Education and Training

Rationale

Advances in biophotonics require research over an exceptionally broad range of disciplines:  biology and medicine, quantum chemistry and optics, materials science and engineering.  Individual researchers can spend entire careers in one subspecialty of any of these disciplines.  Clearly the key to advances in biophotonics is the ability of researchers in each of these fields to understand the strengths and limitations of the others, and to have the broad perspective that enables them to direct their own activities in a way that both draws on and supports the efforts of the others; researchers need to know where they fit in and how they can contribute.  The fundamental aim of the proposed IGERT training program, inasmuch as it extends the traditional discipline-oriented graduate experience, is to impart its students with the broad knowledge needed for them to function and contribute to a trans-disciplinary team of researchers that aims to apply photonics to solve problems in biological systems.

IGERT Fellows will be admitted directly to one of the six departments participating in this program (Chemistry, Chemical Engineering, Electrical Engineering, Biomedical Sciences, Physics, or the Medical School), and this department will be designated the “home department” of the student throughout his/her tenure here.  The student must conform to all regulations and degree requirements of the home department, and the degree obtained by the student is that granted by the home department.  A certificate program in Biophotonics will be established, and students will be granted the certificate upon completion of additional requirements, outlined below. IGERT Fellows will be required to complete the certificate program, and their continued support will be conditioned upon satisfactory progress toward these requirements (as well as those of the home department). But the certificate program is not limited to IGERT Fellows.  Any interested student in one of the participating departments is eligible to pursue the requirements needed to obtain the Biophotonics certificate, and in this way we leverage the IGERT funds to impact a broader range of students than those supported by the grant.

By requiring that each student complete the full degree requirements of one of the participating departments, we will produce scientists that have a strong foundation within a specific discipline, and yet through the IGERT experience these students will also emerge with the broader knowledge needed to interact effectively with researchers trained in other specialized aspects of biophotonics.

IGERT Program Requirements

IGERT students must complete all degree requirements of their home department.  In addition, to obtain the certificate in biophotonics, IGERT-supported students must complete the following requirements. Students pursuing a Ph.D must complete five required courses and at least three courses from a list of electives. The remaining credit hours will be taken from the specific degree program into which they were admitted.  In this manner, students will focus on biophotonics, experimental optical techniques, computational techniques, and research ethics.  The ethics course will cover the basics of research ethics, publications, and presentations.

Required Courses:

^*To be announced - Proposed course with exact course number not available at this time.  These courses will be cross-listed between departments participating in this IGERT.

C.c.2.ii                       Elective Courses

                                 Biology

                                  Chemistry

                                  Chemical Engineering

                                  Electrical Engineering

                                  Physics

                                  Additional General Electives:

Additional courses will be taken from listed graduate courses for the specific area of enrollment of the student.  More importantly, at the University at Buffalo (UB), we are continuing to improve the educational process for our students.  We recognize that the exclusive use of lecture style teaching is largely ineffective in motivating students, stimulating student interest, and constrains students’ learning .  We have successfully converted some of our lecture courses to laboratory courses that incorporate pedagogical techniques that have resulted from engineering and science curriculum reform. Moreover, active-learning environments are used to prepare students for industry by emphasizing working in teams, speaking and writing skills, and solving ill-defined problems . These techniques were central to the report from the Presidential Young Investigator Colloquium on “America’s Academic Future”.  New courses developed for this program will focus on the use of these techniques.

Courses to be Developed:

Biophotonics/Imaging Laboratory

This laboratory course will provide a mechanism to train graduate students in the fundamentals of basic techniques in preparation of biological samples, use of advanced imaging and microspectroscopy instrumentation and finally the integration of the techniques learned in the first parts of this course.  The first trimester of this laboratory will provide students with basic training in cell culture techniques including handling of pathogenic organisms.  Establishment and maintenance of eukaryotic cells will be focused on emphasizing appropriate use of sterile techniques.  Appropriate training in safe handling of pathogenic organisms at the biological level 2 and training (virtual) on handling of biological level 3 pathogens will also be provided.  Techniques in protein purification and modification will be taught using the using state-of-the-art equipment.  Hands-on training on advanced imaging equipment (confocal microscope, atomic force microscope, optical coherence tomograph) will be provided.  Laser alignment and instrument calibration for microspectroscopy will be part of this laboratory course.  Finally, skills acquired in biological and imaging sections will be integrated to provide the students with the necessary experience in operational biophotonics.

