Interregional Network for PhD Education and Research
Department of Biophysics
Professor Sinerik Ayrapetyan, Dean
The Department of Biophysics offers graduate programs leading to PhD degree. The Department is interdisciplinary in its orientation, and it draws on the diverse resources of international scientific community of UNITWIN network.
Programs of instruction and research are conducted in experimental, theoretical, and medical biophysics. In experimental biophysics substantial contributions have been made to structural molecular biology, radiobiology, transport processes with emphasis on biological membranes, the elucidation of the nature of biological sensors and receptors, the understanding of rhythmic behavior of biological systems, and electrochemical inter-cellular information transfer.
Theoretical biophysics includes such diversified areas as non-equilibrium thermodynamics, stochastic methods, transport, regulation and control, modeling of biological systems, application of quantum mechanics to biopolymers, theoretical estimates of forces between membranes, theoretical treatment of intermolecular interactions involving proteins and nucleic acids, and the structure and function of the nervous system.
Medical biophysics involves the application of biophysics to diagnosis and treatment. Medical biophysicists are expected to carry out biophysical research on topics directly related to medical problems, generally in close collaboration with medics, and to act as efficient intermediaries between medics and biomedical engineers.
The students will enjoy a high degree of independence and freedom in the development of research programs, choice of major advisors, and pursuit of dissertation research.
In each program (Biophysics, Biotechnology and Environmental health) the student takes the core courses during the first year. During this period the student becomes familiar to the research interests of the Department and selects an advisor for the Ph.D. dissertation work.
The overall requirements for the Ph.D. programs are described in the following sections followed by the specific requirements for each division.
PROGRAMS LEADING TO THE DOCTOR OF PHILOSOPHY (Ph.D.) DEGREE
Preliminarily it is suggested that the duration of PhD courses will be 3 years (12 semesters, in each 10 weeks). It is expected that during the reporting period 3 cycles of PhD courses will be performed. Courses will be conducted in compliance with PhD international program providing the students 66 credits. The courses will be given by the international team of distinguished scientists. PhD students will have the opportunity to conduct a part of their dissertation in foreign laboratories. PhD dissertation will be supervised by four leading scientists. The graduates will receive an appropriate diploma of the state standard according to regulations of home country. The students will be involved in research projects that will be implemented within the framework of the Network. English and modern computer courses are included in the program.
PhD courses leading to the doctoral degree (66 credits) will consist of the following components:
Theoretical courses (core and supporting) will be realized through DES and will be conducted by a team of leading lecturers from participant institutions (providing 17 credits) and some western institutions (10 credits). PhD students will have the opportunity to conduct a part of their dissertation (to obtain 5 credits out of 35 credits) in foreign laboratories. The duration of core and supporting courses (27 credits total) will be 45 weeks with five semesters, in each-10 weeks. At the end of each semester the examination on current courses will be organized.
In order to be admitted to the program the applicants should present MS degree diploma; 4 photos; 2 letters of recommendation from advanced scientists of the appropriate area. After accepting the documents from the potential students the entrance examinations will be organized to choose the students on the competition basis. The applicants will be examined according to their major and regulations of their home institution and will have to take an English language test. Those applicants who have publications in international journals will have priority in being accepted to the program. The graduates will receive an appropriate diploma of the state standard according to regulations of home countries.
A temporary advisor for each incoming student will be selected. The advisor will meet with the student whenever necessary to advice on course selection, advanced standing, course waivers, examination waivers, and selection of thesis/dissertation advisors. Recommendations concerning advanced standing, course and examination waivers will be submitted to Committee for Management and Programming of the Network. Students must meet with the research groups involved in the project before selecting a dissertation principal advisor.
After selecting a dissertation principal advisor at the end of the first semester, the student together with the principal advisor will select PhD Advisory Board, which will be composed of at least three other members from the participant institutions and one member from a western institution. The scientists will be chosen based on the dissertation topic as well as the eligibility criteria elaborated by the Education Group. The composition of the PhD Advisory Board will be reviewed and approved by the Committee for Management and Programming.
Before the end of the second semester of study an oral examination will be conducted and graded by the PhD Advisory Board. The examination will be administered by four members of PhD Advisory Board and will encompass broad general questions in relevant areas of the selected division. On the basis of the student’s performance in the preliminary examinations and grades in courses, the PhD Advisory Board will recommend that:
Qualifying Examination (Part 1)
At the end of the third semester, each student who has passed the preliminary examination will be examined by the student's Advisory Board, after all course requirements are completed. This will be an oral examination and will be in the major area of the anticipated research specialization. The Advisory Board will assign a pass/fail to the student. A student who fails may be reexamined within one year with the scope of the examination being determined by the Board. The student who fails to pass on the second try will be required to quit his study.
Qualifying Examination (Part 2)
This examination consists of an oral defence of a written research proposal prepared by the student. The proposal and the oral defence will be evaluated by PhD Advisory Board (Pass/Fail). The exam will treat the student’s depth of knowledge in his/her chosen area of specialization as well as his/her ability to write and defend a research proposal. This examination is to be on a topic intended to serve as a basis for the student’s PhD dissertation research. This examination will be at the end of the 4th semester.
