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Stochastic Physics in Biology
Gordon Research Conference

Landscapes, Stochastic Dynamics, and Heterogeneity in Biology

Dates

January 8-13, 2017

Location

Four Points Sheraton / Holiday Inn Express
Ventura, CA

Organizers

Chair:
Jin Wang

Vice Chair:
Wallace F. Marshall

Meeting Description

This Gordon Conference on Stochastic Physics in Biology focuses on research interface where physics meet molecular and cellular biology by bringing together physical scientists and molecular/cell biologists. This conference aims for a quantitative non-equilibrium stochastic description of molecular and cell biology including molecular functions, cell structure formation, gene expressions and cell functions, intra-cellular and intercellular interactions, and cell dynamics, evolution and ecology. The new description will have great implications for biomedicine for human diseases as cancer, stem cell differentiation/tissue engineering, bacteria infections, Alzheimer's disease and Parkinson's disease.

Contributors

Final Meeting Program

Sunday
4:00 pm - 8:00 pmArrival and Check-in
6:00 pmDinner
7:30 pm - 7:40 pmWelcome / Introductory Comments by GRC Site Staff
7:40 pm - 9:30 pmKeynote Session: Stochastic Physics in Molecular and Systems Biology
Discussion Leader: Jin Wang (Stony Brook University, USA)
7:40 pm - 8:10 pmSunney Xie (Harvard University, USA)
"Single Cell Genomics, Where Stochasticity Meets Precision"
8:10 pm - 8:15 pmDiscussion
8:15 pm - 8:45 pmJose Onuchic (Rice University, USA)
"The Genetics and Biophysics of Epithelial-Mesenchymal Transition (EMT): Can Theory Help Cancer Biology"
8:45 pm - 8:50 pmDiscussion
8:50 pm - 9:20 pmMans Ehrenberg (Uppsala University, Sweden)
"Stochastic Impact of Slow Inhibitors of Translation of Messenger RNAs in the Living Bacterial Cell"
9:20 pm - 9:30 pmDiscussion
Monday
7:30 am - 8:30 amBreakfast
8:30 amGroup Photo
9:00 am - 12:30 pmBiomolecular Stochastic Dynamics
Discussion Leader: Ken Dill (Stony Brook University, USA)
9:00 am - 9:30 amWilliam Eaton (National Institute of Diabetes and Digestive and Kidney Diseases, NIH, USA)
"Stochastic Fluctuation of Cell Sickling from Nucleation of Single Hemoglobin S Fibers"
9:30 am - 9:45 amDiscussion
9:45 am - 10:15 amMasaki Sasai (Nagoya University, Japan)
"The 3D Genome Architecture and Transcriptional Regulation"
10:15 am - 10:30 amDiscussion
10:30 am - 11:00 amCoffee Break
11:00 am - 11:30 amMargaret Cheung (University of Houston, USA)
"Molecular Underpinning of Postsynaptic Ca2+/Calmodulin Signaling, Protein Folding and Conformational Changes In Vivo"
11:30 am - 11:45 amDiscussion
11:45 am - 12:15 pmBenjamin Schuler (University of Zurich, Switzerland)
"Dynamics of Unfolded and Intrinsically Disordered Proteins from Single-Molecule Spectroscopy"
12:15 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:30 pm - 9:30 pmCell Fate Decision Making
Discussion Leader: Jose Onuchic (Rice University, USA)
7:30 pm - 8:00 pmJames Ferrell (Stanford University, USA)
"Trigger Waves in Apoptosis"
8:00 pm - 8:10 pmDiscussion
8:10 pm - 8:40 pmJin Wang (Stony Brook University, USA)
"Quantifying Stochastic Cell Fate Decision Making"
8:40 pm - 8:50 pmDiscussion
8:50 pm - 9:20 pmLev Tsimring (University of California, San Diego, USA)
"Correlations and Adaptations Queueing in Enzymatic Networks"
9:20 pm - 9:30 pmDiscussion
Tuesday
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmCell Growth and Transformations
Discussion Leader: Sunney Xie (Harvard University, USA)
9:00 am - 9:30 amChao Tang (Peking University, China)
"Growth Behavior of Microbes: Monod's Problem Revisited"
9:30 am - 9:45 amDiscussion
9:45 am - 10:15 amDaniel Gillespie (Dan T. Gillespie Consulting, USA)
"From the Stochastic Simulation Algorithm to the Small-Voxel Tracking Algorithm"
10:15 am - 10:30 amDiscussion
10:30 am - 11:00 amCoffee Break
11:00 am - 11:30 amQi Ouyang (Beijing University, China)
"Thermodynamics of Biological Systems"
11:30 am - 11:45 amDiscussion
11:45 am - 12:15 pmJonathon Howard (Yale University, USA)
"Neuronal Morphology Driven by Stochastic Branching: Data and Models"
12:15 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:30 pm - 9:30 pmGenomes and Disease Mechanisms
Discussion Leader: Zan Luthey-Schulten (University of Illinois, USA)
7:30 pm - 8:00 pmChenghang Zong (Baylor College of Medicine, USA)
"Effective Detection of Variations in Single Cell Transcriptome"
8:00 pm - 8:10 pmDiscussion
8:10 pm - 8:40 pmWei Wang (Nanjing University, China)