Imaging and Microspectroscopy

This course will provide students with a graduate level course that is focused on the fundamentals in microscopy and spectroscopy.  Focus will be on the theories in spectrometry, multimode fiber technology, detector technology (PMT, APDs and etc.) , and microscopy.  Optics and electronics necessary for imaging and microspectroscopy will be included as part of the curriculum. 

C.c.2.iv                     Research Rotation

Meaningful research rotations foster multidisciplinary perspective, and give students structured practice in collaborative research.  Intermittently during their second and third years, IGERT students will complete a brief (1-semester) project in at least one laboratory or research group outside their home department.  Students will have completed a required or elective course relevant to each project before beginning the corresponding rotation period.  In this manner the student arrives at the host lab at least partially prepared to contribute to the research activities being performed there.  Each project will be performed in conjunction with another student resident in the host lab, and it is expected (but not formally required) that the student’s contribution to the project will be sufficient to warrant co-authorship on a publication resulting from his or her activities (primary authorship is not expected).  Attempts will be made to designate host students who are also IGERT fellows, but logistically this may not be possible in all cases.  Students hosting another fellow gain experience gains some leadership experience as he or she helps to guide the efforts of the visiting student.  Additionally, each student rotator is required to give a 15-minute presentation on the research experience and its outcomes upon completion of the project, and provide a formal report that will demonstrate that the fellow has acquired sufficient operational knowledge of the subject matter of the laboratory that was visited. This report is to be submitted to the advisor and the IGERT program. The grade for this research rotation is determined by the fellow's faculty advisor in consultation with the faculty member that hosted the fellow in their laboratory.   The presentation is made as part of the Multidisciplinary Colliquium.

The Research Rotation is an experience unique to the IGERT program in most of the departments.  The motivation for the Rotation is to prepare students to work as part of a research team, giving them the opportunity to bring some of their own expertise to a group having strengths that lie elsewhere.  As a beneficial side effect, the Rotation will enhance the lessons learned in the classroom.  By applying these lessons to a realistic research problem, the student gains better depth of understanding, acquires a longer-lasting retention, and becomes receptive to learning more about the field.

Faculty participants in the IGERT program will be required to formulate and offer projects for the Research Rotation, making at least one available (or filling at least one) at all times.  Project descriptions will be distributed to all IGERT fellows, including a description of pre-requisites that must be satisfied (e.g., completion of a particular course) to be accepted to the project. Each fellow can elect at any time after the third semester of study to perform a Rotation in one of the available positions.  Decisions regarding placement of the fellows with each project is made by the Steering Committee in consultation with the faculty participant hosting the project.  Each project has a duration of one academic semester (four months), or one three-month summer period.  One industrial internship (described below) may be substituted for one of the three Rotations.

Co-Advisement

Each IGERT fellow will be designated a faculty research advisor from within his or her home department.  The faculty-student selection process will be conducted by the Steering Committee in consultation with the graduate chair of the department.  Additionally, each student will have a designated co-advisor from a second department.  The role of this advisor is to foster the interdisciplinary activities of the student, and in particular to ensure that the student does not become too focused on research activities related to his primary discipline, at the expense of the interdisciplinary aspects of the research.  The co-advisor would normally serve as the host for one of the students Research Rotation periods, and the project performed with the co-advisor is expected to relate to an integral component of the student’s thesis research.  Each student is expected to participate at least half-time in the regular group activities (e.g., weekly meetings) of the co-advisor’s group.  Any research or administratative conflicts that may arise between the student’s advisor and co-advisor will be resolved through petition to the Steering Committee.

