BIMS BIOPHYSICS PROGRAM GUIDELINES

Updated August 2022
Biophysics Director of Graduate Studies (DGS):  Dr. Ilya Levental
Program Administrator:  Mr. Nicholas Barrales

Mission: The Biophysics program is designed to provide students with training in the mechanistic principles and quantitative investigation of living systems, thus preparing them for a career in modern biomedical research or industry.

Admission requirements:  students are admitted to the Ph.D. program in Biophysics through the Biomedical Sciences (BIMS) Graduate Program. BIMS students with an interest in quantitative cell and molecular biology, chemistry and physics of living systems, instrumentation, computational biology, or structural biology would be strong candidates for joining the Biophysics.

Typical course: The program begins with 1.5 years of didactic course work integrated with laboratory research.  The first year is common to all BIMS students:  rotation through three research laboratories and completion of the BIMS Core Course in Integrative Biosciences. By late February of the first year, each BIMS student will select a mentor and declare a degree program (e.g. Biophysics). During the Spring semester of the first year and through the second year of study, Biophysics students will complete the required course work and prepare for the qualifying examination. Students will be evaluated for Advancement to Candidacy based on their overall performance in the program. This evaluation will include performance in course work, research rotations, oral defense of a written thesis proposal, and participation in program activities, including the Journal Club, Research-in-Progress talks, and seminars. Upon completion of required coursework and Advancement to Candidacy Exam, Biophysics students are eligible to earn the M.S. in Biological and Physical Sciences.

After Advancing to Candidacy, students concentrate on conducting independent research under the guidance of a mentor and Thesis Advisory Committee. The student’s research is expected to advance an area in the broad realm of Cellular / Molecular Biophysics. As evidence of this achievement, students will publish research papers, including at least one as first author, and these papers will appear in recognized, peer-reviewed journals. The culmination of the research endeavor is a written dissertation that is presented publicly, and then defended orally before the Thesis Advisory Committee. The final examination for the degree of Doctor of Philosophy is devoted entirely to the candidate’s defense of their dissertation. Student progress through the program is guided by Thesis Advisory Committee and is reviewed at least annually in a formal meeting. This training experience allows students to earn the Ph.D. in Biophysics in four or five years (following the University residency and credit requirements as listed in the Graduate Record).

REQUIRED COURSES

All BIMS students must complete a minimum of 72 hours of graduate credit. A minimum of 22 out of the 72 credit hours must be graded coursework, and no more than 48 of the 72 credit hours can be comprised of Non-Topical Research. Requirements for graduation include the following courses:

• BIMS 6000 – Core Course in Integrative Biosciences Credits: 10
• BIOP 8201 – Biophysical Principles I Credits: 2
• BIOP 8301 – Biophysical Principles II Credits: 2
• CELL 8450 – Effective Science Writing for Grants and Fellowships: 2 (or equivalent writing course)
• BIMS 7100 – Research Ethics Credits: 1
• BIOP 5050 – Biophysical Literature Credits: 1

At least one module of Advanced Methods in Molecular/Cellular Biophysics (2 credits):

• BIOP 8020 Advanced Methods in Molecular Biophysics
• BIOP 8050 Advanced Methods in Cellular Biophysics

At least one module (2 credits) of BIMS or GSAS elective credits.  These include any BIMS courses and many others, though approval by the Director of Graduate Studies is recommended for non-BIMS courses.

A sample (and suggested) curriculum is below:

JOURNAL CLUB

Students will also be required to attend the Biophysics and Physiology journal club throughout their graduate careers.  Associated Course:  BIOP 5050 – Biophysical Literature Credits: 1

FIRST AUTHOR PUBLICATION

At least one first author publication (non-review article) is required for consideration of the Ph.D. degree.  The thesis committee will evaluate the publication for adequate quality and determine whether it is an important contribution to science.

Milestone: PAPER1

QUALIFYING EXAM

Students are expected to write and orally defend the Thesis Proposal by September 1 at the beginning of the third year. The purpose of the Qualifying Examination is to ensure that you have mastered the fundamentals of biophysics relevant to your proposed research and are adequately prepared to begin working full-time on your thesis research. The Exam comprises the preparation of a written research proposal and an oral defense of the proposal to a faculty committee.

The structure of the written document should be similar to the NIH F31 grant application and is described in detail below (detailed instructions are also available from the NIH website). You are expected to present the written proposal to your committee members at least two weeks before the oral defense.

IT IS ESSENTIAL that this proposal presents an original project with original ideas developed and written by the student. While proposals from colleagues, including the student’s mentor, can be used as guidelines, there must be no scientific overlap between your Qualifying Exam written proposal and any other document from either your mentor or other colleagues.

