Biophysics 116 — Introduction to Medical Imaging
This First Year Seminar* surveys the methods of modern medical imaging for clinical and scientific purposes, highlighting basic concepts in chemistry, physics, and biochemistry and especially the biophysical foundations upon which all current tools for biomedical imaging rest. Topics include the underlying science of radiography, computed tomography (X-rays of a selected plane of the body), diagnostic ultrasound, and nuclear medicine. We study magnetic resonance imaging in the context of its historical development and through “reverse engineering.” i.e. understanding how the images are created. This seminar also touches on the societal implications of imaging such as radiation risks, health care costs, and future directions in medical research.
*First Year Seminars are open to Freshmen only.
Biophysics 117 — Introduction to Programming in the Sciences
Interactions with computers are ubiquitous throughout the sciences and engineering, and a general and working knowledge of the structure and architecture of computing languages and interfaces to programming are critical tools for scientists today. Moreover, learning a computer language, writing computer code and translating basic mathematical expressions into algorithms are skills that strongly enforce problem solving and logic and reasoning skills. This course is designed to address these issues through the systematic exploration of computer programming languages and environments. Homework assignments are structured to engage the participants in learning the basic skills that are necessary to interact with computing environments, and specifically Unix, as well as introduce key programming languages and paradigms. The course will be structured as a “working laboratory” with students working individually and as teams to solve the assigned homework problems.
Biophysics 120 — The Discovery of the DNA Double Helix and its Hidden Mysteries
This course introduces students to the field of biophysics and its role in the life sciences. The historical example of the discovery of the structure of DNA by Watson and Crick is discussed, and students will have the opportunity to re-create the original experiments that led to the discovery of how DNA governs inheritance. BIOPHYS 120 will be taught in a format that combines lectures, demonstration experiments, and hands-on student experiments.
Biophysics 130 — DNA Origami
This hands-on First Year Seminar* course explores the theory and methods behind synthetic biology, focusing on one particular technology called DNA origami, which uses folded DNA as building blocks to construct nano-scale objects via self-assembly. This class covers the theoretical underpinnings of DNA origami, then students will work in groups to design, construct, and characterize DNA origami objects. Characterization will be accomplished using modern experimental imaging techniques available in the single molecule analysis in real time (SMART) center and/or within research labs on campus. Beyond learning concepts specific to DNA origami, this course aims to expose students to theoretical and experimental methods used in a broad range of biophysics research. The course ends with discussions on how biological materials might impact the future of science and technology at the University of Michigan and beyond.
*First Year Seminars are open to Freshmen only.
Biophysics 290 — Physics of the Body and Mind
This course covers how the human body functions and malfunctions from a physics perspective by applying basic physical principles to organs, cells, and biomolecules. It employs extensive A/V and CAI material, and is intended for Biophysics majors and/or students interested in the application of physics to biology, biochemistry, physiology, psychology, genetics, medicine, bioengineering and related life sciences. It provides an introduction to topics in biomechanics, biophysics, and medical physics including biosensors.
Biophysics 370 — Physical and Chemical Principles Behind Biology and Medicine
Physical Chemistry is having a major impact on all areas of science that concern the properties of molecules. In particular, the design of pharmaceutical drugs, understanding detailed structure function relationships of proteins, RNA and DNA are highly dependent on the development of physical chemistry concepts.
This course introduces students to physical chemistry (and to the pioneers of these theories) using a biomolecular approach. The underlying principles of quantum mechanics are covered first and then utilized to understand the basic principles of spectroscopy (electronic, vibrational, rotational and magnetic resonance) and other quantum phenomena such as electron/proton tunneling in enzymes. Molecular orbital calculations that can be completed with pencil and paper on simple organic molecules are also covered, giving students a view of theoretical chemistry.
Armed with the tools of quantum chemistry, students shall learn that the laws of thermodynamics can be formulated in terms of the properties of atoms and molecules that make up macroscopic systems. Students will then utilize these concepts to understand the workings of (bio)molecular machines. Mathematical topics are reviewed before using them to develop biophysical chemistry concepts.