Multidisciplinary Colloquia

A Multidisciplinary Colloquium Series on Biophotonics with speakers from all pertinent research areas will be held. Colloquium speakers will include faculty participants, invited external speakers, and IGERT students, who will be required to give 15-minute presentations at the conclusion of each Research Rotation they perform.  All IGERT students will be required to attend the colloquia.  The series serves the purpose of enriching both the academic and social networks among the students and faculty.

Multidisciplinary Efforts in Education and Training

To summarize, the proposed IGERT program requires of its student fellows participation in a wide variety of activities designed to foster a multidisciplinary outlook and broad expertise

·        A diverse set of IGERT students must all complete a common core of coursework together

·        Students must take elective courses outside of their core discipline

·        Each student has a primary advisor and co-advisor from outside the core discipline

·        Three research rotations are required, each involving activities at a level aiming to result in co-authorship of a paper

·        Fellows will be positioned to lead research activities of other students visiting on their rotation

·        All students are required to attend and participate in a Multidisciplinary Colloquium on Biophotonics

C.c.6     Specific Departments and Their Degree Requirements

All departments that are actively participating in this program can easily accommodate the required 16 hours of courses.

Chemical Engineering.

Graduate students in chemical engineering are required to complete 72 credits of study to obtain the Ph.D. degree.  This includes four core curriculum courses: CE 509 Transport Phenomena, CE 525 Advanced Chemical Engineering Thermodynamics, CE 531 Chemical Engineering Analysis I, and CE 561 Applied Chemical Kinetics. Many other graduate courses covering such topic areas as tissue engineering, statistical mechanics, polymers, colloids, and materials science are available as electives, and students may choose elective courses that are closest to their research interests; electives taken outside the discipline are permitted also. A maximum of 30 credit hours can be derived from a completed M.S. degree, with no more than 6 credit hours derived from an M.S. thesis. Students do not need to have an M.S. degree to be admitted to the Ph.D. program. All doctoral candidates are required to actively participate in the Chemical Engineering Seminar Series.

Chemistry

Graduate students in chemistry are required to complete 72 credits of study to obtain the Ph.D. degree.  There are no core curriculum courses required.  Students are required to complete 54 hours within the department.  The remaining 18 can be taken from any department. A maximum of 30 credit hours can be derived from a completed M.S. degree, with no more than 6 credit hours derived from an M.S. thesis. All doctoral candidates are required to actively participate in the Chemistry Seminar Series.

Electrical Engineering

Graduate students in electrical engineering are required to complete 72 credits of study to obtain the Ph.D. degree.  There are no core curriculum courses required.  Students can choose from courses in EE511 Problems in Biomedical Engineering, EE521 Modern Microscopy, EE562 Principles of Medical and Radar Imaging, and EE580 Biomedical Electronics. Many other graduate courses covering such topic areas as electronics design and imaging processing techniques are available as electives, and students may choose elective courses that are closest to their research interests; electives taken outside the discipline are permitted also. A maximum of 30 credit hours can be derived from a completed M.S. degree, with no more than 6 credit hours derived from an M.S. thesis. Students in electrical engineering have to complete the equivalent of the M.S. degree to be admitted to the Ph.D. program. All doctoral candidates are required to actively participate in the Electrical Engineering Seminar Series.

C.c.6.iv                     Physics

Graduate students in Physics are required to complete 72 credit hours of study in Physics and related disciplines, at least 36 of which must be formal course work.  Core curriculum courses that are required by the department are: Graduate laboratory -- PHY 551 or 552; Classical Mechanics -- PHY 509; Electrodynamics I and II -- PHY 513-514; Quantum Mechanics I and II -- PHY 507 - 508, and Statistical Physics I -- PHY 519. In addition, students interested in condensed matter physics are recommended to take elective courses in Introductory Solid State Physics -- PHY 527-528, Quantum Theory of Solids and special topics courses in Modern Optics and the Physics of Semiconductor Nanostructures.  Most students also take one semester of Computational Physics.  Elective courses in related disciplines are also permitted. Up to 12 credit hours can be transferred from an existing MA or MS degree in Physics.  All doctoral candidates are encouraged to participate in the departmental colloquium series, and more advanced students are encouraged to participate in the departmental seminar series.

