Biology presents an astounding diversity of discrete states or species that coexist with each
other over long time intervals. At the sub-cellular scale, molecular competition and positive
feedback maintain cells in specialized epigenetic states, allowing for embryonic development
of complex multicellular organisms. On larger length scales, stable yet dynamic ecosystems
emerge from competition between different species.
This general pattern calls for research with a focus on discrete states, including how they
sustain themselves and how they interact with each other. Statistical mechanics of complex
systems provides a framework for studying universality of collective and cooperative phenomena,
usually through repeated action of identical agents.
I explore the origin and sustainability of many different states, using model systems
from biology. The hypothesis is that competition is the main driver of both discreteness and
diversity, with randomness and cooperation playing auxiliary roles. The research will be guided
by agent based models of biologically relevant examples of competition and diversity:
• Epigenetics and Development,
• Engines of Diversity,
• Epidemics and Host Immunity.
These categories include computational aspects of gene regulation, sustainable self regulation
of ecosystems, mechanisms of speciation facilitated by competition and defense systems. The
latter also including the interplay between diseases and host immune systems.
Fields of interest
Epigenetics (positive feedback and recruitments, among nucleosomes and DNA methylations sites)
Development (Dynamics of formation of early embryo with 3 cell types. Pancreas development)
Phage biology (dynamics of phage lambda infection)
Phage-bacteria interactions (restriction modification systems, abortive infactions, CRISPR)
Plaque formation dynamics: (Spation temporal dynamics of phage-bacteria competition, colony level defence against phage)
Microbial ecology (apparent competition, collapses and reshufling in many species systems)
Toxin-antitoxin systems in bacteria (persister formation, its role in phage defence)
Translation dynamics in E.coli (how does the Shine-Delarne sequence govern protein yield)
Transcription dynamics in bacteria (transcription interference, burstiness, road blocks)
Ecology and diversity in food webs (competitive exclusion, replacement rules and stability in food-webs)
Spatio-temporal models of sessile species (Lichen model, non-hierarchical invasion networks)
Epidemics of infacterous diseases, and host immune systems (influenza, and how new replaces old)
Biological networks (hubs and followers in transcription networks, networks as assembly of tools)
Regulatory feedback systems: (SOS, Toxin-antitoxin-ppGpp, Fe uptake in E.coli, P53, NFkappaBeta, Nanog-Gata6-Oct4).
Social system dynamics (positive feedback, bubble dynamics, emergence of hierarchies in networks, emergent seggregation)
Growth and collapse (limits on resources, and growth fueled by resources by others collapse)
Complex systems and statistical mechanics (self-organization)