Courses & Requirements

Section 1

Content

 


Program Requirements Chart

Requirement Time Allotted Comments
BIOP 401 (Intro to Biophysics) 1st semester 3 hours
32 hours of coursework end of 1st year Met by registering full-time fall, spring, summer. Must complete 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 or equivalent).

experimental in nature, quantitative course required (BIOP 576, BIOP 586C, BIOE 598AGB, ANSC 449, MCB 432 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 2-3 courses required. Hours combined with all coursework listed here (excluding BIOP 590/599) to total 32 hours of coursework required by Graduate College for graduation.
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. At least 32 hours of 599 required for graduation.
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.


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, 179 Loomis.

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.


Biophysics Doctoral Degree Requirements

A.  GENERAL REQUIREMENTS

The Graduate College recognizes three stages in a Doctoral degree program, each accounting for a minimum of 32 hours of course work (including 590 and 599 credits for research, where appropriate).  The total credit hours required for a Ph.D. is a minimum of 96 hours.


Stage I:  Course work taken in consultation with the first year advisor or research advisor, culminating in the successful passing of the Biophysics Qualifying Exam (BQE).  Three lab rotations must be completed by the end of the first semester, resulting in the selection of a research advisor. 

Stage II: Research (Biophysics 599), culminating in the successful passing of the Preliminary Exam.  The Prelim must be passed by the end of the 3rd year.

Stage III:  Research (Biophysics 599), culminating in the successful passing of the Doctoral Exam. 

For the Ph.D. degree, a total of 32 hours of credit in Stage I must be obtained.  The following courses are required#:

  1. Biophysics 401 (3 hours, first year)
  2. Biophysics 595A (research seminar) and 595B (faculty seminar) (5 hours total, first two years)
  3. Biophysics 586 (2 tutorials, 1 hour each, completed before Preliminary Exam)
  4. Biophysics 581-83 (3 lab rotations, 2 hours each, first semester)
  5. MCB 580 – ethics course (1 hour, second year)
  6. Two 500-level courses from the pre-approved Biophysics course list*
  7. Quantitative biology course or experimental lab course**
  8. Additional 400- and/or 500-level biophysics or science courses to make up a total of 32 hours in i. through vii.

#Requirements i-viii must be completed in the first three years, prior to the Preliminary Exam.

* The Biophysics & Quantitative Biology Office provides copies to students annually. 500-level courses in other departments may be petitioned to count towards the Biophysics and Quantitative Biology course requirement.  The main content of the course must be biophysical in nature and a syllabus must be provided with the request. Center approval must be obtained by students prior to registration and receiving credit for non-approved courses.

** If research is computational/quantitative in nature, a lab course is required (BIOC 455, PHYS 552, PHYS 598BP, PHYS 598OM, or equivalent). Conversely, if research is experimental in nature, a computation/quantitative course is required (BIOP 576, BIOP 586C, BIOE 598JM, BIOE 598AGB, ANSC 449, MCB 432, or equivalent).

I. Tutorials and Lab Rotations

The basic requirement is 3 lab rotations (5-weeks in length) and 2 tutorials (8-weeks in length).   Tutorials may not be taken on the same topic as a lab rotation.  Students may take a rotation and a tutorial under the same professor, however, they may not complete a tutorial with their advisor.

All required lab rotations must be taken and completed by the end of the first semester.  A short written report of 6-10 pages is expected for each rotation.  On the basis of the lab rotations, students must select a research advisor by the end of the first semester.  This includes ensuring acceptance by the advisor.

Students may not officially rotate through labs of faculty who are not current members of the Center.  If a student wishes to explore a lab outside Biophysics, they are encouraged to meet with the faculty member unofficially throughout the semester.  If the student ultimately joins a lab outside Biophysics, a Biophysics pro-forma advisor must also be selected.

Each tutorial consists of meeting with a faculty member at least once a week for a 8-week period, and culminates in a written paper of 6-10 pages.  Students should expect to submit two or more drafts, for advice on both scientific content and writing skills.  It is possible to complete two tutorials in a single semester, with the second beginning the eighth week of classes. 

