Talks

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ICTP-ICTS Winter School on Quantitative Systems Biology
Monday, 04 December 2023
Time Speaker Title Resources
09:15 to 09:30 Rajesh Gopakumar (ICTS, India) Welcome remarks
09:30 to 11:00 Jonathan Rodenfels (MPI-CBG, Germany) Energetics of embryonic development
 
11:30 to 13:00 Sunil Laxman (inStem, India) Cell metabolism as an economy - what control strategies do cells use, and how to identify what is at play
 
14:00 to 15:30 Xingbo Yang (Harvard University, USA) Active matter theory and cytoskeletal dynamics
 
Tuesday, 05 December 2023
Time Speaker Title Resources
09:30 to 11:00 Jonathan Rodenfels (MPI-CBG, Germany) Basics and applications in developmental energetics/metabolism
 
11:30 to 13:00 Sunil Laxman (inStem, India) Ideas on Self-organization of metabolic networks, how it can lead to division of metabolic labor
 
14:00 to 15:30 Xingbo Yang (Harvard University, USA) Measurement of spatiotemporal cell metabolism (imaging)
 
Wednesday, 06 December 2023
Time Speaker Title Resources
09:30 to 11:00 Pablo Sartori (IGC, Portugal) Cellular growth as a non-equilibrium chemical process
 
11:30 to 13:00 -- Posters
14:00 to 15:30 -- Posters
Thursday, 07 December 2023
Time Speaker Title Resources
09:30 to 11:00 Jonathan Rodenfels (MPI-CBG, Germany) Energetic cost estimates
 
11:30 to 13:00 Pablo Sartori (IGC, Portugal) Biomass thermodynamics: entropy and enthalpy of biomass, what it is and how to estimate it
 
14:00 to 15:30 Xingbo Yang (Harvard University, USA) Coarse-grained metabolic modeling and flux control
 
Friday, 08 December 2023
Time Speaker Title Resources
09:30 to 11:00 Jonathan Rodenfels (MPI-CBG, Germany) How to measure metabolic/energetic parameters
 
14:00 to 15:30 Pablo Sartori (IGC, Portugal) Yield and dissipation across and within metabolic types
 
Monday, 11 December 2023
Time Speaker Title Resources
09:30 to 11:00 Amitesh Anand (TIFR, India) Redox centers and electron flow
 
11:30 to 13:00 Massimiliano Esposito (University of Luxembourg, Germany) Dynamics and thermodynamics

This course comprises three parts. The first part covers the basics of the dynamical and thermodynamical description of open chemical reaction networks in terms of species concentrations. The second part utilizes the topological properties of chemical reaction networks, encoded in the stoichiometric matrix, to identify the thermodynamic potential and forces controlling entropy production (i.e., dissipation) in open chemical reaction networks. The last part analyzes energy conversion in open chemical reaction networks and introduces circuit theory to study complex chemical reaction networks. The applications of these principles to central metabolism will be examined.
 
14:00 to 15:30 -- Round table
Tuesday, 12 December 2023
Time Speaker Title Resources
09:30 to 11:00 Amitesh Anand (TIFR, India) Resource partitioning and energy metabolism
 
11:30 to 13:00 Massimiliano Esposito (University of Luxembourg, Germany) Using topology: fundamental forces and nonequilibrium potentials

This course comprises three parts. The first part covers the basics of the dynamical and thermodynamical description of open chemical reaction networks in terms of species concentrations. The second part utilizes the topological properties of chemical reaction networks, encoded in the stoichiometric matrix, to identify the thermodynamic potential and forces controlling entropy production (i.e., dissipation) in open chemical reaction networks. The last part analyzes energy conversion in open chemical reaction networks and introduces circuit theory to study complex chemical reaction networks. The applications of these principles to central metabolism will be examined.
 
14:00 to 15:30 -- Career Session
Wednesday, 13 December 2023
Time Speaker Title Resources
09:00 to 11:00 Michael Lynch (Arizona State University, USA) Drift, mutation, and evolution
 
11:30 to 13:00 Sunil Laxman (inStem, India) Metabolic organization - challenges and rules in growth or survival programs
 
14:00 to 15:30 Stuti Srivastav (TIFR, India) Metabolic Plasticity & Bacterial Pathogenesis
 
Thursday, 14 December 2023
Time Speaker Title Resources
09:00 to 11:00 Michael Lynch (Arizona State University, USA) The bioenergetics costs of building and maintaining cells and cell parts
 
11:30 to 13:00 Massimiliano Esposito (University of Luxembourg, Germany) Energy transduction, circuit theory, and metabolism

This course comprises three parts. The first part covers the basics of the dynamical and thermodynamical description of open chemical reaction networks in terms of species concentrations. The second part utilizes the topological properties of chemical reaction networks, encoded in the stoichiometric matrix, to identify the thermodynamic potential and forces controlling entropy production (i.e., dissipation) in open chemical reaction networks. The last part analyzes energy conversion in open chemical reaction networks and introduces circuit theory to study complex chemical reaction networks. The applications of these principles to central metabolism will be examined.
 
14:00 to 15:30 -- Attendee talks
Friday, 15 December 2023
Time Speaker Title Resources
09:30 to 11:00 Francesco Avanzini (University of Padua, Italy) Thermodynamics of Chemical Reaction Networks: From Basic Principles to Metabolism
 
11:30 to 13:00 -- Attendee talks
14:00 to 15:30 -- Round table/ Closing remarks