4 Informal seminars coming up

[Cond.Matt. & Stat.Mech.Section]

INFORMAL SEMINAR on    Statistical Physics
 


Friday, 15 July    -    4:00 p.m.

 

Luigi Stasi Seminar Room,  ICTP Leonardo Building - 1st floor

 



Giovanni BUSSI    ( SISSA, Trieste )

 


"Accelerated sampling of the conformational space in biomolecules: From small proteins to RNAs"



Abstract

 

Recently developed free-energy methods (steered molecular dynamics, well-tempered metadynamics, parallel tempering and solute tempering) will be discussed, and their application to the folding of small proteins and RNA molecules will be shown.  Using these techniques, a proposed model for RNA unwinding is validated and interpreted at atomistic resolution.

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INFORMAL SEMINAR on Statistical Physics
 

 Monday, 18 July    -    4:30 p.m.

 


Luigi Stasi Seminar Room, ICTP Leonardo Building - 1st floor

 


Aleksandra M. WALCZAK    ( Ecole Normale Supérieure, Paris )

 

"Information transmission in  small gene regulatory networks"

 

Abstract

 

Many of the biological networks inside cells can be thought of as transmitting information from the inputs (e.g., the concentrations of transcription factors or other signaling molecules) to their outputs (e.g., the expression levels of various genes). On the molecular level, the relatively small concentrations of the relevant molecules and the intrinsic randomness of chemical reactions provide sources of noise that set physical limits on this information transmission. Given these limits, not all networks perform equally well, and maximizing information transmission provides a optimization principle from which we might hope to derive the properties of real regulatory networks. Inspired by the precision of transmission of positional information in the early development of the fly embryo, I will discuss the properties of specific small networks that can transmit the maximum information. Concretely, I will show how the form of molecular noise drives predictions not just of the qualitative network topology but also the quantitative parameters for the input/output relations at the nodes of the network. I will show how the molecular details of regulation change the networks ability to transmit information.

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INFORMAL SEMINAR on   Statistical Physics
 



Tuesday, 19 July    -    11:30 a.m.

 

Luigi Stasi Seminar Room,  ICTP Leonardo Building - 1st floor

 

Gian Gaetano TARTAGLIA   ( Centre for Genomic Regulation, Barcelona )



"The other side of genomes:   When non-coding is functional and coding is not"

 

Abstract

 

We have recently developed a powerful algorithm to predict protein-RNA associations that we validate using a series of assays including immunoprecipitation of protein-RNA complexes.  At the same time, we work on the prediction of interactomes of amyloid fibrils in the cellular context and develop models for calculating the interaction  potential with molecular chaperones.  A series of bioinformatics tools to predict toxicity under a variety of experimental conditions will be presented.
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INFORMAL SEMINAR on   Statistical Physics
 
 

Wednesday, 20 July    -    4:30 p.m.

 

Luigi Stasi Seminar Room, ICTP Leonardo Building - 1st floor


 

Thierry MORA   ( Ecole Normale Supérieure, Paris )
 

"How cells can improve their sensitivity to concentration changes"

 

Abstract

 

Molecule concentrations are the building blocks of information transmission in living organisms.  Thanks to their molecule receptors, cells are able to sense concentration gradients with high accuracy.  For example, small motile bacteria such as E. coli detect spatial gradients indirectly by measuring concentration ramps (temporal concentration changes) as they swim, and can respond to concentrations as low as 3.2 nM - about three molecules per cell volume.  The noise arising from the small number of detected molecules sets a fundamental physical limit on the accuracy of concentration sensing, as originally shown in the seminal work of Berg and Purcell, but up to now no theory existed for the physical limit of ramp sensing, which is what bacteria actually do.  I will show how such a bound can be derived for different measurement devices, from a single receptor to an entire cell. I will then present a plausible implementation of that bound by a realistic (bio)chemical network, similar to the adaptation system of E. coli.  Finally I will show how energy consumption at the level of the receptors can be used to increase the accuracy by a twofold factor over a passive scheme where no energy is consumed.