Related papers: Molecular Dynamics Simulation of Vascular Network …
The spatial distribution of neuronal cells is an important requirement for achieving proper neuronal function in several parts of the nervous system of most animals. For instance, specific distribution of photoreceptors and related neuronal…
Surface tension-driven flow techniques have recently emerged as an efficient means of shedding light into the rheology of thin polymer films. Motivated by experimental and theoretical approaches in films bearing a varying surface…
Most computer simulations of molecular dynamics take place under equilibrium conditions--in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are…
We examine the shape of droplets atop deformable thin elastomeric films prepared with an anisotropic tension. As the droplets generate a deformation in the taut film through capillary forces, they assume a shape that is elongated along the…
In this work, we present a coupled 3D-1D model of solid tumor growth within a dynamically changing vascular network to facilitate realistic simulations of angiogenesis. Additionally, the model includes erosion of the extracellular matrix,…
Molecular networks guide the biochemistry of a living cell on multiple levels: its metabolic and signalling pathways are shaped by the network of interacting proteins, whose production, in turn, is controlled by the genetic regulatory…
We investigate a two-dimensional network simulator capable of modeling different time dependencies in two-phase drainage displacements. In particular, we focus on the temporal evolution of the pressure due to capillary and viscous forces…
Biological cells can actively tune their intracellular architecture according to their overall shape. Here we explore the rheological implication of such coupling in a minimal model of a dense cellular material where each cell exerts an…
We view a complex liquid as a network of bonds connecting each particle to its nearest neighbors; the dynamics of this network is a chain of discrete events signaling particles rearrangements. Within this picture, we studied a…
Scientists have long sought to understand how vascular networks supply blood and oxygen to cells throughout the body. Recent work focuses on principles that constrain how vessel size changes through branching generations from the aorta to…
The influence of the internal structure of a biological cell (e.g., a leukocyte) on its dynamics and rheology is not yet fully understood. By using 2D numerical simulations of a bilamellar vesicle (BLV) consisting of two vesicles as a cell…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
A simplified model is developed, which allows us to perform computer simulations of the particles transport in an evaporating droplet with a contact line pinned to a hydrophilic substrate. The model accounts for advection in the droplet,…
A hybrid model of molecular dynamics and continuum mechanics is introduced to study a system of vertically shaken granular layers. Despite the simplicity the model shows pattern formation in the granular layers due to the formation of…
We develop a graph-based model of the hydrogen bond network in water, with a view towards quantitatively modeling the molecular-level correlational structure of the network. The networks are formed are studied by the constructing the model…
The dynamics of flow within a material transport network is dependent upon the dynamics of its power source. Responding to a change of these dynamics is critical for the fitness of living flow networks, e.g. the animal vasculature, which…
Non-particulate continuum descriptions allow for computationally efficient modeling of suspension flows at scales that are inaccessible to more detailed particulate approaches. It is well known that the presence of particles influences the…
We implement molecular dynamics simulations in canonical ensemble to study the effect of confinement on a $2d$ crystal of point particles interacting with an inverse power law potential proportional to $r^{-12}$ in a narrow channel. This…
There is now growing evidence of the emergence and biological functionality of liquid crystal features, including nematic order and topological defects, in cellular tissues. However, how such features that intrinsically rely on particle…
Drying of fluids undergoing sol-gel transition in porous media, a process crucial for the consolidation of damaged porous structures in cultural heritage, often leads to skin formation at the surface. This phenomenon significantly hinders…