PEB Discussion Group

2024-2025 Student Organizers:

Marshall McCraw (O’Hern Lab, MEMS)

Latavia Thompson (Physics, Saxena Lab)

Discussion Group Schedule

September 27, 2024

• Karthik Srinivasan (Graduate Student, Dixit Lab, Biomedical Engineering): Exploring low dimensionality in microbiomes using the consumer resource model.
• Yongxu Zhang (Graduate Student, Saxena Lab, Biomedical Engineering): Inference of Neural Dynamics Using Switching Recurrent Neural Networks.

October 25, 2024

• Zhuoyi Liu (Graduate Student, O’Hern Lab, MEMS): Identifying the minimal sets of distance restraints for FRET-assisted protein structural modeling.
• Asmita Jha (Graduate Student, Bewersdorf and LusKing Labs, Cell Biology): FLASH-PAINT Chromatin Labeling: Simultaneous locus and protein labeling.

November 22, 2024

• Avinash Kumar (Postdoc, Zhang Lab, Cell Biology): SNARE assembly and disassembly on membranes
• Garrett Sager (Graduate Student, Clark Lab, MCDB): Lawful scaling of mitochondria in a connectome

December 13, 2024

• Kunyun Wang (Postgraduate Associate, Liang Lab, Neuroscience): Coordination of Local and Global Responses in Individual Mouse Thalamic Local Interneurons
• Zachary Sun (Graduate Student, Murrell Lab, Physics): Active Mechanics of the Cytoskeleton

January 31, 2025

• Brooke Emison (Graduate Student, Dixit Lab, BME): “Detangling Mechanisms of Information Loss in Gene Regulatory Networks During Aging”
• Matthew Leighton (Postdoc, Lynn Lab, Physics): Nonequilibrium Thermodynamics of Free Energy Transduction by Molecular Machines

February 28, 2025

• Farah Abdul-Tahman (Postdoc, Dal Bello Lab, EEB): Copy Number Variants Facilitate Rapid Switching Between Ecological Strategies
• Gabriel Araujo (Post-graduate associate, Chung Lab, Cardiovascular Medicine and MCDB): Uncovering Spatial Metabolic Niches

March 28, 2025

• Christopher King (Graduate student, Breaker Lab, MB&B): A Probabilistic Folding Algorithm for DNA Triplexes
• Kristin Meyer (Assistant Professor, MCDB): Decoding Transcription Factor Dynamics Through Transcriptional Co-condensates

April 25, 2025

• Pranav Kantroo (Graduate Student, Machta Lab, CBB): Parkour in Protein Morphospace
• Andrew Goetz (Graduate Student, Dixit Lab, BME): Non-equilibrium strategies for tuneable ligand specificity in signaling networks”

May 16, 2025

• PEB 2nd Year PEB Student Flash Talks

2022-2023 Student Organizers

Naomi Brandt (O’Hern Lab, Physics)

Emmanuel Mintah (O’Hern Lab, BME)

Discussion Group Schedule

September 29, 2023

• Lam Vo (Graduate Student, Emonet Lab, MCDB): A new adaptation mediated by collective migration

October 27, 2023

• Tianyu Yuan (Graduate Student, Mochrie Lab, Physics): Cohesin distribution encodes chromatin 3D organization via conserved-current loop extrusion
• Isabella Graf (Postdoc, Machta Lab, Physics): How snakes can detect milli-Kelvin changes in temperature

November 17, 2023

• Zion Perry (Graduate Student, Pyle Lab, MCDB): HOTAIR rises: Challenges and lessons learned in studying the long noncoding RNA HOTAIR
• Avinash Kumar (Postdoc, Zhang Lab, Cell Biology): Mechanical forces in membrane fusion, lipid transfer, and mechanosensation

January 26, 2024

• Arthur MacKeith (Graduate Student, O’Hern Lab, MEMS): Image analysis and modeling of mesophyll tissue
• Paul Turner (Professor, EEB and Microbiology): Quantitative biology meets phage therapy

February 23, 2024

• XJ Xu (Graduate Student, Wu Lab, Cell Biology): Emergence of rhythms on the plasma membrane
• Muhammad Noman Almani (Graduate Student, Saxena Lab): µSim: A goal-driven framework for elucidating the neural control of movement through musculoskeletal modeling.

