Development

of a

Biological Physics Curriculum

at the

Physics Department of the University of Illinois

at Urbana-Champaign

Report of Committee, December 4, 2000

Klaus Schulten (chair), Robert Clegg, Enrico Gratton,

Taekjip Ha, Ioan Kosztin, Paul Selvin

History may repeat itself in the development of condensed matter and biological physics: The beginnings of the 20th and 21st century show a remarkable similarity: The 20th century saw discoveries of the atomic level structures of inorganic matter, the 21st century saw the discovery of genes and crystal structures of living matter. These discoveries established the foundations of new eras of research, the era of solid-state physics, materials science and the electronics industry in the 20th century, and the era of systems biology, biomedicine and biotechnology in the 21st century. The UIUC physics department played a great role in the former case, and is today the US academic leader in solid-state physics. The materials research laboratory was initiated on the UIUC campus, and the physics department contributed to the formation of key departments of UIUC's College of Engineering. The UIUC physics department can play a similarly important role in the new century if it applies the same farsighted vision that its leaders showed decades ago.

In fact, the vision of the UIUC physics department can be important for the development of the whole UIUC campus at a crucial moment. On many US university campuses the birth of new laboratories devoted to genomics and postgenomics are being witnessed. Their research efforts are inventorying genes and proteins of living organisms. Our campus is struggling to position itself as an important national institution in these critical endeavors and one wonders with a sense of great trepidation what role UIUC will play ten or twenty years from now.

The role of the University of Illinois at Urbana-Champaign in the future of life science and biotechnology: Actually, one must not worry, provided we built on our strength. The University of Illinois at Urbana-Champaign (UIUC) can place itself far ahead of others that are now leading the genomics and life science gold rush if it realizes its strength and great traditions, and does not try to imitate others and play catch-up. Our strength lies in the integration of physical science into emerging fields; just as this was done in material science and electronics in the past, we can achieve this in systems biology and biotechnology today. Our intuition based on a strong physical background tells us that although taking the inventory of organism is a wonderful achievement, the information accumulated - gene sequences and biopolymer structures - need to be woven into the same intellectual fabric that laid the foundation of 20th Century science and industry, a thorough understanding built on physical principles and mathematics.

We at UIUC can prepare our students and ourselves for the great opportunities that will become available (and are already there) when genes and protein structures have become largely known. The realization is already becoming evident that having taken the inventory leaves much unexplained and does not reveal how this enumerative knowledge can be turned into new medicines and technical products. In addition, our ability to acquire new physical data with such complex systems and to interpret intricately complex interactive systems must improve dramatically, in order to keep pace with the enormous influx of descriptive biological data. New paradigms of the organization and functioning of large complex, interactive living systems will be required. This will require a new style of physically and mathematically trained scientists with sophisticated knowledge of the biological systems as well as a solid physics background. Such training and education in a physics curriculum is not offered presently almost anywhere in the United States, and we have the opportunity to be pioneers in such an endeavor. Within about a year, the genomes of more than hundred organisms will be sequenced and over 20,000 protein structures be solved. Soon thereafter, most proteins from a single organism will be structurally resolved. However, even now we know that knowledge of a relevant gene is not enough. We must know what the gene product is and how it performs its function; knowledge of a protein structure, with notable exceptions, most often reveals little about the physical mechanisms underlying function. Indeed, drug development is still mainly a fishing expedition. Rational design in pharmacology and biotechnology will require an understanding beyond genes and structures, an understanding of function, mechanisms, and system integration.

