Petascale Simulations of Complex Biological Behavior in Fluctuating Environments

Ilias Tagkopoulos, University of California, Davis

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The goal of this research is to use large-scale simulations to investigate the evolution of intricate multi-scale biological systems, focusing on questions regarding the assembly of ecological structures, the emergence of complex traits and the impact of biological phenomena regarding the speed and direction of evolution. The computational work aims to provide valuable insight into the evolution of complex systems and it will ultimately result in a large set of predictions, some of which can be validated experimentally. Specifically, this project will try to elucidate the:

• Evolution of Bacterial Ecology: How do unicellular organisms evolve and adapt in novel environments? How do symbiosis, synergy, host-parasite interactions, bio-film formation and speciation emerge and what environmental parameters (nutrients, rate of mutation, etc.) have a significant impact during the evolution and adaptation of ecological structures? What are the optimal strategies for survival in static and fluctuating environments? How do unicellular organisms internalize the correlation-structure of their environment and rewire their internal networks to facilitate such changes? What is the role of genetic and molecular information transfer processes (lateral gene transfer, quorum sensing, etc) during evolution?
• Evolution of Gene Regulatory and Biochemical Networks: How do evolutionary forces shape the topology, kinetics and organization of biological networks? How and through what mechanisms do robustness to mutations or noise, evolvability and modularity appear and when are these attributes advantageous in evolution? What are the dynamics and the interplay among these characteristics?