March 29, 2024

• Miriam Genuth (Postdoc, Holley Lab, MCDB): A cadherin-ECM code for tissue solidification
• Juan Chen (Postdoc, Luo Lab, MEMS): Disodium Cromoglycate Templates Anisotropic Short-chain PEG Hydrogels

April 26, 2024

• Gustavo Santana (Graduate Student, Emonet Lab, INP): Motion Detection in Olfaction
• David Carcamo (Graduate Student, Lynn Lab, Physics): Exact Statistical Physics Models Minimize Entropy of Large-scale Neural Activity with Loops

May 16, 2024

• 2nd Year PEB Students: Ardavan Abiri, Shoham Benmelech, Alex Calabrese, Hobart Chen, Devon Finlay, Gautham Gopinath, Sam Greenspun, Ao Huang, Keui Li, Yao Lu, Anthony Minnah, Jungmin Nam, Raibat Sarker, Carlton Smith, Anna Su, Latavia Thompson, Nick Weaver, Zhang Wen, Samuel Yu, Roy Zhang, Xinyuan Zheng

2022-2023 Student Organizers

Lauren Harkins (Saltzman Lab, BME)

Jake Sumner (O’Hern Lab, CBB)

Discussion Group Schedule

Friday, September 23rd, 2022

• Ed Stites PhD - “Mutants, Loners, and Bad Influences”
• Binyam Mogessie PhD - “Cytoskeletal ensembles in oocyte meiosis and female reproductive aging”

 Friday, October 28th, 2022

•  Shan Xu PhD - “Enhanced FIB-SEM: A discovery platform to visualize biology across scales”
• Alex Grigas - “Polymer collapse and jamming applied to protein cores” 

Friday, November 18th, 2022

• Arlind Kacirani - “Dimensionality reduction of cataract associated gammaD-crystallin conformational dynamics
• Zachary Sun - “Self-organized criticality in the cell cytoskeleton”

 Friday, January 27th, 2023

• Joseph Shomar - “Distance estimation in walking drosophila”
• Cristina Rodríguez PhD - “Next-generation optical microscopy methods for deep tissue in vivo imaging of the nervous system”

Friday, February 24th, 2023

• Xiaoyi Ouyang - “Mean-field model of branching morphogenesis of dendrites in fly sensory neurons”
• Yuan Ren PhD - “A 5-in-1 in vivo mechanical force transducer”

Friday, March 24th, 2023

• Joey Erwin - “OmcB is a widespread porin-cytochrome complex required for kick-starting growth and nanowire production of electric bacteria” 

Friday, April 28th, 2023

• John Tsang PhD - “Systems immunology of immune set points”
• Yimin Luo PhD - “Substrate anisotropy, crowding, and division drives new collective behaviors in monolayers”
• Allison Didychuk PhD - “Unwrapping the herpesvirus genome packaging machinery”
• Liz Li - “Investigate how long noncoding RNAs establish epigenetic memory”

Friday, May 26th, 2023

• PEB 2nd Year Talks

2021-2022 Student Organizers

Isaac Vock (Simon Lab, MB&B)

Grace Meng (O’Hern Lab, Chemistry)

Discussion Group Schedule

October 29, 2021

• Gregory Tietjen (Assistant Professor, Surgery): Honoring the gift of organ donation through emergency science
• Amir Pahlavan (Assistant Professor, MEMS): Gradient sensing and transport in heterogeneous environments

November 12, 2021

• Jeremy Moore (Graduate Student, Emonet Lab, MCDB): Cell-to-cell variability in chemotactic signal integration
• Hannahmariam Mekbib (Graduate Student, Bewersdorf Lab, BME): Light sheet microscopy for 3D nanoscale imaging

