Gordon Research Conferences
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Conference Program
 
Stochastic Physics in Biology
Foundations and Current Trends
January 13-18, 2013
Four Points Sheraton / Holiday Inn Express
Ventura, CA
Chair:
Hong Qian

Vice Chair:
Steven J. Altschuler

This is the 2nd installment of the new Gordon Research Conference. The meeting is to introduce the foundations for stochastic dynamical descriptions of living processes, and to discuss the trend of current biomedical research, which reveals cellular molecular fluctuations, nonlinear feedbacks, and emergent behaviors at different time scales. It brings together a group of scientists to help establish an emerging new discipline. Researchers will discuss fundamental questions, approaches, and principles relating to how cells function, develop and evolve in the presence of noise and fluctuations at the mesoscopic systems. Emergent phenomenon is a key to understand many of such stochastic systems. A part of the meeting focuses on the current experimental and theoretical areas such as fluctuation measurements and stochastic thermodynamics. It also displays a wide range of new developments and approaches in the application of stochastic measurements and analysis to biological systems and processes. We particularly focus on cellular level gene expression, biochemistry, mechanics, and spatial dynamics, as well as the role of nonlinearity, and their relations to evolution theory. The meeting will help in supporting interdisciplinary research at the interface between physical, biological sciences, and mathematics.


