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The detachment dynamics of a fluid membrane with an isotropic spontaneous curvature from a flat substrate are studied by using meshless membrane simulations. The membrane is detached from an open edge leading to vesicle formation. With…
Many vesicles have a spherical resting shape and exposure to fluid flows induces an exchange between sub-optical area and visible (systematic) deformation, while the total area is conserved. The dynamics which controls the exchange between…
A molecular dynamics simulation of SPC/E water confined in a Silica pore is presented. The pore has been constructed to reproduce the average properties of a pore of Vycor glass. Due to the confinement and to the presence of a strong…
Dynamic organization of the cytoskeletal filaments and rod-like proteins in the cell membrane and other biological interfaces occurs in many cellular processes. Previous modeling studies have considered the dynamics of a single rod on fluid…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
Cell deformability is an essential determinant for tissue-scale mechanical nature, such as fluidity and rigidity, and is thus crucial for understanding tissue homeostasis and stable developmental processes. However, numerical simulations…
Microorganisms swimming through viscous fluids imprint their propulsion mechanisms in the flow fields they generate. Extreme confinement of these swimmers between rigid boundaries often arises in natural and technological contexts, yet…
In equilibrium and supercooled liquids, polymorphism is manifested by thermodynamic regions defined in the phase diagram, which are predominantly of different short- and medium-range order (local structure). It is found that on the phase…
Recent experimental studies have shown that confinement can profoundly affect self-organization in semi-dilute active suspensions, leading to striking features such as the formation of steady and spontaneous vortices in circular domains and…
We present a multiparticle collision dynamics (MPC) implementation of layered immiscible fluids $A$ and $B$ of different shear viscosities separated by planar interfaces. The simulated flow profile for imposed steady shear motion and the…
In active matter systems, deformable boundaries provide a mechanism to organize internal active stresses and perform work on the external environment. To study a minimal model of such a system, we perform particle-based simulations of an…
Blood vessel constriction is simulated with particle-based method using a molecular dynamics authoring software known as Molecular Workbench (WM). Blood flow and vessel wall, the only components considered in constructing a blood vessel,…
Low Reynolds number swimmers frequently move near boundaries, such as spirochetes moving through porous tissues and sperm navigating the reproductive tract. Furthermore, these microorganisms must often navigate non-Newtonian fluids such as…
Lipid vesicles composed of a mixture of two types of lipids are studied by intensive Monte-Carlo numerical simulations. The coupling between the local composition and the membrane shape is induced by two different spontaneous curvatures of…
The red blood cell (RBC) membrane is composed of a lipid bilayer and a cytoskeleton interconnected by protein junction complexes, allowing for potential sliding between the lipid bilayer and the cytoskeleton. Despite this biological…
We analyze the displacements of the particles of a glass-forming molecular liquid perpendicular to a confining solid surface, using extensive molecular dynamics simulations with atomistic models. In the vicinity of an attractive surface,…
We present a novel computational modeling framework to numerically investigate fluid-structure interaction in viscous fluids using the phase field embedding method. Each rigid body or elastic structure immersed in the incompressible viscous…
Blood exhibits a heterogeneous nature of hematocrit, velocity, and effective viscosity in microcapillaries. Microvascular bifurcations have a significant influence on the distribution of the blood cells and blood flow behavior. This paper…
Cellular membranes exhibit a large variety of shapes, strongly coupled to their function. Many biological processes involve dynamic reshaping of membranes, usually mediated by proteins. This interaction works both ways: while proteins…
Hydrodynamics is known to have strong effects on the kinetics of phase separation. There exist open questions on how such effects manifest in systems under confinement. Here, we have undertaken extensive studies of the kinetics of phase…