December 10, 2021

• Farrah Mohammad (Graduate Student Zhou Lab, BME): Investigation of the cellular and molecular mechanisms of glyburide for stroke treatment through single cell sequencing
• Lenoard Scharfen (Graduate Student, Neugebauer Lab, MB&B): Transcriptome-wide probing of nascent RNA structure

January 28, 2022

• Nicole Donnert (Graduate Student, Palm Lab, Microbiology):  Decoding Host-Microbe Interactions in Crohn’s Disease 
• Sonal Shree (Postdoc, Howard Lab, MB&B): Branching morphogenesis of Drosophila Sensory Neurons

February 25, 2022

• Milind Singh (Graduate Student, Colon-Ramos Lab, MCDB): Investigating the mechanisms that lead to PFK-1.1 condensation in vivo
• Isaac Vock (Graduate Student, Simon Lab, MB&B): Improved statistical modeling for differential RNA kinetics analysis

March 25, 2022

• Avinash Kumar (Postdoc, Zhang Lab, Cell Biology): The compliance of NOMPC gating spring and its implication in mechanosensation
• Joseph Shomar (Graduate Student, Clark Lab, Physics): Distance estimation in walking Drosophila

April 29, 2022

• Abdel-Rahman Hassan (Postdoc, Holley Lab, MCDB): In vivo single molecule biophysics during spinal column development
• Yuan Ren (Postdoc, Berro Lab, MB&B): In vivo force measurement with two, one, half, and zero GFP

May 27, 2022

• 2nd year PEB students

2020-2021 Student Organizers

Kyra Thrush (Levine Lab, CBB)

Alex Grigas (O’Hern Lab, CBB)

2020-2021 Schedule

September 25, 2020

• David Van Dijk (Van Dijk lab)
• Alison Sweeney (Sweeney lab)

October 23, 2020

• Henry Mattingly (Postdoc, Emonet lab, MCDB): Are cells information limited?
• Caitlin Davis (Assistant Professor, Chemistry): Spliceosomal U1A protein - SL2 RNA binding affinity increases in cells

December 4, 2020

• Min Wu (Associate Professor, Cell Biology): Single cell pattern formation: Opportunities and challenges
• Jinghua Ge (Postdoc, Cell Biology): Single-molecule force spectroscopy of protein-membrane interactions

January 29, 2021

• Eric Schneider (Associate Professor, Department of Surgery): Understanding physiological response to quantified measures of sub-concussive blast exposure in humans
• Miriam Genuth (Postdoc, MCDB): Ergodic cell state transitons and the reproducibility of embryonic development

February 26, 2021

• Xiaobai Li (Graduate Student, Chemistry): Stresses within the actin meshwork control the turnover of fimbrin during clathrin-mediated endocytosis
• Kyra Thrush (Graduate Student, CBB): Epigentic based modeling of brain aging is linked to Alzheimer’s Disease pathology

March 26, 2021

• Christopher Anderson (Graduate Student, ExPath): Generation of a tissue engineered pulsatile conduit for modified fontan circulation
• Jeremy Moore (Graduate Student, MCDB): Cell-to-cell variation in sensitivity to mixed chemotactic stimuli

April 23, 2021

• Ryosuke Tanaka (Clark lab, Interdepartmental Neuroscience Program): Mechanisms for collision avoidance in walking Drosophila
• Viraaj Jayaram (Emonet lab, Physics): Robust olfactory navigation is shaped by multiple temporal features of turbulent odor plumes

May 28, 2021

• 2nd year PEB students: Sara Siwiecki, Yuxuan Cheng, Daisy Duan, Farrah Mohammed, Anjiabei Wang, Eric Ni, Fidel Arizaga, Grace Meng, Hannahmariam Mekbib, Isaac Vock, Isaiah Yim, Joey Erwin, Joseph Shomar, Kasey Hancock, Lianghui Peng, Tianyu Yuan, XJ Xu, Zachary Sun

2019-2020 Student Organizers:

Catharine Shipps (Malvankar lab, MB&B)
Taylor Schaffner  (Machta lab, Physics)

