A graduate program in Quantitative Biology

Last updated: July 14, 2011 at 3:49 p.m.


The quantitative biology specialization is available only to students enrolled and working toward the PhD degree in one of the seven participating graduate programs: biochemistry, biophysics and structural biology, chemistry, computer science, molecular and cell biology, neuroscience, and physics. Individuals who want to obtain a PhD degree with a specialization in quantitative biology should apply to one of the participating PhD programs as described in the relevant section of this Bulletin. Enrolled PhD students who want to obtain the quantitative biology specialization should contact their PhD program’s graduate program chair or quantitative biology liaison for further information. Students wishing to obtain the specialization are advised also to contact one of the quantitative biology co-chairs for information about participating in the noncurricular educational activities of the quantitative biology program.

Faculty Advisory Committee

Jeff Gelles, Co-Chair

Jané Kondev, Co-Chair, Liaison to Physics PhD Program

Irving Epstein, Liaison to Chemistry PhD Program

Bruce Goode, Liaison to Molecular and Cell Biology PhD Program

Dorothee Kern, Liaison to Biophysics and Structural Biology PhD Program

Eve Marder, Liaison to Neuroscience PhD Program

Christopher Miller, Liaison to Biochemistry PhD Program

Requirements for the Specialization to the Degree of Doctor of Philosophy

Students must complete all requirements for the degree of Doctor of Philosophy in the program in which they are enrolled. In addition, students must successfully complete three of the following four courses: QBIO 120b, BCHM 102a, PHYS 105a, and an approved computational methods course. Other courses may be substituted only with the written approval of the co-chair. The approved computational methods courses are QBIO 110a, COSI 178a, NBIO 136b and BIOL 135b. No more than one of the computational methods courses may be counted toward the three-course quantitative biology specialization requirement.

Courses of Instruction

(100-199) For Both Undergraduate and Graduate Students

QBIO 110a Numerical Modeling of Biological Systems
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Prerequisite: MATH 10a and b or equivalent.
Modern scientific computation applied to problems in molecular and cell biology. Covers techniques such as numerical integration of differential equations, molecular dynamics and Monte Carlo simulations. Applications range from enzymes and molecular motors to cells. Usually offered every second year.

QBIO 120b Quantitative Biology Instrumentation Laboratory
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Focuses on optical and other instruments commonly used in biomedical laboratories to make quantitative measurements in vivo and in vitro. Students disassemble and reconfigure modular instruments in laboratory exercises that critically evaluate instrument reliability and usability and investigate the origins of noise and systematic error in measurements. Usually offered every year.
Mr. Gelles

Cross-Listed Quantitative Biology

BCHM 102a Quantitative Approaches to Biochemical Systems
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Prerequisite: BCHM 100a or equivalent.
Introduces quantitative approaches to analyzing macromolecular structure and function. Emphasizes the use of basic thermodynamics and single-molecule and ensemble kinetics to elucidate biochemical reaction mechanisms. Also discusses the physical bases of spectroscopic and diffraction methods commonly used in the study of proteins and nucleic acids. Usually offered every year.
Mr. Gelles

BCHM 104b Physical Chemistry of Macromolecules II
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Prerequisites: BCHM 104a, CHEM 141a, PHYS 40a or equivalent; and BCHM 100a or equivalent.
Illustrates the basic principles on which biological macromolecules are constructed and by which they function. Describes overall structures of proteins, nucleic acids, and membranes in terms of the underlying molecular forces: electrostatics, hydrophobic interactions, and H-bonding. The energetics of macromolecular folding and of the linkage between ligand binding and conformational changes will also be discussed. Usually offered every year.
Mr. Theobald

BIOL 135b The Principles of Biological Modeling
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Prerequisite: MATH 10a or 10b.
With examples from neuroscience, cell biology, ecology, evolution, and physiology, dynamical concepts of significance throughout the biological world are discussed. Simple computational and mathematical models are used to demonstrate important roles of the exponential function, feedback, stability, oscillations, and randomness. Usually offered every second year.
Mr. Miller

CHEM 147b Advanced Mass Spectrometry Laboratory
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This is an experiential learning course. Prerequisites: A satisfactory grade (C- or better) in CHEM 18b or equivalent and CHEM 25a or equivalent, or permission of the instructor. Organic chemistry is also recommended.
Explores the fundamentals and historical significance of mass spectrometry. Students are trained to perform multidimensional liquid chromatography, and operate four different types of mass spectrometers, including MALDI-TOF MS, ESI-IonTrap MS, GC-MS, and ESI/MALDI-Fourier transform MS and gain practical experience in the following mass spectrometry applications: 1) organic and inorganic structure and reaction mechanism elucidation, 2) biological applications, including proteomics, imaging mass spectrometry, and forensics, and 3) environmental/green chemistry. Students will be briefly exposed to the next generation of mass spectrometry applications, including quantum computation and fusion research. In the last third of the course, students are given free reign to design an independent project based upon personal or thesis research interests. One hour lecture and one afternoon of laboratory per week. Usually offered every second year.
Mr. Pochapsky

COSI 178a Computational Molecular Biology
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Open to advanced undergraduate students and graduate students.
Information and computing technologies are becoming indispensable to modern biological research due to significant advances of high-throughput experimental technologies in recent years. This course presents an overview of the systemic development and application of computing systems and computational algorithms/techniques to the analysis of biological data, such as sequences, gene expression, protein expression, and biological networks. Hands-on training will be provided. Usually offered every other year.
Mr. Hong

NBIO 136b Computational Neuroscience
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Prerequisite: MATH 10a or PHYS 10a or approved equivalents.
An introduction to concepts and methods in computer modeling of neural systems. Topics include single and multicompartmental models of neurons, information representation and processing by populations of neurons, synaptic plasticity and models of learning, working memory, decision making and neuroeconomics. Usually offered every second year.
Mr. Miller

PHYS 105a Biological Physics
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Physical forces in living matter are studied from the perspective offered by statistical mechanics, elasticity theory, and fluid dynamics. Quantitative models for biological structure and function are developed and used to discuss recent experiments in single-molecule biology. Usually offered every second year.
Mr. Hagan