It is actually not difficult to imagine the postgenomics state of the life sciences. We will, for the first time, have a truly global view of the state of an organism. We will know at the various stages of the life cycle the state of expression of all genes and the quantity of all proteins. We will have detailed insight into the structures of active biopolymers, as well as tools that image the morphology of organisms from the atomic level to the cellular level and beyond This information will create a renaissance of physical life science and will set the stage for the physicist. Progress in this new field will be focused on a detailed understanding of the material substrate of living systems, and physicists will make the major contributions to this new field as they now do in condensed matter physics. Biological physics is already a strong discipline, but progress in our physical descriptions has been largely limited by the available information, or rather the lack of it. For example, much of biophysics dealt for decades with a single protein, myoglobin, simply because this was the first protein to be structurally resolved. In the near future, any biomolecular system can be studied by a biological physicist. We will be able to base our choice on functional relevance rather than on what is available. For example, we will be able to investigate all proteins of the photosynthetic and respiratory apparatus that convert light and food energy into the synthesis of ATP, and we will not only be able to study the proteins one by one, but how they assemble and function together.

The role of UIUC’s physics department in a new era merging physical and life sciences: One can safely predict that biological physics will play the same role in the sciences and engineering as condensed matter physics did in the last century. The UIUC physics department is already well positioned for its part in the renaissance of the life sciences provided we orient ourselves appropriately and timely. It has pioneered the field of biological physics in the US over three decades long before any other physics department. We have recently consolidated and extended our faculty, now numbering five primary members (Clegg, Gratton, Ha, Schulten, Selvin) and several affiliated members. However, in keeping with the tradition and mission of an academic institution, faculty hiring must be complemented by a strong teaching program. We suggest to the department to accomplish this through a system of undergraduate and graduate level courses that is described below. This system replaces the single existing biological physics course through a set of three undergraduate and three graduate courses, with possibilities to be expanded and modified in the future (as is required of such a fast moving field). This set of courses will establish biological physics as a core discipline in the UIUC physics department that is commensurate to the other main disciplines in the department, as astrophysics, condensed matter physics, elementary particle physics, and nuclear physics. The suggested courses also address the needs of these latter fields, as well as those of other departments. This is especially apparent in the case of the suggested spectroscopy and non-equilibrium statistical mechanics courses (see below). The courses promise to enrich all graduates of the physics department, irrespective of their chosen fields, familiarizing them with concepts and methods of life science industries that may serve them well in future employment situations.

The biological physics curriculum development committee: During the past three months a committee formed by the entire biological physics faculty developed an outline for a new curriculum. The suggestions are based on deliberations that included other members of the department as well as numerous faculty from related fields such as chemistry, the life sciences, and bioengineering. A curriculum emerged from these discussions that promises to strengthen our department. In addition, it complements teaching in other campus units that strengthens UIUC as a whole. The consultation with faculty from other units revealed that the physics department must play the leadership role in establishing the physical life sciences on our campus, both because of the centrality of the physics discipline, and because of the coherence and size of its participating faculty. The rapid evolution of modern life sciences brought about many new methodologies, as new imaging technologies, new types of spectroscopy, and biological computing, for which an urgent need for a curriculum has emerged. It is clear that these are best taught in physics, especially at this early stage of methodologies. The hiring of new faculty in biological physics has placed the physics department ahead of other units in terms of size and strength, in particular, since the department has also key members from other departments that are affiliated with physics, such as chemistry (Gruebele and Makri). Our faculty members collaborate and communicate closely with these and other chemistry faculty (Luthey-Schulten, Martinez), and we have also well-established affiliations with the life science departments.

The committee has discussed at great length the culture of teaching in the UIUC physics department and accordingly balanced valuable traditions with the particular needs of biological physics, a field that is both broad and highly interconnected with other academic units. The committee adopted the vision that biological physics will be a core field in the UIUC physics department. This vision was reinforced by many voices stating that the future of the physics department hinges on a strong biological physics program.

The number of biological physics courses, together six, actually emerged from deliberations that followed closely the mold of existing physics courses, in particular in the condensed matter field and in the undergraduate service courses curriculum. Below we provide brief explanations for the biological physics courses that draw parallels to existing physics courses. The explanations are followed by a summary of the entire curriculum and by comments regarding the feasibility of realizing the necessary faculty resources.

