BEGIN:VCALENDAR VERSION:2.0 PRODID:researchseminars.org CALSCALE:GREGORIAN X-WR-CALNAME:researchseminars.org BEGIN:VEVENT SUMMARY:Udo Seifert (University of Stuttgart) DTSTART:20200727T140000Z DTEND:20200727T144500Z DTSTAMP:20260404T041159Z UID:BIRS_20w5074/1 DESCRIPTION:Title: From Stochastic Thermodynamics to Thermodynamic Inference\ nby Udo Seifert (University of Stuttgart) as part of BIRS workshop: Mathem atical Models in Biology - from Information Theory to Thermodynamics\n\n\n Abstract\nStochastic thermodynamics provides a universal framework for ana lyzing nano- and micro-sized non-equilibrium systems. Prominent examples a re single molecules\, molecular machines\, colloidal particles in time-dep endent laser traps and biochemical networks. Thermodynamic notions like wo rk\, heat and entropy can be identified on the level of individual fluctua ting trajectories. They obey universal relations like the fluctuation theo rem. Thermodynamic inference as a general strategy uses consistency constr aints derived from stochastic thermodynamics to infer otherwise hidden pro perties of non-equilibrium systems. As a paradigm for thermodynamic infere nce\, the thermodynamic uncertainty relation provides a lower bound on the entropy production through measurements of the dispersion of any current in the system. Likewise\, it quantifies the cost of temporal precision for biomolecular processes and provides a model-free bound on the thermodynam ic efficiency of molecular motors. For a review: U. Seifert\, Annu. Rev. C ondens. Matter Phys. 10\, 171-192\, 2019\n LOCATION:https://stable.researchseminars.org/talk/BIRS_20w5074/1/ END:VEVENT BEGIN:VEVENT SUMMARY:Sarah Harvey (Stanford University) DTSTART:20200727T153000Z DTEND:20200727T161500Z DTSTAMP:20260404T041159Z UID:BIRS_20w5074/2 DESCRIPTION:Title: An Energy-Accuracy Tradeoff in Nonequilibrium Cellular Sensing \nby Sarah Harvey (Stanford University) as part of BIRS workshop: Math ematical Models in Biology - from Information Theory to Thermodynamics\n\n \nAbstract\nSingle celled organisms possess extremely sensitive mechanisms for detecting external chemical concentrations through the binding of ind ividual molecules to cell-surface receptors. Here\, we combine stochastic thermodynamics\, large deviation theory\, and information theory to derive fundamental limits on the accuracy with which single receptors can detect external chemical concentrations through energy-consuming nonequilibrium processes. I will give an overview of these calculations\, starting with e stimation performed by an ideal observer of the entire trajectory of recep tor states. We show that in this case\, no energy consuming non-equilibriu m receptor that can be divided into two pools of bound signaling and unbou nd non-signaling states can outperform a simple equilibrium two-state rece ptor. Next\, I will discuss an energy-accuracy tradeoff for such general n onequilibrium receptors when the estimation is performed by a simple obser vation of the duration the receptor is bound. Our tradeoff reveals that th e simple observer can only attain the performance of the ideal observer in the limit of large receptor energy consumption and size.\n LOCATION:https://stable.researchseminars.org/talk/BIRS_20w5074/2/ END:VEVENT BEGIN:VEVENT SUMMARY:Massimiliano Esposito (University of Luxembourg) DTSTART:20200728T140000Z DTEND:20200728T144500Z DTSTAMP:20260404T041159Z UID:BIRS_20w5074/3 DESCRIPTION:Title: Thermodynamics of Biochemical Reaction Networks: Information\, Accuracy and Speed\nby Massimiliano Esposito (University of Luxembour g) as part of BIRS workshop: Mathematical Models in Biology - from Informa tion Theory to Thermodynamics\n\n\nAbstract\nAfter formulating a nonequili brium thermodynamics for open chemical reaction networks\, the theory will be applied to assess the thermodynamics performance of a dissipative self -assembly scheme. Power-efficiency and noise-dissipation trade-offs will b e discussed\n LOCATION:https://stable.researchseminars.org/talk/BIRS_20w5074/3/ END:VEVENT BEGIN:VEVENT SUMMARY:Thomas Ouldridge (Addenbrooke) (Imperial College London) DTSTART:20200729T140000Z DTEND:20200729T144500Z DTSTAMP:20260404T041159Z UID:BIRS_20w5074/4 DESCRIPTION:Title: Non-Equilibrium Thermodynamics of Catalytic Information Proces sing\nby Thomas Ouldridge (Addenbrooke) (Imperial College London) as p art of BIRS workshop: Mathematical Models in Biology - from Information Th eory to Thermodynamics\n\n\nAbstract\nCatalytic motifs are ubiquitous in c ellular information-processing systems\, from kinase signalling networks t o the central dogma of molecular biology. This ubiquity results from the a bility of catalysts to channel chemical free energy into far-from-equilibr ium information-bearing states\, allowing them to perform non-trivial comp utational operations. This power\, however\, comes at a price. At a fundam ental level\, the need to create non-equilibrium outputs sets thermodynami c constraints on these systems. At a practical level\, catalysts must care fully balance kinetic and thermodynamic factors to ensure that the desired non-equilibrium output is actually reached. The complexity of this task e xplains the comparatively slow progress made with engineering synthetic no n-equilibrium information-processing systems\, as opposed to synthetic sys tems that form complex equilibrium assemblies. I will present our latest w ork - both theoretical and experimental - aimed at overcoming this challen ge to engineer non-equilibrium catalytic systems for information processin g.\n LOCATION:https://stable.researchseminars.org/talk/BIRS_20w5074/4/ END:VEVENT BEGIN:VEVENT SUMMARY:Ilka Bischofs (Max Planck Institute Marburg) DTSTART:20200729T153000Z DTEND:20200729T161500Z DTSTAMP:20260404T041159Z UID:BIRS_20w5074/5 DESCRIPTION:Title: Information Processing by Bacterial Quorum Sensing Systems \nby Ilka Bischofs (Max Planck Institute Marburg) as part of BIRS workshop : Mathematical Models in Biology - from Information Theory to Thermodynami cs\n\n\nAbstract\nBacteria can communicate with each other by means of dif fusive signaling molecules to coordinate their behaviors. The term “quor um sensing” denotes a cell-density dependent regulation of population-le vel behavior and is typically used to describe the sensory function of the se signaling systems. I will give an overview of the diversity of differen t quorum sensing architectures and explain how architecture could affect i nformation processing. I will then focus on a particular type of so-called pump-probe signaling architectures and demonstrate that they could serve other functions than classical quorum sensing. Finally\, I will introduce our attempts to determine network parameters using a FRET-based reporter s ystem in order to quantitatively describe signal processing in B. subtilis with the help of a phenomenological model.\n LOCATION:https://stable.researchseminars.org/talk/BIRS_20w5074/5/ END:VEVENT END:VCALENDAR