II. Seminars

All first year students must take Biophysics 595A (Department Seminar) and Biophysics 595B (Faculty Research Topics Seminar). Biophysics 595B is only required in the first semester. Students are required to register for Biophysics 595A (research seminar) until the end of their second year, for a total of four semesters.

III. Ethics Requirement

Graduate students in the sciences at the University of Illinois are expected to have training in professional ethics.  Graduate students in the Center for Biophysics and Quantitative Biology are required to take the ethics course offered by the School of Molecular and Cellular Biology, MCB 580The course will be offered each fall for second year students.  The course syllabus can be found at: www.life.illinois.edu/mcb/580/.

IV. Grades/Grade Point Average (GPA)

The University of Illinois grades on a 4.00 point plus & minus system (A=4.00; B=3.00; C=2.00; D=1.00; F(fail)=0.00).  In order for the University to calculate the overall Grade Point Average (GPA), the number of hours for a course is multiplied by the numerical equivalent of the letter grade received.  This is done for all graded courses and the sum of all graded courses is divided by the total number of graded hours.  This is the GPA.

The Graduate College minimum GPA requirement for biophysics is 3.00 in all coursework.  If a student’s overall GPA is below 3.00 for a semester, a warning letter will be sent from the Graduate College.  If, after the completion of additional graded hours, the GPA has not been raised, the student will be placed on limited status.  If the student is still on limited status the following semester, they will not be allowed to register for subsequent semesters.  Students on limited status are also ineligible for degree conferral until the limited status is lifted.

In addition, the Center for Biophysics and Quantitative Biology has a minimum GPA requirement of 3.00 for the courses in i., iii.-viii above.  If a student’s GPA in these courses falls below 3.00 for a semester, a warning letter will be sent from the Biophysics Office.  If, after the completion of additional graded hours, the GPA has not been raised, the student will be placed on probation, and can be asked to leave the Program.

Grades of S (satisfactory) and U (unsatisfactory) are given for seminar courses, but not counted toward the GPA.  Likewise, if a course is taken Credit/No Credit, it is not counted toward the GPA.  Hours for these courses will be counted toward the total credit hours for the degree.

1.  Deferred grades are temporary grades given for work not completed for a lab rotation and for Thesis Research (599).  Thesis work will be graded DFR (deferred) until the final examination is passed, when an S or U grade will be granted.  Incomplete work for a lab rotation should be completed by the semester following the receipt of a DFR grade.  The professor must contact the Biophysics and Quantitative Biology office to assign a letter grade, before credit can be received for the course.

2. Excused grades (I for incomplete) are temporary grades given for courses where work is not completed before the end of the semester.  These must be cleared up before the reading day of the following semester.  “I” grades not cleared by the appropriate time will become "F” (“F by rule") and appear on the student’s transcripts as such.  These are counted as F when computing GPA.  Once the work is completed, the professor must submit a grade change with the Biophysics and Quantitative Biology office to replace the F with a letter grade.

V. Petitions

Requests for an exception to a published Graduate College policy or deadline, an official on-line Student Petition Form must be completed by the student on the Graduate College website (http://www.grad.illinois.edu/gsas/petition-record-requests).  Student record requests, such as change of curriculum or add/drop will be completed on a Curriculum Change/Transfer of Credit Form.  The outcome of these requests will be forwarded to the student and the Biophysics and Quantitative Biology Office electronically by the Graduate College.

Students who want to receive 500-level credit for courses in other departments or want to be considered for an exception to a program requirement may petition the Center for Biophysics and Quantitative Biology.  These petitions only require the Center Director approval and a simple email request will suffice.

B.  TEACHING

All Biophysics and Quantitative Biology students are required to teach for a minimum of one semester during their graduate career, though some students may be asked to teach for additional semesters if their advisors do not have an alternative means of support available. Students are strongly urged to complete this requirement in their first few years in the program. There is a limited number of Teaching Assistantships (TA) available through the Center for Biophysics and Quantitative Biology itself.  Most appointments are made through other departments, such as Molecular and Cellular Biology and Physics.  These TAships are highly competitive. 