The outcome of this course will provide students with the ability to understand research problems in biotechnology and medical fields from a physical chemistry perspective.
Biophysics 399 — Research in Biophysics
Research in a modern research laboratory, under the direction and supervision of a faculty member, is a required part of the Biophysics curriculum to prepare students adequately for their future careers as a biophysicist in academic or industrial research.
This course number is used for an individualized research experience under the guidance of a Biophysics faculty member. If a non-Biophysics faculty member serves as the principal mentor, a Biophysics faculty member must be identified as a co-mentor. Students need permission from their biophysics faculty mentor before they can enroll in this course. Typically, students will work on a small, well-defined project that may subsequently turn into a senior or honor's thesis.
The student is expected to work on a research project under the direct supervision of the faculty mentor, who accepts responsibility for all aspects of the student's work. Each credit hour is equivalent to at least four hours a week of actual work in the lab for a 14 week term (minimum 50 hours per term-credit hour). The faculty mentor may delegate some day-to-day supervisory functions to a post-doc or graduate student, but the mentor is nonetheless expected to meet regularly with the student and monitor his or her progress. The mentor is also responsible for assigning a grade at the end of the semester. In case of co-mentorship for a project under the guidance of a non-Biophysics faculty member, the Biophysics co-mentor is expected to take responsibility for the overall appropriateness of the project, ensure that the principal mentor fulfills his or her mentoring obligations towards the student, and, in consultation with the principal mentor, assign a grade.
Students are required to submit a one-page report on his or her research project at the end of the semester. Reports are submitted both to the faculty mentor and to the Biophysics main office for student records.
Biophysics 401 - Special Topics in Biophysics
This course will cover different topics of special interest within Biophysics.
Biophysics 417 — Dynamical Processes in Biophysics
The physical basis of diffusive processes in biology and biochemistry, and optical spectroscopic means for measuring its rates. Topics include: membrane electrical potentials, nerve impulses, synaptic transmission, the physics of chemoreception by cells, motion and reaction kinetics of membrane components, optical microscopy, visible and UV light absorption, fluorescence and phosphorescence, quasielastic light scattering, mathematics of random fluctuations, and chaotic processes in biology.
Biophysics 420 — Structural Biology: The Architecture of Life
Properly folded biological macromolecules help us think, feel and do. When things go wrong they cause disease. What is the physical basis for strings of amino acids (or, sometimes, nucleobases) assembling into well-folded structures in order to perform the tasks essential for life?
This course focuses on an in-depth treatment of topics including secondary and tertiary structures of biological macromolecules including proteins, DNA and RNA, folding and misfolding of proteins, ensemble and single-molecule kinetics, protein-protein interactions and biochemistry of cellular processes.
Biophysics 421 — Structural Biology: Biophysical Controversies
This course builds on the Biophysics 420 sequence and aims at providing a complete understanding of the roles of structure and dynamics on the function of biological macromolecules such as globular proteins, membrane proteins, DNA and RNA. This course also focuses on the analysis and interpretation of various biophysical experimental and computational data for biological macromolecules including x-ray diffraction, microscopic and fluorescence images, multidimensional NMR spectra, EPR spectra, ion-channel recordings and single molecular experimental data. Students will be trained with the steps involved in handling the experimental data to solve and understand the structures of biomolecules.
Biophysics 422 - Experimental Methods in Structural Biology
This course offers a detailed introduction to the fundamental physical principles behind key structural techniques including X-ray crystallography, NMR spectroscopy and cryo-electron microscopy. Students will gain hands-on experience with data processing, analysis and structure calculations/model building.
Biophysics 430 — Medical Physics
This course introduces biomedical imaging techniques and medical physics based therapies, elucidates the physical principles behind them, and discusses the interaction of different kinds of radiation with biological matter. Examples for covered imaging techniques are ultrasound, X-ray imaging, CAT scan, MRI imaging, and positron emission tomography. Relevant radiotherapy methods include the gamma knife, brachytherapy, and proton-beam therapy.
