Table of Contents

Biophysics Student Handbook

Topics	Page Numbers
I. Mission Statement	1
II. Introduction to Biophysics Program	2
III. Information for Prospective Students	2
A. General Admission Requirement	2-3
B. Pre Enrollment Contract	3
IV. Coursework Requirements for 1^st & 2^nd Year Students	4
A. 1^st Year Course Load	4
B. 2^nd Year Course Load	4
C. Foundation Courses	5
D. General Recommendations for Scheduling Classes	5
E. English Courses for Non-domestic Students	6
V. Individual Training Tracks: Coursework Options	7
A. Structural Biology & Molecular Biophysics Track (SBMB)	8
B. Cellular and Integrative Biophysics Track (CIB)	12
C. Biological Imaging and Spectroscopy (BIS)	16
D. Bioinformatics and Computational Biology Track (BCB)	21
VI. Biophysics General Graduate Program Policies	24
A. Ph.D. Candidates and Financial Aid	24
B. Masters Degree Candidates	25
C. Laboratory Internships	26
D. A Few Words About the “Politics” of Internships	28
E. Internship Final Report Form (also see Appendix C)	28
F. Choosing an Advisor/Being Chosen by and Advisor	29
G. When the Advisor/Student Relationship does not work out	29
F. Vacation Policy	30
G. Program Probation, Graduate School Probation and Dismissal	31
H. Ethical and Scientific Misconduct	32
I. Transfer and Dismissal from the Program	32
F. Biophysics Student Association	33
VII. Examination Policies	34
A. General Overview	34
B. The Biophysics “Contract”	34
C. Format of the Written Preliminary Examination	35
1. Examples of Preliminary Exam Questions and Additional Notes	36
2. Additional notes and suggestions regarding the Preliminary Exam	37
E. The Written Qualifying Exam	38
1. Examination Preproposal	38
2. Format of the Written Qualifying Exam	39
3. Evaluation and Grading of the Written Qualifying Exam	42
F. Oral Qualifying Exam	43
G. Thesis and Oral Thesis Defense	44
H. Oral Thesis Defense	45
I. Outcome of the Thesis Defense	45
Appendix A. Biophysics Student Pre-Enrollment Contract	46
Appendix B. Worksheet for First and Second Year Class Schedules	48
Appendix C. Biophysics Research Internship Final Report Form	49
Appendix D. Biophysics Ph.D. Contract Form	50
Appendix E. Timetable/Worksheet for Biophysics Students	55
Appendix F. Student Biographical Sketch Form	56
Appendix G. Example Letter of Advisor’s Pre-proposal Assurance Letter	57
Appendix H. Biophysics/Univ. Graduate Student Leave of Absence Form	58
Appendix I. Faculty Agreement to become a student’s Ph.D. Advisor	59
Appendix J QuickChart for candidacy exam	59

I. Mission Statement of The Ohio State University Biophysics Interdisciplinary Graduate Program

II. Introduction to the OSU Biophysics Graduate Program

Biophysics is a highly integrated discipline that can encompass nearly all aspects of biomedical science, from the interaction of various forms of energy with biologically relevant molecules to the mechanical forces involved with limb movement in an intact organism. What makes biophysics uniquely different from other disciplines of biomedical science is its approach to problems. Simply, the biophysicist examines biological systems through the eyes and tools of a physicist. The biophysicist is trained to understand the underlying interactions of energy and matter in living organisms or molecules and to use highly quantitative physical, statistical and modeling methodologies to unravel complex phenomena. The goal of our program is to provide an educational structure for graduate students at The Ohio State University to develop as scientists at this interface of physics and biology.

We accept students with a wide range of undergraduate training, but all students accepted must have rigorous backgrounds in science and mathematics. There is a great deal of flexibility built into the curriculum to meet the needs of students with varying backgrounds and goals. Importantly, our program emphasizes research experience as the greatest teacher as opposed to exhaustive class work. We want our students learning in the laboratories. Our general philosophy is that graduate education in science is best acquired as a “research apprenticeship” where the most valuable education comes from active participation in research and related independent study. Nevertheless, it is extremely important that all students get sufficient fundamental knowledge in biochemistry, biology, chemistry and physics, regardless of the direction of their research, in order to successfully complete their qualifying exams and move on to a successful career.

