membrane itself…
The article proposes an algorithm to model the collision between arbitrary ellipsoids in viscous fluid. It is composed of several steps, each improving upon the standard procedure employed in the current literature. First, an efficient…
Viscosity is a key property of cell membranes that controls mobility of embedded proteins and membrane remodeling. Measuring it is challenging because existing approaches involve complex experimental designs and/or models, and the…
The viscosity of lipid bilayer membranes plays an important role in determining the diffusion constant of embedded proteins and the dynamics of membrane deformations, yet it has historically proven very difficult to measure. Here we…
Sphericity and roundness are fundamental measures used for assessing object uniformity in 2D and 3D images. However, using their strict definition makes computation costly. As both 2D and 3D microscopy imaging datasets grow larger, there is…
Fluid-structure interactions are a widespread phenomenon in nature. Although their numerical modeling have come a long way, the application of numerical design tools to these multiphysics problems is still lagging behind. Gradient-based…
Atoms at liquid metal surfaces are known to form layers parallel to the surface. We analyze the two-dimensional arrangement of atoms within such layers at the surface of liquid sodium, using ab initio molecular dynamics (MD) simulations…
The motion of an object within a viscous fluid and in the vicinity of a soft surface induces a hydrodynamic stress field that deforms the latter, thus modifying the boundary conditions of the flow. This results in elastohydrodynamic (EHD)…
When considering flows in biological membranes, they are usually treated as flat, though more often than not, they are curved surfaces, even extremely curved, as in the case of the endoplasmic reticulum. Here, we study the topological…
A method to calculate the bending rigidity $\kappa$, saddle-splay modulus $\bar{\kappa}$, and spontaneous curvature $C_0$ of a fluid membrane is proposed. Virtual work for the bending deformations into cylindrical and spherical shapes is…
This paper presents a general and robust method for the fluid-structure interaction of membranes and shells undergoing large displacement and large added-mass effects by coupling an immersed-boundary method with a shell finite-element…
Recent experiments on vesicles formed from block copolymers with liquid-crystalline side-chains reveal a rich variety of vesicle morphologies. The additional internal order ("structure") developed by these self-assembled block copolymer…
We examine the deformation of homogeneous spherical fluid vesicles along their equator by a circular rigid ring. We consider deformations preserving the axial and equatorial mirror symmetries of the vesicles. The configurations of the…
The equations governing the conditions of mechanical equilibrium in fluid membranes subject to bending are revisited thanks to the principle of virtual work. The note proposes systematic tools to obtain the shape equation and the line…
Microorganisms are rarely found in Nature swimming freely in an unbounded fluid. Instead, they typically encounter other organisms, hard walls, or deformable boundaries such as free interfaces or membranes. Hydrodynamic interactions between…
Cells offer numerous inspiring examples where proteins and membranes combine to form complex structures that are key to intracellular compartmentalization, cargo transport, and specialization of cell morphology. Despite this wealth of…