2008, 5(2): 355-388. doi: 10.3934/mbe.2008.5.355

Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment

1. 

Biocomplexity Institute and Department of Physics, Indiana University, Swain Hall West, 727 East Third Street, Bloomington, IN 47405-7105, United States, United States, United States, United States

Received  April 2007 Revised  December 2007 Published  March 2008

The CompuCell3D modeling environment provides a convenient platform for biofilm simulations using the Glazier-Graner-Hogeweg (GGH) model, a cell-oriented framework designed to simulate growth and pattern formation due to biological cells' behaviors. We show how to develop such a simulation, based on the hybrid (continuum-discrete) model of Picioreanu, van Loosdrecht, and Heijnen (PLH), simulate the growth of a single-species bacterial biofilm, and study the roles of cell-cell and cell-field interactions in determining biofilm morphology. In our simulations, which generalize the PLH model by treating cells as spatially extended, deformable bodies, differential adhesion between cells, and their competition for a substrate (nutrient), suffice to produce a fingering instability that generates the finger shapes of biofilms. Our results agree with most features of the PLH model, although our inclu- sion of cell adhesion, which is difficult to implement using other modeling approaches, results in slightly different patterns. Our simulations thus pro- vide the groundwork for simulations of medically and industrially important multispecies biofilms.
Citation: Nikodem J. Poplawski, Abbas Shirinifard, Maciej Swat, James A. Glazier. Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment. Mathematical Biosciences & Engineering, 2008, 5 (2) : 355-388. doi: 10.3934/mbe.2008.5.355
[1]

Marco Scianna, Luigi Preziosi, Katarina Wolf. A Cellular Potts model simulating cell migration on and in matrix environments. Mathematical Biosciences & Engineering, 2013, 10 (1) : 235-261. doi: 10.3934/mbe.2013.10.235

[2]

Thomas Y. Hou, Zuoqiang Shi. Dynamic growth estimates of maximum vorticity for 3D incompressible Euler equations and the SQG model. Discrete & Continuous Dynamical Systems - A, 2012, 32 (5) : 1449-1463. doi: 10.3934/dcds.2012.32.1449

[3]

Eduardo Ibarguen-Mondragon, Lourdes Esteva, Leslie Chávez-Galán. A mathematical model for cellular immunology of tuberculosis. Mathematical Biosciences & Engineering, 2011, 8 (4) : 973-986. doi: 10.3934/mbe.2011.8.973

[4]

Xianhua Tang, Xingfu Zou. A 3/2 stability result for a regulated logistic growth model. Discrete & Continuous Dynamical Systems - B, 2002, 2 (2) : 265-278. doi: 10.3934/dcdsb.2002.2.265

[5]

Qi Wang, Jingyue Yang, Lu Zhang. Time-periodic and stable patterns of a two-competing-species Keller-Segel chemotaxis model: Effect of cellular growth. Discrete & Continuous Dynamical Systems - B, 2017, 22 (9) : 3547-3574. doi: 10.3934/dcdsb.2017179

[6]

Tomás Caraballo, Antonio M. Márquez-Durán, José Real. Pullback and forward attractors for a 3D LANS$-\alpha$ model with delay. Discrete & Continuous Dynamical Systems - A, 2006, 15 (2) : 559-578. doi: 10.3934/dcds.2006.15.559

[7]

Shijin Deng. Large time behavior for the IBVP of the 3-D Nishida's model. Networks & Heterogeneous Media, 2010, 5 (1) : 133-142. doi: 10.3934/nhm.2010.5.133

[8]

Ferdinando Auricchio, Elena Bonetti. A new "flexible" 3D macroscopic model for shape memory alloys. Discrete & Continuous Dynamical Systems - S, 2013, 6 (2) : 277-291. doi: 10.3934/dcdss.2013.6.277

[9]

Mostafa Adimy, Fabien Crauste, Laurent Pujo-Menjouet. On the stability of a nonlinear maturity structured model of cellular proliferation. Discrete & Continuous Dynamical Systems - A, 2005, 12 (3) : 501-522. doi: 10.3934/dcds.2005.12.501

[10]

Claude-Michel Brauner, Michael L. Frankel, Josephus Hulshof, Alessandra Lunardi, G. Sivashinsky. On the κ - θ model of cellular flames: Existence in the large and asymptotics. Discrete & Continuous Dynamical Systems - S, 2008, 1 (1) : 27-39. doi: 10.3934/dcdss.2008.1.27

[11]

R.A. Satnoianu, Philip K. Maini, F.S. Garduno, J.P. Armitage. Travelling waves in a nonlinear degenerate diffusion model for bacterial pattern formation. Discrete & Continuous Dynamical Systems - B, 2001, 1 (3) : 339-362. doi: 10.3934/dcdsb.2001.1.339

[12]

Thomas März, Andreas Weinmann. Model-based reconstruction for magnetic particle imaging in 2D and 3D. Inverse Problems & Imaging, 2016, 10 (4) : 1087-1110. doi: 10.3934/ipi.2016033

[13]

Erika T. Camacho, Christopher M. Kribs-Zaleta, Stephen Wirkus. The mathematical and theoretical biology institute - a model of mentorship through research. Mathematical Biosciences & Engineering, 2013, 10 (5&6) : 1351-1363. doi: 10.3934/mbe.2013.10.1351

[14]

Alexis B. Cook, Daniel R. Ziazadeh, Jianfeng Lu, Trachette L. Jackson. An integrated cellular and sub-cellular model of cancer chemotherapy and therapies that target cell survival. Mathematical Biosciences & Engineering, 2015, 12 (6) : 1219-1235. doi: 10.3934/mbe.2015.12.1219

[15]

Reiner Henseler, Michael Herrmann, Barbara Niethammer, Juan J. L. Velázquez. A kinetic model for grain growth. Kinetic & Related Models, 2008, 1 (4) : 591-617. doi: 10.3934/krm.2008.1.591

[16]

Elena Izquierdo-Kulich, José Manuel Nieto-Villar. Mesoscopic model for tumor growth. Mathematical Biosciences & Engineering, 2007, 4 (4) : 687-698. doi: 10.3934/mbe.2007.4.687

[17]

Hiroshi Matano, Yoichiro Mori. Global existence and uniqueness of a three-dimensional model of cellular electrophysiology. Discrete & Continuous Dynamical Systems - A, 2011, 29 (4) : 1573-1636. doi: 10.3934/dcds.2011.29.1573

[18]

Xinxin Tan, Shujuan Li, Sisi Liu, Zhiwei Zhao, Lisa Huang, Jiatai Gang. Dynamic simulation of a SEIQR-V epidemic model based on cellular automata. Numerical Algebra, Control & Optimization, 2015, 5 (4) : 327-337. doi: 10.3934/naco.2015.5.327

[19]

Xiaojing Xu, Zhuan Ye. Note on global regularity of 3D generalized magnetohydrodynamic-$\alpha$ model with zero diffusivity. Communications on Pure & Applied Analysis, 2015, 14 (2) : 585-595. doi: 10.3934/cpaa.2015.14.585

[20]

Corrado Lattanzio, Pierangelo Marcati. The relaxation to the drift-diffusion system for the 3-$D$ isentropic Euler-Poisson model for semiconductors. Discrete & Continuous Dynamical Systems - A, 1999, 5 (2) : 449-455. doi: 10.3934/dcds.1999.5.449

2016 Impact Factor: 1.035

Metrics

  • PDF downloads (0)
  • HTML views (0)
  • Cited by (0)

[Back to Top]