Discussion group schedule

September 26, 2019

• Jing Yan (Yan lab): Mechanical principles of biofilm formation
• Yuan Ren (Berro lab): Cutting proteins in fission yeast cells

November 14, 2019

• Sam Dundon (Pollard lab): Mitotic microtubules regulate Rho activity and cytokinesis in fission yeast
• Anne Feke (Gendron lab): Illuminating the plant calendar: Photoperiodic regulation of a winter gene

January 31, 2020

• Clorice Reinhardt (Hammes-Schiffer lab): Towards simulation of the active state of ribonucleotide reductase
• Aneysis Gonzalez (Clark lab): Manipulating the kinetics of motion detection in Drosophila

February 28, 2020

• Zach Levine (Levine lab): Disorderd proteing folding as a determinant of human disease
• Ethan Perets (Yan lab): Optical spectroscopy of protein phase-separation

April 24, 2020

• Daniel Seara (Murrell lab): Dissapative signatures of dynamical phases and transitions
• Kevin Hu (Bewersdorf lab): 3-color live cell super-resolution microscopy

May 22, 2020

• 2nd year PEB students: Kate Bridges, Taylor Schaffner, Janua Khanal, Feng Xing, Qian Xu, Kyra Thrush, Haoyu Tang, Xingbo Shang, Ryan Nguyen, Peter Ciaccia

2018-2019 Student Organizers:

Kevin Hu (Bewersdorg lab, Cell Biology)
Elise Bullock (Miller-Jensen lab, BME)

Discussion group schedule

September 21, 2018

• Xiaolei Su (Su lab) Phase separation in T cell signaling
• Victor Beaumont (Loria lab): Chimeric phosphatase demonstrates the importance of active site loop sequence and dynamics

October 26, 2018

• Dipjyoti Das (Holley lab): Organization of embryonic morphogenesis via mechanical information propagation
• Rui Ma (Berro lab): How to pull a membrane tube against turgor pressure during endocytosis

November 16, 2018

• Nandan Pundit (De La Cruz lab): Branched actin network disassembly is force sensitive
• Anna Chen (Ganim/Yan lab): Single-molecule force microsopy studies of dronpa and rhodopsin

January 31, 2019

• Wei-Hsiang Lin (Jacobs-Wagner lab): Non-steady-state dynamics and growth optimization of scalable flux networks
• Keita Kamino (Emonet lab): Adaptive tuning of phenotypic diversity in bacterial chemotaxis

February 15, 2019

• Chris Anderson (Qyang lab): Production of a beating conduit for the modified Fontan procedure
• Neelima Sharma (Venkadesan lab): Dynamics of static finger contact

March 15, 2019

• Bara Badwan (Clark lab): Dynamic nonlinearities enable direction-occupancy in Drosophila elementary motion detectors
• Mary Grace Velasco (Bewersdorf lab): Two-photon STED microscopy for super-resolution imaging in live mice

April 19, 2019

• Michael Grome (Isaacs lab): Vesicle tubulation with self-assembling DNA nanosprings
• Zhe Mei (O’Hern lab): Computational protein redesign using NMR structures

May 22, 2019

• 2nd year PEB students

2017-2018 Student Organizers:

Mary Lou Bailey (Mochrie lab, Applied Physics)
Bara Badwan (Clark lab, MCDB)

Discussion group schedule

September 22, 2017

• Rong Fan (Fan lab): Single cell omics tools for immune oncology
• Michael Mak (Mak lab): Cell matrix dynamics: Experiments and simulations

October 20, 2017

• Nirag Kadakia (Emonet lab): Olfactory sensing in a vast odor space: adaptive mechanisms for robust combinatorial coding
• Dick Kibbey (Kibbey lab): Measuring mitochondrial metabolism by modeling multiordinate mass-isotopomers: from rare disease to diabetes drug

November 17, 2017

• Mahmut Demir (Emonet lab): How do insects navigate odor plumes?
• Peter Williams (O’Hern lab): Computational models of the bacterial cytoplasm

