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Theorique d'Orsay

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Agenda > Séminaires / Seminars > Ph. Statistique Dernier ajout : jeudi 2 octobre 2014.

Séminaire commun LPT/LPTMS 2010-2011

Physique Statistique des Systèmes Complexes

Les séminaires de Physique Statistique des Systèmes Complexes se tiennent le jeudi à 14 heures (sauf indication contraire), soit au LPT (bâtiment 210) en salle 114, soit au LPTMS (bâtiment 100A) en salle 201.

Contact pour les séminaires : Cecile Appert-Rolland et Silvio Franz.


ATTENTION, SALLE INHABITUELLE !!!

-  Jeudi 30 Juin 2011 à 14h, bât. 210, LPT, en Amphi I,

Bertrand Delamotte (LPTMC, Paris)

Processus stochastiques hors de l’équilibre : une approche par les méthodes non perturbatives de renormalisation

Le renouveau des méthodes non perturbatives (i.e. Wilsoniennes) du groupe de renormalisation permettent d’étudier des phénomènes dans les systèmes stochastiques hors de l’équilibre qui étaient hors de portée. Après une revue de l’esprit de ces méthodes ainsi que de certains résultats je me concentrerai sur l’étude des phénomènes critiques dans les systèmes dits de réaction-diffusion ainsi que sur l’équation de Kardar-Parisi-Zhang ou des résultats encourageants ont d’ores et déjà été obtenus.


ATTENTION, JOUR ET HEURE INHABITUELS !!!

-  Mercredi 29 Juin 2011 à 14h15, Salle 201, bât. 100, LPTMS

Roya Zandi (University of California, Riverside)

Self-assembly of icosahedral, prolate and conical capsids

Virus particles come in many sizes and shapes and vary enormously in the number and nature of the molecules from which they are built. Amazingly enough, despite this tremendous diversity, most spherical capsids adopt the structures with icosahedral symmetry and the elongated capsids have almost always hexagonally ordered cylindrical bodies with hemispherical T-number caps centered along 5-, 3- and 2- fold axes. In this talk, I show that the remarkable well-defined geometry of spherical and prolate viruses is the consequence of free energy minimization of a generic interaction between the structural units of viral shells. I also discuss the conical structure of HIV capsids and show that the continuum theory of elastic shells combined with the nonequilibrium assembly process is able to predict the formation of structures pertinent to retroviruses (such as HIV). The minimal model of our assembly yields a unified one-dimensional phase diagram in which the appearance of spherical, irregular, conical and cylindrical structures of retroviruses is seen to be governed by the spontaneous curvature of protein subunits.


-  Jeudi 26 Mai 2011 à 14h, Salle 201, bât. 100, LPTMS

Michael Schindler (ESPCI-Paris)


-  Jeudi 19 Mai 2011 à 14h, Salle 114, bât. 210, LPT

Paul Loubeyre (CEA, DIF, Arpajon)

Propriétés de la matière sous très hautes pressions : les enjeux, les méthodes, les applications

La physique des hautes pressions est un vieux domaine et pourtant encore très actif. Les propriétés des matériaux peuvent maintenant être étudiées sous des pressions du Mbar aussi finement qu’à pression ambiante. L’utilisation de synchrotrons a été essentielle pour cela. Nous présenterons quelques résultats significatifs de ces dernières années, avec un biais de sélection pour nos travaux. Ceux-ci seront mis en perspective des questions suivantes :

‘ Y-a-t-il une nouvelle physique de la matière condensée sous pression ? ‘ ;

‘Quelles sont les applications de ces recherches ?’.


