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8.592

Statistical Physics in Biology

3-0-9 units · Graduate

A survey of problems at the interface of statistical physics and modern biology: bioinformatic methods for extracting information content of DNA; gene finding, sequence comparison, phylogenetic trees. Physical interactions responsible for structure of biopolymers; DNA double helix, secondary structure of RNA, elements of protein folding. Considerations of force, motion, and packaging; protein motors, membranes. Collective behavior of biological elements; cellular networks, neural networks, and evolution.

Spring 2011

Topics

  • Introduction; Master equation
  • Elements of population genetics
  • Evolving populations (forward Kolmogorov)
  • Population genetics (fitness, selection, …)
  • Fixation (backward Kolmogorov)
  • Introduction to sequence alignment
  • Algorithms for sequence alignment
  • Significance of alignments (extreme value distributions)
  • Ionic interactions
  • Polymer theory 1, entropy elasticity, collapse
  • Polymer theory 2, collapse, Random energy model
  • Protein folding I: elements of structure and forces
  • Protein folding II: evolved (designed) foldable proteins
  • Protein folding III: kinetics
  • Protein folding IV:: kinetics
  • DNA (melting)
  • RNA (secondary structure)
  • Protein-DNA interactions I: specific and non-specific binding
  • Protein-DNA interactions II: sequence-dependence & kinetics
  • Microtubules
  • Molecular motors & cell motility
  • Introduction to networks
  • Dynamics on networks 1
  • Dynamics on networks 2
  • Packing of DNA inside cells
  • Cooperativity: hemoglobin and transcription factors

Readings

  • The presentation of material does not follow a specific textbook for this course. The following books are recommended references.
    Listed reading
  • Alberts, Bruce, et al. Molecular Biology of the Cell . 3rd ed. Garland Science, 1994. ISBN: 9780815316190 (hardcover), 9780815316206 (paperback). It is a standard reference to modern biology.
    Listed reading
  • Durbin, Richard, et al. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids . Cambridge University Press, 1998. ISBN: 9780521620413 (hardcover), 9780521629713 (paperback). It describes some of the standard computational methods used in bioinformatics.
    Listed reading
  • Frank-Kamenetskii, Maxim D. Unraveling DNA: The Most Important Molecule of Life . Translated by Lev Liapin. Basic Books, 1997. ISBN: 9780201155846. It presents several relevant topics in a way that should appeal to physical scientists.
    Listed reading
  • Watson, James D., et al. Molecular Biology of the Gene. 5th ed. Cold Spring Harbor Laboratory Press, 2003. ISBN: 9780805346350. It is another standard reference to modern biology.
    Listed reading
  • Nelson, Philip. Biological Physics: Energy, Information, Life . W. H. Freeman, 2003. ISBN: 9780716743729. It is a new textbook by a statistical physicist.
    Listed reading
  • Phillips, Rob, Jane Kondev, et al. Physical Biology of the Cell . Garland Science, 2008. ISBN: 9780815341635.
    Listed reading
  • Howard, Jonathan. Mechanics of Motor Proteins and the Cytoskeleton . Sinauer Associates, 2001. ISBN: 9780878933341.
    Listed reading
  • Finkelstein, Alexei V., and Oleg B. Ptitsyn. Protein Physics: A Course of Lectures. Academic Press, 2002. ISBN: 9780123908797.
    Listed reading
  • Kimball’s Online Biology Textbook ↗
    Listed reading

Prerequisites & course information

Same subject as HST.452[J] Prereq: 8.333 or permission of instructor Acad Year 2027-2028: Not offered Acad Year 2028-2029: G (Fall) 3-0-9 units

Sources