To better organize our curriculum and to provide appropriate mentorship, our program is self-organized into four “training tracks” or divisions. These tracks are oriented toward “experimental approaches” rather than “experimental problems.” To be successful, however, scientists must be “problem oriented” and be willing to embrace any technology or approach that will yield them the answers they are seeking. Scientists who pigeonhole themselves, for example, only as crystallographers, patch clampers, bioinformaticists, magnetic resonance spectroscopists or modelers often have short careers. Therefore, we expect all students to become familiar with a variety of experimental approaches and applications within these tracks while in their graduate training and also to learn and be willing to embrace new technologies as their research problems unfold and the science advances. On the other hand, one cannot be an expert at everything within the few years of graduate education. Therefore, students are best served by also concentrating and developing a high degree of expertise and rigor in one general approach during their graduate training so that they can use this as a springboard for establishing a reputation of expertise and to promote their career development. This is the purpose of the four tracks, which are the following:

Structural Biology and Molecular Biophysics (SBMB)

Description: Three dimensional structure and function of biological molecules, including proteins, nucleic acids, ligands, lipids, and their interactions. Methods include X-ray crystallography, nuclear magnetic resonance, computational modeling, calorimetry, and optical spectroscopy.

Cellular and Integrative Biophysics (CIB)

Description: Applied physics to living animals and plants, including membrane electrochemical behavior, patch clamping, channel biology, intracellular calcium ion regulation, molecular motors, cytoskeleton , muscle contractile function, nerve function, neural integration, bioenergetics and mitochondrial function, free radical biology and biomechanics.

Computational Biology and Bioinformatics (CBB)

Description: The use of high-level computational techniques and computer modeling to address biological problems and to model molecular aspects of living cells. The development and use of computer models, simulations and statistical approaches to interpret large data sets of the genome, proteome and lipid elements of the cell, as well as neural networks and other biologically complex systems.

Biological Imaging and Spectroscopy (BIS)

Description: The application of high-end technology for imaging and detection of chemical and biological processes and structures. Techniques include magnetic resonance (MRI, NMR, EPR, etc.) light/laser spectroscopy, multiphoton and confocal imaging, electron microscopy, optics, fluorescent detection, atomic force microsocopy, positron emission tomography (PET), etc.

III. Information for Prospective and Students Beginning the Program:

A. General Admission Requirements

As mentioned previously, our program admits students with a wide range of science and mathematics backgrounds. Approximately 60% of our incoming students are physics or biophysics majors; about 20% are general chemistry or biochemistry majors and 20% are mathematics, engineering or biology majors. Nevertheless, all students in biophysics need to have general knowledge in physics, mathematics, chemistry and biology.

In general, applicants are encouraged to prepare themselves for a career in biophysics with the following background during their undergraduate training:

1) Physics: through particles and waves, quantum mechanics and thermodynamics.

2) Mathematics: differential and integral calculus. Linear algebra is also highly recommended.

3) Chemistry: inorganic, organic and physical chemistry.

4) Biology: knowledge of at least one biological system, e.g. general biology, microbiology, botany, animal physiology or plant physiology.

Students who have not completed all of the above requirements in the undergraduate degree can pick up some of them in their first year of graduate school. Many of our incoming students need additional background education in at least one of these areas. However, the Admissions Committee reviews the applicant’s undergraduate curriculum to evaluate how successful the student could be in completing these requirements in a timely manner and this is part of their evaluation. As an example, pure physics majors who have had no background in chemistry or biology would have a more difficult time in this program compared to physics majors with a more balanced science background including some chemistry and biology.