The new biological physics curriculum: The suggested curriculum addresses both the needs of undergraduate as well as graduate level instruction, and includes general introductory courses focusing on the broad concepts of the field as well as core courses that prepare students for research and development work in biological physics. The courses in spectroscopy and non-equilibrium statistical mechanics, would satisfy the strongly voiced needs of other fields, e.g., condensed matter physics or chemistry. These courses could be shared with those fields and faculty, broadening the faculty participation and very likely providing better courses than each field could individually achieve.

(Course numbers provided are provisional; each course is to be taught once per academic year; detailed descriptions of the courses are provided at the end of this document)

Physics 350: Introduction to Biological Physics. This course is the biological physics equivalent of Physics 389, Introduction to Solid-State Physics. [to be taught by all biological physics faculty]

Physics 351: Spectroscopic Methods. This course resurrects a popular course on the subject “Optical Methods for the Investigation of Biological Materials” that was taught in the life sciences and ceased to exist after the retirement of Gregorio Weber, whose research area is now continued in physics. A demand for this course has been voiced strongly by a broad group of faculty far beyond biological physics. The course should contain a laboratory section. [to be taught by all faculty in experimental biological physics as well as by some faculty in experimental condensed matter physics]

Physics 352: Computational Biophysics. This course is the biological physics equivalent to Phys 398 “Atomic-Scale Simulation Methods” that has been taught regularly and with great success during the past years. There is only minor overlap between the new course and Physics 398 “Atomic-Scale Simulation Methods”; computational methods included in the new course are more central to biological physics than to condensed matter. Many campus units have expressed a strong demand for this course since computing is expected to become a core methodology in the life sciences and biotechnology, i.e., the new course is likely to become a popular service course. The course should be taught jointly with the chemistry department and should contain a laboratory section. [to be taught by faculty in theoretical biological physics and in theoretical biological chemistry]

Physics 450: Biomolecular Physics. This is an existing ``cafeteria'' course that remains relevant, but will be revised; this is the biological physics equivalent to Phys 489. [to be taught by all biological physics faculty]

Physics 451: Biosystems Physics. This course is the biological physics equivalent of Phys 490, except that the latter builds on Phys 489, whereas Phys 451 does not build on Phys 450. Since the course can be taken independently from Physics 450 it should provide to physics graduate students an alternative ``cafeteria'' course choice. [to be taught by all biological physics faculty]

Physics 463: Non-Equilibrium Statistical Mechanics. This course is the biological physics equivalent to Phys 483. This course prepares graduate students for research in theoretical biophysics, covering stochastic classical and quantum mechanics as well as non-equilibrium statistical mechanics in a biophysics context as well as using examples from other fields.

Phys 498: Advanced Spectroscopy with Biophysical Applications. This course will be initially taught as a special topics course; we expect demand sufficient to warrant a regular course later on. It would be taught jointly with faculty in condensed matter physics and chemistry.

Who can teach the suggested courses: Faculty that can teach one or more of the suggested Physics 350, 352, 450, 451 courses are Clegg, Dahmen, Gratton, Ha, Robinson, Schulten, Selvin, as well as a potentially new faculty to be hired in theoretical biophysics. Physics 351 (spectroscopy) and Physics 463 (non-equilibrium stat.mech.) can be taught by various other members of the physics department. Physics 352 can be taught jointly with chemistry faculty. This co-teaching has the advantage that it will bring in students from other departments and break down departmental walls, a concept which is encouraged on our campus.

Suggested Initial Time Table:

Fall 2001: Physics 352, Chemistry 352 - Computational Biophysics (Kosztin, Luthey-Schulten)

Physics 450 - Biomolecular Physics (Clegg)

Physics 463 – Non-Equilibrium Statistical Mechanics (Schulten)

Spring 2002: Physics 350 - Introduction to Biological Physics (Selvin)

Physics 351 - Spectroscopic Methods (Gratton)

Physics 451 - Biosystems Physics (Schulten)

Fall 2002: Physics 352, Chemistry 352 - Computational Biophysics (Kosztin, Luthey-Schulten)

Physics 450 - Biomolecular Physics (Ha)

Physics 463 - Non-Equilibrium Statistical Mechanics (new biological physics faculty?)