Department Summary

The four principal doctoral programs involved in this IGERT program have sufficient flexibility to accommodate the Biophotonics IGERT requirements within their degree electives.  From the departmental perspectives, the IGERT requirements will appear as department electives.

Visiting Speaker Seminars

We have requested funding for one international speaker to give a seminar.  In addition, we have requested a modest amount of funding for two domestic speakers per year.  These speakers will be respected scientists in the area of biophotonics. 

Role of Undergraduate Students

Finally, in addition to graduate students, researchers at UB have been fortunate to attract some of the best undergraduate students to their research.  These include a number of undergraduate students that were awarded NSF Graduate Research Fellowships and Department of Defense Graduate Research Fellowships based on their undergraduate research efforts. We will continue every effort to enhance our ability to provide stimulating research activities for students interested in photonics and biophotonics. We feel that these students can serve as an excellent source for entry into this IGERT program.

C.c.9     Internships:

Internships in Industry and National Labs will be developed for participating students to broaden their skills and experience.  To date, the following companies and National Labs have agreed to serve as locations for internships for our IGERT Fellows.  We have included a sample of the letters that were provided in support of this proposal in the Supplementary Documentation section.

Advanced Cytometry Instrument Systems (ACIS)

ACIS is a newly established company in Amherst, NY committed to the development of advanced cytometry instruments using the most recent advancements in the field.  The cytometers currently being tested and prototyped will provide new capabilities as well as being modular, smaller and more versatile overall.  The design testing and construction of these devices requires the skills of people trained in many disciplines. Contact/Mentor: Carleton Stewart.

Pixel Physics

Pixel Physics is a Rochester, NY corporation specializing in the design and development of photonic systems for science and industry.  Our areas of interest and specialization include digital imaging systems, spectral imaging, optical MEMS, and laser-based sensing.  Pixel Physics concentrates on emerging technology areas, with particular activity in the space remote sensing, and biophotonics markets. Contact/Mentor: Kevin Kearney.

Coherent

Coherent Inc., is the world´s leading supplier of lasers and lasers and laser-based solutions for medical, scientific and commercial applications. Founded in 1966, they bring customer solutions to light by designing and manufacturing the industry´s most diversified selection of laser-based products. Coherent is focused on two principal market segments: the electro-optical marketplace, and the medical market. Coherent pioneered the development of the medical market for lasers in 1970 by introducing the first laser products used in ophthalmology. In addition, their lasers are now used in such other diverse medical applications as orthopedics, urology, gynecology, neurological surgery and aesthetic surgery. Aesthetic solutions now represent the fastest-growing segment of Coherent´s business, and include such applications as skin resurfacing, hair and tattoo removal, and the treatment of vascular and pigmented lesions. Contact Person: David Kemp.

C.c.9.iv                     Advanced Refractory Technologies (ART)

ART is a privately held company, established in 1981, with operation in Buffalo, NY, and Amesbury, MA, as well as joint ventures Bekaert Dymonics (Belgium) and ART KK (Japan) that uses state-of-the-art technologies in the manufacture of electronic packaging systems, non-oxide ceramic materials, thin-film diamond coatings, metal matrix composites (MMC's) and developmental R&D.  These materials are used by the wireless/telecommunications, microelectronics/semiconductor, transportation/military, biomedical, aerospace, electronic/industrial, energy and nuclear industries. Contact/Mentor: Roger Storm.

