Center for Biophysics and Quantitative Biology

Courses & Requirements

Program Requirements Chart

Requirement Time Allotted Comments
BIOP 401 (Intro to Biophysics) 1st semester 3 hours
Min of 32 hours of coursework end of 1st year Met by registering full-time fall, spring, summer. Must complete 32 hrs before allowed to register for BIOP 599 after passage of BQE.
Quantitative Biology OR Lab Course end of 3rd year If research is:
quantitative in nature, lab course required (BIOC 455, PHYS 598BP, PHYS 598OM, CHEM 483, PATH 521, ECE 460, CHEM 445, CHEM 570 or equivalent).

experimental in nature, quantitative course required (ANSC 542, MCB 571, BIOP 576, BIOP 586C, BIOE 598AGB, BIOE 598TL, BIOE 505, ANSC 449, MCB 432, CHBE 571, INFO 490, STAT 530, CHEM 492DS, CPSC 567, ChBE 584 or equivalent).
500-level Biophysics coursework end of 3rd year 2 courses from pre-approved list. The Director may approve other 500-level courses upon request if a syllabus is provided and main content of course is biophysical in nature.
400- & 500-level coursework prior to Prelim Min 2 courses required.
BIOP 581, 582, 583 (Lab Rotations) end of 1st semester 2 hours (3 rotations required)
BIOP 586 (Tutorials) end of 3rd year 1 hour (2 tutorials required)
BIOP 590 (Individual Research) spring semester 1st year until passage of BQE At least 1 semester required before taking BIOP 599
BIOP 595 A (Seminar) 1st and 2nd year 1 hour (4 hours required)
BIOP 595 B (Faculty Research Seminars) fall semester 1st year 1 hour
BIOP 599 (Thesis Research) after passage of BQE through graduation Graded DFR until graduation, then graded S or U. (32 hours max applied toward degree).
Qualifying Exam (BQE) before end of 2nd year - offered spring only Passage based on: written exam, oral exam, total academic record, student's objectives and motivation, research potential, acceptance into research group (additionally, International students must pass EPI).
Preliminary Exam end of 3rd year
If more than 5 years elapse before the final exam, a 2nd prelim must be passed before allowed to defend.		 20-30 minute oral exam to examine the validity of the research and test the student's fitness to carry out independent research. Does not require publishable data! 20-30 page proposal submitted to committee; 1-page project summary report to Biophysics office.
Final Exam not sooner than 6 months after Prelim, but before end of 5 years Public presentation and defense of thesis work. 50-60 minute presentation, then Question & Answer session.
Teaching 2nd or 3rd year Minimum of one semester. Preferably 50% time.
Ethics course 2nd year Minimum of one semester course on ethics in science. MCB 580 meets requirement; offered in fall.

English Proficiency Interview (EPI)
International students only

1st-2nd year
(3 attempts allowed)		 International students with less than 24 on iBT are required to pass EPI test before serving as a TA. Also required for passage of BQE.
Annual Review by faculty or Director annually Students receive Progress Report from BIOP office annually. If requested, students must provide 2-page synopsis of work completed/progress toward degree.


NOTES:

Tutorials may NOT be taken on the same topic as a lab rotation and cannot be taken with advisor!!

Tutorials = Meet with professor to determine subject to research. Write a 6-10 page paper on readings agreed upon by student and the professor.

Lab Rotations = Meet with professor weekly to determine research work and progress.


Biophysics Doctoral Degree Requirements

  1. General Requirements
    1. Tutorials and Lab Rotations
    2. Grades/Grade Point Average (GPA)
  2. Teaching
    1. TA Orientation
    2. English Proficiency Requirements
  3. Examinations
    1. Biophysics Qualifying Examination
    2. Preliminary Exam
    3. Final Exam
  4. Requirements for the Master of Science Degree
  5. Satisfactory Academic Progress
  6. Degree Conferral Procedure

Courses

401.  Introduction to Biophysics
Same as PHYS 475. 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.

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.

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.

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.

576.  Computational Chemical Biology
Same as CHEM 576.  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

581.  Lab Rotation #1
Laboratory research methods; familiarization of first-year graduate students with experimental methods used in research in Biophysics & Quantitative Biology.  Required of all first-year students majoring in Biophysics & Quantitative Biology.  Prerequisite:  First-year graduate status and consent of department; concurrent registration in BIOP 582 and BIOP 583. 2 hours.

582.  Lab Rotation #2
Laboratory research methods; familiarization of first-year graduate students with experimental methods used in research in Biophysics & Quantitative Biology.  Required of all first-year students majoring in Biophysics & Quantitative Biology.  Prerequisite:  First-year graduate status and consent of department; concurrent registration in BIOP 581 and BIOP 583.  2 hours.

583.  Lab Rotation #3
Laboratory research methods; familiarization of first-year graduate students with experimental methods used in research in Biophysics & Quantitative Biology.  Required of all first-year students majoring in Biophysics & Quantitative Biology.  Prerequisite:  First-year graduate status and consent of department; concurrent registration in BIOP 581 and BIOP 582. 2 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.

586C.  Hands-On Course in Computational Biology
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. 3 hours.

590. Individual Topics 

These topics can also be used for BIOP 586 (tutorial) topics and BIOP 599 (thesis research).

Bioph 590 Individual Topics.
Prerequisite: Consent of the Department.
2-10 hours.
For Independent Study Registration In This Course, Students Must Contact The Program Office, 318C Roger Adams Laboratory.

