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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

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