Related papers: Selective sweeps in growing microbial colonies
We study the effect of discreteness on various models for patterning in bacterial colonies. In a bacterial colony with branching pattern, there are discrete entities - bacteria - which are only two orders of magnitude smaller than the…
We introduce a general theoretical framework to study the shape dynamics of actively growing and remodeling surfaces. Using this framework we develop a physical model for growing bacterial cell walls and study the interplay of cell shape…
Competition during range expansions is of great interest from both practical and theoretical view points. Experimentally, range expansions are often studied in homogeneous Petri dishes, which lack spatial anisotropy that might be present in…
Defective interfering particles (DIPs) are virus-like particles that occur naturally during virus infections. These particles are defective, lacking essential genetic materials for replication, but they can interact with the wild-type virus…
Chemical reactions inside cells are generally considered to happen within fixed-size compartments. Needless to say, cells and their compartments are highly dynamic. Thus, such stringent assumptions may not reflect biochemical reality, and…
Colonies of bacteria endowed with a pili-based self-propulsion machinery are ideal models for investigating the structure and dynamics of active many-particle systems. We study Neisseria gonorrhoeae colonies with a molecular-dynamics-based…
An ab-initio numerical study of the density-dependent, evolutionary stable dispersal strategy is presented. The simulations are based on a simple discretei generation island model with four processes: reproduction, dispersal, competition…
Aggregation-diffusion equations are foundational tools for modelling biological aggregations. Their principal use is to link the collective movement mechanisms of organisms to their emergent space use patterns in a concrete mathematical…
Microbial colonies are experimental model systems for studying the colonization of new territory by biological species through range expansion. We study a generalization of the two-species Eden model, which incorporates local…
We study a three-species cyclic model whose organisms are vulnerable to contamination with an infectious disease which propagates person-to-person. We consider that individuals of one species perform an evolutionary self-preservation…
A stochastic model is used to assess the effect of external parameters on the development of submerged biofilms on smooth and rough surfaces. The model includes basic cellular mechanisms, such as division and spreading, together with an…
Microbial communities routinely have several alternative stable states observed for the same environmental parameters. Sudden and irreversible transitions between these states make external manipulation of these systems more complicated. To…
The growth of multicomponent structures in simulations and experiments often results in kinetically trapped, nonequilibrium objects. In such cases we have no general theoretical framework for predicting the outcome of the growth process.…
Bacteria build multicellular communities termed biofilms, which are often encased in a self-secreted extracellular matrix that gives the community mechanical strength and protection against harsh chemicals. How bacteria assemble distinct…
Bacterial colonies growing on surfaces are shaped by mechanical stresses transmitted through the community, governed by the balance between cell growth and steric and cell-substrate interactions. Using overdamped dynamics simulations of…
We study how changes in population size and fluctuating environmental conditions influence the establishment of seed banks in plants. Our model is a modification of the Wright-Fisher model with seed bank, introduced by Kaj, Krone and…
Dispersal is an important strategy that allows organisms to locate and exploit favorable habitats. The question arises: given competition in a spatially heterogeneous landscape, what is the optimal rate of dispersal? Continuous population…
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predicting, understanding and…
Bacterial colonies are abundant on living and nonliving surfaces and are known to mediate a broad range of processes in ecology, medicine, and industry. Although extensively researched, from single cells to demographic scales, a…
Bacteria such as Escherichia coli (E. coli) exhibit biased motion if kept in a spatially non-uniform chemical environment. Here, we bring out unique time-dependent characteristics of bacterial chemotaxis, in response to a diffusing spatial…