B. The Biophysics Pre-Enrollment Contract

The OSU Biophysics Graduate program has developed the concept of “contracts.” These are written agreements between the student and the Graduate Program or the student’s Graduate Committee. We have both a “Pre-Contract,” which is an initial agreement between the student and the Graduate Program regarding the educational plan, and a general Biophysics “Contract” which expands the Pre-contract and includes the content of the Preliminary and Qualifying Examination and any additional coursework needed for career development.

A blank “Pre-contract” for incoming students to use as they design the curriculum for their first two years is included in Appendix A. It includes only general requirements of all students in the program and does not represent the specialized training that is expected of students in each of the four tracks. The requirements of the contract can be met in a number of ways. 1) The student could have met the requirements in previous undergraduate or graduate education, 2) through new undergraduate or preferably graduate level courses at Ohio State and 3) by evidence of self-study of equivalent material and/or proof by oral or written examinations provided by the graduate faculty.

A note on biochemistry: With very few exceptions, all areas of modern biophysics require some background in biochemistry. Within it is encompassed the “language of biology” to the extent that even if a student’s research is, for example, in pure magnetic resonance imaging or pure computational bioinformatics, it is necessary to learn the language in order to communicate with other biophysicists and biological scientists and to get a general understanding of the molecular basis of living organisms.

IV. General Course Load Requirements for 1^st and 2^nd Year Students

A. First Year Course Load

By the end of the summer of the first year of enrollment, students must achieve a MINIMUM of 20 total graduate credit hours of which 17 credit hours are Biophysics Foundation Courses. Foundation courses (listed below) are identified by the Biophysics Graduate Committee as critical, graded courses that are universally applicable and fundamental to developing a knowledge base in biophysics and the language and methods of biology. Included in the 17 credit hours, all first year students must complete the 3-quarter Introduction to Biophysics series (Neuroscience 702, XXX, Physics 780.20; 10 total credits) and a suitable graduate level Biochemistry series. The Biophysical Chemistry Series is also considered a primary part of the foundation course requirements, and is required if the student has had no physical biochemistry background and is recommended for all others. Note that 20 credit hours can be completed in 3 quarters by taking two, 3-4 credit hour courses per quarter, (i.e. considered a minimum course load for first year students). Failure to be on schedule to meet these requirements in the first year will result in a status of “Program Probation,” possible loss of support and/or loss of active status in the program. Note: students can petition the Graduate Committee for specific graded courses to be considered among this fundamental list which might be unique to the student’s career goals or background.

Students in the first year are required to seek permission of the Graduate Studies Chair or Program Director BEFORE dropping scheduled courses. There are no University rules requiring this, but failure to get permission to drop a course may result in change of status in the program.

First year students are expected to be actively involved in research rotations during the entire first year of enrollment. A minimum of 2 credit hours of 999 (Thesis Research) is required each quarter. Enrollment in the Biophysics Seminar series (1 c) is also required for Au, Wi and Sp quarters (see below for all students). During the autumn quarter, students may be asked to also enroll in Biochemistry Seminar Program 796, which is a combined OSBP/Biophysics/MCDB/NGSP graduate seminar designed to help students with developing a career in science.

B. Second Year Course Load

Prior to the General Qualifying Exam, all students must achieve a MINIMUM of 12 ADDITIONAL credits of recommended and approved coursework within the “Core” curriculum of their designated training track for a total of 32 credit hours of combined “Foundation” and “Core” curriculum. Note that this requirement does not include research credit hours (999) or seminar credit hours (e.g. Physics 801) and is considered an absolute minimum. Most training tracks will require larger course requirements than this minimum. Students with unique research directions may petition the Biophysics Graduate Committee to combine coursework from different research tracks or to add alternate but appropriate courses to meet their specific needs. Students with previously attained M.S. degrees and extensive graduate school training can also petition the Graduate Committee to waive some of these requirements based on proof of previous training. Waiving requirements does not necessarily involve transfer of credits. Approval of direct transfer of credit to The Ohio State Graduate School can only occur from credits earned at comparable U.S. Universities with the joint approval of the Biophysics Graduate Committee and the Graduate School.

