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We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to…
We present a collision model for phase-resolved Direct Numerical Simulations of sediment transport that couple the fluid and particles by the Immersed Boundary Method. Typically, a contact model for these types of simulations comprises a…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
Two separate algorithms for calculating the intermediate states, using cellular automata and the initial conditions in the rate matrix for the diffusion-collision model are introduced. They enable easy and fast calculations of the folding…
A coarse-grained molecular model, which consists of a spherical particle and an orientation vector, is proposed to simulate lipid membrane on a large length scale. The solvent is implicitly represented by an effective attractive interaction…
The evolution, regulation and sustenance of biological complexity is determined by protein-protein interaction network that is filled with dynamic events. Recent experimental evidences point out that clustering of proteins has a vital role…
A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…
A micro-hydromechanical model for granular materials is presented. It combines the discrete element method (DEM) for the modeling of the solid phase and a pore-scale finite volume (PFV) formulation for the flow of an incompressible pore…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
Cellular aggregates play a significant role in the evolution of biological systems such as tumor growth, tissue spreading, wound healing, and biofilm formation. Analysis of such biological systems, in principle, includes examining the…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…
We study the particle-scale dynamics that give rise to bulk flow behaviours of highly concentrated particle-fluid mixtures using discrete element method (DEM) simulations. We utilize boundary conditions of a stress-controlled shear cell and…
We develop an immersed-boundary approach to modeling reaction-diffusion processes in dispersions of reactive spherical particles, from the diffusion-limited to the reaction-limited setting. We represent each reactive particle with a…
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…
Intracellular signaling often arises from ligand-induced oligomerization of cell surface receptors. This oligomerization or clustering process is fundamentally a cooperative behavior between near-neighbor receptor molecules; the properties…
We define a lattice model for the interaction of a polymer with water. We solve the model in a suitable approximation. In the case of a non-polar homopolymer, for reasonable values of the parameters, the polymer is found in a non-compact…
Blebs are cell protrusions generated by local membrane-cortex detachments followed by expansion of the plasma membrane. Blebs are formed by some migrating cells, for example primordial germ cells of the zebrafish. While blebs occur randomly…
In this article we present a construction of a family particle systems that converge after scaling to the solution a non-linear SDE of Reaction-Diffusion type.
Partial differential equations are a convenient way to describe reaction- advection-diffusion processes of signalling models. If only one cell type is present, and tissue dynamics can be neglected, the equations can be solved directly.…