Article

Lattice gas cellular automation model for rippling and aggregation in myxobacteria

Department of Mathematics, Interdisciplinary Center for the Study of Biocomplexity, University of Notre Dame, Notre Dame, IN 46556-5670, USA
Physica D Nonlinear Phenomena (Impact Factor: 1.83). 05/2004; DOI: 10.1016/j.physd.2003.11.012

ABSTRACT A lattice gas cellular automation (LGCA) model is used to simulate rippling and aggregation in myxobacteria. An efficient way of representing cells of different cell size, shape and orientation is presented that may be easily extended to model later stages of fruiting body formation. This LGCA model is designed to investigate whether a refractory period, a minimum response time, a maximum oscillation period and non-linear dependence of reversals of cells on C-factor are necessary assumptions for rippling. It is shown that a refractory period of 2–3 min, a minimum response time of up to 1 min and no maximum oscillation period best reproduce rippling in the experiments of Myxococcus xanthus. Non-linear dependence of reversals on C-factor is critical at high cell density. Quantitative simulations demonstrate that the increase in wavelength of ripples when a culture is diluted with non-signaling cells can be explained entirely by the decreased density of C-signaling cells. This result further supports the hypothesis that levels of C-signaling quantitatively depend on and modulate cell density. Analysis of the interpenetrating high density waves shows the presence of a phase shift analogous to the phase shift of interpenetrating solitons. Finally, a model for swarming, aggregation and early fruiting body formation is presented.

Download full-text

Full-text

Available from: Mark Alber, Jun 28, 2015
0 Followers
 · 
105 Views
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The study of how cells interact to produce tissue development, homeostasis, or diseases was, until recently, almost purely experimental. Now, multi-cell computer simulation methods, ranging from relatively simple cellular automata to complex immersed-boundary and finite-element mechanistic models, allow in silico study of multi-cell phenomena at the tissue scale based on biologically observed cell behaviors and interactions such as movement, adhesion, growth, death, mitosis, secretion of chemicals, chemotaxis, etc. This tutorial introduces the lattice-based Glazier-Graner-Hogeweg (GGH) Monte Carlo multi-cell modeling and the open-source GGH-based CompuCell3D simulation environment that allows rapid and intuitive modeling and simulation of cellular and multi-cellular behaviors in the context of tissue formation and subsequent dynamics. We also present a walkthrough of four biological models and their associated simulations that demonstrate the capabilities of the GGH and CompuCell3D.
    Methods in cell biology 01/2012; 110:325-66. DOI:10.1016/B978-0-12-388403-9.00013-8 · 1.44 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: This paper reviews recent progress in modeling collective behaviors in myxobacteria using lattice gas cellular automata approach (LGCA). Myxobacteria are social bacteria that swarm, glide on surfaces and feed cooperatively. When starved, tens of thousands of cells change their movement pattern from outward spreading to inward concentration; they form aggregates that become fruiting bodies. Cells inside fruiting bodies differentiate into round, nonmotile, environmentally resistant spores. Traditionally, cell aggregation has been considered to imply chemotaxis, a long-range cell interaction. However, myxobacteria aggregation is the consequence of direct cell-contact interactions, not chemotaxis. In this paper, we review biological LGCA models based on local cell–cell contact signaling that have reproduced the rippling, streaming, aggregating and sporulation stages of the fruiting body formation in myxobacteria.
    Advances in Complex Systems 11/2011; 09(04). DOI:10.1142/S0219525906000860 · 0.79 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: A two-dimensional multiscale model is introduced for studying formation of a thrombus (clot) in a blood vessel. It involves components for modelling viscous, incompressible blood plasma; non-activated and activated platelets; blood cells; activating chemicals; fibrinogen; and vessel walls and their interactions. The macroscale dynamics of the blood flow is described by the continuum Navier-Stokes equations. The microscale interactions between the activated platelets, the platelets and fibrinogen and the platelets and vessel wall are described through an extended stochastic discrete cellular Potts model. The model is tested for robustness with respect to fluctuations of basic parameters. Simulation results demonstrate the development of an inhomogeneous internal structure of the thrombus, which is confirmed by the preliminary experimental data. We also make predictions about different stages in thrombus development, which can be tested experimentally and suggest specific experiments. Lastly, we demonstrate that the dependence of the thrombus size on the blood flow rate in simulations is close to the one observed experimentally.
    Journal of The Royal Society Interface 08/2008; 5(24):705-22. DOI:10.1098/rsif.2007.1202 · 3.86 Impact Factor