The research proposal: should be a detailed document outlining the background and conduct of the proposed dissertation research and should be designed to answer a significant question in the field of his/her study. The student may consult someone in the course of preparing the proposal, but the written document must represent the student's own work. The principal advisor may aid in the development of specific aims and construction of a topical outline for the dissertation proposal. The advisor also may direct the student to relevant literature and may edit an initial draft. However, the advisor should not act as a co-author. The research proposal will be judged on standard criteria, including, but limited to, the student's grasp of the field, significance of the proposed work, originality and depth of thoughts and feasibility of the experimental approach. The proposal will be submitted to the PhD Advisory Board at least one month prior to an oral presentation of the proposal. At the oral defense, the student will answer questions on related topics; the questions focus on (but are not restricted to) the student's program area. The PhD Advisory Board, chaired by the dissertation advisor, will administer the exam. The student must pass the exam by the majority of votes of the Board. The PhD Advisory Board will communicate the data and results of the exam. If the student does not satisfactorily complete this part of the exam, the PhD Advisory Board will make appropriate recommendations, which may include modifying the proposal and re-taking the exam, completing remedial course work, or dismissal from the program.
Admission to candidacy: A student is admitted to candidacy for the degree of Doctor of Philosophy upon meeting the following standards:
Dissertation research, role of the PhD Advisory Board: The student’s Advisory Board will meet regularly with the student throughout the course of his/her dissertation research to evaluate progress and advice. The Advisory Board is also responsible for evaluating and accepting the final written dissertation and conducting the student’s oral dissertation defence. Acceptance of the dissertation will be by majority of votes of the Advisory Board and is subject to the approval of Committee for Management and Programming.
Laboratory rotations: The laboratory where the student is intended to pass the rotation will be selected by the student’s Advisory Board. The aims of the laboratory rotations are:
It is advisable that all students regardless of their previous laboratory experience participate in the lab rotations and should not repeat a rotation in with the same mentor. The student is expected to put at least 12 hours per week during each rotation.
The rotation schedule will be designed to obtain the maximum lab (clinical) experience within the framework of courses and additional graduate responsibilities. There will be a Summer Rotation for students who enter the program early or those who enter in January and wish to satisfy their rotation requirement before the fall semester. Data for these alternate rotation schedules may be obtained from the PhD Advisory Board. At the end of each rotation the students will be required to write a brief report (3-5 pages) describing their project. This report should be given to the research advisor and, after his/her final draft, must be submitted to the PhD Advisory Board one week after the end of the rotation. The student will be responsible for submitting this report and the failure to do so will result in an incomplete grade. At the end of the core courses, i.e. after receiving 15 credits, the final examination will be organized. Starting from the 4th semester the students will continue their study in the supporting courses according to their chosen directions (tracks). The main tracks of the program will be discussed and finalized during the first meeting of the consortium. By the end of the 4th semester the dissertation subject and the members of the Advisory Board of each student will be finalized and approved by Committee for Management and Programming.
The supporting courses will also have practical and theoretical parts. The laboratory rotations will be organized in specialized laboratories of participant institutions and the theoretical part will be taught by the invited lecturers of both participant institutions and leading western universities through DES. By the end of the 5th semester the examinations and seminars on the subjects of the dissertation works will be organized for each student and only after receiving the approval from Committee for Management and Programming, they will finalise their dissertation thesis under the leadership of members of the PhD Advisory Board.
Core Courses in Biophysics (15 credits)
1. Biological Information (1 credit)
Information theory and its application in biology discussed. Topics: physico-chemical principles of information transfer at the molecular level, including DNA, RNA, proteins, peptides, storage and retrieval of information in the brain; molecular modification of information by radiation, chemical, and biological methods.
2. Molecular Biophysics I (1 credit)
Introduction to the major areas of molecular biophysics and their foundations in chemistry and physics. Will include: molecular interactions, structural analysis through diffraction techniques, macromolecular physical chemistry, the effects of physical forces on biological structures, and thermodynamics systems.
3. Molecular Biophysics II (1 credits)
Conformation of Biological Macromolecules. Will include: Structure of ferments, nucleic acids and other biological polymers; the role of hydrogen bonds, hydrofobic forces and ion bonds in stabilization of the different structures of biomacromolecules will be discussed.
4. Processes in Biological Systems (1 credit)
This course is concerned the fundamental physical and physico-chemical treatment of various kinetic processes underlying the normal function of biological systems. Topics include: no equilibrium processes, thermodynamics and statistical mechanics, osmotic and hydrostatic forces, membrane permeation and potentials, and the mechanisms of excitability.
5. Cellular Biophysics I: Membrane Transport (2 credits)
Fundamental theory and principles of transport processes and membrane phenomena in biological systems. Serves as a basis for discussion of representative biological examples, including: transport involving water, non-electrolytes, and electrolytes. Theories and principles developed to the state of current research knowledge.
6. Cellular Biophysics II:
Structure and Function of Neuromuscular System (2 credits)
Current concepts and experimental approaches to study the cellular bases for nerve and muscle structure and function. Topics: bioelectric phenomena, membrane excitability, mechanochemistry, bioenergetics, and current theories of muscle contraction. The course is self-contained and independent of Cellular Biophysics I.
