Plots and Scotch — The CMU Biophysics Seminar Series

Indrajit Badvaram

Department of Biophysics, Johns Hopkins University

Physics of membrane shape sensing by a single protein

Richard Gillilan

Cornell High Energy Synchrotron Source

High-pressure limited proteolysis uncovers widespread and functionally important conformational dynamics on the whole proteome scale

Krista Freeman

Department of Biological Sciences, University of Pittsburgh

Seeing is believing: Structural insights on bacteriophage immunogenicity

Matthew Wohlever

Department of Cell Biology, University of Pittsburgh

The Mechanism of Substrate Recognition and Membrane Extraction by the AAA Protein Msp1

Christopher Aldrich

Department of Physics, Carnegie Mellon University

Quantitative principles of bacterial physiology at different temperatures

Sarthak Gupta

Department of Physics, Syracuse University

Active Chromatin Dynamics Drives Nuclear Bulge Formation

Saheli Mitra

Department of Physics, Carnegie Mellon University

Novel helical Trp- and Arg-rich antimicrobial peptides locate near membrane surfaces and rigidify lipid model membranes

Frank Heinrich

Department of Physics, Carnegie Mellon University & NCNR/NIST

Autonomous measurements of peptide-membrane structures with neutron reflectometry

Tafadzwa Chigumira (1) &

Deb Sankar Banerjee (2)

(1) Department of Biological Sciences and (2) Department of Physics, Carnegie Mellon University

Ripening of nuclear condensates is governed by the interplay between chromatin stiffness and condensate properties

Gabrielle Illava

Department of Chemistry & Chemical Biology, Cornell University

Biomolecular adaptations to oxygen and development of anoxic X-ray scattering techniques

Vadim Frolov

Ikerbasque Research Professor, UPV/EHU and Biophysics Institute (CSIC-UPV/EHU)

Smart material approach to cellular membrane remodelling

Frank Heinrich

Department of Physics, Carnegie Mellon University & NCNR/NIST

Peripheral Membrane Proteins. Experimental Structure and Simulation

Huijing Wang

Department of Computational and Systems Biology, University of Pittsburgh

Dynamics and Fitness Implications of Nonlinearities in Bacterial Regulatory Networks

Azam Shafieenezhad

Department of Physics, Indiana University – Purdue University Indianapolis

Malavika Varma

Department of Physics, Carnegie Mellon University

Xinzhi Li

Department of Physics, Northeastern University

Statistical Mechanics of Biological Tissues

Sebastian Himbert

Department of Physics and Astronomy, McMaster University, Canada

Functional and Functionalized Red Blood Cell Membranes

David P. Siegel

Givaudan Flavors Corp.

Why we should study inverted cubic phases for a better understanding of membrane trafficking

(or: A prospectus for a fishing expedition, with a sketch of a map.)

Fernanda Pérez

Department of Physics, Carnegie Mellon University

Haozhen Wang

Advanced Science Research Center, The City University of New York

Logan Carpenter

Department of Physics, Carnegie Mellon

Callaghan Cylke

Department of Physics, Carnegie Mellon University

Inferring the Stochastic Dynamics of Bacterial Growth and Shape Fluctuations

Samuel Foley

Department of Physics, Carnegie Mellon University

Asymmetry and Phase Coexistence: From van der Waals to Lipid Bilayers

David P. Siegel

Givaudan Flavors Corp.

Do antimicrobial & fusion-catalyzing peptides act by changing membrane curvature energy?
Clues from Helfrich theory and peptide effects on Q_II phase stability.

Stephanie Tristram-Nagle

Department of Physics, Carnegie Mellon University

Use of x-ray and neutron scattering to anchor MD simulations of membranes with additives

Deb Sankar Banerjee

Department of Physics, Carnegie Mellon University

Centrosome size regulation

Saheli Mitra

Department of Physics, Carnegie Mellon University

Understanding the interaction of the ionic liquids with bio-membranes

Minaspi Bantawa

Department of Physics, Georgetown University

Role of microscopic interactions and network topology in linear and non-linear mechanics of soft gels

