Interdisciplinary PhD in Structural and Computational Biology and Quantitative Biosciences

Biophysics Seminar (CHEM 872)

The Biophysics Seminar is a research literature-based course that covers current topics in the field of molecular biophysics.  The course is a requirement for first-, second-, and third-year Biophysics students.

The course emphasizes rigorous design, interpretation, and reproducibility. Students learn to apply critical analysis to cutting-edge subjects in biophysics. Student presenters identify the premise, cover the paper figure by figure, evaluate results and explain the technical aspects.

Presentations help students develop communication skills. Vigorous discussions moderated by students with the help of the faculty trainer ensure that students develop a critical approach to understanding the conceptual basis and technical pitfalls of the subject under study. Students broaden their view of how physical ideas can be applied to biological problems.

The course has different formats depending on the semester.

In the Fall semester, the course consists of three modules, each one focusing on a different topic. Each module is led by a Biophysics trainer who is responsible for selecting the topic and three research papers. Each module starts with a lecture overview of the topic. In the following weeks, students present the papers.  The presenter and the faculty member collaborate in moderating the discussion.  Presenters are typically second-year students.

In the Spring semester, first-year students, who will have recently joined a thesis lab, present a paper that is foundational for their research project.  Their advisor is invited to serve as faculty moderator.

History of topics and contributors to the Biophysics Seminar

Semester (main instructor) Faculty Topics
Fall 2022 (Senes) Ci Ji Lim See and Feel: methods to study protein-nucleic acids interactions at single-molecule level
Yongna Xing Mathematical models in biology
Alessandro Senes Structural prediction in the age of AlphaFold
Spring 2022 (Senes) Jackson, Kirchdoerfer, Lim, Grant, Bergmann, Kaçar, Notbohm, Van Lehn, Li, Friedrich, McNeel, Romero, Butcher First-year students presented a paper related to their own thesis topic. Each student's advisor joined as co-moderator.
Fall 2021 (Senes) Chad Rienstra NMR in Biochemistry: Much More Than Structures
Tim Grant Recent methodological advances in cryo-EM
Josh Coon Native Mass Spectrometry and its utility for structural biology
Spring 2021 (Senes) Reid Van Leih Functional Consequences of Lipid Phase Behavior
John Yin Biophysical measures and models of virus growth in cells
Aaron Hoskins Biophysical studies of genome organization
Fall 2020 (Senes) Liz Wright Cryo-EM
Andy Buller Mutagenesis strategies for understanding and improving enzyme function
Pupa Gilbert Machine learning in Biology
Spring 2020 (Senes) Jeremy Rogers Label free optical imaging
John Cowgill (Chanda Lab) Unnatural amino acid incorporation in biophysical studies of proteins
Raunak Sinha Biophysics of phototransduction
Fall 2019 (Jackson) Meyer Jackson Membrane Mechanics
Silvia Cavagnero Metamorphic Proteins
Alessandro Senes Bacterial Cell Division
Spring 2019 (Record) Tom Record Biophysics of Transcription Initiation
Alessandro Senes Membrane Biophysics
Liz Wright Cryo-EM
Fall 2018 (Jackson) Randy Goldsmith Technology for making measurements on single molecules
Meyer Jackson Fusion pores
Yongna Xing New frontiers in cryo-EM
Spring 2018 (Jackson) Alessandro Senes Single Molecule Approaches for Membrane Proteins
Megan McClean Signal Transduction at the Single-Cell Level
Ophelia Venturelli Modeling and Analysis of Synthetic Gene Regulatory Circuits
Fall 2017 (Jackson) Nate Sherer Visualizing viruses
Meyer Jackson Two-photon microscopy
Philip Romero Directed evolution
Spring 2017 (Record) Tom Record Ensemble and single molecule spectroscopic studies of transcription initiation
Sam Butcher Cryo-EM
Vatsan Raman Protein allostery
Fall 2016 (Murphy) Sam Gelman Molecular structures of amyloid fibrils
Jeff Harden Biomechanics of single molecules
