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Subdiffusion has been proposed as an explanation of various kinetic phenomena inside living cells. In order to fascilitate large-scale computational studies of subdiffusive chemical processes, we extend a recently suggested mesoscopic model…
Brownian dynamics simulations are an increasingly popular tool for understanding spatially-distributed biochemical reaction systems. Recent improvements in our understanding of the cellular environment show that volume exclusion effects are…
The relationship between cell density and velocity is often assumed to be negative, reflecting crowding-induced suppression of movement. However, observations across systems reveal a more nuanced picture: while some emphasize contact…
The effect of disorder in the energetic heights and in the physical locations of fence barriers encountered by transmembrane molecules such as proteins and lipids in their motion in cell membranes is studied theoretically. The investigation…
Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
The diffusion of active microscopic organisms in complex environments plays an important role in a wide range of biological phenomena from cell colony growth to single organism transport. Here, we investigate theoretically and…
During cell migration, cells become polarized, change their shape, and move in response to various internal and external cues. Cell polarization is defined through the spatio-temporal organization of molecules such as PI3K or small GTPases,…
Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to…
A topic of intense current investigation pursues the question how the highly crowded environment of biological cells affects the dynamic properties of passively diffusing particles. Motivated by recent experiments we report results of…
The composition of cellular metabolism is different across species. Empirical data reveal that bacterial species contain similar numbers of metabolic reactions but that the cross-species popularity of reactions is so heterogenous that some…
Brownian diffusion of rod-like polymers in the presence of randomly distributed spherical obstacles is studied using molecular dynamics (MD) simulations. It is observed that dependence of the reduced diffusion coefficient of these…
The interior of cells is crowded thus making it important to assess the effects of macromolecules on the folding of proteins. Using the Self-Organized Polymer (SOP) model, which is a coarse-grained representation of polypeptide chains, we…
The formation of dynamical clusters of proteins is ubiquitous in cellular membranes and is in part regulated by the recycling of membrane components. Mean-field models of out-of-equilibrium cluster formation with recycling predict a broad…
The dispersal of cells from an initially constrained location is a crucial aspect of many physiological phenomena ranging from morphogenesis to tumour spreading. In such processes, the way cell-cell interactions impact the motion of single…
Mathematical models of motility are often based on random-walk descriptions of discrete individuals that can move according to certain rules. It is usually the case that large masses concentrated in small regions of space have a great…
Biomolecular condensates are small droplets forming spontaneously in biological cells via phase separation. They play a role in many cellular processes, but it is unclear how cells control them. Cellular regulation often relies on…
The motion of a eukaryotic cell presents a variety of interesting and challenging problems from both a modeling and a computational perspective. The processes span many spatial scales (from molecular to tissue) as well as disparate time…
The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be…
Cellular biology exists embedded in a world dominated by random dynamics and chance. Many vital molecules and pieces of cellular machinery diffuse within cells, moving along random trajectories as they collide with the other biomolecular…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…