Generalized Langevin equations for a driven tracer in dense soft colloids: construction and applications

We describe a tracer in a bath of soft Brownian colloids by a particle coupled to the density field of the other bath particles. From the Dean equation, we derive an exact equation for the evolution of the whole system, and show that the density field evolution can be linearized in the limit of a dense bath. This linearized Dean equation with a tracer taken apart is validated by the reproduction of previous results on the mean-field liquid structure and transport properties. Then, the tracer is submitted to an external force and we compute the density profile around it, its mobility and its diffusion coefficient. Our results exhibit effects such as bias enhanced diffusion that are very similar to those observed in the opposite limit of a hard core lattice gas, indicating the robustness of these effects. Our predictions are successfully tested against molecular dynamics simulations.Comment: 21 pages, 7 figure

Scaling of the glassy dynamics of soft repulsive particles: a mode-coupling approach

We combine the hyper-netted chain approximation of liquid state theory with the mode-coupling theory of the glass transition to analyze the structure and dynamics of soft spheres interacting via harmonic repulsion. We determine the locus of the fluid-glass dynamic transition in a temperature -- volume fraction phase diagram. The zero-temperature (hard sphere) glass transition influences the dynamics at finite temperatures in its vicinity. This directly implies a form of dynamic scaling for both the average relaxation time and dynamic susceptibilities quantifying dynamic heterogeneity. We discuss several qualitative disagreements between theory and existing simulations at equilibrium. Our theoretical results are, however, very similar to numerical results for the driven athermal dynamics of repulsive spheres, suggesting that `mean-field' mode-coupling approaches might be good starting points to describe these nonequilibrium dynamics.Comment: 11 pages, 8 figure

Quantitative field theory of the glass transition

We develop a full microscopic replica field theory of the dynamical transition in glasses. By studying the soft modes that appear at the dynamical temperature we obtain an effective theory for the critical fluctuations. This analysis leads to several results: we give expressions for the mean field critical exponents, and we study analytically the critical behavior of a set of four-points correlation functions from which we can extract the dynamical correlation length. Finally, we can obtain a Ginzburg criterion that states the range of validity of our analysis. We compute all these quantities within the Hypernetted Chain Approximation (HNC) for the Gibbs free energy and we find results that are consistent with numerical simulations.Comment: 6 pages, 2 figures + supplementary information -- a few minor errors of the published version have been fixe

On the entropy of protein families

Proteins are essential components of living systems, capable of performing a huge variety of tasks at the molecular level, such as recognition, signalling, copy, transport, ... The protein sequences realizing a given function may largely vary across organisms, giving rise to a protein family. Here, we estimate the entropy of those families based on different approaches, including Hidden Markov Models used for protein databases and inferred statistical models reproducing the low-order (1-and 2-point) statistics of multi-sequence alignments. We also compute the entropic cost, that is, the loss in entropy resulting from a constraint acting on the protein, such as the fixation of one particular amino-acid on a specific site, and relate this notion to the escape probability of the HIV virus. The case of lattice proteins, for which the entropy can be computed exactly, allows us to provide another illustration of the concept of cost, due to the competition of different folds. The relevance of the entropy in relation to directed evolution experiments is stressed.Comment: to appear in Journal of Statistical Physic

Static replica approach to critical correlations in glassy systems

We discuss the slow relaxation phenomenon in glassy systems by means of replicas by constructing a static field theory approach to the problem. At the mean field level we study how criticality in the four point correlation functions arises because of the presence of soft modes and we derive an effective replica field theory for these critical fluctuations. By using this at the Gaussian level we obtain many physical quantities: the correlation length, the exponent parameter that controls the Mode-Coupling dynamical exponents for the two-point correlation functions, and the prefactor of the critical part of the four point correlation functions. Moreover we perform a one-loop computation in order to identify the region in which the mean field Gaussian approximation is valid. The result is a Ginzburg criterion for the glass transition. We define and compute in this way a proper Ginzburg number. Finally, we present numerical values of all these quantities obtained from the Hypernetted Chain approximation for the replicated liquid theory.Comment: 34 pages, 1 figure - to be published on J.Chem.Phys. for a special issue on the Glass Transitio

Field theoretic formulation of a mode-coupling equation for colloids

The only available quantitative description of the slowing down of the dynamics upon approaching the glass transition has been, so far, the mode-coupling theory, developed in the 80's by G\"otze and collaborators. The standard derivation of this theory does not result from a systematic expansion. We present a field theoretic formulation that arrives at very similar mode-coupling equation but which is based on a variational principle and on a controlled expansion in a small dimensioneless parameter. Our approach applies to such physical systems as colloids interacting via a mildly repulsive potential. It can in principle, with moderate efforts, be extended to higher orders and to multipoint correlation functions

Can the jamming transition be described using equilibrium statistical mechanics?

When materials such as foams or emulsions are compressed, they display solid behaviour above the so-called `jamming' transition. Because compression is done out-of-equilibrium in the absence of thermal fluctuations, jamming appears as a new kind of a nonequilibrium phase transition. In this proceeding paper, we suggest that tools from equilibrium statistical mechanics can in fact be used to describe many specific features of the jamming transition. Our strategy is to introduce thermal fluctuations and use statistical mechanics to describe the complex phase behaviour of systems of soft repulsive particles, before sending temperature to zero at the end of the calculation. We show that currently available implementations of standard tools such as integral equations, mode-coupling theory, or replica calculations all break down at low temperature and large density, but we suggest that new analytical schemes can be developed to provide a fully microscopic, quantitative description of the jamming transition.Comment: 8 pages, 6 figs. Talk presented at Statphys24 (July 2010, Cairns, Australia