-  Jeudi 12 Mai 2011 à 14h, Salle 201, bât. 100, LPTMS

Laurence Calzone (Institut Curie-Paris)

Boolean approach to cell fate decision in response to death receptor engagement

A mathematical model of cell fate decision between survival, apoptosis and necrosis following activation of death receptors FAS and TNFR was developed and analyzed. It is based on the most consistent facts extracted from the literature and recapitulated using a discrete modelling formalism. The model represents a generic high-level view of interplay between NFkB pro-survival pathway, RIP1-dependent necrosis and apoptosis pathways in response to death receptor-mediated signals. First, analysis of the stable steady states of the wild type model shows robust segregation of cellular responses to receptor engagement. Then, the model is capable to recapitulate many experimental observations showing how knockdown of certain proteins, some not yet performed, or diverse drug treatments influence cell fate decision in a qualitative manner. Moreover, some in silico experiments simulate the effect of ligand removal at different stages of the pathways and suggest experimental settings to further validate and specialize the model for a particular cell type. Finally, the model is reduced to a conceptual 3-node model that recapitulates the main ideas of the decision process and exhibits mutual inhibition of the three pathways. Our wild type and mutant simulations qualitatively matches most published data, and provides novel insights to restore apoptosis in defective cells. The in-depth analysis of model properties further proposes several predictions. Some of them provide hints about possible scenarios in forcing or restoring a phenotype in mutants. All versions of the model give some insight on the main decision (or bifurcation) points at which the cell decides if it survives or dies and if it dies, how it does it. With our systems biology analyses, the principal actors involved in these decisions were identified.


-  ANNULE : Jeudi 28 Avril 2011 à 14h, Salle 201, bât. 100

Arnab Chatterjee (Centre de Physique Théorique, Université de la Méditerranée Aix Marseille II, Marseille, France)

ATTENTION, CE SEMINAIRE EST ANNULE !!!!

Noise induced phase transition in kinetic models of opinion dynamics

We propose a model of continuous opinion dynamics, where mutual interactions can be both positive and negative. Different types of distributions for the interactions, all characterized by a single parameter p denoting the fraction of negative interactions, are considered. Results from exact calculation and numerical simulations indicate the existence of a universal continuous phase transition at p = p_c below which a consensus is reached. In addition, the ordered and disordered regimes show characteristic features close to reality.


ATTENTION, JOUR ET HEURE INHABITUELS !!!

-  Mardi 26 Avril 2011 à 11h, Salle 201, bât. 100

Martial Mazars (LPT - Orsay)

Interactions à longue portée et simulations numériques

Au cours des 15 dernières années, d’important progrès dans l’optimisation des sommes d’Ewald pour la prise en compte des interactions à longue portée ont été réalisés. En particulier dans le calcul des diverses contributions dans l’espace réciproque par l’introduction d’algorithmes de transformée de Fourier rapide (FFT - SPME, P3M) et aussi à l’aide de méthodes algébriques multi-échelle (Multigrid methods). Ces techniques ont permis d’améliorer très significativement, tant qualitativement que quantitativement, les simulations portant sur des systèmes complexes par exemple dans les calculs portant sur les bio-macromolécules (protéines, ADN, ARN, etc.).

Cependant, les sommes d’Ewald restent assez mal adaptées pour prendre en compte avec efficacité certains problèmes essentiels pour la modélisation des molécules, tels que la polarisabilité des atomes et/ou des blocs moléculaires et aussi dans des systèmes plus simples en matière condensée, comme les effets induits par la polarisation des milieux diélectriques ou pour des systèmes ayant des conditions aux limites non périodiques ou partiellement périodiques.

Je commencerai par donner une description assez générale des méthodes d’Ewald. Puis, je montrerai quelques résultats récents concernant l’influence de la longue portée des interactions (en loi de puissance inverse) sur la stabilité des phases hexatiques et des solides dans les monocouches, ainsi que leur influence sur la compétition entre le scénario KTHNY et la formation de frontière entre les grains (grain boundary induced melting) pour la fusion des solides bidimensionnels.

Enfin, comme alternative aux méthodes d’Ewald pour les interactions électromagnétiques, je décrirai les principes d’un algorithme basé sur la méthode des éléments finis (Finite Element Method), méthode utilisée fréquemment pour la résolution numérique des équations aux dérivées partielles. 