Air Force Research Laboratory, Materials and Manufacturing Directorate
Polymer Core Technology Area:  Photonics

AFRL/ML is an approximately 800 individual organization with greater than $250M yearly combined budget, tasked to investigate novel materials and manufacturing issues for the Air Force.  The fundamental research at AFRL/ML encompasses all aspects of materials and thus numerous unique facilities, both experimental and computational, are maintained and available for research.  Specifically, current efforts focused on photonics and nonlinear optics in the Polymer Core Technology Area include 1) synthesis of ultra-large two-photon absorbing chromophores, associated photophysics and development of potential application technologies including optical microfabrication, data storage, and nondestructive investigation; 2) synthesis of hierarchical organic-inorganic nanoelements including dendrimers, core-shell nanoparticles and metal-organic chelates for unique optically induced charge transfer; 3) nanofabrication techniques based on holographically induced photochemistries to control alignment and aggregation of nanoelements in precise patterns for filters, circuitry and sensors; and 4) investigation of biology and development of bio-harvesting concepts for artificial photonic devices, such as elucidating the role of the protein shell in the nonlinear response of green fluorescent protein (GFP), assembling virus particles into photonic band gap materials or characterizing and assembling mesostructures (100-500 nm) from marine organisms in waveguide devices .Contact/Mentor: Rich Vaia.

Laser Photonic Technology (LPT)

LPT is a company with more than 10 years of experience developing optical materials, lasers and working with customers to find innovative solutions. LPT has successfully developed laser targeting devices for use in fluoroscopic surgical procedures, an analytical device for assessing uniformity of engineered and natural tissues, fiber optic chemical sensors, and, through partnerships with other companies, a wide range of solid state tunable laser products intended for research and light industrial applications. Contact/Mentor: Martin Castevens.

C.c.9.vii                   Other New York State Institutions

Two other New York State Institutions will host students through an internship program:

1) The Center for Imaging Science at the Rochester Institute of Technology has 36 research and teaching laboratories dedicated to specialized areas of imaging science, including electronic imaging, digital image processing, remote sensing, medical imaging, color science, optics, and chemical imaging. Contact/Mentor: Ian Gately.

2) The Center for Advanced Thin Film Technology at the State University of New York at Albany has served as a unique environment to pioneer, develop, and test new ideas within a technically aggressive yet economically competitive research environment. The mission of the Center is to act as a research, development, education, and economic outreach resource for industries that manufacture, use, or supply microelectronics, electronics, optoelectronics, bioelectronics, nanotechnology and telecommunications devices and components. Contact/Mentor: James Castracane.

Soft Skills Development

IGERT trainees will have several opportunities to practice and hone their communication and research planning skills as part of the IGERT requirements. 

·        As part of the research rotation experience, each student will be required to give a 15-minute presentation on his project activities.  He or she will also contribute to the writing of a journal article that is expected from the project activities

·        Trainees must prepare, semi-annually, written reports detailing their progress and plans for the coming period.

·        A written research proposal must be presented to the Fellow’s Ph.D. thesis committee plus at least one member of the IGERT Steering Committee.  Approval of the thesis proposal must be obtained for continued IGERT support.

·        Other, less formal activities (e.g., presentation in group meetings) will form part of the regular research experience of each student.

Diversity

Diversity of all kinds promotes innovation in research.  Persons of different educational and cultural backgrounds bring to the table of ideas perspectives unique to their experience.  Each individual must be encouraged to voice his or her ideas regarding the research activites of the other IGERT participants. A primary vehicle for this exchange is the Multidisciplinary Colloquium.  Active efforts will be made by the faculty participants at the colloquia to encourage students to speak up and contribute to the discussions.

Integral to the proposed IGERT program is diversity of undergraduate training.  Many students will come into the program with B.S.-level degrees in engineering, chemistry, physics, or biology.  Each arrives with different experiential emphases acquired from the undergraduate discipline and the institution.  Cultural diversity will also be fostered through efforts to recruit traditionally underrepresented students into the IGERT program, so that the admissions procedure will yield a more diverse group of trainees and graduates than would result under a more passive recruiting strategy.

Program Goals and Evaluation:

We plan to follow the goals and evaluation criteria set forth in Table 1 below.  Specifically, we will monitor our program and attempt to improve our graduate program in quality and diversity.

Table 2: Goals and Evaluation Criteria for Education and Training