Shiladitya Banerjee & Markus Deserno

Department of Physics, Carnegie Mellon University

Deb Sankar Banerjee

Department of Physics, Carnegie Mellon University

Dynamic size control with growth promoters and growth inhibitors

Stephan Wimmi & Andreas Diepold

Max-Planck-Institute for Terrestrial Microbiology

Logan Carpenter

Department of Physics, Carnegie Mellon

Koen Martens

Department of Physics, Carnegie Mellon

Dennis Michalak

Department of Physics, Carnegie Mellon

Michal Skruzny

Max Planck Institute for Terrestrial Microbiology, SYNMIKRO, Marburg, Germany

Stephanie Tristram-Nagle

Department of Physics, Carnegie Mellon University

Journal Club: “Location of the Hydrophobic Surfactant Proteins, SP-B and SP-C, in Fluid-Phase Bilayers“

Bartosz Turkowyd

Department of Physics, Carnegie Mellon University

Journal Club: “Establishing Live-Cell Single-Molecule Localization Microscopy Imaging and Single-Particle Tracking in the Archaeon Haloferax volcanii“

John Nagle

Department of Physics, Carnegie Mellon University

Critique of a derivation of the relation between monolayer and bilayer area compression moduli

Samuel Foley

Department of Physics, Carnegie Mellon University

Journal Club: “Stabilizing Leaflet Asymmetry under Differential Stress in a Highly Coarse-Grained Lipid Membrane Model“

Shiladitya Banerjee

Department of Physics, Carnegie Mellon University

Mechanical feedback promotes bacterial adaptation to antibiotics

Frank Heinrich

Department of Physics, Carnegie Mellon University & NCNR/NIST

Journal Club: “Deep mutational scanning reveals the structural basis for α-synuclein activity“

John Nagle

Department of Physics, Carnegie Mellon University

Papers that purport to measure the bending modulus from the size distribution of vesicles

Jonathan Fritz

Department of Physics, Carnegie Mellon University

The role of pulmonary surfactant proteins in lipid phase coexistence suppression

Fred Lanni

Department of Biological Sciences, Carnegie Mellon University

The finite-well particle-in-a-box and evanescent field in optical TIR

Frank Heinrich

Department of Physics, Carnegie Mellon University & NCNR/NIST

Monte Carlo and MD simulations of KRAS at the membrane and comparison to experiment

Markus Deserno

Department of Physics, Carnegie Mellon

Why do science when you can photoshop?
A few vignettes from a Chamber of Horrors.

Shashank Markande

Department of Physics, Georgia Tech

A study of symmetric structures in soft materials: three-periodic surfaces & two-periodic sets of strings

Dennis Michalak

Department of Physics, Carnegie Mellon

Journal Club: “Spin-Dependent Electron Transport through Bacterial Cell Surface Multiheme Electron Conduits“

Jana Kainerstorfer

Department of Biomedical Engineering, Carnegie Mellon

Diffuse optical imaging for biomedical application

Huaiying Zhang

Department of Biological Sciences, Carnegie Mellon

Phase separation in telomere elongation of ALT cancer

Peter Kasson

Department of Molecular Physiology and Biological Physics, University of Virginia

Individual-based modeling of COVID-19 spread: how individual actions matter in pandemic control

Stephan Uphoff

Department of Biochemistry, University of Oxford

Visualising DNA repair and mutagenesis at the single-molecule level in bacteria

Michael Murrell

Department of Biomedical Engineering, Yale University

Tissue pressure drives traction-independent cellular flows

Hanna Salman

Department of Physics and Astronomy, University of Pittsburgh

Cell-size control and inheritance dynamics in bacteria

David Hoogerheide

NIST Center for Neutron Research, National Institute of Standards and Technology

The Physics of Floating Bilayers

Frank Heinrich

Department of Physics, Carnegie Mellon University & NCNR/NIST

Neutron Reflectometry and MD Simulations of Flexible Membrane Proteins

Deb Sankar Banerjee

Department of Physics, Carnegie Mellon University

Organelle Size Control: positive feedback, size bistability and symmetry breaking

Ilya Levental

Department of Molecular Physiology and Biological Physics, University of Virginia

Plasma membranes are asymmetric in lipid unsaturation, packing and protein shape

Henry Chu

Department of Chemical Engineering, Carnegie Mellon University

Bridging stimulated deterministic motions between non-living and living systems: Diffusiophoresis & Chemotaxis

Stephanie Tristram-Nagle

Department of Physics, Carnegie Mellon University

Elastic and Structural Interactions of Engineered Cationic Antimicrobial Peptides (eCAPs) WLBU2 and D8 with Bacterial Lipid Model Membranes