Non-equilibrium physics of driven living matter

Chatterjee, Purba

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https://hdl.handle.net/2142/112945 Copy

Description

Title

Non-equilibrium physics of driven living matter

Author(s)

Chatterjee, Purba

Issue Date

2021-05-13

Director of Research (if dissertation) or Advisor (if thesis)

Goldenfeld, Nigel D

Doctoral Committee Chair(s)

Dahmen, Karin A

Committee Member(s)

• Kim, Sangjin
• Hughes, Taylor L

Department of Study

Physics

Discipline

Physics

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

• active matter
• self-propelled particles
• driven systems
• phase transition
• intrinsic stochasticity
• gene regulation
• DNA supercoiling

Abstract

In this dissertation, I explore how complex macroscopic collective phases emerge from stochastic interactions of the components of a biological system. In addition, I examine the conditions for non-equilibrium transitions from one stable phase to another. This dissertation is divided into two parts. Part I concerns systems broadly classified as active matter. I focus on three specific examples of emergent collective phases in active systems: flocking, chemotactic aggregation, and emergent elasticity. 1. Flocking:- I study the transition to long-range orientational order in polar active systems with a simple agent-based model for flocking, as well as its derived stochastic hydrodynamics. Through exact Gillespie simulations and analytical calculations, I show that binary interactions are insufficient to generate polar order, in agreement with experimental studies on actomyosin assays. However, noisy three-body interactions are both necessary and sufficient to capture the complete phenomenology of the flocking transition at high densities. I further show that imposition of skewed noise statistics can generate artifactual polar order with just two-body interactions. Moreover, the intrinsic stochasticity of microscopic interactions predicts a new phase at low densities mediated by just two-body interactions. This phase, characterized by transient local order, has been identified experimentally in fish schools. 2. Chemotactic aggregation:- I develop a field-theoretic description for active systems, based on a density functional description of crystalline materials modified to capture orientational ordering. I enumerate the many advantages offered by this framework in studying collective phases in active systems, with particle resolution, but on diffusive timescales. Modifying it to describe run and tumble chemotaxis, I show that this model can capture particle aggregation in an externally imposed constant attractant field, as observed for phototactic or thermotactic agents. I also show that this model captures particle aggregation through self-chemotaxis, an important mechanism that aids quorum dependent cellular interactions. 3. Emergent elasticity:- I demonstrate that agent-based models, with simple rules governing the reaction of individual agents to controlled perturbations, can capture experimentally-observed emergent elastic responses in biological systems. I also motivate a formal elastic theory for active systems based on a density functional description of crystalline materials, and discuss the potential as well as the challenges of this formalism. Part II concerns transcription, the process by which molecular machines called RNA polymerases (RNAPs), synthesize messenger RNA (mRNA) from the genome. I study the purely mechanical regulation of collective modes of RNAP dynamics through transcription-induced DNA supercoiling. I formulate a continuum deterministic model for the translocation of RNAPs on a typical gene, where the speed of an RNAP is coupled to the local DNA supercoiling as well as the density of RNAPs on the gene. Moreover, I propose that transcription factors can act as physical barriers to the diffusion of DNA supercoils. I show that unlike existing theories, this model successfully recapitulates the recent experimental observation that DNA supercoiling drives a transition from cooperative to antagonistic RNAP dynamics when RNAP loading is interrupted. The novel hypotheses that form the basis of this model have important implications for transcription dynamics in the genomic context, where genes may affect each other's transcription efficiencies from a long distance via supercoil diffusion. As such, this work presents an important stepping stone towards understanding the collective dynamics of the molecular machines involved in gene expression.

Graduation Semester

2021-08

Type of Resource

Thesis

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http://hdl.handle.net/2142/112945

Copyright and License Information

Copyright 2021 Purba Chatterjee

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