These topics can also be used for BIOP 586 (tutorial) topics and BIOP 599 (thesis research).

  1. Bioelectricity—Grosman, Jakobsson, Y Lu, and Sligar.
  2. Bioenergetics—Crofts, Hammes-Schiffer, Y Lu, and Sligar.
  3. Cellular Biophysics—Belmont, Chemla, Dar, Gruebele, Hergenrother, Jin, Kong, Kuhlman, Leckband, Y Lu, Oldfield, Schroeder, Z Schulten, and Zhang.
  4. Dynamics of Macromolecules—Aksimentiev, Belmont, Chemla, Gennis, Grosman, Gruebele, Hammes-Schiffer, Huang, Leckband, Y Lu, Martinis, Nair, Oldfield, Rienstra, Z Schulten, Schroeder, Selvin, Shukla, Silverman, Sligar, and Tajkhorshid.
  5. Fluorescence Spectroscopy—Dar, Gennis, Gruebele, Leckband, Y Lu, Schroeder, Selvin, and Zimmerman.
  6. Kinetics—Crofts, Dar, Das, Gerlt, Grosman, Gruebele, Jakobsson, Leckband, Y Lu, Martinis, Oldfield, K Schulten, Shukla, Silverman, and Sligar.
  7. Computational Biophysics—Aksimentiev, Dar, Hammes-Schiffer, Hergenrother, Huang, Jakobsson, Leckband, Y Lu, Nair, Oldfield, Olsen, Rienstra, K Schulten, Z Schulten, Shukla, Sinha, and Tajkhorshid.
  8. Membrane Biophysics—Aksimentiev, Crofts, Das, Fratti, Gennis, Gillette, Grosman, Jakobsson, Kraft, Leckband, Oldfield, Rienstra, Selvin, Shukla, Sligar, and Tajkhorshid.
  9. Molecular Biophysics—Aksimentiev, Belmont, Chemla, Crofts, Das, Gerlt, Grosman, Gruebele, Hammes-Schiffer, Huang, Jin, Leckband, Y Lu, Martinis, Nair, Oldfield, Olsen, Rienstra, Schroeder, K Schulten, Z Schulten, Selvin, Shukla, Silverman, Sligar, Tajkhorshid, and Zhao.
  10. Photosynthesis—Crofts and Shukla.
  11. Protein-Lipid Interactions—Crofts, Das, Fratti, Gennis, Kong, Oldfield, Rienstra, Sligar, and Tajkhorshid.
  12. Macromolecular Structure—Aksimentiev, Belmont, Crofts, Das, Gerlt, Grosman, Huang, Jin, Kong, Leckband, Y Lu, Martinis, Nair, Oldfield, Olsen, Procko, Rienstra, Schroeder, K Schulten, Selvin, Silverman, Sligar, and Tajkhorshid.
  13. Cerebral Energy Metabolism—Hergenrother.
  14. Magnetic Resonance—Jin, Oldfield, and Rienstra.
  15. Complex Systems—Anastasio, Dar, Gruebele, Kuehn, T Lu, Rienstra, K Schulten, and Z Schulten.
  16. Computational Neurobiology—Anastasio, Gillette, Hergenrother, Nair, and Nelson.
  17. Statistical Mechanics of Genomes—Kuehn, Olsen, Z Schulten, and Sinha.
  18. History of Biophysical Research—Govindjee.
  19. Systems Biology—Anastasio, Dar, Gruebele, Kuehn, Kuhlman, T Lu, Y Lu, Z Schulten, Sinha, and Zhao.
  20. Matrix Biophysics—Kong.
  21. Stochastic Gene Expression/Gene Regulation—Belmont, Dar, Kuhlman, T Lu, Z Schulten, and Sinha.
  22. Nanobiophysics—Aksimentiev, Y Lu, Schroeder, and Sligar.
  23. Transmembrane Transport—Aksimentiev, Grosman, Procko, and Tajkhorshid.
  24. Bio-Imaging Development—Gruebele, Y Lu, Rienstra, Schroeder, Selvin, and Sligar.
  25. In vivo Transport and Diffusion—Kong and Z Schulten.
  26. Bio-Inspired Materials—Kong, Y Lu, Schroeder, and Zimmerman.
  27. Computational Genomics—Sinha.
  28. Stem Cells—Kong and Z Schulten.
  29. Ion Channels—Gillette, Grosman, Jakobsson, Selvin, Shukla, and Sligar.
  30. Single-Molecule Biophysics—Chemla, Grosman, Kuhlman, Leckband, Schroeder, Z Schulten, Selvin, and Sligar.
  31. Synthetic Biology— T Lu, Y Lu, Silverman, Zhang, and Zhao.
  32. Protein-DNA and/or Protein-RNA Interactions—Chemla, Huang, Kuhlman, Y Lu, Schroeder, Z Schulten, Silverman, Sinha, and Zimmerman.
  33. Live Cell Imaging—Belmont, Dar, Gruebele, Kuhlman, Y Lu, Schroeder, and Zhang.   
  34. Drug Discovery—Dar, Das, Hergenrother, Oldfield, Shukla, Tajkhorshid, Zhao, and Zimmerman.
  35. Experimental Evolution–-Kuehn, Y Lu, Procko, Silverman, and Zhao.
  36. Microbial Ecosystems—Kuehn and T Lu.

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 Quantitative 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.