-  Jeudi 31 Mars 2011 à 14h, Salle 114, bât. 210

Camille Aron (Rutgers University)

Symmetries of generating functionals of Langevin processes

The dynamics of classical system in interaction with a thermal bath can often be described by Langevin processes. We deal with multiplicative and colored noise. We present a study of the symmetries of the generating functionals associated to these processes, in and out of equilibrium. We treat both Martin-Siggia-Rose-Janssen-deDominicis and supersymmetric formalisms. We summarize the relations between observables that these symmetries imply including fluctuation-dissipation theorems, fluctuation theorems, and Schwinger-Dyson equations.


-  Jeudi 17 Mars 2011 à 14h, Salle 201, bât. 100

Luca Giorgetti (Institut Curie, Paris)

Non-cooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs

A paradigm in transcriptional regulation is that a graded increase in transcription factor (TF) concentration is translated into a digital on/off transcriptional response by cooperative TF binding to adjacent cognate sites in cis-regulatory sequences. This digital type of response underlies the sharp definition of boundaries among body parts during development. Here we show that NF-kB, a key TF controlling the inflammatory and immune transcriptional responses, is instead an analogical transcriptional regulator relying on the usage of homotypic clusters of high-affinity binding sites. We observed that gradually increasing concentrations of NF-kB in the cell nucleus are translated into gradually increasing levels of transcriptional activity of NF-kB inflammatory target genes. We provide a thermodynamic interpretation of the experimental observations by combining quantitative measurements and a minimal physical model of an NF-kB dependent promoter. We show that NF-kB does not bind cooperatively to adjacent sites in a cluster ; conversely, independent binding of NF-kB to adjacent sites promotes RNA Pol II recruitment in an additive fashion, thus resulting in a graded transcriptional response. These findings reveal a novel paradigm in the usage of clustered TF binding sites, which may be relevant in all biological conditions in which the transcriptional output must be proportionate to the strength of an environmental input.


-  Jeudi 10 Mars 2011 à 14h, Salle 114, bât. 210

Remarque :

Max Ebbinghaus soutiendra sa thèse (co-tutelle) en Allemagne, et ce séminaire sera l’occasion de présenter ses travaux de thèse coté français.

Max Ebbinghaus (LPT, Orsay / Dpt Theoretical Physics, Sarrebruck)

Models for efficient bidirectional transport in axons

Intracellular transport along microtubules is bidirectional because molecular motors of different types drag intracellular cargo in opposite directions. Models taking into account the mutual exclusion of motors on the microtubules turn out to be unrealistically inefficient on static networks due to jam formation.

In this talk, I will propose a possible solution to overcome this problem and recover efficient transport : We consider a stochastic lattice gas model with two particle species which includes dynamics of the underlying lattice. This model allows for a transition from a jammed to a homogenous phase with good transport properties. In particular, the flux of particles along the lattice becomes density-dependent if the lattice is dynamic enough. This is a necessary condition for a non-vanishing transport capacity in extremely elongated geometries such as axons. Our results are generic for several types of lattice dynamics but rely on a limited lifetime of a lattice site which inhibits the formation of clusters.

The effect of lattice dynamics is furthermore compared to another mechanism enhancing transport properties, namely lane formation due to motor-motor interactions. It turns out that these two mechanisms are not exclusive, but could rather contribute in a cooperative way to the efficiency of bidirectional transport.


-  Jeudi 3 Mars à 14h, salle 114, bât. 210

Martin Trulsson (Department of theoretical Chemistry, Université de Lund, Suède) : Simulations of classical fluids in hyperspherical geometry

Simulations are becoming increasingly important in our understanding of the complex na- ture of charged and polar fluids. It is thereby important to describe these correctly.

We perform and analyze simulations of classical charge and polar fluids in the hyperspher- ical geometry, S3. Special focus has been on Stockmayer and simple water (SPC/E and TIP3P) models. Size dependencies (ranging from 300 to 10000 particles) and different ways to obtain the dielectric constant, εr, are investigated. Good agreement is found with simu- lations performed with periodic boundary conditions. We furthermore go on to investigate effective interactions of ions in these dielectric fluids and review some of the recent work in this field.


