BI529
Biomolecules: Molecular Driving Forces
Tu Th 1:30--3:30 in Higgins 275.
Office hours: To be announced.


Course description | Text | Grading policy | Academic Integrity Policy | Homework | Class Notes | Demos | Tests

BI529 Biomolecules: Molecular Driving Forces
Course Description

This is a course on statistical thermodynamics and its applications in biology and chemistry. Following the excellent book, Molecular Driving Forces of Dill and Bromberg, the course includes a self-contained treatment of mathematics beyond single variable calculus and elementary probability theory. What is the free energy of an ensemble of RNA molecules? Why is protein folding cooperative? What is the critical point in a phase transition? How does Langmuir adsorption explain the saturation effect one sees in gene expression microarrays? These are the types of questions that will be addressed in this course.

The basic notions of entropy, enthalpy, free energy, etc. are fundamental to a mathematically precise understanding of molecular folding events. For instance, one of the research problems facing synthetic biology, a rapidly emerging discipline with enormous transformative potential, is to develop sensors for single molecules, for instance by use of RNA conformational switches. The design of such molecules depends on computations of the Boltzmann partition function, energy of hybridization, etc., all of primary focus of our lab. Thus, apart from following this excellent text of Dill and Bromberg, we plan to illustrate some of the basic principles by applying thermodynamics to the formation of RNA structures, kinetics of folding, etc.

"There is now an enormous amount of information on the events that take place in living systems at the molecular level. However, much of this information is qualitative and descriptive, even when the components involved are known and the structures of many of them (proteins and nucleic acids) have been determined. Many ingenious experiments have been done to establish which phenomena take place, but most of them do not address the question of why things happen the way they do. This is where the physical sciences, including thermodynamics, can make an essential contribution to biology." (Themis Lazaridis and Martin Karplus, page 3, "Microscopic basis of macromolecular thermodynamics", Thermodynamics in Biology, ed Enrico di Cera, Oxford University Press (2000))

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Reading

Required Text
  1. Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience Authors: Ken Dill, Sarina Bromberg. Paperback, Second edition, ISBN-10: 0815344309, ISBN-13: 978-0815344308, Publication Date: December 3, 2010.

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Grading Policy

To be explained in class.

Academic Integrity Policy

Boston College values the academic integrity of its students and faculty. It is your responsibility to familiarize yourself with the university’s policy on academic integrity: here. If you have any questions, always consult your professor.

If you are stuck and need ideas for your homework, then please come to me -- that is the purpose of office hours.

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