Spring 2003: Physics 350 - Introduction to Biological Physics (Selvin)

Physics 351 - Spectroscopic Methods (Gratton)

Physics 451 - Biosystems Physics (Schulten)

Physics 498 - Advanced Spectroscopy with Biophysical Applications (Clegg)

Rationale for the new curriculum: The suggested curriculum will make our department more attractive to new generations of undergraduate and graduate students who are very likely to seek a biological physics specialization and expect systematic instruction, lest they will choose other schools. The close integration of biological physics with research and teaching in other campus units will likely attract many students from outside the department to the suggested courses. The new curriculum will also make the department and the whole campus more competitive for grants that insist increasingly on strong teaching efforts. Finally, the new curriculum strengthens the department in the general area of molecular physics, a discipline that promises to rise to the same prominent level as solid-state physics has done in shaping the electronics industry.

Can the physics department afford the new curriculum: The new curriculum places significant demands on the department, in particular during the initial stage when five new courses (Physics 350, 351, 352, 451, 452) need to be developed along with a special topics course in advanced spectroscopy. In the long run, 2.5 regular biological physics courses will be taught every fall and 3.0 courses every spring; this implies that, in the worst case, three biological physics faculty will not be available for the teaching of other physics courses, in the best case (other faculty teaching Physics 351, 452) 1.5 in the fall and 2.0 in the spring will not be available.

A demand of 1.5 – 3.0 full courses taught by biological physics faculty appears to be a high, but desirable investment in a new field of study that is considered important for the future of the physics department and, in fact, for the future of the whole UIUC campus. To judge this demand in relative terms one may compare the suggested graduate curriculum with that in condensed matter physics:

Courses in Condensed Matter Physics:

Physics 435 Theory of Semiconductors and Semiconductor Devices

Physics 430 Surface Physics

Physics 489 Solid State Physics I (taught every term)

Physics 490 Solid State Physics II

"Feeder" Courses for Condensed Matter Physics:

Physics 442 Classical Electromagnetic Radiation

Physics 462 Statistical Mechanics and Kinetic Theory

Physics 480 Quantum Mechanics I

Physics 481 Quantum Mechanics II

Physics 483 General Field Theory

Physics 485 Advanced Field Theory

Courses in Biological Physics:

Physics 450 Biomolecular Physics

Physics 451 Biosystems Physics

“Feeder” Courses for Biological Physics:

Physics 462 Statistical Mechanics and Kinetic Theory

Physics 463 Non-Equilibrium Statistical Mechanics (new)

(other physics courses, e.g., Physics 480, are also “feeder” courses for Biological Physics, but to a much lesser degree than they are for Condensed Matter Physics; in fact, Biological Physics, in the past, had to train graduate students to a very large degree “on the job”, much more so than Condensed Matter Physics had to do)

While the suggested curriculum places a significant burden on the department, it has to be realized that an intellectually complete program in biological physics requires a minimum number of courses. Hence, if the number of faculty in biological physics is relatively small, it requires a higher percentage of faculty devoted to the field, compared to a larger field such as condensed matter physics. This is particularly true because biological physics does not benefit from "feeder" courses in physics as much as condensed matter physic does.

Summary: The Physics Department has made already a great commitment in strengthening its faculty engaged in biological physics research and in doing so has proven worthy of its leadership role in US physics; many other US universities try to follow the same course today. We should now take the second bold and farsighted step and build a strong curriculum in biological physics that matches the high quality of our other physics teaching. Biological Physics asks for a lot to be granted its new curriculum. It is up to the rest of the physics faculty to decide if history has a chance to repeat itself making biological physics a program that can bring the same glory to the physics department as solid state physics did half a century ago. If the answer is that it can we must be bold and willing to take a big step.

