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Biophotonics DE

Designated Emphasis in Biophotonics

I. Introduction

Description of the field, its importance, and recent developments

Biophotonics is the technology of generating and harnessing light and other forms of radiant energy to visualize, measure, analyze, and manipulate biological systems and materials.  Biophotonics is used at all scales of biology and medicine, from identification and analysis of organic and biological molecules, to cellular and tissue imaging and manipulation, and, at the largest scale, in the development of light-based surgical tools and whole body imaging. This field also spans the range of technical activities from basic scientific discovery in the realm of molecular and cellular mechanisms to the engineering of new tools for medical diagnostics and treatments. The field of biophotonics lies at the intersection of the optical communications and biotechnology revolutions. When applied to biomedical problems, this new field holds tremendous promise for producing widely used and economically viable optical devices for an array of applications ranging from screening for the predisposition of diseases, providing new implantable therapeutic and diagnostic devices, providing minimally-invasive therapies, and contributing to the fundamental understanding of biological mechanisms that are directly relate to human health.

Unique strengths in this field on the Davis campus

Given such importance in the new biology and technology interface, a center for research activities in all of these areas has been established. The Center for Biophotonics Science and Technology (CBST) has both a research goal and an educational goal. It is toward achieving the stated educational goals that faculty members of this Center have proposed to establish a new Designated Emphasis in Biophotonics.

Affiliated Ph.D. programs

Due to its intrinsically interdisciplinary nature, the preparation of graduate students in the area of biophotonics requires the broad participation of many of the already widely spanned Graduate Programs, both departmentally-based programs and graduate groups, that exist on the UC Davis campus.  Faculty members participating in this DE come from the Graduate Groups of Biophysics, Biochemistry and Molecular Biology, as well as the Departmentally-based Graduate Programs of Applied Science, Biomedical Engineering, and Physics. Faculty members from the Designated Emphasis in Biotechnology and several other Graduate Programs have also expressed interest in participating.

II.  Academic program of the Designated Emphasis in Biophotonics

  • Requirements for admission – all graduate students admitted to the Ph.D. program of the above-listed Graduate Groups and Departmentally-based Graduate Programs will automatically be eligible for admission to the Designated Emphasis in Biophotonics if they intend to complete their dissertation research in the field of biophotonics and choose a faculty advisor who is a member of the DE in Biophotonics. Even though the admission requirement for these different programs are distinct and different, the DE in Biophotonics welcomes the diversity in training background and will design an individual curriculum for each student who takes advantage of that breadth.
  • Curriculum – In addition to the primary disciplinary knowledge and skills provided by the student’s Ph.D. degree program, this DE in Biophotonics requires that each student  must master a minimum of materials from two major fields of knowledge: modern biology including some fundamental underpinning of diseases and current status in optical science and engineering. The required courses have been selected to provide training in the application of the most modern photonics methods to the fields of biological and medical research. These courses will contribute to the understanding of the basic biological mechanisms, the basic physical techniques and the fundamentals of implementing modern medical biotechnology. The CBST will offer research opportunities within the broad range of the Center’s activities, with research programs associated with not only campus projects but those at the UCD Medical Center and the Lawrence Livermore National  Laboratory.
  • Seminar series - The Designated Emphasis in Biophotonics will offer a seminar and a colloquium series each year for the students as well as researchers within the Center. In the first series, distinguished external speakers will be invited to present their research insights, in part to stimulate the students into thinking about new topics of research, and in part to initiate more collaborative projects between the Senior Scientists (Post-doctoral Fellows and faculty members) and the guest speakers. The second seminar series will give the project spokesperson and student researchers from each of the projects a chance to discuss their current results, to challenge their peers, and to initiate new cross-thrust projects. We envision the Distinguished Speaker’s forum to be held monthly, while the Science Seminar series will be a weekly program with a new course designation to be integrated into the Biophysics Program: BPH 292. Students are encouraged to attend the colloquium on voluntary basis; the year-long (3 quarter) seminar series, will be a requirement of the DE curriculum.
  • Fellowship opportunities -Top graduate students chosen to participate in the research activities of the Center will be recommended for one of two types of fellowships. The CBST will offer a number of CBST Graduate Fellowships each year. These Fellowships are for two-year periods with the possibility for one additional year on renewal. In addition, an equal number of top students will be recommended for the LLNL Student Employee Fellowships. These five-year fellowships are provided by LLNL on merit basis for those students whose projects have the joint sponsorship and participation of UCD faculty and LLNL senior staff members.
  • Core Courses

1. Required course in Biology:

BIM 202 Cell and Molecular Biology for Engineers (Simon) or MCB 221A Physical Biochemistry

Other specialty courses in this segment could include:     

BIM 214 – Blood Cell Biomechanics (Simon)
MCB 221 B,C, D, Metabolism & Regulation, Molecular, Cell Biology
MCB 241 – Membrane biology (Crowe, Voss)
MCB 242 Muscle Biophysics (Baskin)
MIC 263 - Principles of Protein – Nucleic Acid Interactions (Kowalczykowski)

2. Required course in Optical Science and Technology:

EAD 271 Optical Methods in Biophysics (Yeh/ Parikh)

Other specialty courses in this segment could include:

EAD 229 – Computational Molecular Modeling (Jensen)
EAD 273 – X-ray Spectroscopy and Synchrotron Radiation (Cramer)
EAD 289B – New and Emerging Techniques for Probing Biomolecular Structure and Dynamics (Balhorn)
EAD 289E – Special Topics in Biomedical Technologies (Matthews)
EEC 235 - Photonics
EEC 236  - Nonlinear Optical Applications
BPH 231 - Magnetic Resonance in Biology (Jue)

  • Impact on Normative Time of affiliated Ph.D. programs – The additional requirements for the DE in Biophotonics constitute a minimum of the two core courses and a year-long seminar series. The total number of units will be 2x4 units for the core courses and 3x1 unit for the seminar courses. This amounts to 11 additional units, or between one to two quarters of course work.  Most if not all of this work can be part of the electives for the student’s Ph.D. program.
  • Qualifying Examination and Dissertation Committees – We anticipate that the student will be ready for his/her Ph.D. Qualifying Examination once he has completed the Program’s requirement and the two-course requirement of the Designated Emphasis. The Qualifying Examination will assess the student’s level of knowledge and preparedness within the Designated Emphasis, as well as the Ph.D. program. Satisfactory performance on the Qualifying Examination for the Ph.D. will be judged independently from performance on the DE.  At least one member from the DE in Biophotonics will participate in the Qualifying Examination.  The DE member will be recommended by the Executive Committee of the DE, in consultation with the student, and will be appointed by the Graduate Council. The student’s dissertation committee will include a member of the DE in Biophotonics who will be recommended by the Executive Committee of the DE, in consultation with the student, and will be appointed by the Graduate Council. The dissertation topic will be relevant to the field of Biophotonics.

Degree conferral process

The Designated Emphasis will be awarded solely in conjunction with the Ph.D. and will be signified by the degree designation “Ph.D. in X with Emphasis in Biophotonics,” where X is the Ph.D. program.