We shall study the principles and the mechanisms employed by living organisms to sense, process information and adapt to the surrounding environmental conditions. Basics of information theory (entropies, information, Shannon's channel capacity, compression and rate distortion theory) will be introduced as needed during the lectures. Aspects and methods related to statistical physics will be presented throughout the course.
Physics of reception and biochemical signaling • Chemical kinetics and Gillespie algorithm • Chemical Langevin limit • Phenotypic diversity in populations, single cell and population averages • Fluctuation-dissipation relations
Overview of signal transduction pathways and mechanisms of cellular response • Biological examples: photoreceptors, olfactory receptors and two-component systems • In silico evolution and genomics
Cooperativity, allosteric transitions, induced fit, ultrasensitivity, proofreading • Biological examples: bacterial chemotaxis, early response of T-cell immune receptors
Adaptation in neuroscience and cellular responses • Biological examples: Vision, two-component systems and chemotaxis • Functions of adaptation
Principal and Independent Component Analysis • Statistical significance of PCA, relation to random matrices • Compressive sensing. Biological examples: Population genetics, odor discrimination in olfaction
Information flow, Exploration/exploitation, Bellman equation • Biological examples: Signaling and development, Foraging, Olfactory searches