Program in Biophysics Graduate Student Handbook

Courses - Biophysics and Computational Biology Program

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401. Introduction to Biophysics
Review of membrane and cell biophysics designed to introduce the theoretical and mathematical bases of bioelectricity, photobiology and biomolecular motors. Prerequisite: One year each of college-level mathematics and physics; one year each of college level biology and chemistry recommended. 3 hours.

417. Modeling Neural Systems
Same as BIOE 417, MCB 417, and NEUR 427. Application of computer modeling and simulation techniques to the nervous system; Hodgkin-Huxley formalism, single neuron models, central pattern generators, large networks, lateral inhibition, Hopfield models, back-propagation, self-organization and development. Programming assignments and projects to be carried out in scheduled computer laboratory time. Prerequisite: MCB 401or 414 or BIOP 401; or consent of instructor. 4 hours.

419. Brain, Behavior & Information Processing
Same as MCB 419, BIOE 419 and NEUR 419. Exploration of the neural basis of animal behavior. Emphasis on the information processing problems that animals face in complex natural environments and how nervous systems have evolved to solve these problems. Introduction to the use of computer modeling and simulation techniques for exploring principles of nervous system design and function. Current literature in computational neurobiology and neuroethology will be incorporated in readings and class discussion. Prerequisite: CS 101; and PHYS 102 or PHYS 212; and MCB 252; or equivalent or consent of instructor. 3 hours.

420. Molecular Biophysics
Same as MCB 425. Examines structure and function of biological macromolecules and supramolecular assemblies; methods for three-dimensional structure determination. Specific topics include: diffraction methods, protein structure and the molecular basis of enzyme catalysis, antibody structure and function, virus structure and assembly; membrane proteins, microtubules and other supramolecular assemblies, nucleic acid structure, protein-nucleic acid interactions. Prerequisite: MCB 354; CHEM 440, or equivalent; or consent of instructor. 3 hours.

432. Photosynthesis
Same as CPSC 489, and IB 421. Comprehensive description of photosynthesis. Topics include: the photosynthetic membranes, light absorption, electron and proton transfer, photophosphorylation, water oxidation, RUBP carboxylase/oxygenase, photorespiration, whole plant photosynthesis, gas exchange and atmospheric interactions, and impacts of global environmental change. Prerequisite: IB 420, MCB 354, MCB 450, BIOP 401, or equivalent; or consent of instructor. 3 hours.

470. Computational Chemical Biology
Same as CHEM 470. Hands-on introduction to the simulation of biological molecules and bioinformatics. Topics included the principles of molecular modeling, molecular dynamics and monte carlo simulations, structure prediction in the context of structural and functional genomics, and the assembly of integrated biological systems. Course counts towards the CSE option. Prerequisite: One semester of undergraduate biology and organic chemistry and statistical thermodynamics or consent of instructor. Recommended: proficiency in Matlab and CS 101 or equivalent. 3 or 4 hours.

540. Topics in Biophysical Chem
Same as CHEM 576, and MCB 556. Topics of importance in research in biophysical chemistry are discussed with emphasis on physical background and current applications; topics may be chosen from among the following: NMR and ESR spectra of biological macromolecules; x-ray diffraction studies of macromolecules; kinetics and statistical mechanics of helix coil transitions; physical approaches to the refolding and assembly of multi-subunit proteins; fluorescence spectroscopic studies on macromolecules; and light scattering from macromolecules in solution. Prerequisite: CHEM 444 or equivalent, or CHEM 472. 4 hours.

550. Biomolecular Physics
Same as MCB 550, and PHYS 550. Physical concepts governing the structure and function of biological macromolecules; general properties, spatial structure, energy levels, dynamics and functions, and relation to other complex physical systems such as glasses; recent research in biomolecular physics; physical techniques and concepts from theoretical physics emphasized. Designed for students without appreciable background in biology and chemistry. Prerequisite: CHEM 104 or equivalent; PHYS 485 or PHYS 487 or equivalent; or consent of instructor. 4 hours.

586. Special Topics in Biophysics (Tutorials)
Advanced course/tutorials on topics of interest in biophysics, such as electrophysiology, radiation biology, bioenergetics, protein structure, or the physics of muscular contraction. Prerequisite: Consent of instructor. 1 to 4 hours.

586 N. Introduction to Neuromorphic Engineering
Hands on experience building neurons, synapses and simple neural networks from analog circuits. Prerequisite: Consent of instructor. 2 hours.

586 ZZ. Molecular Biophysics Literature Section
Concurrent enrollment in BIOP 420 is required. Graduate standing is required. All Biophysics graduate students enrolled in BIOP 420 are required to enroll in this section. 1 hour.

590. Individual Topics
For graduate students wishing to study individual problems or topics not assigned in other courses. Prerequisite: Consent of department. 2-10 hours.

The current topics covered in BIOP 590 are listed below, with the names of faculty members you should contact if you are interested. These topics can also be used for BIOP 586 (tutorial) topics and BIOP 599 (thesis research).