The Biophysics and Quantitative Biology Office will inform students each fall and spring when the School of Molecular and Cellular Biology is accepting applications.  Students will be asked to complete an application on-line.  Students may also apply for TAships in other departments.  Most applications are due the semester prior to the proposed assignment (MCB TA applications for fall are due in mid-April; those for spring are due in mid-November), so students should submit applications to the appropriate departments well in advance for full consideration.  Sometimes TAships can be arranged through the advisor's lab.  This option should be discussed with the advisor directly.  TA's are appointed for one semester, though some departments offer an option to renew the next semester.  TAships are generally not offered over the summer, so other means of support must be arranged.

I. TA Orientation

Before students are allowed to act as TAs for a University course, they must pass the Graduate Academy for College Teaching program.  This program is held one week prior to the beginning of classes in the fall and spring semesters.  Students will attend large and small group sessions; be videotaped teaching a short lesson; and have the tape reviewed.  There are also follow-up sessions later in the semester that offer further training opportunities.  Follow-up sessions are not required for Biophysics and Quantitative Biology students, but may be attended if of interest to the students.

II. English Proficiency Requirements

All non-native English speaking international students must pass the English Proficiency Interview (EPI) test before they can be enrolled in an orientation session or be appointed as a Teaching Assistant.  It is also a graduation requirement of the University and of the Center for Biophysics and Quantitative Biology.  Even U.S. citizens or permanent resident aliens must sit for the exam if English is not their native language.  An exemption from the exam can be granted only if a student attended both high school and college in English speaking institutions. 

    If any of the following have been passed prior to enrollment at UIUC, the scores will be accepted in lieu of the EPI test:

    TSE passed with a score of 50
    iBT* speaking sub-section passed with a score of 24
    IELTS* speaking sub-section passed with a score of 8

      *scores must be less than 2 years old on the 1st day of class the semester the student enters the U of I

The EPI test is offered every semester during specified weeks.  Information will be disseminated from the Biophysics and Quantitative Biology Office regarding test dates and times.  The exam is held at the Armory and the exams start promptly at the time indicated.  Students taking the exam must bring a picture ID card and will need to arrive at least 15 minutes early to check in.

Results of the exam are sent to the Biophysics and Quantitative Biology Office approximately two weeks after the test date.  The exam is scored pass/conditional pass/fail.  If a passing grade is not earned, the exam must be taken again the following semester, but only after participation in language improvement activities have occurred.  These improvement activities include: taking an English as a Second Language course (ESL 504, 506, etc., which may be repeated as needed); or hiring a private, OIR-approved tutor for a minimum of 10 hours to help improve English abilities.  Students are required to take the EPI test each semester until they pass it.  It is also is a requirement for successful passage of the BQE.  The University of Illinois only allows a student to take the EPI test three times.  If the student fails the exam the third time, they will be required to take one of the alternate exams at their own expense until a passing score is achieved.

If a student receives a total score of 102 or less on the iBT, they will also be required to take the ESL Placement Test (EPT) when they arrive on campus.  The score received on the EPT determines the need for any ESL courses at the University of Illinois.  These courses must be completed before the student will be allowed to TA or graduate.

C.  EXAMINATIONS

There are three exams leading to a Ph.D. degree in Biophysics and Quantitative Biology.

I.  Biophysics Qualifying Examination

The first of these is the Biophysics Qualifying Exam (BQE), which must be passed by the end of the second year in the program.  Students are expected to sit for the exam in their first year.  The exam is administered every spring. 

Passage of Biophysics 401 and a biochemistry and physical chemistry course are strongly suggested before attempting to take the BQE.  Regular attendance at seminars; study of past exams; and a good knowledge of the Center faculty’s research have also proven to be helpful. 

The BQE has both written and oral components: 

  • The written BQE tests the student's general knowledge of Biophysics and Quantitative Biology.  It contains three sections (Experimental; Computational/Quantitative; Fundamentals of Biophysics).  Six questions (out of 12 available) must be attempted, with at least one in each section.

  • The oral BQE reviews biophysics knowledge further, especially in areas not mastered on the written exam, and determines the student’s progress in course work, research, and other programmatic matters. 

