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Stochastic Physics in Biology

Gordon Research Conference

Landscapes, Stochastic Dynamics and Heterogeneity in Biology

January 8 - 13, 2017

Chair Jin Wang

Vice Chair Wallace F. Marshall

Four Points Sheraton / Holiday Inn Express

1050 Schooner Drive

Ventura, CA, US

Venue and Travel Information

Venue

Office Manager: Tim Andraka

Office Manager Email: FourPoints_SM@grc.org

Office Phone: 805-856-9561

Conference 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.

Conference Program

Sunday
4:00 pm - 8:00 pm	Arrival and Check-in
6:00 pm - 7:00 pm	Dinner
7:30 pm - 7:40 pm	Introductory Comments by GRC Site Staff / Welcome from the GRC Chair
7:40 pm - 9:30 pm	Keynote Session: Stochastic Physics in Molecular and Systems Biology Discussion Leader: Jin Wang (Stony Brook University, USA)
7:40 pm - 8:10 pm	Xiaoliang Sunney Xie (Harvard University & Peking University, USA) "Single Cell Genomics, Where Stochasticity Meets Precision"
8:10 pm - 8:15 pm	Discussion
8:15 pm - 8:45 pm	Jose Onuchic (Rice University, USA) "The Genetics and Biophysics of Epithelial-Mesenchymal Transition (EMT): Can Theory Help Cancer Biology"
8:45 pm - 8:50 pm	Discussion
8:50 pm - 9:20 pm	Mans Ehrenberg (Uppsala University, Sweden) "Stochastic Impact of Slow Inhibitors of Translation of Messenger RNAs in the Living Bacterial Cell"
9:20 pm - 9:30 pm	Discussion
Monday
7:30 am - 8:30 am	Breakfast
8:30 am - 9:00 am	Group Photo
9:00 am - 12:30 pm	Biomolecular Stochastic Dynamics Discussion Leader: Ken Dill (Stony Brook University, USA)
9:00 am - 9:30 am	William 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 am	Discussion
9:45 am - 10:15 am	Masaki Sasai (Nagoya University, Japan) "The 3D Genome Architecture and Transcriptional Regulation"
10:15 am - 10:30 am	Discussion
10:30 am - 11:00 am	Coffee Break
11:00 am - 11:30 am	Margaret Cheung (University of Houston, USA) "Molecular Underpinning of Postsynaptic Ca²⁺/Calmodulin Signaling, Protein Folding and Conformational Changes In Vivo"
11:30 am - 11:45 am	Discussion
11:45 am - 12:15 pm	Benjamin Schuler (University of Zurich, Switzerland) "Dynamics of Unfolded and Intrinsically Disordered Proteins from Single-Molecule Spectroscopy"
12:15 pm - 12:30 pm	Discussion
12:30 pm - 1:30 pm	Lunch
1:30 pm - 4:00 pm	Free Time
4:00 pm - 6:00 pm	Poster Session
6:00 pm - 7:00 pm	Dinner
7:30 pm - 9:30 pm	Cell Fate Decision Making Discussion Leader: Jose Onuchic (Rice University, USA)
7:30 pm - 8:00 pm	James Ferrell (Stanford University, USA) "Trigger Waves in Apoptosis"
8:00 pm - 8:10 pm	Discussion
8:10 pm - 8:40 pm	Jin Wang (Stony Brook University, USA) "Quantifying Stochastic Cell Fate Decision Making"
8:40 pm - 8:50 pm	Discussion
8:50 pm - 9:20 pm	Lev Tsimring (University of California, San Diego, USA) "Correlations and Adaptations Queueing in Enzymatic Networks"
9:20 pm - 9:30 pm	Discussion
Tuesday
7:30 am - 8:30 am	Breakfast
9:00 am - 12:30 pm	Cell Growth and Transformations Discussion Leader: Xiaoliang Sunney Xie (Harvard University & Peking University, USA)
9:00 am - 9:30 am	Chao Tang (Peking University, China) "Growth Behavior of Microbes: Monod's Problem Revisited"
9:30 am - 9:45 am	Discussion
9:45 am - 10:15 am	Daniel Gillespie (Dan T. Gillespie Consulting, USA) "From the Stochastic Simulation Algorithm to the Small-Voxel Tracking Algorithm"
10:15 am - 10:30 am	Discussion
10:30 am - 11:00 am	Coffee Break
11:00 am - 11:30 am	Qi Ouyang (Beijing University , China) "Thermodynamics of Biological Systems"
11:30 am - 11:45 am	Discussion
11:45 am - 12:15 pm	Jonathon Howard (Yale University, USA) "Neuronal Morphology Driven by Stochastic Branching: Data and Models"
12:15 pm - 12:30 pm	Discussion
12:30 pm - 1:30 pm	Lunch
1:30 pm - 4:00 pm	Free Time
4:00 pm - 6:00 pm	Poster Session
6:00 pm - 7:00 pm	Dinner
7:30 pm - 9:30 pm	Genomes and Disease Mechanisms Discussion Leader: Zan Luthey-Schulten (University of Illinois, USA)
7:30 pm - 8:00 pm	Chenghang Zong (Baylor College of Medicine, USA) "Effective Detection of Variations in Single Cell Transcriptome"
8:00 pm - 8:10 pm	Discussion
8:10 pm - 8:40 pm	Wei Wang (Nanjing University, China) "Cell-Fate Decision Mediated by the P53-Centered Signaling Network"