-  Mardi 16 Novembre à 14h, salle 114

Stefan Grandner (Institut für Theoretische Physik, Technische Universität Berlin) : Structural properties of charged colloidal suspensions under confinement

Confinement effects in charged colloidal suspensions are of great interest for technical applications. We consider charged colloidal silica spheres solved in water as a model system to investigate structural properties where the particles are modeled on a coarse-grained level using Derjaguin-Landau-Verwey-Overbeek theory, i.e., the counter- and saltions are treated implicitly. Employing canonical and grand-canonical Monte-Carlo simulations the impact of several system parameters as density, wall separation and wall charges on characteristic lengths and freezing behavior is investigated. The importance of the surface charges of the slit pore is motivated by Colloidal-Probe Atomic-Force-Microscope experiments predicting an enhancement of the amplitudes of structural forces. Therefore we used a modified model from linearized Poisson-Boltzmann theory taking wall counterions into account. The difference to former models which failed to describe this behavior is the wall charge dependence of the screening parameter of the fluid-wall interaction which yields a non- monotonic behavior of the repulsion. As a consequence we found a strong impact of the wall charge on the in-plane structuring and charge-induced fluid-solid transitions.

-  Jeudi 27 Janvier 2011 à 14h, Salle 201, bât. 100

Hiroki Ohta (University of Tokyo, Japan)

Avalanches in a zero-temperature random-field Ising model

Understanding laws in collective dynamics is a central issue in the field of the statistical physics. As a case, we discuss the zero-temperature Glauber dynamics of a random-field Ising model on a Bethe lattice. In this system, collective dynamics, so-called avalanches, occur near the spinodal line. For the initial condition that all spins are down, we derive an exact time evolution equation closed by an order parameter, which enables us to determine the critical exponents for the spinodal transition. We also discuss its relevance to the nonergodic transition in a kinetically constrained spin model.


-  Jeudi 20 Janvier 2011 à 14h, Salle 201, bât. 100

Pierfrancesco Urbani (Physics Department, University of Rome, La Sapienza)

High density expansion for Euclidean Random Matrices

Euclidean random matrices appear in a wide range of physical con texts. However they are deeply related to the study of vibration al spectrum for systems with topological disorder. In particular one can obtain a detailed formulation for the dynamical structu re factor of such systems in terms of euclidean random matrices of Laplacian type. We describe two formailsms for the high densi ty expansion of such matrices through which new results have bee n recently obtained : the first one is a combinatorial approach a nd is very useful to extract the perturbative expansion in a pow erful way ; the second formalism is based on a field theory refo rmulation of the problem and is very useful to study the infrare d behaviour of the dynamical structure factor to all orders in p erturbation theory.


-  Jeudi 13 Janvier 2011 à 14h, Amphi I, 2e étage, bât. 210.

(Attention, salle inhabituelle)

Asja Jelic (LPT, Orsay)

Quenching and annealing in the 2D XY model

Topological defects are often used as fingerprints for the passage of a system through a phase transition in the far past, with applications going from cosmology to condensed matter. In this talk I will discuss the out of equilibrium dynamics of the 2D XY model when cooled across the Kosterlitz-Thouless (KT) phase transition, focusing on the evolution of the growing correlation length and the density of topological defects (vortices). I will first discuss the time and temperature dependence of the growing correlation length after an infinitely rapid quench from above the transition temperature to the quasi-long range order region. This analysis clarifies the different dynamic roles played by bound and free vortices. These results are then used as input to revisit the Kibble-Zurek mechanism in thermal phase transitions in which the disordered state is plagued with topological defects. We provide a theory of quenching rate dependence in systems with the KT-type transition that goes beyond the equilibrium scaling arguments.

Reference : A. Jelic and L. F. Cugliandolo, Quench dynamics of the 2dXY model, [arXiv:1012.0417]


-  Jeudi 6 Janvier 2011 à 14h, Salle 114, bât. 210.