7. Membranes (1 credits)
Biophysical aspects of model and biological membranes. Topics: chemical composition and physical properties of membranes, structure-functional relationships, model systems, lipid-protein interactions and other selected topics of biological interest. Presented alternate years, fall semester.
8. Ion Channels (2 credits)
Ion channels are responsible for information transmission in biological cells. They generate nerve and muscle electrical activity, control the secretion of hormones, and account for sensory transaction. This course will examine ion channels from the molecular level up to their role in controlling cellular processes. The course will be a combination of lectures, problem sets, and student seminars on current topics.
9. Radiation Biophysics (1 credit)
Studies radiation effects on water properties. Radiation-induced excitation, oxidation, reduction, and dissociation examined particularly in biomolecules. Reactions of primary spacious produced in radiolysis of water reviewed. Biological implications discussed. Emphasis is made on the analysis of radiation effects by magnetic resonance methods.
10. Mathematical biophysics (1 credit)
This course will present theoretical aspects of biology and biophysics. Various aspects of chemical physics, quantum mechanics, and statistical mechanics, together with thermodynamics relevant to biophysics solutions, proteins, cell membranes, and transport will be covered in the first semester. Appropriate aspects of mathematics will be reviewed. The second semester will concern applications to theoretical biology, including mathematical modeling. Both linear and nonlinear problems of biology will be studied.
11. Computers and their Applications In Biomedicine (2 credits)
An intermediate level approach to the range of applications of computer techniques in biomedical research and in the clinics. Emphasis is placed upon hand-on experience with existing applications software, development of special purpose programming, and analysis of algorithms and their hardware implementations to accomplish typical computational tasks.
Supporting Courses in Biophysics
1. Medical Biophysics (1 credit)
Involves application of physical and physiochemical principles to diagnosis and treatment. Course describes the design of diagnostic and therapeutic instruments. Scope and limitations of these techniques are discussed in context of appropriate medical situations, as are methods for quantitative evaluation of diagnostic information.
2. Statistical Thermodynamics (1 credit)
Brief review of the elementary principles of thermodynamics and statistical mechanics. Emphasis on application of statistical mechanical treatment to the variety of biological and biologically important phenomena. Topics: phase transition, macromolecular configuration, transport phenomena, and theory of polymeric solution. The statistical mechanical aspects of biological evolution as expressed by fluctuation considered.
3. Nerve System Theory (1 credits)
Responses and interactions of single cells; nerve nets; receptive fields, visual adaptation, size and space perception; information processing; general principles of nervous system structure and function.
4. Instrumental Techniques in Biology and Medicine (1 credit)
Surveys modern techniques of gas chromatography-mass spectrometry, including some laboratory experience in the use and maintenance of GC/MS instrumentation. Other topics include ionization methods, spectra interpretation, computerized data acquisition systems, and biomedical applications.
5. Evolvent of Life (1 credit)
Following brief review of history of theories on origin of life; course focuses on current theories and on their foundations in stellar evolution, geochemistry, molecular biology, and paleontology. Emphasizes thermodynamic and kinetic constraints of chemical evolution to select the most plausible mechanisms. Different fundamental biochemical processes are discussed with an attempt to come up with plausible theories for their evolution. The general characterization of living systems are discussed in considering the possible existence of extraterrestrial life.
6. Engineering and Physical Principles of Clinical Biophysics I (2 credits)
Offered to medical students and graduate students in electrical engineering, physics, and biophysics. Intended to familiarize them with the advances in medical technology as well as with underlying principles of physics and engineering. Emphasizes application of existing and forthcoming technology to medical problems. Students are encouraged to develop innovative ideas regarding new or improved technological solutions to pertinent medical problems.
7. Engineering and Physical Principles of Clinical Biophysics II (2 credits)
Continuation of BPH 16. Topics: use of ultrasound, electric pacing of heart, diagnostic radiology (including computerized tomography, magnetic resonance imaging, radiation therapy, and intensive care instrumentation).
8. Experimental Biophysics (1 credit)
Intensive laboratory experience with contemporary biophysical techniques: quasi-elastic laser scattering from cells and polymers, electrophysiology of membrane transport, fluorescence probe studies of membranes, dynamics of muscle contraction and psychophysics of vision. Lab reports are presented orally each week. Students are expected to do a brief independent project. LAB
9. Isotopes and Their Applications (2 credits)
Intended primarily for biochemists, pharmacologists, physiologists, as well as for medical researchers, interested in the application of isotopes as tracers, isotopic dilutants, probes of molecular structure and dynamics of chemical behavior at the molecular level. Topics: isotope effects and their utilization in isotope production and in chemical, biochemical, physiological research; methods of radioisotope production, measurement and assay techniques including mass spectrometry, magnetic resonance, infrared and Raman spectroscopy; major routes for the synthesis of single and multilabeled compounds; detection techniques for radioisotopes; atomic and molecular tracers in biological systems; isotope dilution analysis in pharmacology and toxicology; potential uses in clinical laboratory and in routine clinical practices.