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:20260422T185741Z UID:BIRS_20w5074/1 DESCRIPTION:Title: From Stochastic Thermodynamics to Thermodynamic Inference\nby Udo Seifert (University of Stuttgart) as part of BIRS workshop: Mathematical Models in Biology - from Information Theory to Thermodynamics\n\n\nAbstrac t\nStochastic thermodynamics provides a universal framework for analyzing nano- and micro-sized non-equilibrium systems. Prominent examples are sing le molecules\, molecular machines\, colloidal particles in time-dependent laser traps and biochemical networks. Thermodynamic notions like work\, he at and entropy can be identified on the level of individual fluctuating tr ajectories. They obey universal relations like the fluctuation theorem. Th ermodynamic inference as a general strategy uses consistency constraints d erived from stochastic thermodynamics to infer otherwise hidden properties of non-equilibrium systems. As a paradigm for thermodynamic inference\, t he thermodynamic uncertainty relation provides a lower bound on the entrop y production through measurements of the dispersion of any current in the system. Likewise\, it quantifies the cost of temporal precision for biomol ecular processes and provides a model-free bound on the thermodynamic effi ciency of molecular motors. For a review: U. Seifert\, Annu. Rev. Condens. Matter Phys. 10\, 171-192\, 2019\n LOCATION:https://researchseminars.org/talk/BIRS_20w5074/1/ END:VEVENT BEGIN:VEVENT SUMMARY:Sarah Harvey (Stanford University) DTSTART:20200727T153000Z DTEND:20200727T161500Z DTSTAMP:20260422T185741Z UID:BIRS_20w5074/2 DESCRIPTION:Title: An Energy-Accuracy Tradeoff in Nonequilibrium Cellular Sensing\nb y Sarah Harvey (Stanford University) as part of BIRS workshop: Mathematica l Models in Biology - from Information Theory to Thermodynamics\n\n\nAbstr act\nSingle celled organisms possess extremely sensitive mechanisms for de tecting external chemical concentrations through the binding of individual molecules to cell-surface receptors. Here\, we combine stochastic thermod ynamics\, large deviation theory\, and information theory to derive fundam ental limits on the accuracy with which single receptors can detect extern al chemical concentrations through energy-consuming nonequilibrium process es. I will give an overview of these calculations\, starting with estimati on performed by an ideal observer of the entire trajectory of receptor sta tes. We show that in this case\, no energy consuming non-equilibrium recep tor that can be divided into two pools of bound signaling and unbound non- signaling states can outperform a simple equilibrium two-state receptor. N ext\, I will discuss an energy-accuracy tradeoff for such general nonequil ibrium receptors when the estimation is performed by a simple observation of the duration the receptor is bound. Our tradeoff reveals that the simpl e observer can only attain the performance of the ideal observer in the li mit of large receptor energy consumption and size.\n LOCATION:https://researchseminars.org/talk/BIRS_20w5074/2/ END:VEVENT BEGIN:VEVENT SUMMARY:Massimiliano Esposito (University of Luxembourg) DTSTART:20200728T140000Z DTEND:20200728T144500Z DTSTAMP:20260422T185741Z UID:BIRS_20w5074/3 DESCRIPTION:Title: Thermodynamics of Biochemical Reaction Networks: Information\, Accura cy and Speed\nby Massimiliano Esposito (University of Luxembourg) as p art of BIRS workshop: Mathematical Models in Biology - from Information Th eory to Thermodynamics\n\n\nAbstract\nAfter formulating a nonequilibrium t hermodynamics for open chemical reaction networks\, the theory will be app lied to assess the thermodynamics performance of a dissipative self-assemb ly scheme. Power-efficiency and noise-dissipation trade-offs will be discu ssed\n LOCATION:https://researchseminars.org/talk/BIRS_20w5074/3/ END:VEVENT BEGIN:VEVENT SUMMARY:Thomas Ouldridge (Addenbrooke) (Imperial College London) DTSTART:20200729T140000Z DTEND:20200729T144500Z DTSTAMP:20260422T185741Z UID:BIRS_20w5074/4 DESCRIPTION:Title: Non-Equilibrium Thermodynamics of Catalytic Information Processing\nby Thomas Ouldridge (Addenbrooke) (Imperial College London) as part of BIRS workshop: Mathematical Models in Biology - from Information Theory to Thermodynamics\n\n\nAbstract\nCatalytic motifs are ubiquitous in cellular information-processing systems\, from kinase signalling networks to the c entral dogma of molecular biology. This ubiquity results from the ability of catalysts to channel chemical free energy into far-from-equilibrium inf ormation-bearing states\, allowing them to perform non-trivial computation al operations. This power\, however\, comes at a price. At a fundamental l evel\, the need to create non-equilibrium outputs sets thermodynamic const raints on these systems. At a practical level\, catalysts must carefully b alance kinetic and thermodynamic factors to ensure that the desired non-eq uilibrium output is actually reached. The complexity of this task explains the comparatively slow progress made with engineering synthetic non-equil ibrium information-processing systems\, as opposed to synthetic systems th at form complex equilibrium assemblies. I will present our latest work - b oth theoretical and experimental - aimed at overcoming this challenge to e ngineer non-equilibrium catalytic systems for information processing.\n LOCATION:https://researchseminars.org/talk/BIRS_20w5074/4/ END:VEVENT BEGIN:VEVENT SUMMARY:Ilka Bischofs (Max Planck Institute Marburg) DTSTART:20200729T153000Z DTEND:20200729T161500Z DTSTAMP:20260422T185741Z UID:BIRS_20w5074/5 DESCRIPTION:Title: Information Processing by Bacterial Quorum Sensing Systems\nby Il ka Bischofs (Max Planck Institute Marburg) as part of BIRS workshop: Mathe matical Models in Biology - from Information Theory to Thermodynamics\n\n\ nAbstract\nBacteria can communicate with each other by means of diffusive signaling molecules to coordinate their behaviors. The term “quorum sens ing” denotes a cell-density dependent regulation of population-level beh avior and is typically used to describe the sensory function of these sign aling systems. I will give an overview of the diversity of different quoru m sensing architectures and explain how architecture could affect informat ion processing. I will then focus on a particular type of so-called pump-p robe signaling architectures and demonstrate that they could serve other f unctions than classical quorum sensing. Finally\, I will introduce our att empts to determine network parameters using a FRET-based reporter system i n order to quantitatively describe signal processing in B. subtilis with t he help of a phenomenological model.\n LOCATION:https://researchseminars.org/talk/BIRS_20w5074/5/ END:VEVENT END:VCALENDAR