Outlines of Suggested Courses

Physics 350 (Prepared by Paul Selvin)

Title: Introduction to Biological Physics

Summary: This course is an introduction to biological physics covering many scales: from the microscopic behavior of individual biomolecules, to cellular responses, to systems (e.g. vision) to whole populations (e.g. food webs). It is primarily a survey course although a few topics (such as the role of diffusion) will be covered in more detail so students can get a sense of both the breadth and possible depth of field.

Prerequisites. This course is intended for undergraduate students who have completed the 111-114 series and have a familiarity with differential equations. A biology course is not a prerequisite but is desirable.

Role of course in physics curriculum. This course will be part of a new biological physics emphasis for physics majors. It is anticipated that the emphasis will include the standard physics core requirements (including statistical mechanics, Physics 361), a year of introductory chemistry (plus organic chemistry, recommended, but not required), an introductory biology and also biochemistry course, Physics 350, plus one other, more advanced biophysics course such as Physics 351, Physics 450, Biophysics 301 or Biophysics 320.

Outline.

A. Experimental Techniques with Applications. Includes an introduction to interaction of electromagnetic waves with biological matter and applications in spectroscopy (absorption, fluorescence, Raman, NMR, EPR) and medical imaging (CAT, PET, MRI). Also includes modern molecular techniques such as AFM (atomic force microscopy), and optical traps, each with a particular biological application.

B. Structure and dynamics of biomolecules, including: equilibrium, kinetics, fluctuations (including diffusion). Basics of equilibrium configurations and fluctuations from equilibrium. Diffusion and Brownian motion, with applications including synaptic transmission in nerves. Some molecular dynamics simulations and computer models will be used to aide in understanding and to introduce idea of modeling.

C. Molecular Biophysics, including: ion transport and ion channels, molecular motors (RNA polymerase, F1-Fo ATPase, Kinesin and myosin), photosynthesis. This section will end by examining whole systems such as vision beginning with the first elementary steps of photon absorption, to cellular changes, to brain recognition. Photosynthesis and chemotaxis can also be similarly analyzed. Computer simulations will also be used here.

D. Theoretical Modeling of systems: including food webs, population dynamics.

Physics 351 (Prepared by Enrico Gratton)

Title: Spectroscopic Methods

Summary: This course introduces the basic spectroscopic methods for the study of optical properties of biological materials and for imaging of biological samples. Emphasis is on modern techniques and instrumentation.

Prerequisite: The course is intended for advanced undergraduates and beginning graduates students in physics, chemistry, engineering, and life sciences. Basic knowledge of experimental physics, optics and mathematics is required.

Role of course in physics curriculum: The course will provide students with a working knowledge of modern optical instrumentation. The course should be taken by all physics students (both undergraduate and graduate) who intend to specialize in experimental Biological Physics. The course is likely to draw students from life science and bioengineering.

Outline: Introduction to optical properties of biological materials; Absorption (UV/VIS) Theory; Absorption (UV/VIS) Instrumentation; Absorption (IR) Theory; Absorption (IR) Instrumentation; Linear and circular dichroism; Dynamic light scattering; Scattering in turbid media: Theory; Optical properties of tissues; Scattering in tissues: Instrumentation; Synchrotron radiation, EXAFS; Synchrotron radiation: Instrumentation; Fluorescence principles: Excitation-emission; Fluorescence steady-state: Instrumentation; Fluorescence anisotropy; Fluorescence time-domain; Fluorescence frequency-domain; Multiphoton excitation; Pump-probe methods: Stimulated emission; Microscopy full-field: Theory; Microscopy full-field: Instrumentation; Microscopy laser-scanning: Theory; Microscopy laser-scanning: Instrumentation; Fluctuation spectroscopy: Theory; Fluorescence Correlation Spectroscopy (FCS): diffusion and populations; FCS: chemical kinetics; FCS: Instrumentation; Single molecule spectroscopy; Spatio-temporal correlations.

Lab sessions: UV-VIS absorption; Tissue spectroscopy; Steady-state fluorescence; Microscopy; Fluctuation spectroscopy.

Comments: The course is organized in 30 lectures (biweekly) and 5 laboratory sessions, each one to be completed within three weeks. Suggested credit 4-5 h. Material for this course has been prepared already by the Experimental Biophysics Group, that has taught several lab sessions for courses in chemistry and life sciences.