Sylvain Prolhac (Technische Universität München)

Exact scaling functions in the one-dimensional Kardar-Parisi-Zhang universality class.

The Kardar-Parisi-Zhang (KPZ) equation describes the stochastic evolution of a growing surface. In one dimension, exact scaling functions for the fluctuations of the height of the interface around its mean value have been obtained, for various boundary conditions. These scaling functions have been derived first for microscopic realizations of the KPZ equation such as the asymmetric simple exclusion process and the polynuclear growth model. More recently, some of these scaling functions have been obtained directly from the Cole-Hopf solution of the KPZ equation using the replica method.


-  Vendredi 17 Décembre 2010 à 14h, Salle 201, bât. 100.

Martin Evans (School of Physics, University of Edinburgh)

Models of Switching in Biophysical Contexts

In this talk I will give an overview of how statistical mechanical models may be brought to bear on the study of populations of organisms (e.g. microbes) that may switch between different phenotypical states. At the microscopic level one may consider the dynamics that lead to the switching on or off of certain genes. At the macroscopic level one can consider how heterogeneity within a population is maintained through switching and what is the best switching strategy for the population in the face of a changing environment. I will focus on two simple models, one for a genetic switch and one for the growth of a population in an environment which produces catastrophic events, both of which may be solved exactly.


-  Jeudi 16 Décembre 2010 à 14h, Salle 114, bât. 210.

Frederic van Wijland (MSC, Paris)

Grandes déviations et dynamiques lentes dans des liquides modèles

Les outils émanant de la théorie des grandes déviations temporelles permettent d’analyser certains phénomènes sous un jour nouveau. C’est le cas notamment de la dynamique de certains fluides, qui est extraordinairement ralentie à température suffisamment basse. Pour un mélange binaire de particules en interaction, les trajectoires suivies par le système dans son espace des phases se séparent en deux catégories distinctes. Nous aborderons à la fois les approches numériques et analytiques permettant de caractériser les propriétés dynamiques de ce genre de systèmes.


-  Jeudi 2 Décembre 2010 à 14h, Salle 201, bât. 100.

Antoine Venaille (Atmospheric and Oceanic Sciences (AOS)- Princeton)

Mécanique statistique des anneaux et jets océaniques

L’océan est peuplé de tourbillons organisés en anneaux de 200 km de diamètre. Ces anneaux restent cohérents pendant des mois, voire des années, et dérivent lentement vers l’ouest. Nous proposons une explication de ce phénomène par la mécanique statistique d’équilibre des écoulements turbulents géophysiques.

Nous montrons l’existence d’une analogie formelle entre la formation de ces anneaux et la formation de bulles en thermodynamique, et discutons de l’application de ces idées à la description de jets cohérents dirigés vers l’est, comme le Gulf Stream. Enfin, nous décrivons l’existence de transitions de phase dans la structure des écoulements, associées à des propriétés thermodynamiques étonnantes, comme l’inéquivalence entre les ensembles statistiques ou l’existence de chaleurs spécifiques négatives.


-  Jeudi 25 Novembre 2010 à 14h, Salle 201, bât. 100.

Aleksandra Walczak (LPT - ENS)

The effects of negative selection on non-independently evolving sites

To understand how existing organisms evolved to their present form, one can compare statistical features of genomes within a population to predictions of evolutionary models. Theoretical developments have produced a good understanding of how positive selection at a few sites affects genetic variation at linked (i. e. inherited together) neutral sites and of how strong selection at many sites affects variation at linked neutral sites. Recent sequence data from a variety of populations indicates that moderate selection acting on linked sites may be common and simulations show that it can have a significant impact on observed sequence variation. I will present a newly developed framework which allows us to understand the expected patterns of genetic variation when weak or moderate selection acts on many linked sites. I will show that in this limit the probability of allelic configurations cannot be described by any neutral model, indicating that it is possible to detect selection from patterns of sampled allelic diversity. I will then combine this analysis with the structured coalescence approach to trace the ancestry of individuals through the distribution of fitnesses within the population. I will show that selection alters the statistics of genealogies compared to neutral population with varying size, building a basis for a way to detect negative selection in sequence data.