Proposal Instructions:

Your proposal should describe the research plan for one person (you) for a three-year period. It should follow the format of an NIH application with five sections. Remember that in evaluating your proposal, reviewers will be looking for more than the protocols for your experiments; they will mostly be looking to ensure that you can explain the rationales behind your experiments, the justifications for their importance, and the possible interpretations of various outcomes. In short, the scientific ideas that are part of a research project are at least as important, if not more important, than the technical methods. Your proposal should contain the following sections. The page lengths indicated are very rough suggestions, but the total length of sections I-IV should not exceed 8 pages (including figures but excluding Literature Cited).

1. SPECIFIC AIMS (1 page)

First, state your overall objective, concisely and realistically. This objective should describe what the

research is expected to accomplish and what hypothesis is to be tested. Then list the major experimental

goals (i.e. specific aims} that will be completed to achieve that overall objective during the course of your

study.

1. BACKGROUND AND SIGNIFICANCE (1-2 pages)

Briefly describe the background for your proposal, critically evaluate existing knowledge, and specifically identify the knowledge gaps that the project is intended to fill. State concisely the importance of the research described in this proposal by relating the specific aims to longer term objectives beyond the scope of the proposed 3-year study.

III. PRELIMINARY STUDIES (2-3 pages)

Provide an account of any experiments you have already carried out that might be pertinent to the research plan. You may also briefly review the history of the project and relevant work accomplished by others in your lab. If you have not yet started experiments relevant to the proposed project, this section will include more the latter than the former. If the project is new to your lab, this section can be very short. Appropriate figures, graphs or tables should be included, if available.

Do not delay preparing your Qualifying Proposal to accumulate more preliminary results. Your experimental skills at the bench are only one small facet of the exam. The most important consideration is your ability to think logically and present your proposed research in clear and insightful ways. While Preliminary Studies in an actual NIH application, by an independent investigator, would be required to make a compelling case for the proposed experiments, your Qualifying Proposal is not an actual application, nor are you an independent investigator. It is unwise to delay preparing your proposal to get more preliminary results, rather the opposite is true.  You will get good feedback from your committee about the design of your experiments. If you are considering delaying your Qualifying Exam beyond the end of the spring semester of your 2^nd year, you should speak with the Director of Graduate Studies.

1. EXPERIMENTAL DESIGN AND METHODS (3-4 pages)

Explain in detail the experimental design and procedures that will be used to accomplish the specific aims

of the project. For standard experimental approaches (eg DNA sequencing or ELISA), cite an

appropriate reference for the method; no need to detail experimental specifics. For more specialized methods specific to your project, describe the approaches with sufficient detail to be understood by a reviewer not entirely familiar with your field of research. Discuss how data will be analyzed and interpreted. Discuss the potential difficulties and limitations of the proposed procedures and alternative approaches to achieve the aims.

1. LITERATURE CITED

Use complete literature citations, including all authors and titles. The bibliography need not be exhaustive,

but should be relevant and current.

FORMATTING:  The suggested lengths for each section refer to single-spaced text in easily readable type sizes such as Arial 11pt, with at least 0.5-inch margins, as required for NIH format. This is a minimum, all reviewers appreciate adequate spacing in the document. Try to avoid exceeding a total of 8 pages, excluding Literature Cited. You and your reviewers will probably appreciate liberal use of subheadings, which help organizing the material.  For example, if you have three specific aims, you will probably have three major subdivisions if Part IV, and additional subheadings within these.  Since this format is essentially that of an NIH grant, it may be useful for you to study examples of these, either from your mentor, your committee members, or other colleagues.

ORAL EXAMINATION:  The written Proposal will be presented evaluated by the student’s selected Thesis Advisory Committee. For the Oral examination, the student should present the written proposal in approximately similar format, with the background, justifications, aims of the research, preliminary data and proposed experiments (not necessarily in that order).  During the examination, the committee will discuss these aspects with the student to probe the student’s depth of knowledge on relevant topics and ability to think critically about aspects of their Proposal.

The committee may decide to award a full pass, conditional pass, or fail. The committee will provide detailed critiques to the student in order to meet the conditions to fully pass, or to help improve the thesis proposal and the oral defense in the case of a fail. The student must pass the qualifying exam on the second attempt or the program will recommend dismissal from the School of Medicine.

Milestone: PHDDISSERT

COMMITTEE:

The Thesis Advisory Committee includes the thesis advisor(s), and at least three other tenure track faculty members (minimum of four members). Eligible faculty are those recognized by the School of Medicine. Eligible faculty generally do not include faculty with clinical appointments, except those with secondary appointments in a basic science department, or those with approved membership on the Graduate Faculty. Faculty with primary appointments in departments in the School of Engineering and Applied Sciences (i.e., Biomedical Engineering, Chemical Engineering, etc.) are generally eligible.