Physics 352 (Prepared by Ioan Kosztin and Klaus Schulten)

Title: Computational Biophysics

Summary: This course introduces concepts and applications of biomolecular modeling methods and bioinformatics. Emphasis will be on visualization, computer simulation, analysis of simulation results,

quantum chemistry methods, protein sequences, genomics linking an atomic perspective with function and genome. The course will be based on case studies of several well-studied biomolecules, integrating physical modeling, sequence analysis, and genomics.

Prerequisite: The course is intended for advanced undergraduate and beginning graduate students in the physical and chemical sciences interested in learning how to apply the concepts and methods of their

field of specialty in the biological sciences. The course is also suitable for graduate students from life sciences interested in extending and deepening their knowledge in the mathematical and physical foundations of molecular modeling and bioinformatics. Basic knowledge of molecular and cell biology, as well as of mathematics, physics and chemistry is required.

Role of course in physics curriculum: The course will provide students with a working knowledge of biomolecular modeling and bioinformatics. The course should be taken by all physics students (both undergraduate and graduate) who intend to specialize in Biological Physics. The course is likely to draw students from life science and bioengineering. The course will be taught jointly with the Chemistry department.

Outline: Molecular Graphics; Protein data bases; Amino acid sequence analysis; Empirical force fields of biopolymers; Molecular Dynamics; O(N) algorithms for long-range interactions; Thermodynamic properties; NVT, NpT ensemble simulations; Correlation and response functions; Gene banks and gene sequence analysis; Homology and comparative modeling; Evolutionary and phylogenetic analysis; Monte Carlo simulations; Free energy calculations; Steered Molecular Dynamics; Quantum chemical calculation of force fields; Ab-initio Molecular Dynamics (Car-Parinello method);

Comments: The course will include regular lab sections; teaching in a lecture room will alternate with teaching in a computer laboratory. Material for this course has been prepared by the Theoretical Biophysics Group, that has taught several modeling courses, and by the Chemical Biology program that has taught previously a related course with emphasis on bioinformatics.

Physics 450 (Prepared by Bob Clegg )

Title: Molecular Biological Physics: concepts and application of biological physics

Summary: This course has been taught continuously for over twenty years. In the last few years, it has had an enrollment of between 30 - 40 students. The course emphasizes a molecular point of view. Biomolecules are introduced, as well as the integration of these macromolecules into complex, interconnected supramolecular assemblies.

Prerequisite: The audience consists of graduate students from physics (on the average about 1/2 of the class), chemistry, biophysics, bioengineering and biological disciplines with the appropriate background. Advanced undergraduates have taken the course. It is a cafeteria course, and as such the course has many physics graduate students who are not specializing in biological physics. The prerequisites are a background in quantum mechanics and statistical thermodynamics. There are no biology or biochemistry requirements; the necessary concepts and background are introduced in the course.

Role of course in physics curriculum: Physics 450 is the standard biological physics cafeteria course. It is required for the physics graduate students as one of the four cafeteria courses offered in the physics department (students must take two of these). It is presently the only course offered in biological physics in the physics department. It is effectively required for all physics graduate students specializing in biological physics.

Outline: Introduction to protein structure; Polymer statistics; Protein structure and spin glasses; Energy landscape for protein folding; Protein folding and stability; Models of the helix-coil transition in biomacromolecules; Nucleic acid and chromatin structures; Fluctuations; Cooperative conformational changes; Elasticity of DNA; Synthesis and formation of biomolecules; DNA supercoiling; Protein-DNA complexes; Inter- and Intra-molecular interactions; Physical characteristics and structure of water; Aqueous solutions of macromolecules; Ion-solvent interactions; ion-polyion interactions; Charged surfaces; Debye-Hueckel theory; Poisson-Boltzmann theory; Short introduction to spectroscopy – fluorescence and NMR; Application of new techniques to biomolecules; Cellular trafficking; Molecular motors; Topics in molecular evolution; Up-to-date new exciting biophysics topics; Introduction of the biological cell from a physics point of view.