-  Mardi 16 Novembre à 14h, salle 114, bât. 210.

Stefan Grandner (Institut für Theoretische Physik, Technische Universität Berlin) : Structural properties of charged colloidal suspensions under confinement

Confinement effects in charged colloidal suspensions are of great interest for technical applications. We consider charged colloidal silica spheres solved in water as a model system to investigate structural properties where the particles are modeled on a coarse-grained level using Derjaguin-Landau-Verwey-Overbeek theory, i.e., the counter- and saltions are treated implicitly. Employing canonical and grand-canonical Monte-Carlo simulations the impact of several system parameters as density, wall separation and wall charges on characteristic lengths and freezing behavior is investigated. The importance of the surface charges of the slit pore is motivated by Colloidal-Probe Atomic-Force-Microscope experiments predicting an enhancement of the amplitudes of structural forces. Therefore we used a modified model from linearized Poisson-Boltzmann theory taking wall counterions into account. The difference to former models which failed to describe this behavior is the wall charge dependence of the screening parameter of the fluid-wall interaction which yields a non- monotonic behavior of the repulsion. As a consequence we found a strong impact of the wall charge on the in-plane structuring and charge-induced fluid-solid transitions.


-  Jeudi 18 Novembre 2010

Pas de séminaire pour cause de worshop MMT10 au LPT


-  VENDREDI 22 Octobre 2010, Salle 114, bât. 210.

Ines Weber (Univ. Sarrebrucken)

Fluctuations of intracellular filaments

Microtubules are highly dynamic biopolymer filaments involved in a wide variety of biological processes like cell division and intracellular transport. These filaments are semi-flexible polymers, i.e. their bending energy is comparable to the thermal energy. Even though they form a rather stiff and highly cross-linked structural network, it has been shown that they typically exhibit significant bends on all length scales.

We study microtubule fluctuations and their mechanical properties like the persistence length using single filament tracking. Furthermore we present a model for buckling of semi-flexible filaments under the action of thermal and non-thermal forces. We investigate a system in which molecular motors deform filaments against a background network. The force-generating motors can stochastically unbind and rebind to the filament during the buckling process generating rapid step-like force fluctuations.


-  VENDREDI 15 Octobre 2010 à 14h, Salle 201, bât. 100.

A. Nihat Berker (Sabanci University)

Inverted Tricriticality and Apollonian Tulips in A Plenitude of Exactly Soluble Statistical Mechanics with Quenched Randomness

The distinctive phase transition phenomena of magnetic systems with frozen disorder are studied with renormalization-group theories that are numerically exact for d=3 hierarchical lattices and that have proven to be quite indicative for the physical lattices. A pedagogical introduction will be followed by recent results, including inverted tricritical points [1], finite-temperature spin-glass order induced by quenched dilution, asymmetric quantum spin-glass phase diagrams. On scale-free small-world spin-glass networks, the calculated local magnetizations and local spin-glass order parameters exhibit, as function of temperature, complex tulip patterns.[2] The conversion of first-order phase transitions to second order and the strong violation of critical phenomena universality, predicted by this approach, has recently been confirmed by numerical simulation.[3]

[1] V.O. Özçelik and A.N. Berker, Phys. Rev. E 78, 031104 (2008).

[2] C.N. Kaplan, M. Hinczewski, and A.N. Berker, Phys. Rev. E 79, 061120 (2009).

[3] A. Malakis, A.N. Berker, I.A. Hadjiagapiou, and N.G. Fytas, Phys. Rev. E 79, 011125 (2009).


-  Jeudi 7 Octobre 2010, journée des nouveaux entrants au LPT, pas de seminaire.


-  Jeudi 30 Septembre 2010 à 14h, Salle 114, bât. 210.