All Biophysics students are required to enroll in Biophysics seminar classes for Fall, Winter and Spring quarters of each year of enrollment. Conflicts with other course requirements and teaching assignments must be prior-approved by a Director of the Program or the Graduate Studies Chair. For those students who have passed the candidacy exam but want to take a class for credit, the inclusion of the Biophysics seminar could result in more than three credit hours, the minimum required for the full-time status by the Graduate School. If this occurs, students need to notify a Director of the Program or the Graduate Studies Chair. They may then not register for the seminar but are still required to attend in the same amount of seminars as required for a passing grade if taken for credit.

C. Accepted Biophysics “FOUNDATION” Courses

Biophysics (Required)

Neuroscience 702 (3 cr hr) required (cellular biophysics)

Biophysics 702b (3 cr hr) required (methodological approaches to biophysical studies)

Physics 780.20 (4 cr hr) Introduction to Biophysics

Physical Biochemistry (Highly recommended, required if no Physical Chemistry)

Physical Biochemistry 721.01, 721.02, 721.03

Biochemistry (At least One Graduate Level Biochemistry Series Required)

Biochemistry and Molecular Biology 613,614 (615 optional) 4 cr hr ea

Biochemistry 511 5 cr hr

Molecular and Cellular Biochemistry 761 (Proteins), Biochemistry 766 (Nucleic Acids), Biochemistry 763 (Membranes)

Biochemistry Laboratory Courses

Biochemistry 521 Laboratory 5 cr hr

Biochemistry 706 Protein, Enzyme, Molecular Biology Laboratory 5 cr hr

Integrated Life Sciences

Physiology 601, 602 5 cr hr ea

Plant Physiology 630, 631 3 cr hr ea

Microbiology 520, 521 5 cr hr ea

Medical Microbiology 625, 626 5 cr hr ea

Molecular Genetics 605, 606 4 cr hr ea

Cell Biology (Mol. Gen) 607 3 cr hr

Computer Science

Computer Science Engineering (CSE) 459 Languages series (recommend Java C, C++ Unix)

(Note this series is an undergraduate course but is acceptable to meet “Foundation Course” Requirements.

CSE 502 (Object oriented Programming for Scientists and Engineers), 3 Cr Hr

Or CSE 560 (Systems Software Design, Development and Documentation) 5 Cr Hr

D. General Recommendations For Scheduling Classes

In your first quarter of enrollment you will be asked to plan a curriculum for the first two years (See Form in Appendix B). Based on the Current Graduate School Handbook (http://www.gradsch.ohio-state.edu/Depo/PDF/Handbook/Handbook.pdf) Graduate Associates holding 50 percent or greater appointments as Research Assistants (RAs) or Teaching Assistants (TAs) must register for at least nine (9) credit hours per quarter, except in summer, when the minimum is seven (7). University Fellows must maintain a course load of 15 cr hours for each quarter of fellowship support and students with no substantial teaching requirements should target similar course loads. Doctoral students who have passed the General Candidacy Examination must register for at least three (3) credit hours each quarter; registration during summer quarters is optional for these students. Students holding the titles “Graduate Fellow,” regardless of the source of the funds, must register for a minimum of 15 credit hours each quarter the appointment is held.

The Graduate School Handbook (available at http://www.gradsch.ohio-state.edu/Depo/PDF/Handbook/Handbook.pdf) currently defines the minimum of 135 graduate credit hours beyond the baccalaureate degree that is required to earn a doctoral degree. Students do not receive graduate credit for courses listed with numbers of 400 or below. If a master’s degree has been earned by the student, this minimum is reduced. Note, that sufficient credit hours is rarely a problem for students.

It is highly recommended that students with teaching assistant responsibilities limit their first teaching quarter to only two graduate level courses of 3 or more graded credit hours. These should generally fall within the “Foundation Courses” of the program. The remaining credits should be made up of 999 credits with the particular faculty the student is rotating or working with. Fellowship students or students without substantial teaching requirements should generally take approximately three graded courses per quarter over the first year.

In choosing courses to take, two recommended sources you should be familiar with include a) the Recommended Courses under each program track (this document), and b) the University Course Offerings Bulletin http://www.ureg.ohio-state.edu/course/ .