January 19, 2018

• Daniel Seara (Murrell lab): Non-canonical actomyosin interactions drive stabilizing F-actin bending fluctuations
• Simon Mochrie (Mochrie lab): Analysis of single particle tracks reveals the biochemistry of DNA binding proteins in living cells

February 16, 2018

• Margarida Agrochao (Clark lab): Which neurons regulate walking speed in fruit flies?
• Zachary Levine (Levine lab): Intrinsically disordered protein folding and the thermodyamics of amyloid diseases

March 16, 2018

• Catherine Matulis (Clark lab): Distributed contrast adaptation in Drosophila visual circuits
• Alvaro Sanchez (Sanchez lab): Emergent simplicity in microbial community assembly

April 20, 2018

• Jack Treado (O’Hern lab): Proteins without a backbone: A new perspective on the structural properties of protein cores and cavities
• Ben Machta (Machta lab)

May 25, 2018

• 2nd year PEB students

2016-2017 Student Organizers:

Curran Oi ( Regan  lab, MB&B)
Olivier Trottier (Howard lab, Physics)

Discussion group schedule

September 23, 2016

• David Baddeley (Baddeley lab): Drowning in detail? Getting high quality quantitative results from super-resolution microscopy
• Wei Liu (Yan lab): A sum frequency generation study of SpyTag modified BsIA biofilm protine at interface

October 21, 2016

• Emilio Salazar (Clark lab): Fast timescale tuning to correlations in Drosophila’s ON and OFF elementary motion detectors
• Sujoy Ganguly (Howard lab): Mathematical modeling of dendrite morphogenesis

November 18, 2016

• Stefan Elrington (Barrett lab): Magnetic resonance imaging of biological solids: P-31 and H-1 NMR/MRI in bone apatite
• Joshua Burt (Murray lab): Hierarchical organization of microcircuit specialization in human cortex

January 20, 2017

• Michael Mak (Mak lab): Multiscale mechanobiology in cancer and development
• Stephanie Loeb (Kim lab): Towards the design and characterization of photothermal nanomaterials for sustainable solar water treatment

February 17, 2017

• Michael Lacy (Berro lab): Visualizing heterogeneous single-molecular dynamics of eisosome protein Pil1p in live cells
• Alexandra Signoriello (O’Hern lab): Computational modeling of stissue developent

March 17, 2017

• Sangjin Kim (Jacobs-Wagner lab): Modeling spatio-temporal dynamics of RNA polymerases in gene regulation: Lessons from highway traffic
• Andrew Barentine (Bewersdorf and Baddeley labs):  Nono-scale imaging at warp speed

April 21, 2017

• Gilad Kaufman (Osuji lab): Interfacial engineering in microdroplets as a tool to make microcapsules
• Jennifer Gaines (O’Hern lab): Computational studies of protein cores and protein core mutations

May 19, 2017

• 2nd year PEB students

2015-2016 Student Organizers:

Susan Pratt (Mochrie lab, Physics)
Sandy Hernandez (De La Cruz lab, MB&B)

Discussion group schedule

September 18, 2015

• Madhusudhan Venkadesan (Venkadesan lab): Evolution of the human foot
• Nikhil Malvankar (Malvankar lab): Seeing in believing: Imaging electron transfer in bacterial pili reveals a new mechanism for respiration and energy sharing

October 23, 2015

• Srinivas Gorur-Shandilya (Emonet lab): Gain control in olfactory receptor neurons
• Dpjyoti Das (Holley lab): Can too much order be a problem? - A story of how disorder prevents scoliosis

November 20, 2015

• Ken Buck (Forscher lab): apCAM adhesion sites are mechanically isolated from retrograde actin flow by local Arp2/3complex-dependent actin assembly
• Pablo Sartori (Howard lab): How curvature regulates the beat of Chlamydomonas agella

January 22, 2016

• Michael Murrell (Murrell lab): Cellular Reconstitution to Understand Mechanical Force Production in Biology
• Austin Elam (De La Cruz lab): S3D Colin Binds Actin Filaments but Does Not Sever Them

