Physics of Molecular and Cellular Processes

Krastan B. Blagoev is a Program Director at the US National Science Foundation and has an academic position at Johns Hopkins University. Herbert Levine Hasselmann Professor of Bioengineering at Rice University. He is a pioneer in using theory to expand experimental findings and in the development of well-parameterized computational models that can be used to garner new insights into biomedical systems. A main research project in his group combines theoretical approaches with advanced laboratory experiments to understand directed cell motion in eukaryotic cells and to elucidate both signal transduction and cellular mechanics aspects of this critical process. Additional areas of research include calcium-based cell signaling (most recently at the neuronal synapse), the statistical mechanics of Darwinian evolution, and pattern formation in microorganism colonies. Levine is an elected member of the American Academy of Arts and Sciences, an elected member of the National Academy of Science, a fellow of the American Physical Society, past chair of the American Physical Society's Division of Biological Physics. He is the author of more than 225 peer-reviewed publications. His research has been featured in the New York Times, Scientific American, the Today Show and many other popular science forums. Levine is a co-director of CTBP and consultant for JASON, which is an independent group of scientists that advises the U.S. government on matters of science and technology. Also, Dr. Levine is the coordinator of an international network of graduate students conducting research into the Physics of Living Systems.

Part I. The non-equilibrium nature of living systems.- 1.1 Introduction.- 1.2 Equilibrium and non-equilibrium thermodynamics and statistical physics.- 1.3 Organization and evolution of life.- 1.4 The physics of biomolecules.- 1.5 The physics of proteins: The special role of water. Folding, unfolding and misfolding. Active sites, allostery. Molecular motors (e.g. flagellar motor) and the use of free energy. Protein-protein interactions and their role in cell signaling.- 1.6 Physics of DNA and RNA: Electrostatistics, folding, unfolding, topology, geometry, accessibility. Protein-DNA interactions and chromatin structure.- 1.7 Physics of metabolism: Energy production and charge transport. Network analysis. Bacterial growth laws. Mitochondrial structure and function.- 1.8 Physics of Cytoskeletal proteins. Polymerization kinetics and applications to actin and microtubules. Nucleation dynamics. Kinesin, Dynein and Myosin as non-equilibrium walkers.- 1.9 Physics of Viruses.- Part II. The Physics of the Cell.- 2.1 Physics of the cell membrane: real and model membranes, Helfrich free energy. Embedded protein, including surface receptors. Membrane fusion and fission, application to viral entry, endo- and exo-cytosis.- 2.2 Dynamics in the cell. Transport via passive diffusion versus active transport. Targeting to organelles via molecular signals. Scaffolds and compartments for chemical reaction control. The cytoskeletal network and its role in cell mechanics.- 2.3 Genetic networks. Transcriptional dynamics, examples from phage and bacteria. Control of translation, for example via small RNAs. Role of chromatin structure for eukaryotic systems.- 2.4 Signal transduction: Receptor subtypes (GPCR, Tyrosine kinase, ion channels) and kinetics. Phosphorelay in the Map Kinase pathway. Second messenger dynamics, including amplification in e.g. calcium signaling. Adaptation and chemotacis in bacteria.- Part III. The Physics of the Organism.- 3.1 Cell division - DNA replication. Bacteria cell size determination, contractile ring placement and dynamics; Eukaryotic cell division mitotic spindle, cell cycle checkpoints.- 3.2 DNA damage and repair, chromosome instability, damage checkpoints, telomere dynamics and chromosome instability.- 3.3 Cell motion types of bacterial motion: swimming versus gliding. Crawling of eukaryotic cells; adhesion complexes, active forces due to contraction and polymerization. Chemotaxis and durotaxis.- 3.4 Cellular decisions sporulation in Bacillus,Dictyostelium. Stem cells versus differentiated cells. Landscapes in non-equilibrium systems. The origins of multicellularity.