A Parallel Implementation of the Cellular Potts Model for Simulation of Cell-Based (2009)
Nan Chen, James A. Glazier, Jesús A. Izaguirre
The Cellular Potts Model (CPM) has been used in a wide variety of biological simulations. However, most current CPM implementations use a sequential modified Metropolis algorithm which restricts the...
Trevor Cickovski, Chengbang Huang, Rajiv Chaturvedi, Tilmann Glimm, Mark Alber, ...
2004 DRAFT IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2 We present COMPUCELL3D, a software framework for three-dimensional simulation of morphogen-esis in different organisms....
Experimental growth law for bubbles in a "wet" 3D liquid foam (2007)
Lambert, Jérôme, Mokso, Rajmund, Cantat, Isabelle, Cloetens, Peter, Delannay, Renaud, Glazier, James A., ...
We used X-ray tomography to characterize the geometry of all bubbles in a liquid foam of average liquid fraction $\phi_l\approx 17 %$ and to follow their evolution, measuring the normalized growth...
Trevor Cickovski, Kedar Aras, Maciej Swat, M. H. Merks, Tilmann Glimm, H. George E, ...
Scientific applications are typically developed using procedural languages such as C or Fortran to gain performance, but often at the cost of reduced flexibility. As software complexity increases,...
Poplawski, Nikodem J., Swat, Maciej, Gens, J. Scott, Glazier, James A.
A central question in developmental biology is how cells interact to organize into tissues? In this paper, we study the role of mesenchyme-ectoderm interaction in the growing chick limb bud using...
Viscous instabilities in flowing foams: A Cellular Potts Model approach (2005)
Sanyal, Soma, Glazier, James A.
The Cellular Potts Model (CPM) succesfully simulates drainage and shear in foams. Here we use the CPM to investigate instabilities due to the flow of a single large bubble in a dry, monodisperse...
Contact-inhibited chemotaxis in de novo and sprouting blood-vessel growth (2005)
Merks, Roeland M. H., Perryn, Erica D., Shirinifard, Abbas, Glazier, James A.
Blood vessels form either when dispersed endothelial cells (the cells lining the inner walls of fully-formed blood vessels) organize into a vessel network (vasculogenesis), or by sprouting or...
Dan, Debasis, Mueller, Chris, Chen, Kun, Glazier, James A.
The Cellular Potts Model (CPM) is a robust, cell-level methodology for simulation of biological tissues and morphogenesis. Both tissue physiology and morphogenesis depend on diffusion of chemical...
A framework for three-dimensional simulation of morphogenesis (2005)
Trevor M. Cickovski, Chengbang Huang, Rajiv Chaturvedi, Tilmann Glimm, H. George, E. Hentschel, ...
Abstract—We present COMPUCELL3D, a software framework for three-dimensional simulation of morphogenesis in different organisms. COMPUCELL3D employs biologically relevant models for cell clustering,...
Vasconcelos, Igor F., Cantat, Isabelle, Glazier, James A.
We discuss a method to reconstruct an approximate two-dimensional foam structure from an incomplete image using the extended Potts mode with a pinned lattice we introduced in a previous paper. The...
A texture tensor to quantify deformations (2003)
Aubouy, Miguel, Jiang, Yi, Glazier, James A., Graner, François
Under mechanical deformation, most materials exhibit both elastic and fluid (or plastic) responses. No existing formalism derived from microscopic principles encompasses both their fluid-like and...
A texture tensor to quantify deformations: the example of two-dimensional flowing foams (2003)
Asipauskas, Marius, Aubouy, Miguel, Glazier, James A., Graner, François, Jiang, Yi
In a continuum description of materials, the stress tensor field $\bar{% \bar{\sigma}}$ quantifies the internal forces the neighbouring regions exert on a region of the material. The classical theory...
On Cellular Automaton Approaches to Modeling Biological Cells (2002)
Mark S. Alber, Maria A. Kiskowski, James A. Glazier, Yi Jiang
We discuss two di#erent types of Cellular Automata (CA): lattice-gasbased cellular automata (LGCA) and the cellular Potts model (CPM), and describe their applications in biological modeling.
A Model of Convergent Extension in Animal Morphogenesis (1999)
In this paper we argue that the pattern of cell movements in the morphogenetic process known as convergent extension can be understood as a energy minimization process, provided the cell-cell...
Stochastic Simulation of Benign Avascular Tumour growth using the Potts Model. (1999)
Emma L. Stott, Nick F. Britton, James A. Glazier, Mark Zajac
We simulate the growth of a benign avascular tumour embedded in normal tissue, including cell sorting that occurs between tumour and normal cells, due to the variation of adhesion between different...
Foam Drainage: Extended Large-Q Potts Model Simulation (1996)
We study foam drainage using the large-Q Potts model extended to include gravity on a three dimensional lattice. Without adding liquid, homogeneously distributed liquid drains to the bottom of the...
Dynamical mechanisms for skeletal pattern formation in the vertebrate limb.
Hentschel, H. G. E., Glimm, Tilmann, Glazier, James A., Newman, Stuart A.
We describe a 'reactor-diffusion' mechanism for precartilage condensation based on recent experiments on chondrogenesis in the early vertebrate limb and additional hypotheses. Cellular...
Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth
Merks, Roeland M. H., Perryn, Erica D., Shirinifard, Abbas, Glazier, James A.
Blood vessels form either when dispersed endothelial cells (the cells lining the inner walls of fully formed blood vessels) organize into a vessel network (vasculogenesis), or by sprouting or...
3D Multi-Cell Simulation of Tumor Growth and Angiogenesis
Shirinifard, Abbas, Gens, J. Scott, Zaitlen, Benjamin L., Popławski, Nikodem J., Swat, Maciej, Glazier, James A.
We present a 3D multi-cell simulation of a generic simplification of vascular tumor growth which can be easily extended and adapted to describe more specific vascular tumor types and host tissues....