CompuCell3D-based Ph.D. and Master Theses

2025

• Multicellular Agent-Based Computational Modeling Approaches to Investigate Cell- and Tissue Scale Effectors of Collective Migration Within an In Vivo Context. Tien Comlekoglu, PhD, Biomedical Engineering - School of Engineering and Applied Science, University of Virginia; 2025.

• A Cellular Potts Model to describe tumor infiltration in confined in vivo tissues. Sofia Giordano, Masters Thesis, Politecnico di Torino, 2025.

• Clonal Dynamics in Barrett's Oesophagus and Oesophageal Adenocarcinoma. E Black. Ph.D. Thesis, 2025. doi.org/10.17863/CAM.115012

• A cellular model for the mechanistic simulation of biological response to radiation damage. OR García. Ph.D. Thesis, 2025 (spanish)

2024

• Modeling the Spatio -Temporal Effect of 2,3, 7,8 Tetrachlorodibenzo-P-Dioxin on Hepatic Gene Expression Marri, Daniel Kwabena. Michigan State University PhD Dissertation. ProQuest Dissertations & Theses,  2024. 

• Clonal Dynamics in Barrett’s Oesophagus and Oesophageal AdenocarcinomaEmily Black, PhD Thesis Emmanuel College University of Cambridge (2024). https://doi.org/10.17863/CAM.115012

• "Modelling Three Dimensional Morphology of Retinal Pigment Epithelium". Akinwale Famotire, Masters Thesis, Georgia State University, 2024. doi: https://doi.org/10.57709/37395530

• "A Multiscale Model To Study Atp-Induced Calcium Signaling In Larval Zebrafish Tailfin Wound Response". Mothieshwar Jayaraman Krishnan. Purdue University Graduate School. Masters Thesis. doi: 10.25394/PGS.26396806.v1

2023

• "CompuCell3D model of cell migration reproduces chemotaxis". Pedro Cenci Dal Castel. Masters Thesis, Instituto de Fısica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil, 2023.

• "Computational systems biology approaches to investigate cellular senescence" - Sharmilla Chandrasegaran, Ph.D. Newcastle University (September 2023)

• "Breaking Barriers in Multiscale Agent-Based Models: Effects of Cell Individuality on Viral Infection Treatment and A Path for Cross-Platform Validation" - Juliano Ferrari Gianlupi, Ph.D. Indiana University (August 2023)

2021

• "Multicellular Multiscale Spatial Modeling of The Immune Response to Pathogens And Cancer" - Josua Oscar Aponte-Serrano, Ph.D. Indiana University (December 2021)

• "Developing a multi scale cellular automata simulation model of a vascularised brain tumour environment to predict angiogenic potential of brain endothelial cells" - Elena Sophie Engstler, MSc in Neuroscience King's College London, University of London (September 2021) (and a poster)

• "Modelling of Cell Movements and Aggregations During Early Nephrogenesis" - Pauli Tikka, Ph.D. University of Heidelberg (April 2021)

2020

• "Modeling Cell Mediated Interactions in Epithelial Tissue Organization and Repair" Priyom Adhyapok, Ph.D. Indiana University, Department of Physics (August 2020)

2019

• "The Emergence of Biofilms: Computational and Experimental Studies". Sheraton Muniraj, V. PhD Thesis, University of Amsterdam (June 2019)

2018

• "Computational Modeling Of Metastatic Cancer Migration Through A Remodeling Extracellular Matrix" Yen T. Nguyen Master of Science Chemical Engineering Oklahoma State University Stillwater, Oklahoma (July 2018)

2016

• "Integrative Modeling of Microcirculatory Transport and Cell Responses in Liver and Retinal Homeostasis and Disease" - Xiao Fu, Ph.D. Indiana University, Department of Physics (May, 2017)

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, Ph.D. 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 (October, 2014)

• High-throughput simulation studies of angiogenesis – Margriet Palm, CWI, Amsterdam, Netherlands (September, 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)

2013

• 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 (February, 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)

2005

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

• Computational modeling of angiogenesis: from matrix invasion to lumen formation. -Sonja E.M. Boas, Ph.D. CWI and Leiden University (2005)

2004

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