E. English Courses for Non-Domestic Students

All students who have come from non-English speaking countries and have English as a second language must fulfill the University requirements in English. The courses for English are “100” level courses and they do not contribute to your total credit hour requirements for graduation. They are considered remediation courses by the program and do not fulfill any part of ongoing curriculum expectations of the Biophysics program. Arriving students must be evaluated by the “Spoken English Program,” (SE, 075 ARPS Hall, 2-5005). Before going, ask the Biophysics Program Administrator for a 100-W form so that the Biophysics Program can pay for the exam. Students who pass this exam automatically qualify to teach, if required. Students who do not pass generally enroll in Spoken English 104 and/or 105, depending on the recommendation of the SE Program. The 105 Course is extremely valuable because it instructs students how to teach in an American University. At the beginning of the 105 course, students are given a “Mock Teaching Trial.” At this point, individuals who do extremely well in the trial can sometimes pass out of Spoken English 105. At the end of the 105 course the students are also given a Mock Teaching Trial, usually given around finals week. They have the choice of practice teaching biology, chemistry, or physics and a representative of the Biophysics Program or one of those teaching programs will be in attendance.

The written English course is also a requirement for students from non-English speaking countries. It should be taken during the first year, but can be postponed to a later quarter so that it does not interfere with the many courses offered in autumn and winter quarters.

IV. Individual Training Tracks: Coursework Options

Introduction

The following paragraphs describe the range of curriculum that each student should consider when deciding to specialize in one of the four training directions. In many ways these options are very incomplete, but provide you with a starting point to design your curriculum and the kinds of courses and course loads you should expect to carry. At each point along the way, as your career and your graduate education progress you should meet regularly with your career advisor, with your research mentor, the director of your specific training track, your Graduate Committee and other faculty to help you select the courses. If your research area does not clearly fit within a training track, work with a Program Director or the Grad Studies Chair to identify a faculty who can provide you with the feedback you will need. It is very common that a student’s curriculum falls between two or more tracks, so don’t be concerned. These are just guidelines.

The descriptions that follow are under constant revision and sometimes courses that are offered have been dropped, changed or moved to other quarters, so please refer to the OSU Course Offerings Bulletin for more information. http://www.ureg.ohio-state.edu/course/

Many students get overwhelmed by seeing all of these courses that are offered and think they “cannot possibly do all that they would like or is expected.” Ohio State has one of the most diverse curriculums in the world and therefore many options are available. It is important to understand that each student’s curriculum in this program is different and should be tailored to their needs. Again, please choose carefully and work with your advisor and committee to come up with a plan that is feasible, rigorous but also enjoyable.

A. Structural Biology and Molecular Biophysics Track (SBMB)

Students specializing in Structural Biology and Molecular Biophysics, besides having a solid background in physics and biophysics, must have an extensive knowledge of biochemistry. Although there is much overlap, the program in Biophysics differs from that in Biochemistry primarily in that students often approach the subject from a physics or fundamental chemistry background, and less often from a biology-oriented background. Secondly, an emphasis is placed on physical biochemistry, kinetics and three-dimensional structure of proteins and other molecules rather than more traditional molecular biology and biochemistry topics. The following objectives should be met through formal graduate coursework, previous undergraduate coursework (when approved), or more informal, but approved mechanisms such as study groups or independent study under the direction of biophysics faculty.

Objectives for acquiring a general background.

1. Solid background in basic graduate level biochemistry and molecular biology. Requirements in these areas can be met in a number of ways. For example, one highly recommended series is the protein course Molecular and Cellular Biochemistry 761 (autumn), followed by Biochemistry 766, nucleic acids (winter) and Biochemistry 763, membranes (spring). This series is well received by students focusing on molecular structure, but certain aspects such as metabolism and molecular biology are missing. Another series, Biochemistry 613,614 (Fall/Winter series) is more inclusive of traditional Biochemistry curriculum. This course is also recommended but some students have found that it emphasizes areas of biochemistry that are not t