Committee Representation: At least one faculty member on Thesis Committee must be from outside the home department of the thesis mentor, thus acting as the representative of the Graduate Faculty. Moreover, at least one faculty is required to be a member of the Biophysics program Steering Committee or designated as a representative of the Biophysics program. Faculty with secondary or guest appointments in the home department are not eligible to act as the Biophysics representative.

Thesis Committee Chair: The committee and student will nominate one Chair who will guide the proceedings and serve as the primary point of contact between the student and Thesis Committee. The Thesis Committee Chair should not be the student’s thesis Advisor.

DEFENSE:

The dissertation represents the summation of the student’s independent research. It must be an independently completed document that reports the results of your thesis research and makes a significant contribution into a Biophysics topic of biomedical research (broadly defined). There is no specific format, but generally the thesis document is separated into Chapters that including Introduction, Methods, Results, Discussion, Future Directions, etc. Preparation of this document will take a significant amount of time and time away from research work is expected.  At the final meeting of the Thesis Advisory Committee, the student should seek approval from their committee members (including the thesis advisor) to proceed with preparation of the dissertation and scheduling of the Thesis Defense.

The dissertation is to be prepared in consultation with the mentor. When the document is complete to the satisfaction of both the student and mentor it should be submitted to the rest of the committee at least two weeks prior to the Defense date. All Dissertation Committee members must agree to the Defense date and must be present for the Defense. To schedule the defense, contact the Program Administrator (Carrie Walker) and DGS (Ilya Levental), who will help find a room, disseminate information to the community, and begin the process of graduation.

The oral thesis defense consists of a formal presentation to the Thesis Advisory Committee, your scientific colleagues, and the public. This presentation is intended to convey the key aspects of the written dissertation and should be between 30-50 minutes, not including questions. Personal statements and acknowledgements are welcomed and encouraged. After 1hr of the public defense, there will be a question-and-answer session with the Thesis Advisory Committee to deeply probe aspects of the project, results, directions, and interpretations of the presented work.

If all members of the Thesis Advisory Committee agree that the thesis represents a significant scientific advance that was credibly defended by the student, the student is awarded their Ph.D degree.

Milestone: PHDDEFENSE

Upon approval from the Thesis Advisory Committee to proceed with preparation of the thesis, the student should contact the Program administrator and DGS, who will provide important information for the process of completing graduation and thereafter.

After successful defense of their thesis, the student must submit their thesis to the UVA library (see below), complete their Final Exam form, and ensure that they are in good academic standing. The deadlines for submission of all relevant forms to SIS are August 1, December 1, and May 1 (for summer, fall, and spring graduation, respectively).

The student’s academic appointment officially ends at the end of the semester in which they completed their thesis defense (check UVA registrar / academic calendar for specific dates). However, health insurance and other benefits may expire earlier, so it is important to get detailed information from the Program Administrator.

SUMMATION OF THESIS TO UVA LIBRARY

Doctoral students must upload the final, approved version of the dissertation to the University Library’s digital repository, also known as LIBRA, by the same due dates as for the Final Exam form.

Information regarding the repository, the submission process and copyright law is available through the LIBRA web site. Please note the following:

• The title page of the dissertation should be formatted according to the approved template. Signatures of the dissertation committee members should appear only on the final examination form. These signatures should not appear on the title page of the document that is uploaded to LIBRA.
• Students are responsible for ensuring that they upload the final, approved version of their thesis. Documents submitted to LIBRA cannot be deleted or corrected.
• The thesis title submitted to the department in step three above will appear in the LIBRA upload interface. If the title listed in LIBRA does not match the final title of the thesis, the student must stop the upload process and inform his or her departmental graduate administrator of the correct title. The thesis title listed in SIS, LIBRA and the student’s transcript should be identical.

LIBRA will accept the thesis as a single PDF document up to 100MB. Students also have the option to upload supplemental files.

Formatting Requirements

There are no formatting requirements or restrictions; however, students should adhere to traditional physical standards if they wish to purchase bound copies from UVA Printing and Copying Services.

Milestone: LIBRA

SURVEY OF EARNED DOCTORATES

All students are required to complete the National Science Foundation’s Survey of Earned Doctorates

Milestone: SURVEY

REQUIREMENTS FOR DUAL DEGREE PROGRAM

The Biophysics Program welcomes students from the Medical Scientist Training Program. Students in the MSTP are in an accelerated curriculum and generally complete their Graduate Requirements within 4 years. MSTP students have the core course BIMS 6000 waived and are required to complete 18 credits of graded coursework (instead of the standard 24) based on their completed work from the basic sciences portion of the MD curriculum.