The BQE committee recommends to the Director whether or not a student should pass and thus be admitted to Ph.D. candidacy.  These recommendations are based not only on the exam performance, but also on the total academic record, the student's research potential, and the nature of the student's objectives and motivation.  Formal admission to the Ph.D. candidacy also requires that the student be accepted into the research group of a Biophysics and Quantitative Biology faculty member who then serves as the student's official advisor.
As noted earlier, non-native English speaking international students must pass the EPI test in order to satisfy the requirements of the Qualifying Examination.

Rules for BQE Grading

In order to avoid confusion with complicated schemes of combinations of scores, here are the simple BQE Guidelines:

  1. 4 or more passes (out of 6 written questions attempted)
    Students who receive 4 or more passes on the written BQE will not be required to retake the written BQE.

    Students may be asked to retake the oral exam, depending upon their performance during the oral exam on any of the questions they did not pass, and/or any unanswered questions about their proposed research, progress with other program requirements, and related matters.

  2. 3 or more fails (out of 6 written questions)
    Students who receive 3 or more fails on the written BQE must unconditionally retake both the written and oral portions of the BQE.

  3. All other scores
    Students receiving scores not falling into either category above should be prepared for a thorough oral examination on the BQE questions.  The BQE Committee will decide the final outcome of the exam based on the performance at the oral: retaking the oral, or retaking both the written and oral parts of the BQE.

II. Preliminary Exam

The second exam, the Preliminary Exam, examines the student's thesis proposal and his/her knowledge and ability to pursue in-depth research in their chosen area. The primary purpose of the Preliminary Exam is to examine the validity of the thesis proposal and to test the student's fitness to carry out independent research.  Students are expected to take the Preliminary Exam before the end of their third year.  Students are also expected to have completed all coursework and tutorials prior to their prelim. 

The exam is oral and is administered by an ad hoc committee recommended by the student's advisor, who serves as the chair of the committee.  The committee is appointed by the Graduate College with the recommendation of the Center Director. The Chair and a majority of the committee must be members of the Graduate College and the Center for Biophysics and Quantitative Biology.  At least half of the members must be tenured faculty.

It is the student's responsibility to ensure that the committee is appointed at least two weeks prior to the proposed exam date.  The student, with the permission of his/her advisor, initiates the appointment of the committee through the Center for Biophysics and Quantitative Biology Office, who will complete the appropriate paperwork for the Graduate College.  Additionally, the Biophysics Office requires a one-page, double-spaced Project Summary Report from the student for their file. 

The Preliminary Exam is based on a 20-30 page (double-spaced) thesis proposal presented to the committee. The proposal should include an Introduction, Methods and Materials, Preliminary Results, Proposed Work, and References.  Figures and captions should be incorporated into the text.  It is the student's responsibility to see that the thesis proposal is in the hands of the committee at least two weeks before the committee meets.

At the start of the oral exam, the student presents a 20- to 30-minute outline of the proposed work.  The committee then examines the student regarding facets of the proposal that need clarification and makes suggestions which may facilitate the approach to the problem.  Finally, the committee may raise questions of a more general nature, to test the adequacy of preparation for the proposed work, and general knowledge of Biophysics and Quantitative Biology.

At the conclusion of the oral examination, the chairperson of the committee will initiate the approval of the Preliminary Examination Result (PER) form and announce one of three possible decisions:

  1. Pass
  2. Fail
  3. Defer (the same committee must re-examine the student within 180 calendar days of the original exam and the outcome must be pass or fail)

III. Final Exam      

The third exam is the Final Exam, which is a presentation and defense of the student's thesis work.  The Final Exam committee is appointed by the Graduate College upon the recommendation of the Center Director.  As with the Prelim, the student initiates the appointment of this committee through the Biophysics and Quantitative Biology Office, who prepares the paperwork for the Graduate College. 

The composition of the committee for the Final Exam has the same requirements as for the Preliminary Exam and is usually the same as that for the Preliminary Exam; however, a change in the direction of the thesis or departure of original faculty may require changes in the committee. 

The Final Exam may not be taken sooner than 6 months after the Preliminary Exam.  Doctoral candidates must complete all requirements for the degree so as not to exceed five years after their first registration in the Graduate College.  (See Petition section if there is need for exception to this rule, e.g., time extension.)