Vivien Lecomte (Laboratoire de Probabilités et Modèles Aléatoires, Chevaleret) : Large deviations in (non-)equilibrium 1d transport models

 Interacting classical particles diffusing in 1d have provided in recent years an interesting playground to study non-equilibrium. The dynamics of these models is described by an evolution operator, which can be written as a spin chain Hamiltonian H. One is interested in the steady state properties and in the probability that the system presents an atypical current flow. These are described by large deviation functions (ldf).

 Finding the ldf amounts to determining the ground state of H — a correspondence which provides an interesting bridge between classical and quantum problems. I will present different methods (Bethe Ansatz, fluctuating hydrodynamics) used to compute the ldf and to characterize its singularities — which correspond to dynamical phase transitions. Some class of systems also present an intriguing duality between non-equilibrium and equilibrium, that reveal for instance the origin of long-range correlations induced by e.g. contact with reservoirs of different chemical potential.


-  Vendredi 17 Septembre 2010 à 11h, Salle 201, bât. 100.

Julian Talbot (Laboratoire de Physique Théorique de la Matière Condensée, Université Pierre et Marie Curie) : Computational studies of granular systems : Effect of particle shape and granular ratchets

Granular materials occur in many different settings. In nature, they are present in sand dunes, avalanches and planetary rings. In the chemical industry most of the stored, processed, conveyed and handled chemicals are in granular form. Although they have been studied for over a century, it is only relatively recently that a fundamental-level understanding of the properties of granular systems has started to emerge. Numerical simulation has contributed considerably to this development. In this talk, I will present two examples from our recent work.

In the first, we investigate the effect of shape on the behavior of granular systems under shear with event-driven simulations of hard inelastic dumbbells in two dimensions. The dumbbells are randomly orientated at low packing fraction, but show an increasingly preferred alignment with the shear direction as the packing fraction increases.

Brownian ratchets have fascinated scientists for nearly a century. A ratchet effect is possible whenever there is a breakdown of detailed balance and a lack of spatial symmetry. I will discuss a class of heterogeneous granular particles, the simplest of which is an asymmetric piston composed of two materials with different inelasticities. When immersed in a bath of thermalized particles, this device develops a net drift velocity and is able to perform work. Recent experimental studies seem to confirm the effect and also reveal the important role of dry friction


-  Jeudi 9 Septembre 2010 à 14h, Salle 201, bât. 100.

Steffen Klamt (Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg) : Qualitative Modeling of cellular Signaling Networks : Concepts, Algorithms and Applications

A central goal of systems biology is the construction of predictive models of biomolecular networks. Cellular networks of moderate size have been modeled successfully in a quantitative way based on differential equations. In large-scale networks, knowledge of mechanistic details and kinetic parameters is often too limited to allow for the set-up of predictive quantitative models. In my talk I will present methods for qualitative and topology-based analysis of cellular signal transduction networks based on three different (but related) modeling formalisms : interaction graphs, logical/Boolean networks, and qualitative differential equations. Albeit the simplest models possible, interaction graphs allow us to identify important properties such as signaling paths, feedback loops or global causal dependencies. Based on these structural features one can make qualitative predictions (ups and downs) on the effect of perturbations giving us a valuable tool to detect inconsistencies between knowledge and measured data. Logical or Boolean models can be derived from interaction graphs by constraining the logical combination of edges. Using a hypergraphical representation of Boolean networks and introducing some novel techniques for their analysis we made this qualitative modeling approach also amenable to large-scale signaling networks. These techniques include qualitative simulation of stimulus-response experiments and the identification of proper intervention strategies enforcing or repressing a particular behavior. Recently we introduced a novel method to transform Boolean networks into a system of differential equations by which essential dynamic features of the network can be studied. I will also discuss algorithmic problems related to the analysis of interaction graphs (e.g. computation of shortest positive/negative paths) and logical networks (e.g. computation of minimal intervention sets). Practical application examples - including a large-scale model of EGF signaling - demonstrate that our methods deliver verifiable predictions and hypotheses on network function driving the iterative cycle between experiment and modeling.