Contributors

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 pmFoundations and Current Approaches
Discussion Leader: Peter von Hippel (Univ. of Oregon)
7:40 pm - 8:15 pmKen Dill (Stonybrook)
"Physics of proteomes"
8:15 pm - 8:30 pmDiscussion
8:30 pm - 9:05 pmElliot Elson (Washington University School of Medicine)
"Fluctuation measurements"
9:05 pm - 9:20 pmDiscussion
9:20 pm - 9:25 pmMichael Halter (NIST)
"Predicting rates of cell state change due to stochastic fluctuations using a data-driven landscape model"
9:25 pm - 9:30 pmDiscussion
MONDAY
7:30 am - 8:30 amBreakfast
8:30 amGroup Photo
9:00 am - 12:30 pmStochasticity: Biology meets Physics
Discussion Leader: Nancy Thompson (UNC)
9:30 am - 10:05 amMans Ehrenberg (Univ. Uppsala)
"Accuracy, fidelity, and central dogma"
10:05 am - 10:20 amDiscussion
10:20 amCoffee Break
10:50 am - 11:25 amTom Chou (UCLA)
"Stochastic nucleation and self assembly in cell biology"
11:25 am - 11:40 amDiscussion
11:40 am - 12:15 pmPeter von Hippel (Univ. Oregon)
"Fluctuations in replication"
12:15 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session I
6:00 pmDinner
7:30 pm - 9:30 pmEmergent Phenomena in Cellular Biology
7:30 pm - 7:50 pmDiscussion Leader: Chao Tang (Peking Univ./UCSF)
"Cellular decision making under noisy conditions"
7:50 pm - 8:25 pmJames Ferrell (Stanford Univ.)
"Feedback and cell fate switching"
8:25 pm - 8:40 pmDiscussion
8:40 pm - 9:15 pmX. Sunney Xie (Harvard)
"Single Cell Dynamics Probed by Imaging and Sequencing"
9:15 pm - 9:30 pmDiscussion
TUESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmFluctuations and Stochasticity at All Scales
Discussion Leader: X. Sunney Xie (Harvard)
9:10 am - 9:45 amJohan Elf (Univ. Uppsala)
"Fluctuations in cellular regulations"
9:45 am - 10:00 amDiscussion
10:00 am - 10:05 amElizabeth Read (UC Irvine)
"Stochastic effects in intra-host HIV evolution"
10:05 am - 10:10 amDiscussion
10:10 am - 10:15 amAnand Banerjee (NIH)
"Stochastic nature of clathrin-coated pit assembly"
10:15 am - 10:20 amDiscussion
10:20 amCoffee Break
10:50 am - 11:25 amDaniel Needlman (Harvard Univ.)
"Self-organizing subcellular structures"
11:25 am - 11:40 amDiscussion
11:40 am - 12:15 pmSusan Rosenberg (Baylor College of Medicine)
"Stress-induced mutation and evolvability"
12:15 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session I
6:00 pmDinner
7:30 pm - 9:30 pmThermodynamics and Stochastic Open Systems
Discussion Leader: Ken Dill (Stonybrook)
7:40 pm - 8:15 pmUdo Seifert (Univ. Stuttgart)
"Stochastic thermodynamics"
8:15 pm - 8:30 pmDiscussion
8:30 pm - 9:05 pmMassimiliano Esposito (University of Luxembourg)
"Open systems dynamics"
9:05 pm - 9:20 pmDiscussion
9:20 pm - 9:25 pmSrabanti Chaudhury (Los Alamos National Laboratory)
"Universality of Poisson indicator and Fano factor of transport event statistics in ion channels and enzyme kinetics"
9:25 pm - 9:30 pmDiscussion
WEDNESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmIntegrating stochastic dynamic models with measurements
9:00 am - 9:30 amDiscussion Leader: Ivet Bahar (U. Pittsburgh)
"Coarse-graining supramolecular structure and dynamics for subcellular simulations"
9:30 am - 10:05 amDenis Tsygankov (UNC)
"Cellular signaling dynamics and models"
10:05 am - 10:20 amDiscussion
10:20 amCoffee Break
10:50 am - 11:25 amJian-shu Cao (MIT)
"Statistics and single molecules"
11:25 am - 11:40 amDiscussion
11:40 am - 12:15 pmSui Huang (Institute for Systems Biology)
"Population dynamics with phenotype conversion in mammalian cell"
12:15 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session II
6:00 pmDinner
7:00 pm - 7:30 pmBusiness Meeting
Nominations for the next Vice Chair; Fill out Conference Evaluation Forms; Discuss future Site & Scheduling preferences; Election of the next Vice Chair
7:30 pm - 9:30 pmForce, Mechanics, and Polarity of Cells
7:30 pm - 7:50 pmDiscussion Leader: William Loomis (UCSD)
"Chemotactic motility"
7:50 pm - 8:25 pmLani Wu (UTSW)
"Cellular polarity circuit"
8:25 pm - 8:40 pmDiscussion
8:40 pm - 9:15 pmMichael Murrell (Univ. Chicago)
"Biomechanics of cells"
9:15 pm - 9:30 pmDiscussion
THURSDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmBiological Dynamics in Space and Time
Discussion Leader: Samuel Isaacson (Boston Univ.)
9:10 am - 9:45 amMark Goulian (Univ. Penn)
"Cell variability in phosphorelay signaling"
9:45 am - 10:00 amDiscussion
10:00 am - 10:05 amSrividya Iyer Biswas (Univ. Chicago)
"Scaling of fluctuations in exponential growth and division in single cells"
10:05 am - 10:10 amDiscussion
10:10 am - 10:15 amNika Shakiba (Univ. Toronto)
"A Compartmental Probabilistic Model of Heterogeneity in Reprogramming to Pluripotency"
10:15 am - 10:20 amDiscussion
10:20 amCoffee Break
10:35 am - 11:10 amMatt Scott (Waterloo)
"Stochastic reaction diffusion"
11:10 am - 11:30 amDiscussion
11:30 am - 12:05 pmDoug Barrick (Johns Hopkins Univ.)
"Protein dynamics and landscape"
12:05 pm - 12:30 pmDiscussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session II
6:00 pmDinner
7:30 pm - 9:30 pmStochastic Nonlinear Dynamics, Models and Computations
Discussion Leader: Elliot Elson (Washington Univ.)
7:40 pm - 8:15 pmAlbert Goldbeter (Univ. Brussels)
"Biological clocks"
8:15 pm - 8:30 pmDiscussion
8:30 pm - 9:05 pmRachel Kuske (UBC)
"Stochastic models of biological systems"
9:05 pm - 9:20 pmDiscussion
9:20 pm - 9:25 pmSandeep Choubey (Brandeis Univ.)
"Dynamics of transcription initiation from electron microscopy images of transcribing polymerases"
9:25 pm - 9:30 pmDiscussion
FRIDAY
7:30 am - 8:30 amBreakfast
9:00 amDeparture

Funding for this conference was made possible (in part) by 1 R13 GM 105239 from NIGMS. The views expressed in written conference materials or publications and by speakers and moderators do not necessarily reflect the official policies of the Department of Health and Human Services; nor does mention by trade names, commercial practices, or organizations imply endorsement by the U.S. Government.

 
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