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The reaction of volatile matter plays an important role in the process of bringing matter from the surface of the planet to the atmosphere. Therefore, by simulating the mixing and chemical reaction process of volatile matter in the…
Eukaryotic cells adhere to extracellular matrix during the normal development of the organism, forming static adhesion as well as during cell motility. We study this process by considering a simplified coarse-grained model of a vesicle that…
Experimental studies of cell motility in culture have shown that under adequate conditions these living organisms possess the ability to organize themselves into complex structures. Such structures may exhibit a synergy that greatly…
Proteins in photosynthetic membranes can organize into patterned arrays that span the membrane's lateral size. Attractions between proteins in different layers of a membrane stack can play a key role in this ordering, as was suggested by…
We study, by means of mean field calculations and Monte Carlo simulations of a lattice-gas model, the distribution of adhesion sites of a bilayer membrane and a supporting flat surface. Our model accounts for the many-body character of the…
The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results…
We present a multi-scale model to study the attachment of spherical particles with a rigid core, coated with binding ligands and in equilibrium with the surrounding, quiescent fluid medium. This class of fluid-immersed adhesion is…
Cell-cell adhesion is one the most fundamental mechanisms regulating collective cell migration during tissue development, homeostasis and repair, allowing cell populations to self-organize and eventually form and maintain complex tissue…
We consider the dynamic wetting and dewetting processes of films and droplets of complex liquids on planar surfaces, focusing on the case of colloidal suspensions, where the particle interactions can be sufficiently attractive to cause…
The phase behavior of stabilized dispersions of macromolecules is most easily described in terms of the effective interaction between the centers of mass of solute particles. For molecules like polymer chains, dendrimers, etc., the…
Realistic examples of reaction-diffusion phenomena governing spatial and spatiotemporal pattern formation are rarely isolated systems, either chemically or thermodynamically. However, even formulations of `open' reaction-diffusion systems…
Dynamical reaction-diffusion processes and meta-population models are standard modeling approaches for a wide variety of phenomena in which local quantities - such as density, potential and particles - diffuse and interact according to the…
A simple three-dimensional model of a fluid whose constituent particles interact via a short range attractive and long range repulsive potential is used to model the aggregation into large spherical-like clusters made up of hundreds of…
Rebinding kinetics of molecular ligands plays a critical role in biomachinery, from regulatory networks to protein transcription, and is also a key factor for designing drugs and high-precision biosensors.In this study, we investigate…
Living cells employ excitable reaction-diffusion waves for internal cellular functions, in which curvature-inducing proteins are often involved. However, the role of their mechanochemical coupling is not well understood. Here, we report the…
The endoplasmic reticulum (ER), a cellular organelle that forms a cell-spanning network of tubes and sheets, is an important location of protein synthesis and folding. When the ER experiences sustained unfolded protein stress, IRE1 proteins…
This paper introduces diffusion protein language model (DPLM), a versatile protein language model that demonstrates strong generative and predictive capabilities for protein sequences. We first pre-train scalable DPLMs from…
Many animals have patterned fur, feathers, or scales, such as the stripes of a zebra. Turing models, or reaction-diffusion systems, are a class of mathematical models of interacting species that have been successfully used to generate…
Single-molecule fluorescence imaging of adsorption onto initially-bare surfaces shows that polymer chains need not localize immediately after arrival. In a system optimized to present limited adsorption sites (quartz surface to which…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…