Reid van Lehn Molecular simulations of the biological hydrophobicity scale
Spring 2016 (Jackson) Silvia Cavagnero Prion Proteins: Folding and Aggregation
Aaron Hoskins The Biophysics of Gene Expression
Cindy Czajkowski Conformational transitions in ligand-gated channels
Fall 2015 (Jackson) Katie Henzler-Wildman Using NMR to investigate protein function
Qiang Cui Long-scale molecular dynamics simulations for biomolecules
Doug Weibel Bacterial motility
Spring 2015 (Jackson) Matthew Merrins Quantitative Imaging of Metabolism
Thomas Brunold Spectroscopic and Computational Insights into Metalloenzyme Mechanisms
Lloyd Smith Proteomics by Mass Spectrometry
Fall 2014 (Jackson) Julie Mitchell Data science in biophysics
Brian Fox Biophysical approaches to defining enzyme mechanism
Katrina Forest Macromolecular crystallography
Spring 2014 (Jackson) Regina Murphy Intrinsically disordered proteins
Yongna Xing Chaperone and anti-chaperone function
Alessandro Senes Membrane protein folding
Fall 2013 (Jackson) Jim Weisshaar Super-resolution fluorescence microscopy in live cells
Martin Zanni Excitons in biophysics
Doug Weibel Single molecule force measurements
Spring 2013 (Jackson) Randy Goldsmith Single Molecule Biophysics:  Techniques and Technology
Milo Westler Biomacromolecule interactions as probed by NMR spectroscopy
Sam Butcher Small Angle X-ray Scattering of Biological Systems
Fall 2012 (Jackson) Pupa Gilbert Biomineralization
Meyer Jackson Voltage probes
Baron Chanda Temperature sensors
Spring 2012 (Jackson) Jeff Hardin Biophysical approaches using light microscopy with FRET
Aaron Hoskins Translation and the Ribosome
Tom Record Probing large scale conformational changes in the operation of the RNA polymerase molecular machinery
Fall 2011 (Jackson) Thomas Brunold Spectroscopic Insights into Metalloprotein Structure-Function
Robert Fettiplace Mechanically-Gated Channels
Silvia Cavagnero The protein unfolded state under physiological conditions
Spring 2011 (Jackson) Qiang Cui Membrane deformation and function of membrane proteins
Brian Fox Photo Allosteric Regulation of Protein Function:
Cindy Czajkowski Pentameric Ligand Gated Channel receptor structure-function
Fall 2010 (Jackson) Regina Murphy Protein Misfolding and Aggregation: Focus on Amyloid Proteins
Yongna Xing Metal Ions in Protein Structure and Function
Meyer Jackson Membrane elasticity and membrane fusion
Spring 2010 (Jackson) Arun Yethiraj Conformations of macromolecules
Alessandro Senes Structural and functional roles of hydrogen bonding in proteins
Martin Zanni Exciton models for quantitative interpretation of infrared and CD spectra of proteins
Fall 2009 (Jackson) Baron Chanda Principles of electromechanical coupling
George Phillips X-ray scattering by proteins
Sam Butcher RNA folding
Spring 2009 (Jackson) Julie Mitchell First principles approaches in molecular modeling
Qiang Cui Biophysical studies of binding
Tom Record Effects of small solutes
Fall 2008 (Jackson) Silvia Cavagnero Protein folding: basic concepts and leading mechanisms
Katrina Forest X-ray crystallography
Thomas Brunold Applications of spectroscopic and computational tools in bioorganic chemistry
Spring 2008 (Jackson) Tom Record Transcription
Jim Weisshaar Structure of the nucleoid in bacteria
Fall 2007 (Jackson) Jim Weisshaar Sub-diffraction-limit fluorescence (PALM, STED, STORM)
Meyer Jackson Ion channels
Doug Weibel Biological imaging - AFM optical microscopy
Spring 2007 (Jackson) Doug Weibel Cell motility
Qiang Cui Force as a probe in biophysics
Baron Chanda Voltage-dependent gating of ion channels
Fall 2006 (Jackson) Tom Record Kinetics and thermodynamics of protein-DNA interactions
Regina Murphy Formation of amyloid fibrils
Katrina Forest, Jim Keck X-ray crystallography
Spring 2006 (Jackson) Ching Kung Thermo- and mechanosensitive ion channels
George Phillips Simplified models of the dynamics of proteins
Sam Butcher RNA and DNA dynamics
Fall 2005 (Jackson) Tom Record In vitro protein folding
Meyer Jackson, Qiang Cui Ion Permeation: Experiment and computational studies
Jim Weisshaar Organization of the cell membrane