The final form of the thesis, at the time of deposit after a successful defense, must conform to the rules specified by the Graduate College.  At the time of the defense, the thesis must be in essentially final form.

The Final Exam is a public exam, and the recommended format is a 50-minute formal presentation as a public seminar, with a short question period from the audience.  The examination committee will then question the candidate in detail in a private meeting.
At the conclusion of the oral examination, the chairperson of the committee will announce one of three possible decisions:

  1. Passed, and the committee will sign the FER/TDA forms.
  2. Passed, but with revisions and the committee will sign the approval forms at a later date.
  3. Failed, and the student will not be admitted to another examination.

Specific information on the Final Examination procedures can be found under F. Degree Conferral Procedure.  The Graduate College also provides information regarding forms, thesis preparation, and electronic submission, which can be accessed via the web at: http://www.grad.illinois.edu/thesis-dissertation.

D.  REQUIREMENTS FOR THE MASTER OF SCIENCE DEGREE

Students are not admitted into a program leading to a Master's degree.  The Master’s degree is not awarded to students continuing toward the doctoral degree in the program, or to students who are transferring to another Ph.D. program on campus.  However, under certain circumstances, a student may be awarded a terminal Master of Science degree.  The requirements are as follows:

  • a total of 32 hours of credit in biophysics courses and related subjects.  

  • 10 hours of 500-level biophysics courses with a minimum GPA of 3.25.   These 10 hours do not include seminar courses (Biophysics 595A/B) nor research units (Biophysics 590/599) and can include no more than 2 hours of tutorials (Biophysics 586).   500-level courses in other departments count towards this 500-level formal course requirement if they are on the approved Biophysics course list.

  • At least 4 hours of research (Biophysics 590 or 599) is required, with the work presented as a thesis (which is submitted to the Graduate College after the advisor’s approval) or research paper (which is submitted only to the advisor and/or Center Director).  The paper should be a concise account of the student's research, in the style and format of an appropriate scientific journal, except that it should include a more detailed introduction to the area of investigation, and it may include a greater degree of speculation in the discussion.  Bibliographic references should include complete titles. The paper should be between 10-50 typed, double-spaced pages, excluding figures and numbered references, which should be attached to the paper.

The evaluation of the paper will be made by the student's Biophysics 590/599 advisor.  The advisor has the option of calling for an oral examination based on the research paper/thesis. Additionally, the Center Director can review the paper.  After the evaluation of the paper, one of three possible decisions will be made by the Center Director:

  1. The paper is approved, and the student will be granted a Master’s degree.
  2. The paper should be revised and resubmitted within one month.
  3. The student failed and will not be granted a Master’s degree.

E.  SATISFACTORY ACADEMIC PROGRESS

Unless there are very unusual circumstances, the following conditions must be met for a graduate student to be making satisfactory academic progress, and to be eligible for reappointment as an assistant or trainee:

  • A student should give evidence of continuous effort and progress.  Beginning with the end of the first academic year, and thereafter, the student should give evidence of continuous effort and progress in research. 

  • A student should have a primary research advisor by the beginning of the second semester in the program.  If a student leaves a lab, they must arrange for a new advisor within the same semester.  The only exception is official leave from the University, such as medical leave.

  • A student should complete 32 hours of courses by the end of three semesters, following the outlines of the program requirements above.  If this condition is not met, he/she will not be appointed as a graduate assistant/trainee after that time without special permission from the Center Director. This rule does not apply to special status students.

  • Students should enroll for the maximum amount of course credit (including 590 and 599) for which they are eligible, usually 12-16 hours per semester (4-8 hours in the summer).  A minimum of 8 hours of course work is required at all times, except with permission from the Center Director.  International students must maintain an enrollment of 12 hours for the fall and spring terms to maintain their visa status.

  • A doctoral student should complete all requirements for the degree not later than five years after entering graduate school with the B.S. degree.  Continuation beyond this time requires special permission from the Center Director and the Graduate College, in response to a petition from the student's research advisor.

  • A student who has a GPA below 3.0 after two semesters is making unsatisfactory academic progress and may be released from the program.

