Phase-Field Modeling of Interactive Biological Networks: From Zombie Ants to Slime Molds
Restricted (Penn State Only)
- Author:
- Ghanbari, Farshad
- Graduate Program:
- Engineering Science and Mechanics (PHD)
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- January 06, 2023
- Committee Members:
- Christian Peco, Chair & Dissertation Advisor
Francesco Costanzo, Major Field Member
John Pecchia, Outside Field Member
Albert Segall, Program Head/Chair
Pinlei Chen, Outside Unit Member
Reuben Kraft, Outside Field Member - Keywords:
- Phase-field
Finite elements
Adaptive biological netwroks
Mathematical modeling
Physarum polycephalum
Ophiocordyceps unilateralis - Abstract:
- Many problems in science and engineering involve moving boundaries. Some well-known examples include fluid-structure interaction, dendritic solidification, and crack propagation. Numerical treatment of such problems requires solving partial differential equations (PDEs) on moving domains with boundary conditions that hold on unknown and moving interfaces. Phase-field modeling has gained popularity within the computational mechanics community as a powerful tool to address the difficulties associated with solving interface problems by reformulating the moving boundary problem as PDEs on a known and fixed computational domain. In recent years, the phase-field method has been used to model complex problems in biology, such as avascular and vascular tumor growth, embryonic development, and interactive biological networks. These networks, in different forms and scales, are ubiquitous in nature. Well-known examples of biological networks include vertebrate cardiovascular and respiratory systems, social insect nests, fungi mycelial networks, and the true slime mold Physarum polycephalum networks. Among these examples, living organisms that forage their surroundings for food, such as fungi and slime molds, exhibit sophisticated interplay between their networks and their environment. The fungi mycelial networks, when viewed globally, forage their environment, find nutrient sources, and efficiently transport the nutrients to other parts of the mycelium, creating a multi-source multi-sink transport network. Perhaps the most well-known organism that utilizes a complex, highly adaptive, and optimized network morphology to interact with its surroundings is the true slime mold P. polycephalum. In this work, we develop a high-fidelity computational multiphysics multispecies framework based on the phase-field method to explain the mechanics of various biological systems, including the parasitic fungus Ophiocordyceps unilateralis and the slime mold P. polycephalum. We then validate the model by providing extensive two and three-dimensional examples and comparing the results with experiments. These comparisons reveal that the simulations closely resemble the behavior of real organisms, proving the proposed model to be an excellent tool for studying interactive biological networks.