Comments: This course has been constantly evolving over the past years. There are approximately 45 lectures given each fall semester. A term paper is required. This is a relatively difficult course to teach due to the breadth of the topic.

Physics 451 (Prepared by Klaus Schulten)

Title: Biosystems Physics

Summary: This course provides an introduction to self-organization and multi-scale processes in single and multiple cells from the theoretical physics perspective. The course will be based on case studies from the fields

of photosynthesis, vision, signaling, motion, morphogenesis, and neural information processing. Physical concepts, mathematical techniques, and computational methods required in cellular and multi-cellular biophysics will be introduced. Emphasis will be on the multi-scale organization and multi-level mechanisms of integral facilities of living systems. The latter mechanisms link various domains of physics, like classical and quantum mechanics, stochastic processes, self-organization, networks, and non-linear dynamics. The course will view biological systems as information processing devices and combine a top-down (whole organism, genomics) with a bottom-up (molecular) description.

Prerequisite: The course has the same requirements as Biophys 450 and can be taken together with or separately from Phys450. Students need to have a basic working knowledge of differential equations as they typically arise in physics and in scientific computing.

Role of course in physics curriculum: This course provides an alternative (to Phys450) cafeteria course choice for students interested in the physics of biological organization and information processing,

rather than in the physics of biomolecular systems and processes. For physics graduate students that specialize in biological physics this is an essential course. Other students will benefit from an introduction to systems with emergent behavior that the course provides.

Outline: Bacterial Photosynthesis: Architecture of the cellular apparatus; Participating proteins and their functions; Formation of the apparatus; Physical mechanisms underlying the function of individual components; Coordination of functions of multiple components. Life cycle of slime mold amoebae: Biological clocks and signaling; Organization of amoeba motion; Morphogentic fields from reaction-diffusion processes in amoebae colony; Normal mode analysis of pattern formation; Chemotaxis; Cellular automata to describe self-aggregation of multi-cellular slug from colony of individual amoebae; Organization principles for

slug motion and development; Slime mold genomics. Vision: Molecular sensing; Signal amplification through G-Proteins; Synaptic transmission; Neural spikes; Cable equation; Morphogenesis of visual maps in LGN and cortex. Neural computation: Associative networks; Self-organizing maps; Visual maps; Motor maps; Visuo-motor control.

Comments: This course will be given as a Phys 498 course in spring 2001. A 1992 textbook on the neural processing part written by Klaus Schulten exists and will be updated.

Physics 463 (Prepared by Klaus Schulten)

Title: Non-equilibrium Statistical Mechanics

Summary: Living systems are sustained by non-equilibrium processes. On the one hand, self-organization, order and faithful replication exist due to energy consuming non-equilibrium processes, on the other hand cellular processes occur at physiological temperature and the physical mechanisms selected for cellular facilities need to be robust against thermal disorder. The course introduces classical and quantum stochastic dynamics as well as non-linear stochastic processes with emergent order that provide the fundamental descriptions for biological dynamics. Stochastic transport, linear and non-linear reaction-diffusion systems, chemical kinetics and master equations, and stochastic molecular electronics are methods that will be illustrated in the framework of observed cellular behavior and analysis of experimental data.

Prerequisite: The course is suitable for graduate students in physical and life sciences as well as engineering with basic knowledge in physics and mathematics. Students should master fundamental classical and quantum mechanics as well as the rudimentary theory of partial differential equations. The course will not introduce the background for the biological examples employed, but rather directs students to the literature for self-study. The level of the course will be that of Jackson : "Classical Electromagnetism".