February 19, 2016

• John Murray (Murray lab): Population-level Dynamics and Coding in Prefrontal Cortex During Working Memory
• Shari Yosinski (Reed lab): Controlling Bioparticles with Electric Fields

March 18, 2016

• Jared Rovny (Barrett lab): MRI of Bones, or What is NMR Anyways?
• Emily Wong (De La Cruz lab): Regulation and physiological function of the DEAD-box protein Dbp5

April 22, 2016

• Yao Zhao (Mochrie lab): 3D Reconstruction of Fluorescently Labeled Membranes
• Lynn Liu (Solomon lab): The Role of Phosphorylation in Cell Cycle Protein Stability

May 20, 2016

• 2nd year PEB students

2014-2015 Student Organizers:

Julie Park (H. Lin lab, Cell Biology)
Stefan Elrington (Barrett lab, Physics)

Discussion group schedule

September 26, 2014

• Research: Hyeran Kang (De La Cruz lab): Site-specific cation release drives actin filament severing by vertebrate cofilin
• Research: Erdem Karatekin (Karatekin lab): Control of fusion pore nucleation and dynamics by SNARE proteins

October 24, 2014

• Research: Ellen White (Miranker lab): Self-assembly and stability of a small beta-helix
• Research: Ramesh Ramji (Miller-Jensen lab): Microdevices enabling single cell analysis

November 21, 2014

• Research: Alejandro Virrueta (O’Hern lab), Hard sphere models: Predicting methionine side-chain dihedral angles
• Research: Ying Guo (Yan lab), Thermal stability of vertebrate visual pigments is correlated to molecular evolution of vision

January 16, 2015

• Research: Diego Caballero (O’Hern lab), Equilibrium transitions between side chain conformations in leucine and isoleucine
• Research: Sarah Schreiner (King lab), Tethering of chromatin to the nuclear envelope supports stable nuclear mechanics

February 20, 2015

• Research: Betsy Speltz (Regan lab), Synthetic proteins for synthetic biology
• Research: Aaron Lewis (De Camili, Dufresne, Prum labs), Development of gyroid membranes in butterfly scale cells

March 20, 2015

• Research: Ross Boltyanskiy (Dufresne lab), Mechanical response of single cells to stretch
• Research: Xiongfe Fu (Emonet lab), Phenotypic diversity and collective behavior in chemotactic migratory waves

April 17, 2014

• Research: Ziad Ganim (Ganim lab), Structural Resolution in Single Molecule Experiments
• Research: Shirin Bahmanyar (Bahmanyar lab), Nuclear stiffness protects against mitotic errors

May 16, 2014

• 2nd year PEB students

2013-2014 Student Organizers:

Diego Caballero (O’Hern Lab, Physics)
Lynn Liu (De La Cruz lab, MB&B)

Discussion group schedule

September 20, 2013

• Research: David Taylor(Wang lab): RNA-induced structural activation of the CRISPR-associated Cas9 endonuclease
• Research: Danny Schlingman (Regan lab): The nuclesome unwinds into two states at physiological forces and ionic strengths

October 18, 2013

• Research: Julien Berro (Berro Lab): Molecular Mechanisms of Actin Dynamics during Clathrin-Mediated Endocytosis
• Research: Alex Kwan (Kwan Lab): Functional dissection of local and long-range neural circuits

November 15, 2013

• Research: Martha Braun (Karatekin Lab), FisB Mediated Membrane Fission During Sporulation in Bacillus subtillis
• Research: Fang Huang (Brewersdorf Lab), Localization Nanoscopy Goes Fast and 3D

January 17, 2014

• Research: Miriam Amiram (Isaacs Lab), Super natural materials: expanding the genetic code for the production of exotic biopolymers
• Research: Caroline Laplante (Pollard Lab), Real time super-resolution microscopy of the cytokinetic apparatus of fission yeast

February 21, 2013

• Research: Kathryn Rosowski (Horsley Lab), A role for mechanics in stem cell differentiation
• Research: Joe Howard (Howard Lab), Beat Generation: From single molecules to the collective motion of vilia and flagella

