Related papers: Statistical dynamics of spatial-order formation by…
Over the past decade, advances in super-resolution microscopy and particle-based modeling have driven an intense interest in investigating spatial heterogeneity at the level of single molecules in cells. Remarkably, it is becoming clear…
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…
To celebrate Hans Frauenfelder's achievements, we examine energy(-like) "landscapes" for complex living systems. Energy landscapes summarize all possible dynamics of some physical systems. Energy(-like) landscapes can explain some…
Spatial awareness in mammals is based on internalized representations of the environment---cognitive maps---encoded by networks of spiking neurons. Although behavioral studies suggest that these maps can remain stable for long periods, it…
Motivated by earlier numerical evidence for a percolation-like transition in space-time jamming, we present an analytic description of the transient dynamics of the deterministic traffic model elementary cellular automaton rule 184…
We present a systematic study of the influence of cell geometry on the orientational distribution of microtubules (MTs) nucleated from a single microtubule organizing center (MTOC). For simplicity we consider an elliptical cell geometry, a…
We consider a partial differential equation model for the growth of heterogeneous cell populations subdivided into multiple distinct discrete phenotypes. In this model, cells preferentially move towards regions where they feel less…
Based on a recently proposed non-equilibrium mechanism for spatial pattern formation [cond-mat/0312366] we study how morphogenesis can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of…
Cell lineage decisions occur in three-dimensional spatial patterns that are difficult to identify by eye. There is an ongoing effort to replicate such patterns using mathematical modeling. One approach uses long ranging cell-cell…
Predicting spatial gene expression from routine H\&E enables large-scale molecular profiling, yet current models treat this as isolated pointwise tasks, thereby overlooking essential biological structures like gene coordination and spatial…
Biological cells with all of their surface structure and complex interior stripped away are essentially vesicles - membranes composed of lipid bilayers which form closed sacs. Vesicles are thought to be relevant as models of primitive…
The complexity of gene regulatory networks in multicellular organisms makes interpretable low-dimensional models highly desirable. An attractive geometric picture, attributed to Waddington, visualizes the differentiation of a cell into…
We simulate static memory materials on a two-dimensional lattice. The bulk properties of such materials depend on boundary conditions. Considerable information can be stored in various local patterns. We observe local probabilities…
We consider random search processes alternating stochastically between diffusion and ballistic motion, in which the distribution function of ballistic motion directions varies from point to point in space. The specific space dependence of…
We study a simple swarming model on a two-dimensional lattice where the self-propelled particles exhibit a tendency to align ferromagnetically. Volume exclusion effects are present: particles can only hop to a neighboring node if the node…
We consider the problem of communicating a sequence of concepts, i.e., unknown and potentially stochastic maps, which can be observed only through examples, i.e., the mapping rules are unknown. The transmitter applies a learning algorithm…
Mechanical interactions among cells in a growing microbial colony can significantly influence the colony's spatial genetic structure and, thus, evolutionary outcomes such as the fates of rare mutations. Here, we computationally investigate…
Understanding to what extent stem cell potential is a cell-intrinsic property, or an emergent behavior coming from global tissue dynamics and geometry, is a key outstanding question of systems and stem cell biology. Here, we propose a…
Most models of biological pattern formation are simulated on continuous domains even though cells are discrete objects that provide internal boundaries to the diffusion of regulatory components. In our previous papers on simulating…
This chapter investigates some mechanisms behind pattern formation driven by competitive-only or repelling interactions, and explores how these patterns are influenced by different types of particle movement. Despite competition and…