Biophysics 433 — Biocomplexity
This course explores concepts of nonlinear dynamics in biological systems. It covers fixed points, logistic maps, chaotic oscillators, waves in excitable media and spatio-temporal pattern formation in biological systems ranging from cells to organs such as the brain and populations.
Biophysics 435 — Biophysical Modeling
This course introduces students to the basic concepts of biophysical modeling. Methods such as molecular dynamics and Brownian Dynamics simulations, as well as larger-scale models for regulatory networks are covered and the associated computational tools are introduced.
Biophysics 440 — Biophysics of Diseases
This course deconstructs current and emerging diseases in terms of the malfunctioning of nucleic acids, proteins, and membranes and interactions between them. The diseases covered will include Alzheimer’s, Parkinson’s, Creutzfeldt-Jakob disease (or Mad-Cow disease), HIV, a variety of bacterial infections, and other biological disorders. A variety of biophysical methods for dissecting diseases at the atomic level will be surveyed, including NMR spectroscopy, X-ray crystallography, cryo-electron microscopy, single molecule imaging, and computational methods.
The course will emphasize how a basic biophysical understanding of diseases can guide the rational design of therapeutics, to include:
- Infectious diseases
- The Molecules of Life: Biophysical Principles
- Viral Infections
- Bacterial Infections
- Health Conditions
- Rational Approaches to Drug Discovery
Biophysics 445 — Introduction to Information Theory for the Natural Sciences
This course introduces the basic tools of Information Theory -- Entropy, Relative Entropy and Information - and highlights their utility with applications drawn from various disciplines. After introducing the basics of probability theory and information theory, other topics like coding, data compression, channel capacity, thermodynamics, population dynamics, gene transcriptions, network science are explored.
Biophysics 450 — Laboratory Techniques in Biophysics
This hands-on course teaches essential laboratory skills in Biophysics. Experiments cover sample preparation techniques, such as protein expression and purification; modern research methods such as atomic force microscopy, optical tweezers, NMR, X-ray crystallography, and computational techniques such as molecular dynamics simulation. The final project will allow students to explore a topic of interest in greater depth.
Biophysics 454 — Biophysical Chemistry II: Macromolecular Structure and Dynamics
This course builds on the CHEM 451-453 sequence and aims at providing an understanding of the structure and dynamics of biological macromolecules. After introducing the necessary nomenclature and reviewing thermodynamic principles, modern techniques to characterize the structure and dynamics of biopolymers is the focus. Sedimentation, electrophoresis, mass spectrometry, X-ray diffraction, scattering, and spectroscopic techniques such as absorption, circular dichroism, fluorescence, and NMR are covered. Both physical principles and practical applications in the Life Sciences are highlighted.
Biophysics 463 — Mathematical Modeling in Biology
The complexity of the biological sciences makes interdisciplinary involvement essential and the increasing use of mathematics in biology is inevitable as biology becomes more quantitative. Mathematical biology is a fast growing and exciting modern application of mathematics which has gained worldwide recognition. In this course, mathematical models that suggest possible mechanisms which may underlie specific biological processes are developed and analyzed. Another major emphasis of the course is illustrating how these models can be used to predict what may follow under currently untested conditions. The course moves from classical to contemporary models at the population, organ, cellular, and molecular levels.
Biophysics 495 — Senior Seminar (Professional Development in Biophysics)
This course teaches professional skills such as writing research articles, reviews, grant proposals, and preparing and giving poster presentations and scientific talks. The scientific publishing process, including peer review, will be discussed and ethical rules and considerations explored. All students will draft an application for an NSF Graduate Fellowship, which will be extensively critiqued by other students and the instructor.
Biophysics 498 — Senior Thesis
This course gives Biophysics majors (at the senior level) the opportunity to cap their educational experience with a senior thesis based on their research. It will typically be a continuation of Biophysics 399.
Biophysics 499 — Honors Thesis
This course gives Biophysics Honors concentrators (at the senior level) the opportunity to cap their educational experience with an honors thesis based on their research. It is typically a continuation of Biophysics 399.