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Nonequilibrium Physics in Biology: December 3 – 7, 2018

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Organized by: Jin Wang, Ken Dill, Michael Douglas, Jose Onuchic

The aim of this workshop is to bring together leading researchers from around the world to discuss current progress in uncovering emergent phenomena and design principles that allow living systems to function, develop and evolve under nonequilibrium conditions. It will be organized to encourage discussion between diverse research communities of fundamental physical, mathematical and biological questions in nonequilibrium dynamics across many spatial and temporal scales. This will be the very first workshop dedicated to nonequilibrium physics and mathematics in biology at the Simons Center. We hope this becomes the Woodstock of Nonequilibrium Physics in Biology.

The topics for the workshop discussions include:

  1. Search for the possible principles and emergent laws based on nonequilibrium dynamics and thermodynamics for biology.
  2. The mathematical foundations and underlying geometrical/topological connections behind the nonequilibrium dynamics and thermodynamics as well as the implications to biology.
  3. How nonequilibrium dynamics and thermodynamics determine the structure, dynamics and functions of the intracellular and intercellular networks.
  4. How nonequilibrium dynamics and thermodynamics shape the evolution and ecology.

Biology poses challenging questions from the point of view of current physics and mathematics. For example, are there underlying“laws of life”?  If so, what are they?  If such laws can be found, what is the physics and mathematics behind them? The physicist Schrödinger asked how the creation of order by living things, which must follow physical laws, could be consistent with the Second Law of Thermodynamics. His answer was that living systems can never be in thermodynamic equilibrium and must always exchange material, energy and information with a larger environment. Thus, to quantify a living system requires a nonequilibrium description. While the physics and mathematics of equilibrium systems is well developed, nonequilibrium physics and mathematics remain a fundamental challenge to the physics and mathematics community. In other words, we will need to develop new physics and mathematics to quantify the laws of life.

There has been significant recent progress in the physics and mathematics of nonequilibrium dynamics.  Recent work has suggested that the nonequilibrium dynamics is governed by both the underlying landscape and by the steady state probability flux. The flux has a nonconservative (nonzero curl) component which measures the degree of the detailed balance breaking, and quantifies the departure from the equilibrium. On the other hand, the recent developments of nonequilibrium thermodynamics have suggested forms for the thermodynamic driving forces and associated fluctuating statistics for nonequilibrium systems. Interestingly, this recent progress has also suggested geometrical, topological and gauge field descriptions of these driving forces. All of these progresses suggest the possibility of underlying emergent laws. Mutual information optimization and Maximum Caliber have been recently suggested as criteria to test hypotheses about biological function under nonequilibrium conditions against the data. These emergent laws and rich mathematical and physical structures are waiting to be explored.

On the biology front, there are also many challenging questions. These include, how the departure from equilibrium influences cell signaling, gene regulations, epigenetics, the structure and dynamics of intracellular circuitry, cell cycles, cell structures and dynamics, stem cell differentiation and development, neural networks and brain functions, ecology and finally evolution itself, in terms of sensitivity, speed, adaptivity, energy cost, stability, robustness and evolvability. In addition, there are challenging practical questions such as how specific characteristics of the nonequilibrium dynamics of the human body can play a role in diseases such as cancer, aging, immune dysfunction, bacterial infections, Alzheimer’s disease and Parkinson’s disease, etc.