  • A graduate assistant who performs inadequately, or irresponsibly, in a teaching or research position may be removed from the position with no commitment of alternative support and may be released from the program.

Annual Reviews

The Center for Biophysics and Quantitative Biology conducts annual reviews for all students.  This process helps keep students on track toward the timely completion of their degree.  The initial stage of  review consists of a written Progress Report from the Biophysics & Quantitative Biology Office each year, which lists all requirements met and those still outstanding.

If deemed necessary, the director or advisor can call for a more thorough review by a small faculty committee, consisting of two to four members.   This committee can be a potential Prelim and/or Final Exam committee.  These reviews will help facilitate working relationships between faculty and students, and provide the student with more contacts who may be aware of new or alternative methods or studies, something a single advisor may be unaware of. 

The reviews by progress report and/or committee are mandatory for all students.  If requested, students are to provide their committee with a two-page synopsis of the work that has been completed, and the progress they have made each year.  This synopsis will be reviewed by the committee and discussed with the student at a brief meeting, to be arranged by the student.

The Biophysics and Quantitative Biology Office will monitor the review process.  The Office will remind the appropriate students to make preparations for these annual meetings, and keep records of the recommendations of their committees. 

F. DEGREE CONFERRAL PROCEDURE

When preparing for their final defense, students should arrange to meet with the Center Administrative Coordinator, to verify that all Center requirements necessary to graduate have been fulfilled

Students should verify all deadline dates with the Center office or Graduate College early in the semester priorto the planned graduation, to ensure the timely deposit of the appropriate forms and paperwork.

Ph.D. degrees are conferred three times a year:  May, August, and December.

The Graduate College mandates official University policy and procedures in regard to student theses, including specified formatting of the document.  Below are the specific procedures for the final defense.  

  • The Final Exam must be passed at least one and one-half months before the conferral date.  Students must be registered during the semester that the final defense is taken.  [NOTE: If a student is registered for the summer and defends prior to the first day of the fall semester, the student does not need to register for the fall.  Students do not need to deposit the same semester nor be registered to deposit. However, if the thesis is not deposited before the same semester as the defense, the decision not to register will affect student insurance and any RA appointments held, both of which require the student to be registered.] 

  • Students should indicate that they plan to graduate while registering via UI Integrate/Enterprise. If a student fails to meet the requirements for graduation, they must add their name the following semester – it will not be done automatically.

  • Students, working with their advisors, should select the faculty for the final committee. Once all have agreed to a date and time, students must reserve a location for the exam.  Once all arrangements have been completed, the student must inform the Biophysics and Quantitative Biology Office of the specific details, along with the thesis title.  This must be done at least two weeks before the exam.  Once the information is received, the office personnel will complete the required paperwork and submit it to the Graduate College on the student’s behalf.  Exams are public and will be announced to the Biophysics community prior to the examination. 

  • The Graduate College approves of the committee members and sends the Final Examination Result (FER) form AND Thesis/Dissertation Approval (TDA) form to the Biophysics and Quantitative Biology Office.  Arrangements must be made to retrieve these forms from the office prior to the date of the exam, either via an email sent to the advisor or hard copies to be picked up in person. 

  • The final committee members must sign both the FER/TDA forms at the conclusion of the final examination.  Results do not need to be unanimous, but both forms must be signed appropriately.

  • The FER and TDA forms must be returned to the Center office immediately after completion of the defense, to secure the Director’s signature, prior to submission to the Graduate College.  Forms are invalid without the Director’s signature.  The TDA form will be returned to the student after the department thesis format check.

  • After the final defense, a copy of the final thesis must be submitted to the Center Office for the department format check.  Once the check has been completed and corrections have been discussed with the student, the on-line department format check form will be prepared by the office personnel and submitted to the Graduate College.  Without the departmental approval, the Graduate College will not perform any format checks or accept the thesis for deposit.

  • The final thesis and original signed TDA forms must be deposited by the student to the Graduate College at least two and one-half weeks before the graduation date.  The thesis must be deposited electronically.  The original TDA form should be submitted in person to 204 Coble Hall, along with other required Graduate College paperwork.  Check with the Thesis Office for other required forms.

       

       
Section 2

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