The Herpes & Phage Virology Group

Department of Physics, Carnegie Mellon University
Principal Investigator: Alex Evilevitch




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1. Physical Virology (graduate course, 12 units)

For the course poster, click here.

The course covers latest methods in biological physics as well as fundamentals in physics of DNA, protein self-assembly and membranes, using viruses as a physical object. It also provides introductory level biochemistry and molecular biology lectures so that students with any major can participate in the course. Being an interdisciplinary and up-to-date research field involving fundamental theory and numerous applications, the emerging field of biophysical virology is aimed to attract students from any of the natural science disciplines (physics, chemistry and biology).

Learning Outcomes

State-of-the-art account of recent advances in the experimental analysis and modeling of structure, function and dynamics of viruses. It is an interdisciplinary course that integrates a review of relevant experimental techniques, such as cryo-electron microscopy, atomic force microscopy, microcalorimetry, light scattering and mass spectrometry with the latest results on the biophysical and mathematical modeling of viruses. The course comprehensively covers the structure and physical properties of the protein envelopes that encapsulate and hence protect the delicate viral genome, their assembly and disassembly, the organization of the viral genome, infection, evolution, as well as applications of viruses in Biomedical Nanotechnology.

Course Content

Principles of Virus Symmetry, Virus Crystallography and Cryo-EM, Capsid Assembly, Nucleic Acid Packaging and Ejection, Virus Exit and Release, Virus Recognition and Attachment, Virus Entry, Virus Structures in the Cell, Human Immunodeficiency Virus, Virus Nanotechnology and Biomedicine, Viral Structure, Function and Dynamics via Mass Spectrometry

2. Physics I for Engineering Students (undergraduate course, 12 units)

This is a first semester, calculus-based introductory physics course. Basic principles of mechanics and thermodynamics are developed. Topics include vectors, displacement, velocity, acceleration, force, equilibrium, mass, Newton's laws, gravitation, work, energy, momentum, impulse, temperature, heat, equations of state, thermodynamic processes, heat engines, refrigerators, first and second laws of thermodynamics, and the kinetic theory of gases.
All Semesters: 12 units
Prerequisites: Corequisites: 21-120

3. Microbiology: Biophysics and Molecular Biology (graduate course, 12 units)

For the course poster, click here.

The course provides introductory level molecular biology that is aimed for students from all disciplines of natural science. It covers microbiology, genetics, genomics and virology, as well as related biophysics of RNA and DNA packaging, protein self-assembly and molecular motors. We also review the latest biophysical methods with a focus on single molecule techniques that have revolutionized the biological sciences.

4. Thermo Physics I (undergraduate course, 10 units)

The three laws of classical thermodynamics, which deal with the existence of state functions for energy and entropy and the entropy at the absolute zero of temperature, are developed along phenomenological lines. Elementary statistical mechanics is then introduced via the canonical ensemble to understand the interpretation of entropy in terms of probability and to calculate some thermodynamic quantities from simple models. These laws are applied to deduce relationships among heat capacities and other measurable quantities and then are generalized to open systems and their various auxiliary thermodynamic potentials; transformations between potentials are developed. Criteria for equilibrium of multicomponent systems are developed and applied to phase transformations and chemical reactions. Models of solutions are obtained by using statistical mechanics and are applied to deduce simple phase diagrams for ideal and regular solutions. The concept of thermodynamic stability is then introduced and illustrated in the context of phase transformations.
Fall: 10 units
Prerequisites: 33234 and 33232

5. Physics II for Science Students (undergraduate course, 12 units)

This is the second semester course that follows 33-111. Electricity and magnetism is developed, including the following topics: Coulomb's law, polarization, electric field, electric potential, DC circuits, magnetic field and force, magnetic induction, and the origins of electromagnetic waves.
Fall and Spring: 12 units
Prerequisites: 21120 and 33111 Corequisites: 21-122