"Cell-Fate Decision Mediated by the P53-Centered Signaling Network"
8:40 pm - 8:45 pmDiscussion
8:45 pm - 8:55 pmBin Zhang (Massachusetts Institute of Technology, USA)
"Towards Predictive Modeling of Three Dimensional Genome Organization"
8:55 pm - 9:00 pmDiscussion
9:00 pm - 9:10 pmMingyang Lu (Jackson Laboratory, USA)
"Interrogating the Robustness of Gene Regulatory Circuits by RACIPE and Cancer Dynamics"
9:10 pm - 9:15 pmDiscussion
9:15 pm - 9:25 pmSteve Presse (Arizona State University, USA)
"Hydrodynamic Hunters"
9:25 pm - 9:30 pmDiscussion
Wednesday
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmCell Structure and Dynamics
Discussion Leader: Wallace Marshall (University of California, San Francisco, USA)
9:00 am - 9:30 amJean-Francois Joanny (ESPCI Paris, France)
"Stochastic Cell Structures and Dynamics"
9:30 am - 9:45 amDiscussion
9:45 am - 10:15 amDavid Weitz (Harvard University, USA)
"Stochastic Contributions of Molecular Motors"
10:15 am - 10:30 amDiscussion
10:30 am - 11:00 amCoffee Break
11:00 am - 11:30 amFrank Julicher (Max Planck Institute for the Physics of Complex Systems, Germany)
"Phase Separation in the Cell Cytoplasm"
11:30 am - 11:45 amDiscussion
11:45 am - 12:15 pmNed Wingreen (Princeton University, USA)
"Protein Phase-Separation in and out of Cells"
12:15 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:00 pm - 7:30 pmBusiness Meeting
Nominations for the Next Vice Chair; Fill in Conference Evaluation Forms; Discuss Future Site and Scheduling Preferences; Election of the Next Vice Chair
7:30 pm - 9:30 pmWhole Cells
Discussion Leader: Chao Tang (Peking University, China)
7:30 pm - 8:00 pmZan Luthey-Schulten (University of Illinois, USA)
"Whole Cell Stochastic Modeling"
8:00 pm - 8:10 pmDiscussion
8:10 pm - 8:40 pmHong Qian (University of Washington, USA)
"Emergent Landscape: Macroscopic Thermodynamics of Mesoscopic, Stochastic Biochemical Kinetics, One Elementary Reaction at a Time"
8:40 pm - 8:50 pmDiscussion
8:50 pm - 9:20 pmAndre Levchenko (Yale University, USA)
"Mapping Populations onto Phenotypic Planes: Predictive Analysis of Noisy Cellular Decision Making"
9:20 pm - 9:30 pmDiscussion
Thursday
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmEvolution and Ecology
Discussion Leader: Mans Ehrenberg (Uppsala University, Sweden)
9:00 am - 9:30 amNigel Goldenfeld (University of Illinois at Urbana-Champaign, USA)
"Fluctuation-Induced Turing Patterns in Ecology and Biofilms"
9:30 am - 9:45 amDiscussion
9:45 am - 10:15 amJeff Gore (Massachusetts Institute of Technology, USA)
"Building Microbial Communities from the Bottom-Up"
10:15 am - 10:30 amDiscussion
10:30 am - 11:00 amCoffee Break
11:00 am - 11:30 amKen Dill (Stony Brook University, USA)
"How Some Cell Behaviors Are Encoded in the Physical Chemistry of the Proteome"
11:30 am - 11:45 amDiscussion
11:45 am - 12:15 pmThomas Kuhlman (University of Illinois at Urbana-Champaign, USA)
"Real Time Transposable Element Activity in Individual Live Cells"
12:15 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:30 pm - 9:30 pmCell Dynamics and Functions
Discussion Leader: Nigel Goldenfeld (University of Illinois at Urbana-Champaign, USA)
7:30 pm - 7:55 pmYuhai Tu (IBM Thomas J. Watson Research Center, USA)
"Physics of Information Processing in Biological Systems"
7:55 pm - 8:00 pmDiscussion
8:00 pm - 8:10 pmJie Liang (University of Illinois at Chicago, USA)
"Exact Time-Evolving Probability Landscapes of Stochastic Networks from Chemical Master Equation: Theory, Optimal State Space, and the ACME Algorithm"
8:10 pm - 8:15 pmDiscussion
8:15 pm - 8:25 pmChunhe Li (Fudan University, China)
"A Self-Enhanced Transport Mechanism Through Long Noncoding RNAs for X Chromosome Inactivation"
8:25 pm - 8:30 pmDiscussion
8:30 pm - 8:40 pmAo Ma (University of Illinois at Chicago, USA)
"A Structure-Based Mechano-Chemical Model for Microtubule Assembly Dynamics"
8:40 pm - 8:45 pmDiscussion
8:45 pm - 8:55 pmStephen Hagen (University of Florida, USA)
"Multiple Modes of Quorum Sensing in Streptococcus mutans: Integrating Internal Noise with Environmental Heterogeneity"
8:55 pm - 9:00 pmDiscussion
9:00 pm - 9:10 pmJian Liu (National Institutes of Health, USA)
"Dynamic Criticality Underlies Fidelity of Bacterial Plasmid Segregation"
9:10 pm - 9:15 pmDiscussion
9:15 pm - 9:25 pmXiao Wang (Arizona State University, USA)
"A Synthetic Biology Approach to Waddington Landscape and Cell Fate Determination"
9:25 pm - 9:30 pmDiscussion
Friday
7:30 am - 8:30 amBreakfast
9:00 amDeparture
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