Role of course in physics curriculum: The course is intended for graduate students who wish to specialize in Theoretical Biophysics, Computational Biology or Chemical Kinetics as well as for physics students who seek a working knowledge of non-equilibrium statistical mechanics. All theoretical biophysics students, and some condensed matter physics students, chemistry, bioengineering, life science and engineering students are expected to take this course. The course had been given previously as a special topics course (Physics 498 NSM) with 7-14 students taking it for credit. The course is a prerequisite for thesis research in Theoretical Biophysics. The course could be taught by physics faculty outside of biological physics; teaching of the course may alternates between biogical physics and condensed matter faculty with a respective periodic change of emphasis.

Outline: Classical Dynamics under the influence of stochastic forces; Einstein and Smoluchowski diffusion equation; Solution of the Smoluchowski equation; Noise-induced limit cycles and neural dynamics; Rates of diffusion-controlled reactions; Adjoint Smoluchowski equation; Field theory and spectral expansion method; Generalized moment expansion of correlation functions; Examples of generalized moment expansion; Master equation; Linear response theory; Theory of echoes and hysteresis; Stochastic quantum mechanics; Quantum systems coupled to classical bath; Spin-Boson model; Path integral presentation.

Comments: The course has been taught already three times as a Physics498 course; detailed lecture notes and a web site with lecture notes, problem sets, solutions, and term projects exists. A textbook is being developed.

Physics 498 (Prepared by Bob Clegg)

Title: Concepts in Spectroscopy with Biophysical Applications

Summary: This is an advanced spectroscopic course that will be offered to students wishing to acquire a description of the interaction of radiation with matter on a molecular scale. The course will cover spectroscopic transitions, providing the basic theoretical background, as well as an in-depth description of how different aspects of the data are interpreted in terms of the molecular properties of the chromophores and their environments. The theoretical description of experiments and data analysis for extracting molecular information will be provided. The interactions between electromagnetic fields and molecules will be covered from a semi-classical point of view. The course will cover spectroscopic transitions involving molecular electronic transitions and magnetic resonance. Vibrational molecular characteristics will be covered integrated with spectroscopic transitions, but vibrational spectroscopy will not be covered separately in detail. The examples will emphasize biophysical experimental systems.

Prerequisite: The audience consists of graduate students (and advanced undergraduates with the appropriate background) from the physics, chemistry, biophysics, bioengineering and biological disciplines with the appropriate background. This course is useful for many disciplines and areas of research, not only those in biological physics. The prerequisites are an advanced undergraduate course (more than just a cursory introduction as part of another course) in quantum mechanics and statistical thermodynamics. An advanced undergraduate course in classical electromagnetism is not necessary, but the necessary background must be acquired as the course proceeds. The emphasis of this course is different from that of the undergraduate spectroscopy course Physics 351.

Role of course in the physics curriculum: No equivalent course is being taught, in spite of many research groups on the UIUC campus employing advanced spectroscopic measurement and theory. Hence, there is an urgent need for this course, and an expressed demand from other departments, that such a course be offered by our physics faculty. This course can be taken by any of our physics graduate students who passed the qualifying exam. Topics that are more advanced, or new, in these subjects will be introduced at the appropriate level.

Outline: Review of quantum mechanical concepts; Hydrogen -like atoms; Molecular orbitals; Spin; Solution of Maxwell equations in Coulomb gauge; Time-dependent perturbation theory; Fermi’s golden rule; Electronic transitions; Transition dipole moments; Selection rules; Absorption and emission rates; Vibrations and rotations in electronic transitions; Frank Condon approximations; Line widths and broadening. Polarizabilities and molecular spectroscopy; Dispersion forces; Molecular rotation contributions to polarizability ; Solvent effects and Lippert equations; Optical resonance; Magnetic properties of molecules; Two photon excitations and non-linear effects; Light sources and light detectors; Electronics for data acquisition and analysis; ESR and NMR spectroscopy.

Comments: As this course is presently conceived, it should give graduate students the background needed for consulting the recent literature and for working with the modern instrumentation and analysis methods. This is not a survey course and it is not limited to only new biophysical applications of spectroscopy. The biophysical applications, including both more established techniques as well as the up-to-data novel developments, will serve as examples. The contents of the latter part of the course will evolve in time much more that the more formal part.