March 21, 2014

• Research: Corey Wilson (Wilson Lab), Controlling the Flow of Energy Through a Protein Matrix
• Research: Junyi Jiao (Zhang Lab), Single Molecule Manipulation Study of Gp41 Folding in HIV-1 Infection and Drug Resistance

April 18, 2014

• Research: Aleksander Rebane (Zhang Lab), Data analysis of Single-Molecule Trajectories from Optical Tweezers
• Research: Nicholas Frankel (Emonet lab) Trade-offs in Bacterial Chemotaxis and the Adaptation of Non-Genetic Diversity

May 18, 2012

• Research: Shyam Krishnakumar (Rothman Lab) Regulation of Membrane Fusion at the Neuronal Synapse
• Research: PEB second-year students

2012-2013 Student Organizer:

Yao Zhao (Mochrie Lab, Applied Physics)

Discussion group schedule

September 28, 2012

• Research: Xinming Zhang (Zhang lab): Optical tweezers: powerful tools to study protein folding
• Research: Sarah Schreiner (King lab): Role of chromatin in mechanically buffering cytoskeletal forces at the nuclear envelope

October 26, 2012

• Research: Chuck Sindelar (Sindelar Lab): Finding kinesin (3D): using new high-resolution imaging methods to examine the brave journey of a molecular motor
• Literature: Matt Akamatsu (Pollard Lab): Measuring Molecular Motor Forces In Vivo: Implications for Tug-of-War Models of Bidirectional Transport

November 16, 2012

• Research: Alice Qinhua Zhou (Regan and O’Hern Labs), The Power of Hard Sphere Model
• Research: Wendell Smith (O’Hern Lab), Molecular Simulations of the Fluctuating Conformational Dynamics of Intrinsically Disordered Proteins

December 14, 2012

• Research: Robert McDougal (Shepherd-Willhite Lab), Challenges and Progress in the Computational Study of Neuronal Calcium Waves
• Research: Nick Sawyer (Regan Lab), Sequence Analysis of Repeat Protein Modules to Guide Protein Design

January 25, 2013

• Research: Ross Boltyanskiy (Dufresne Lab), Probing Mechanical Homeostasis of Individual Cells
• Research: Katie Rosowski (Horsley Lab), A Role for Mechanics in Stem Cell Differentiation

February 22, 2013

• Research: Damon Clark (Clark Lab), 3-Point Correlations in Motion Estimation
• Research: Patrick McMillen (Holley Lab), Cell Adhesion and Extracellular Matrix Assembly during Zebrafish Segmentation

March 29, 2013

• Research: Stuart Campbell (Campbell Lab), Multi-scale Studies of Cardiac Myofilament Activation
• Research: Christian Cyron (Humphrey Lab), Micromechanical Continuum Approach for the Computational Analysis for Biopolymer Networks

April 26, 2013

• Research: Murat Acar (Acar Lab), Understanding the Evolution of a Natural Gene Network Between Closely-Related Yeast Species
• Research: Ivan Surovtsev (Jacobs-Wagner lab), Mesoscale Dynamics of Bacterial Cyroplasm

May 18, 2012

• Research: PEB second-year students

2011-2012 Student Organizers:

Ross Boltyanskiy (Dufresne Lab, Physics)
Nick Sawyer (Regan Lab, MB&B)

Discussion group schedule

September 16, 2011

• Systems Biology Symposium

October 21, 2011

• Research: Yongli Zhang (Zhang Lab), Single-molecule studies of ATP-dependent chromatin remodeling and protein folding
• Research: Michael Sneddon (Emonet Lab), Stochastic coordination of multiple flagellar motors improves performance in bacterial chemotaxis

November 17, 2011

• Research: Daniel Schlingman (Regan Lab), The Effects of Histone Mutations on the Rate of Chromatin Remodeling
• Research: Doug Kelley (Ouellette Lab), Bug turbulence? Studying collective behaviors of C. riparius with Lagrangian particle tracking