Talk Schedule

Time Title Speaker Location
8:00am   Breakfast Simons Center Cafe
8:45am   Workshop Begins N/A
9:00am Folding and protein interactions inside the cell Martin Gruebele SCGP 102
9:45am Kinetics and thermodynamics of DNA replication and other molecular information processes Pierre Gaspard SCGP 102
10:30am Coffee Break N/A N/A
11:00am QUANTUM THERMODYNAMICS: From black mold to black holes Marlan Scully SCGP 102
11:45am Novel spectroscopic probes of conical intersections, chirality and photosynthetic charge and energy transfer with quantum and x-ray light Shaul Mukamel SCGP 102
12:30pm Lunch Break N/A Simons Center Cafe
2:00pm Non-equilibrium thermodynamics of nanoscale systems Chris Jarzynski SCGP 102
2:45pm Experimental Measurement of Information-Content in Mutational Ensembles Felix Ritort SCGP 102
3:30pm Coffee Break N/A N/A
4:00pm Optimal Cellular Information Transmission Pieter Ten Wolde SCGP 102
4:45pm Understanding Life One Photon at a Time Steve Presse SCGP 102

Time Title Speaker Location
8:00am   Breakfast Simons Center Cafe
8:30am Maximum Caliber: an inference principle for nonequilibrium statistical mechanics. Ken Dill SCGP 102
9:15am Oscillatory enthalpic changes during early embryogenesis driven by the cell cycle Joe Howard SCGP 102
10:00am Coffee Break N/A N/A
10:30am Towards Decoding the Metabolic Plasticity in Cancer: Coupling of Gene Regulation and Metabolic Pathways Jose Onuchic SCGP 102
11:15am Quantifying landscape and flux for nonequilibirum biological systems Jin Wang SCGP 102
12:00pm Lunch Break N/A Simons Center Cafe
1:00pm SCGP Weekly Talk – Peter G. Wolynes N/A 102
2:00pm Coffee Break N/A N/A
3:00pm Tissues as Active Systems Jacques Prost SCGP 102
3:45pm Exploiting fluctuations to climb gradients faster Thierry Emonet SCGP 102

Time Title Speaker Location
8:00am   Breakfast Simons Center Cafe
9:00am Cellular Pattern Formation via Notch Signaling Herbert Levine SCGP 102
9:45am Dynamic instability from non-equilibrium structural transitions on the energy landscape of microtubule Ao Ma SCGP 102
10:30am Coffee Break N/A N/A
11:00am Physical properties of suspensions of active particles Jean Francois Joanny SCGP 102
11:45am Accuracy of position determination in Ca$^{2+}$ signaling Karsten Kruse SCGP 102
12:30pm Lunch Break N/A Simons Center Cafe
2:00pm Topology and dynamics in active and living matter Cristina Marchetti SCGP 102
2:45pm Theoretical Tool Bridging Cell Polarities with Development of Morphologies Kim Sneppen SCGP 102
3:30pm Coffee Break N/A N/A
4:00pm Affinity maturation of antibodies and the puzzle of HIV low spike density Mehran Kardar SCGP 102
4:45pm From caging to super-diffusive behavior in tumor growth Dave Thirumalai SCGP 102
6:00pm   Conference Dinner N/A

Time Title Speaker Location
8:00am   Breakfast Simons Center Cafe
9:00am   Rama Ranganathan SCGP 102
9:45am Bottom-up Assembly of Microbial Communities: Modeling, Analysis and Engineering Ting Lu SCGP 102
10:30am Coffee Break N/A N/A
11:00am Self-Organization and Mechanics in the Cell Michael Shelley SCGP 102
11:45am Thermodynamics of open chemical reaction networks: Energy and information transduction in biology Massimiliano Esposito SCGP 102
12:30pm Lunch Break N/A Simons Center Cafe
2:00pm Title:The decision landscapes in living cells Andre Levchenko SCGP 102
2:45pm Truth is in the Disorder and Noise Kingshuk Ghosh SCGP 102
3:30pm   Workshop Discussions N/A
4:30pm   Laufer Center Gathering N/A

Time Title Speaker Location
8:00am   Breakfast Simons Center Cafe
9:00am The biological catch bond suppresses fluctuations in nonequilibrium systems Jason Wagoner SCGP 102
9:45am Coffee Break N/A N/A
10:15am Emergence of a stable nonequilibrium bacteria-phage collective state from multi-scale feedback Hong-Yan Shih SCGP 102
12:00pm   Workshop End N/A