Phase transitions in fluids and biological systems

In this thesis, I consider systems from two seemingly different fields: fluid dynamics and microbial ecology. In these systems, the unifying features are the existences of global non-equilibrium steady states. I consider generic and statistical models for transitions between these global states, and I relate the model results with experimental data. A theme of this thesis is that these rather simple, minimal models are able to capture a lot of functional detail about complex dynamical systems. In Part I, I consider the transition between laminar and turbulent flow. I find that quantitative and qualitative features of pipe flow experiments, the superexponential lifetime and the splitting of turbulent puffs, and the growth rate of turbulent slugs, can all be explained by a coarse-grained, phenomenological model in the directed percolation universality class. To relate this critical phenomena approach closer to the fluid dynamics, I consider the transition to turbulence in the Burgers equation, a simplified model for Navier-Stokes equations. Via a transformation to a model of directed polymers in a random medium, I find that the transition to Burgers turbulence may also be in the directed percolation universality class. This evidence implies that the turbulent-to-laminar transition is statistical in nature and does not depend on details of the Navier-Stokes equations describing the fluid flow. In Part II, I consider the disparate subject of microbial ecology where the complex interactions within microbial ecosystems produce observable patterns in microbe abundance, diversity and genotype. In order to be able to study these patterns, I develop a bioinformatics pipeline to multiply align and quickly cluster large microbial metagenomics datasets. I also develop a novel metric that quantifies the degree of interactions underlying the assembly of a microbial ecosystem, particularly the transition between neutral (random) and niche (deterministic) assembly. I apply this metric to 16S rRNA metagenomic studies of 6 vertebrate gastrointestinal microbiomes and find that they assembled through a highly non-neutral process. I then consider a phase transition that may occur in nutrient-poor environments such as ocean surface waters. In these systems, I find that the experimentally observed genome streamlining, specialization and opportunism may well be generic statistical phenomena.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Physics

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2013

Author dc:creator

• Sipos, Maksim

Contributors dc:contributor

• Goldenfeld, Nigel D.
• Oono, Yoshitsugu
• Weaver, Richard L.
• Chemla, Yann R.

• microbiome
• clustering
• transition to turbulence
• directed percolation
• directed polymers
• evolution
• ecology
• neutral theory
• niche theory
• Metagenomics

Statement dc:rights

• Copyright 2013 Maksim Sipos

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/44295

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/44295