CompuCell3D-based Ph.D. and Master Theses

2014

• "Modeling Tissue Polarization and Symmetry Breaking in Development and Disease", Julio M. Belmonte, Ph.D. Indiana University, Department of Physics, December, 2014

• Simulation of electrochemical and stochastic systems using just in time compiled declarative languages, Andy Somogyi,Indiana University, Department of Physics, December, 2014

• MODELOS FORMALES PARA LA SIMULACIÓN DE LA EPIDERMIS HUMANA, Carlos Alfonso Castaneda Marroquin, Universidad Autonome de Madrid, Spain (Oct 1st 2014)

• High-throughput simulation studies of angiogenesis Margriet Palm, CWI, Amsterdam, Netherlands (Sept 30th 2014)

• Mathematical Modelling of Cancer Growth and Development: Adhesion, Stem Cells and Structure, John Watson Kelly, University of Dundee, Scotland, September 2014

• Modeling interactions between a tumor cell and its host epithelium, Eline Boghaert, Princeton University, (2014)

2014

• Advances in modelling of epithelial to mesenchymal transition – T. Abdulla, Ph.D Loughborough University (June, 2013)

• Modeling interactions between a tumor cell and its host epithelium – D.S. Laman Trip, Bachelor degree, Leiden University, Mathematical Institute (June, 2013)

• Integrative modelling of angiogenesis in the bovine corpus luteum – Sotiris Prokopiou, Ph.D. University of Nottingham, Centre for Mathematical Medicine and Biology, School of Mathematical Sciences (Feb, 2013)

• Modelagem e simulação de mobilidade celular – Eduarda D. Susin, Bacharel em Física, Universidade Federal do Rio Grande do Sul, Instituto de Física (2013)

2012

• Multi-Scale Cell-Based Computational Models of Vertabrate Segmentation and Somitogenesis Illuminate Coordination of Developmental Mechanisms Across Scales – Susan D. Hester. Ph.D. Indiana University, Department of Physics (April, 2012)

• Vascular Patterning and Its Application in Cancer and Choroidal Neovascularization – A. Shirinifard, Ph.D. Indiana University, Department of Physics (March, 2012)

2011

• Mathematical modelling of cancer cell invasion of tissue: discrete and continuum approaches to studying the central role of adhesion – Vivi Andasari, Ph.D. University of Dundee, Divison of Mathematics (2011)

• Essential operating principles of cellular morphogenesis – Jesse Aaron Engelberg, Ph.D. University of California, San Francisco with the University of California, Berkeley (2011)

• Emergent networks: A slime mold simulation – Niklas B. Semmler, Bachelor Opleiding Kunstmatige Intelligentie, University of Amsterdam, Faculty of Science (June, 2011)

2009

• Cell based 3 dimensional computational model for gastrulation in chick embryos – Willemijn Magda Elly Maria Spoor, Ph.D. Dundee University, College of Life Sciences (2009)

2007

• Cell positioning in the Drosophila pupal retina – David Ernfrid Larson, Ph.D. Washington University, Division of Biology and Biomedical Sciences (Dec, 2007)

• Dynamic spatio-temporal interaction of morphogens, forces and growth in embryonic morphogenesis – Ying Zhang, Ph.D. Indiana University, Department of Physics (2007)

• Tumour growth and response to ionizing radiation in a modified cellular Potts model – Daniel Lea, Master's Thesis, University of Surrey (2007)

• Empirical Evaluation of Design Patterns in Scientific Application – Kedar Aras, Master's Thesis, Univ. of Notre Dame, Dept. of Computer Science & Eng. (2005)

• BIOLOGO: A Domain-Specific Language For Morphogenesis – Trevor M. Cickovski, Master's Thesis, Dept. of Computer Science & Eng., Univ. of Notre Dame (2004)