Required
Students are required tot ake the following:
BIOL 662 - Discussions on Research Integrity and Ethics in Academic Research
This course is a combination of lectures and discussions, and covers topics mandated by the NIH that pertain to
ethical conundrums basic and clinical scientists face during everyday affairs in the laboratory. The lectures are designed to be interactive and thought provoking, pairing information sessions with case studies. Students are made aware of Purdue University's Statement on Scientific Integrity; University, domestic, and some international rules and guidelines associated with various aspects of scientific research; as well as resources and hotlines available to researchers in need of advice. In addition, the course covers topics pertaining to students interested in careers outside of basic science, including the ethics of university-industry relations, issues pertaining to big pharma, clinical trials, science policy, and diversity, equity and inclusion (DEI).
BIOL 695 - Biophysics Grant Writing
The instructor will lead trainees through all components of modern NIH grant proposals, including sections devoted to the implementation of rigor and reproducibility, authentication of key biological and chemical resources, and data and material sharing plans, with an emphasis on biophysical projects. The instructor will also teach trainees how to develop a strong scientific foundation for a hypothesis-driven biophysics research project, and the class will collectively evaluate the strengths and weaknesses of various premises in each of the individual grant proposals being developed by trainees. At the end of the semester, students will evaluate each other’s grants in a mock peer review session with rigor and reproducibility as a key review criterion. A key outcome of this course is to produce, at minimum, the framework for fundable proposals that would enable trainees to secure funding after the supported period of the MBTP.
BIOL 696 - Frontiers in Biophysics Seminar Series
An MBTP preceptor will work with MBTP trainees in the Spring prior to each academic year to identify and invite outside speakers who are thematically appropriate for sponsoring departments. MBTP trainees will meet with these invited speakers during an informal lunch, where the speaker is invited to talk about their own career progression. 4th year graduate students will also give formal research seminars in this series, and remaining slots will be filled by local faculty (such as new hires) or speakers representing alternative biophysics career paths. MBTP trainees will enroll in this course (BIOL 696) every semester until they graduate. In the spring semester of their 4th year, they will give a practice talk that is critiqued by a small group of faculty preceptors and the other 4th year MBTP trainees. The trainee will then revise their presentation, and the final version will be given as a formal seminar in the series.
PHYS570E - Introduction to Biophysics
The objective is to educate and train individuals to apply the concepts and methods of the physical sciences to the solution of biological problems. Students will be introduced to a physical description of a wide range of phenomena, from molecular and cell mechanisms to the function of the human brain. This introductory overview of frontiers in Photobiophysics, Neurophysics, bioinformatics and Synchrotron based biological spectroscopy will help students broaden their views. This course prepares physics students for research and development work in an interdisciplinary/medical environment. Topics include molecular forces in biological structures, cell organization, structure and function of proteins, nucleic acids, and biological membranes, flow of genetic information, biological thermodynamic and kinetic (enzymatic reactions), electrostatic interactions in biology, physico-chemical basis of neuron signaling (membrane potentials, action potential generation and propagation, synaptic transmission, sensory receptor function), interaction of biological molecules with light (primary processes in photosynthesis, vision), functional studies of brain.
Elective
Students are required to take at least two of the following:
BIOL 51101 - Introduction to X-ray Crystallography
Introduction to macromolecular structure determination by XRC which balances theory and practice, with 60% of the course lecture-based and 40% lab-based. The five 3-week modules cover (i) Crystallization, (ii) Data Collection, (iii) Molecular Replacement, (iv) Experimental Phasing, and (v) Model Building and Refinement, Validation, and Visualization. The goal of the course is to equip students with the necessary tools to develop and independently execute an XRC project, starting from construct design to publication. By the end of the course, students should be familiar with the (i) structure determination pipeline, (ii) theory behind X-ray diffraction methods, (iii) methods for crystallization, (iv) phasing options for solving a crystal structure, and (v) contemporary XRC software.
BIOL 51202 - Methods And Measures In Biophysical Chemistry
Biological applications of physical methods including absorption spectroscopy (UV-Vis, FTIR and Raman and CD spectroscopy), fluorescence spectroscopy and super high-resolution imaging, spin resonance methods (NMR and ESR spectroscopy), mass and thermodynamic based methods (thermophoresis, analytical ultracentrifugation, ITC and surface plasmon resonance) and diffraction/structural methods using NMR, cryo-EM and X-ray scattering/crystallography. Each topic is treated at an introductory level with examples from the literature. The course objective for students is to obtain a general understanding of the physical principles underlying each of the techniques, as well as the basic ability to apply the technique to biological systems of interest.
BIOL 595W - Cryo-Electron Microscopy; 3D Reconstruction of Macromolecules
CryoEM is a revolutionary structural biology method that allows the determination of the atomic structures of viruses and protein complexes to elucidate the structural basis of their functions. The course will introduce cryo-EM principles, including instrumentation, sample preparation, data collection, and data analysis. The students will also learn how to determine a protein complex or virus structure to 2-3 Å resolution using a GPU-accelerated Linux workstation or cluster.
BIOL 563 - Protein Bioinformatics
In this course, trainees are introduced to bioinformatics databases, tools, algorithms, techniques, and literature focusing on computational approaches for studying protein sequences, structures, and function. Topics include protein structure and function prediction, sequence and structure database search, protein-protein docking predictions, protein-ligand interactions, and computational drug screening.
MCMP 570 - Molecular Interactions and Drug Targets.
This class will cover the identification, qualification, and validation of therapeutic targets and introduces “-omics”-based approaches. It also covers membrane receptor theory, enzymes as drug targets, biophysics of protein-ligand interactions, measurement of molecular interactions with an emphasis on in-house instrumentation (SPR, ITC, MST, fluorescence polarization, NMR etc.), and computational approaches to drug design, including AI.
MCMP 690 - Computer-Aided Drug Design
The overarching goal of the course is to introduce trainees to the theory and practice of computer-aided drug design. During this course, classical approaches to designing small molecules and biologics will be discussed, along with an introduction to machine learning in drug design. Upon completion, students should be able to independently use several computational techniques for their research in pharmaceutical sciences or chemical biology.
CHEM 638 - Biophysical Chemistry
This biophysical chemistry course introduces students to free energy, physical and chemical equilibria, thermodynamics of metabolism, biological redox reactions, active and passive transport, ligand binding and cooperativity, diffusion and sedimentation, noncovalent interactions in proteins, and basic kinetics.