Description

The Summer School is co-sponsored by the European Science Foundation through the PESC activity Exploring the Physics of Small Devices, and it is open to students world-wide and will take place along two weeks in which there will be a total of six courses on the following subjects: - Stochastic Thermodynamics. Massimiliano Esposito, Université Libre de Bruxelles, Belgium - Evolution and Statistical Mechanics. José A. Cuesta, Universidad Carlos III de Madrid, Madrid, Spain. - Statistical Physics of Networks and Proteins. Paolo de los Rios, EPF de Laussane, Laussane, Switzerland. - Systems Biology. Jordi García-Ojalvo, UPC, Barcelona, Spain. - Neurobiology and Behavior. Gonzalo G. de Polavieja, Instituto Cajal (CSIC) Madrid, Spain. - Experiments in Soft Matter. Francesc Sagues, Universitat de Barcelona, Barcelona, Spain. Further information about the School can be found at the web page: http://benasque.org/2012gss/ Applications to attend the school can be submitted through the school web page until June 15. Fellowships covering the lodging cost will be available.

Organizers
Fernando Falo, Jesús Gómez-Gardeñes (local organizers) J.M. Parrondo, P. Colet, F. Falo, J.A. White and M.A. Rodríguez (Scientific Organizers)

Speaker
Zev Bryant

Description B-DNA becomes unstable under superhelical stress and is able to adopt a wide range of alternative conformations including strand-separated DNA and Z-DNA. Localized sequence-dependent structural transitions are important for the regulation of biological processes such as DNA replication and transcription. To directly probe the effect of sequence on structural transitions driven by torque, we have measured the torsional response of a panel of DNA sequences using single molecule assays that employ nano- sphere rotational probes to achieve high torque resolution. The responses of Z-forming d(pGpC)n sequences match our predictions based on a theoretical treatment of cooperativetransitions in helical polymers. “Bubble” templates containing 50–100 bp mismatch regions show cooperative structural transitions similar to B-DNA, although less torque is required to disrupt strand–strand interactions. Our mechanical measurements, including direct characterization of the torsional rigidity of strand-separated DNA, establish a framework for quantitative predictions of the complex torsional response of arbitrary sequences in their biological context.

Speaker
Endre Szemerédi

Description The chaos and order will be defined relative to the problems. (1) Arithmetic progressions. This part is connected to a problem of Erdos and Turan from the 1930’s: related to the van der Waerden theorem, they asked if the density version of that result also holds: Is it true that an infinite sequence of integers of positive (lower) density contains arbitrary long arithmetic progressions? The first result in this direction was due to K.F. Roth, who proved that any sequence of integers of positive (lower) density contains a three-term arithmetic progression. We are going to give a short history of the generalization of Roth’s result and give some ideas about the “easiest” proof of Roth’s result. (2) Long Arithmetic progression in subset sums. We are going to give exact bound for the size of longest arithmetic progression in subset sums. In addition, we describe the structure of the subset sums, and give applications in number theory and probability theory. (3) Embedding sparse graphs into large graphs. We are going to describe and illustrate a method to embed relatively sparse graphs into large graphs. This will include the case of Pósa’s conjecture, El Zahar’s conjecture, and tree embedding under different conditions. Among others, we shall give several generalizations of the central Dirac Theorem, both for graphs and hypergraphs. The methods are elementary.

Speaker
Zev Bryant

Description DNA gyrase is a molecular motor that harnesses the free energy of ATP hydrolysis to introduce negative supercoils into DNA. A critical step in this reaction is the formation of a chiral DNA wrap. Here we observe gyrase structural dynamics using a single-molecule assay in which gyrase drives the processive, stepwise rotation of a nanosphere attached to the side of a stretched DNA molecule. Analysis of rotational pauses and measurements of DNA contraction reveal multiple ATP-modulated structural transitions. DNA wrapping is coordinated with the ATPase cycle and proceeds by way of an unanticipated structural intermediate that dominates the kinetics of supercoiling. Our findings reveal a conformational landscape of loosely coupled transitions funneling the motor toward productive energy transduction, a feature that may be common to the reaction cycles of other DNA and protein remodelling machines.

Speaker
Zev Bryant

Description Cytoskeletal motors drive the transport of organelles and molecular cargoes within cells and have potential applications in molecular detection and diagnostic devices. Engineering molecular motors with controllable properties will allow selective perturbation of mechanical processes in living cells and provide optimized device components for tasks such as molecular sorting and directed assembly. Biological motors have previously been modified by introducing activation/deactivation switches that respond to metal ions and other signals. Here, we show that myosin motors can be engineered to reversibly change their direction of motion in response to a calcium signal. Building on previous protein engineering studies and guided by a structural model for the redirected power stroke of myosin VI, we have constructed bidirectional myosins through the rigid recombination of structural modules. The performance of the motors was confirmed using gliding filament assays and single fluorophore tracking. Our strategy, in which external signals trigger changes in the geometry and mechanics of myosin lever arms, should make it possible to achieve spatio temporal control over a range of motor properties including processivity, stride size and branchpoint turning.