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SUMMARY:Udo Seifert (University of Stuttgart)
DTSTART;VALUE=DATE-TIME:20200727T140000Z
DTEND;VALUE=DATE-TIME:20200727T144500Z
DTSTAMP;VALUE=DATE-TIME:20240329T132540Z
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/
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BEGIN:VEVENT
SUMMARY:Sarah Harvey (Stanford University)
DTSTART;VALUE=DATE-TIME:20200727T153000Z
DTEND;VALUE=DATE-TIME:20200727T161500Z
DTSTAMP;VALUE=DATE-TIME:20240329T132540Z
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/
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BEGIN:VEVENT
SUMMARY:Massimiliano Esposito (University of Luxembourg)
DTSTART;VALUE=DATE-TIME:20200728T140000Z
DTEND;VALUE=DATE-TIME:20200728T144500Z
DTSTAMP;VALUE=DATE-TIME:20240329T132540Z
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;VALUE=DATE-TIME:20200729T140000Z
DTEND;VALUE=DATE-TIME:20200729T144500Z
DTSTAMP;VALUE=DATE-TIME:20240329T132540Z
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;VALUE=DATE-TIME:20200729T153000Z
DTEND;VALUE=DATE-TIME:20200729T161500Z
DTSTAMP;VALUE=DATE-TIME:20240329T132540Z
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/
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