8:40 pm - 8:45 pm	Discussion
8:45 pm - 8:55 pm	Bin Zhang (Massachusetts Institute of Technology, USA) "Towards Predictive Modeling of Three Dimensional Genome Organization"
8:55 pm - 9:00 pm	Discussion
9:00 pm - 9:10 pm	Mingyang Lu (Jackson Laboratory, USA) "Interrogating the Robustness of Gene Regulatory Circuits by RACIPE and Cancer Dynamics"
9:10 pm - 9:15 pm	Discussion
9:15 pm - 9:25 pm	Steve Presse (Arizona State University, USA) "Hydrodynamic Hunters"
9:25 pm - 9:30 pm	Discussion
Wednesday
7:30 am - 8:30 am	Breakfast
9:00 am - 12:30 pm	Cell Structure and Dynamics Discussion Leader: Wallace Marshall (University of California, San Francisco, USA)
9:00 am - 9:30 am	Jean-Francois Joanny (ESPCI Paris, France) "Stochastic Cell Structures and Dynamics"
9:30 am - 9:45 am	Discussion
9:45 am - 10:15 am	David Weitz (Harvard University, USA) "Stochastic Contributions of Molecular Motors"
10:15 am - 10:30 am	Discussion
10:30 am - 11:00 am	Coffee Break
11:00 am - 11:30 am	Frank Julicher (Max Planck Institute for the Physics of Complex Systems, Germany) "Phase Separation in the Cell Cytoplasm"
11:30 am - 11:45 am	Discussion
11:45 am - 12:15 pm	Ned Wingreen (Princeton University, USA) "Protein Phase-Separation in and out of Cells"
12:15 pm - 12:30 pm	Discussion
12:30 pm - 1:30 pm	Lunch
1:30 pm - 4:00 pm	Free Time
4:00 pm - 6:00 pm	Poster Session
6:00 pm - 7:00 pm	Dinner
7:00 pm - 7:30 pm	Business 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 pm	Whole Cells Discussion Leader: Chao Tang (Peking University, China)
7:30 pm - 8:00 pm	Zan Luthey-Schulten (University of Illinois, USA) "Whole Cell Stochastic Modeling"
8:00 pm - 8:10 pm	Discussion
8:10 pm - 8:40 pm	Hong 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 pm	Discussion
8:50 pm - 9:20 pm	Andre Levchenko (Yale University, USA) "Mapping Populations onto Phenotypic Planes: Predictive Analysis of Noisy Cellular Decision Making"
9:20 pm - 9:30 pm	Discussion
Thursday
7:30 am - 8:30 am	Breakfast
9:00 am - 12:30 pm	Evolution and Ecology Discussion Leader: Mans Ehrenberg (Uppsala University, Sweden)
9:00 am - 9:30 am	Nigel Goldenfeld (University of Illinois at Urbana-Champaign, USA) "Fluctuation-Induced Turing Patterns in Ecology and Biofilms"
9:30 am - 9:45 am	Discussion
9:45 am - 10:15 am	Jeff Gore (Massachusetts Institute of Technology, USA) "Building Microbial Communities from the Bottom-Up"
10:15 am - 10:30 am	Discussion
10:30 am - 11:00 am	Coffee Break
11:00 am - 11:30 am	Ken Dill (Stony Brook University, USA) "How Some Cell Behaviors Are Encoded in the Physical Chemistry of the Proteome"
11:30 am - 11:45 am	Discussion
11:45 am - 12:15 pm	Thomas Kuhlman (University of Illinois at Urbana-Champaign, USA) "Real Time Transposable Element Activity in Individual Live Cells"
12:15 pm - 12:30 pm	Discussion
12:30 pm - 1:30 pm	Lunch
1:30 pm - 4:00 pm	Free Time
4:00 pm - 6:00 pm	Poster Session
6:00 pm - 7:00 pm	Dinner
7:30 pm - 9:30 pm	Cell Dynamics and Functions Discussion Leader: Nigel Goldenfeld (University of Illinois at Urbana-Champaign, USA)
7:30 pm - 7:55 pm	Yuhai Tu (IBM Thomas J. Watson Research Center, USA) "Physics of Information Processing in Biological Systems"
7:55 pm - 8:00 pm	Discussion
8:00 pm - 8:10 pm	Jie 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 pm	Discussion
8:15 pm - 8:25 pm	Chunhe Li (Fudan University, China) "A Self-Enhanced Transport Mechanism Through Long Noncoding RNAs for X Chromosome Inactivation"
8:25 pm - 8:30 pm	Discussion
8:30 pm - 8:40 pm	Ao Ma (University of Illinois at Chicago, USA) "A Structure-Based Mechano-Chemical Model for Microtubule Assembly Dynamics"
8:40 pm - 8:45 pm	Discussion
8:45 pm - 8:55 pm	Stephen Hagen (University of Florida, USA) "Multiple Modes of Quorum Sensing in Streptococcus mutans: Integrating Internal Noise with Environmental Heterogeneity"
8:55 pm - 9:00 pm	Discussion
9:00 pm - 9:10 pm	Jian Liu (NIH, USA) "Dynamic Criticality Underlies Fidelity of Bacterial Plasmid Segregation"
9:10 pm - 9:15 pm	Discussion
9:15 pm - 9:25 pm	Xiao Wang (Arizona State University, USA) "A Synthetic Biology Approach to Waddington Landscape and Cell Fate Determination"
9:25 pm - 9:30 pm	Discussion
Friday
7:30 am - 8:30 am	Breakfast
9:00 am	Departure