December 16, 2011

• Research: Abhi Nath (Miranker / Rhoades Labs), Computationally Identifying Small-Molecule Modulators of IAPP Toxicity
• Research: Farren Isaacs (Isaacs Lab), Programming genomes to expand life’s functional repertoire

January 20, 2012

• Research: Aaron Mertz (Dufresne Lab), Active surface tension of cohesive cell colonies
• Research: Seng Fatt Liew (Cao Lab), Structural colors of butterfly wings

February 17, 2012

• Research: Jamie Schwendinger-Schreck (Holley Lab), Deciphering the network of /her/hes/ genes in zebrafish segmentation
• Research: Eben Olson (Levene Lab), Analyzing brightness distribution with fluorescence cumulant analysis

March 16, 2012

• Research: Matt Akamatsu (Pollard Lab), Assembly and stoichiometry of cytokinesis precursor nodes in fission yeast
• Research: Kristina Herbert (J. Steitz Lab), Regulation and Mechanism of Pri-miRNA Processing

April 15, 2011

• Research: Alice Zhou (O’Hern / Regan Labs), The power of hard sphere models: Explaining side-chain dihedral angle distributions of Thr and Val
• Research: Sarah Schreiner (King Lab), The role of peripheral chromatin in nuclear integrity

May 18, 2012

• Research: Michael Bradley (De La Cruz Lab), ATPase coupling in the processive RNA helicase NS3 from hepatitis C virus 
• Research: Jared Harwayne-Gidansky (O’Hern Lab), Minimal energy packings of weakly semiflexible polymers: Application to targeted self-assembly of nanostructures

2010-2011 Student Organizers:

Garrett Cobb (Rhoades Lab, MB&B)
Aaron Mertz (Dufresne Lab, Physics)

Discussion group schedule

September 17, 2010

• Research: Ross Boltyanskiy (Dufresne Lab), ‘Spirochete cell mechanics and membrane fluidity’ 
• Literature: Matt Akamatsu (Pollard Lab), Bipedal Locomotion in Crawling Cells.

October 22, 2010

• Literature: Marcus Bosenberg (Bosenberg Lab), Mutagenic Patterns and Mechanisms in Melanoma
• Research: Nivedita Mitra (Yan Lab), Purification of Family B G-Protein-Coupled Receptors Using Nanodiscs

November 19, 2010

• This SDG meeting was replaced by the IGPPEB Fall Retreat

December 17, 2010

• Research: Kathryn Miller-Jensen (Miller-Jensen lab), ‘HIV as a model system to understand how promoter architecture regulates transcriptional activation’
• Research: Dorina Saro (Sung Lab), ‘Role of FANCM complxes in DNA repair

January 21, 2011

• Research: William Pontius (Emonet lab), ‘Mutual constraints on chemotactic tracking and exploration imposed by a fluctuation-response relationship’
• Research: Alice Zhou (O’Hern and Regan Lab), ‘Predicting the atomic details of protein-protein interactions: How simple can a model be?’

February 18, 2011

• Research: Brad Parry (Jacobs-Wagner lab), ‘Beyond Diffusion: Particle Mobility in the Bacterial Cytoplasm’
• Research: Fabio Parisi (Kluger Lab), ‘Copy Number Analysis in Tumor Samples’

March 25, 2011

• Research: Callen Hyland (Forscher lab), ‘Mechanics of Regenerating Aplysia Neurons’
• Research: J.D. Humphrey (Humphrey lab), ‘Mechanotransduction and Vascular Mechanical Homeostasis Across Multiple Scales’

April 15, 2011

• Research: Jared Harwayne-Gidansky, ‘Understanding Polymer Collapse Through Exact Enumeration’
• Research: George Sirinakis (Zhang lab) ‘The RSC chromatin remodeling ATPase translocates DNA with high force and small step size’

May 20, 2011

• Research: Dorthe Julich and Garrett Cobb (Holley & Rhoades Labs), Using FCS to observe integrin clustering in live zebrafish embryos
• Literature: Tim Craggs (Grindley / Joyce lab), Monitoring multiple distances within a single molecule using switchable FRET: Nature Methods, Kapanidis Lab