1. Bioelectricity--Jakobsson and Sligar.
2. Bioenergetics--Crofts, Dawson, Martinez, Rienstra, Sligar, and Wraight.
3. Cellular Biophysics--Belmont, Chemla, Clegg, Cox, Golding, Hergenrother, Kong, Timp and Wang.
4. Dynamics Of Macromolecules--Baranger, Clegg, Gennis, Grosman, Gruebele, Ha, Kelleher, Leckband, Nair, Oldfield, Rienstra, Z Schulten, Selvin, Silverman, Spies, and Tajkhorshid.
5. Fluorescence Spectroscopy--Baranger, Clegg, Gennis, Gruebele, Ha, Selvin, Silverman and Spies.
6. Kinetics--Baranger, Chemla, Clegg, Crofts, Gerlt, Golding, Grosman, Gruebele, Jakobsson, Kelleher, Price, K Schulten, Silverman, Sligar and Spies.
7. Computational Biophysics--Anastasio, Baranger, Golding, Hergenrother, Jakobsson, Kelleher, Martinez, Nair, Nelson, Oldfield, Olsen, Price, K Schulten, Z Schulten, Tajkhorshid and Zhong.
8. Membrane Biophysics--Clegg, Crofts, Gennis, Gillette, Grosman, Ha, Jakobsson, Kraft, Leckband, Oldfield, Rienstra, Selvin, Tajkhorshid, Timp, Wang and Wraight.
9. Molecular Biophysics--Baranger, Belmont, Chemla, Clegg, Crofts, Gerlt, Gruebele, Ha, Leckband, Martinez, Martinis, Nair, Oldfield, Olsen, Rienstra, K Schulten, Z Schulten, Silverman, Sligar, Tajkhorshid, Timp, Wang, Wraight, and Zhao.
10. Muscle Biophysics--Dawson and Selvin.
11. Photosynthesis--Crofts and Wraight.
12. Protein-Lipid Interactions--Clegg, Crofts, Gennis, Kong, Oldfield, Rienstra, Tajkhorshid and Wraight.
13. Radiation Biophysics and Oncology--Ducoff and Martinez.
14. Senescence--Ducoff and Zhong.
15. Vision--Anastasio, Cox and Martinez.
16. Macromolecular Structure--Belmont, Clegg, Crofts, Gerlt, Huang, Kelleher, Kong, Lu, Nair, Oldfield, Olsen, Rienstra, K Schulten, Selvin, Silverman, Sligar, and Tajkhorshid.
17. Cerebral Energy Metabolism--Dawson and Hergenrother.
18. Magnetic Resonance--Dawson and Rienstra.
19. Complex Systems--Anastasio, Cox, Feng, Golding, Gruebele, Nelson, Price, Rienstra, K Schulten, Z Schulten and Zhong.
20. Computational Neurobiology--Anastasio, Cox, Feng, Hergenrother, Nair, Nelson and Zhong.
21. Quantum Biology--Martinez and Timp.
22. Statistical Mechanics of Genomes--Olsen and Z Schulten.
23. History of Biophysical Research--Govindjee.
24. Systems Biology--Golding and Price.
25. Stochastic Gene Expression/Gene Regulation--Golding.
26. Information Processing--Golding.
27. Matrix Biophysics--Kong.

590B. Bioinformatics
Topics covered include: central dogma and introduction to macromolecular sequences; sequencing methods and physical mapping of genomes; genome data and databases; algorithms for gene finding; statistical methods; pattern recognition; local sequence homology and scoring (BLAST tools); phylogenetic analysis and molecular evolution; tree building methods; RNA structure methods; protein structure and analysis; protein sequence comparison and Dayhoff matrices; Gribskov-Eisenberg profiles; 3d-1d profiles and their construction; homology modeling and scoring of homology models; amphipaticity and hydrophobicity analysis and membrane structure; structure modeling with PDFs; hidden homology in proteins using Markov models and hidden homology from structural criteria. Meets for eight weeks in the spring semester. Prerequisite: Consent of instructor. 1 hour.

590C. Hands-On Course in Computational Biology
Meets for eight weeks in the fall semester. The course will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. The course will be based on case studies including the properties of membranes, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, signaling pathways, visual receptors, and photosynthesis. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers and steered molecular dynamics simulations. The course is designed for graduate students biophysics who seek to extend their research skills to include computational and theoretical expertise. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon where students will be able to set up and run simulations. Prerequisite: Consent of instructor. 1 hour.

590M. Biophysics of Membrane Proteins
Meets for eight weeks in the spring semester. Prerequisite: Consent of instructor. 1 hour.

590P. Photosynthesis: Challenges for the 21st Century
Concurrent enrollment in Bioph 432 is required. Graduate standing is required. Prerequisite: See Bioph 432. 1 unit.

595. Biophysics Seminars
Survey of literature in one area of biophysics, with special emphasis on student reports. Approved for both letter and S/U grading. May be repeated for a total of 4 hours. Prerequisite: Graduate standing in Biophysics and Computational Biology. 1 to 2 hours.

599. Thesis Research
Research may be conducted in any area under investigation in a faculty laboratory, subject to the approval of the faculty member concerned and the department in which the research is to be done. Approved for S/U grading only. 0 to 16 hours.