The Glazier-Graner-Hogeweg Model: Extensions, Future Directions, and Opportunities for Further Study

One of the reasons for the enormous success of the Glazier-Graner-HogewegGlazier-Graner-Hogeweg Model (GGH) model is that it is a framework for model building rather than a specific biological model. Thus new ideas constantly emerge for ways to extend it to describe new biological (and non-biological) phenomena. The GGH model automatically integrates extensions with the whole body of prior GGH work, a flexibility which makes it unusually simple and rewarding to work with. In this chapter we discuss some possible future directions to extend GGH modeling. We discuss off-lattice extensions to the GGH model, which can treat fluids and solids, new classes of model objects, approaches to increasing computational efficiency, parallelization, and new model-development platforms that will accelerate our ability to generate successful models. We also discuss a non-GGH, but GGH-inspired, model of plant development by Merks and collaborators, which uses the Hamiltonian and Monte-Carlo approaches of the GGH but solves them using Finite Element (FE) methods.

[1]  R. O. Erickson,et al.  Symplastic growth and symplasmic transport. , 1986, Plant physiology.

[2]  Roeland M. H. Merks,et al.  Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodeling. , 2006, Developmental biology.

[3]  Nan Chen,et al.  A Parallel Implementation of the Cellular Potts Model for Simulation of Cell-Based Morphogenesis , 2006, ACRI.

[4]  Hans Meinhardt,et al.  Models and Hypotheses , 1976 .

[5]  W. H. Weinberg,et al.  Theoretical foundations of dynamical Monte Carlo simulations , 1991 .

[6]  J. H. Priestley,et al.  STUDIES IN THE PHYSIOLOGY OF CAMBIAL ACTIVITY. II. THE CONCEPT OF SLIDING GROWTH , 1930 .

[7]  Nicholas J Savill,et al.  Control of epidermal stem cell clusters by Notch-mediated lateral induction. , 2003, Developmental biology.

[8]  Paulien Hogeweg,et al.  Computing an organism: on the interface between informatic and dynamic processes. , 2002, Bio Systems.

[9]  Roeland M. H. Merks,et al.  Dynamic mechanisms of blood vessel growth , 2006, Nonlinearity.

[10]  A. Argon,et al.  Brittle-to-ductile transitions in the fracture of silicon single crystals by dynamic crack arrest , 2001 .

[11]  N. Perrimon,et al.  The emergence of geometric order in proliferating metazoan epithelia , 2006, Nature.

[12]  J. Glazier,et al.  Model of convergent extension in animal morphogenesis. , 1999, Physical review letters.

[13]  P. Hogeweg,et al.  Evolving mechanisms of morphogenesis: on the interplay between differential adhesion and cell differentiation. , 2000, Journal of theoretical biology.

[14]  Gerson G. H. Cavalheiro,et al.  High Performance Simulations of the Cellular Potts Model , 2006, 20th International Symposium on High-Performance Computing in an Advanced Collaborative Environment (HPCS'06).

[15]  D. Gillespie A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions , 1976 .

[16]  A. Deutsch,et al.  A New Mechanism for Collective Migration in Myxococcus xanthus , 2007 .

[17]  A. B. Bortz,et al.  A new algorithm for Monte Carlo simulation of Ising spin systems , 1975 .

[18]  J. Lockhart An analysis of irreversible plant cell elongation. , 1965, Journal of theoretical biology.

[19]  Jesús A. Izaguirre,et al.  COMPUCELL, a multi-model framework for simulation of morphogenesis , 2004, Bioinform..

[20]  Tatsuzo Nagai,et al.  A dynamic cell model for the formation of epithelial tissues , 2001 .

[21]  J. Glazier,et al.  Solving the advection-diffusion equations in biological contexts using the cellular Potts model. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[22]  Jelena Pjesivac-Grbovic,et al.  A multiscale model for avascular tumor growth. , 2005, Biophysical journal.

[23]  Roeland M. H. Merks,et al.  A cell-centered approach to developmental biology , 2005 .

[24]  P. Hogeweg,et al.  Multilevel Selection in Models of Prebiotic Evolution: Compartments and Spatial Self-organization , 2003, Origins of life and evolution of the biosphere.

[25]  J. H. Priestley,et al.  STUDIES IN THE PHYSIOLOGY OF CAMBIAL ACTIVITY , 1930 .

[26]  Wouter-Jan Rappel,et al.  Self-organized Vortex State in Two-Dimensional Dictyostelium Dynamics , 1998, patt-sol/9811001.

[27]  Gerard T. Barkema,et al.  Monte Carlo Methods in Statistical Physics , 1999 .

[28]  Koo-Chul Lee,et al.  Rejection-free Monte Carlo technique , 1995 .

[29]  Andreas Deutsch,et al.  Rippling patterns in aggregates of myxobacteria arise from cell-cell collisions. , 2001, Physical review letters.

[30]  Jim Haseloff,et al.  A Computational Model of Cellular Morphogenesis in Plants , 2005, ECAL.