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 research premise of an article, cover the paper figure by figure, evaluate results, address the rigor of statistical methods, 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.
Fall semesters: the course consists of three modules, each one focusing on a different biophysical 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.
Spring semesters: 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 2024 (Senes) | Joshua Brockman | Acquiring and quantifying super-resolution microscopy data |
| Katrina Forest | Building a cell | |
| Meyer Jackson | 2-photon microscopy | |
| Spring 2024 (Senes) | Grant, Xuhui Huang, Jackson, Landick, Notbohm, Rienstra, Rizvi, Venturelli, Xing | First-year students presented a paper related to their own thesis topic. Each student's advisor joined as co-moderator. |
| Fall 2023 (Senes) | Jacob Notbohm | Statistical analysis and data integrity |
| Xuhui Huang | Harnessing the Power of Machine Learning in Studying Protein Dynamics | |
| Martin Zanni | Linking three aspects of a typical amyloid disease: aggregation mechanism, structure, and physiology | |
| Spring 2023 (Senes) | Forest, Henzler-Wildman, Huang, Li, Lim, Notbohm, Romero, Sinha, Smith, Zanni | First-year students presented a paper related to their own thesis topic. Each student's advisor joined as co-moderator. |
| 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) | Bergmann, Butcher, Friedrich, Grant, Jackson, Kaçar, Kirchdoerfer, Li, Lim, McNeel, Notbohm, Romero, Van Lehn | 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 |