Table of Contents

Preface : why the physical microbe?.
1. Introduction.
1.1. Diversity.
1.2. Size.
1.3. Energy.
1.4. Food.
1.5. Diffusion versus size 2. Growth.
2.1. Exponential growth.
2.2. Stationary phase.
2.3. Lag phase and decline.
2.4. Balanced growth.
2.5. Partitioning of resources.
2.6. Individual cells in balanced growth 3. Gene regulatory networks.
3.1. Transcription and translation.
3.2. Representation of networks and pathways.
3.3. Gene regulation basics.
3.4. Deterministic models for gene regulation 4. Stochastic gene expression.
4.1. Variability at low copy number.
4.2. Modeling stochastic expression.
4.3. Bursts of gene expression.
4.4. Protein distributions with both transcription and translation.
4.5. Intrinsic and extrinsic noise.
4.6. Noise reduction and stability through feedback 5. Phenotypic switching.
5.1. Two types of persisters.
5.2. Toxin-antitoxin systems and HipBA.
5.3. Bet-hedging by phenotypic switching 6. Communication.
6.1. Chemical communication.
6.2. Pheromone triggered transitions of nonlinear systems.
6.3. Electrical communication 7. Bacillus subtilis competence and sporulation : the final exam.
7.1. Competence decision by noisy autofeedback.
7.2. Phosphorelay sensor for sporulation.
7.3. A mutually repressing circuit inhibits competence.
7.4. Input from intercellular communication. Physical biology is a fusion of biology and physics. This book narrows down the scope of physical biology by focusing on the microbial cell; exploring the physical phenomena of noise, feedback, and variability that arise in the cellular information-processing circuits used by bacteria. It looks at the microbe from a physics perspective, asking how the cell optimizes its function to live within the constraints of physics. It introduces a physical and information-based (as opposed to microbiological) perspective on communication and signalling between microbes.