A thin film model for corotational Jeffreys fluids under strong slip

We derive a thin film model for viscoelastic liquids under strong slip which obey the stress tensor dynamics of corotational Jeffreys fluids.Comment: 3 pages, submitted to Eur. Phys. J.

Critical holes in undercooled wetting layers

The profile of a critical hole in an undercooled wetting layer is determined by the saddle-point equation of a standard interface Hamiltonian supported by convenient boundary conditions. It is shown that this saddle-point equation can be mapped onto an autonomous dynamical system in a three-dimensional phase space. The corresponding flux has a polynomial form and in general displays four fixed points, each with different stability properties. On the basis of this picture we derive the thermodynamic behaviour of critical holes in three different nucleation regimes of the phase diagram.Comment: 18 pages, LaTeX, 6 figures Postscript, submitted to J. Phys.

Biophysical Perspective: The Latest Twists in Chromatin Remodeling

International audienceIn its most restrictive interpretation, the notion of chromatin remodeling refers to the action of chromatin remodeling enzymes on nucleosomes with the aim to displace and remove them from the chromatin fiber (the effective polymer formed by a DNA molecule and proteins). This local modification of the fiber structure can have consequences for the initiation and repression of the transcription process and, when the remodeling processes spreads along the fiber, also results in long-range effects essential for fiber condensation. There are three regulatory levels of relevance that can be distinguished for this process: the first is the intrinsic sequence preference of the histone octamer which rules the positioning of the nucleosome along the DNA, notably in relation to the genetic information coded in DNA, the second is the recognition or selection of nucleosomal substrates by remodeling complexes, and the final one the motor action on the nucleosome exerted by the chromatin remodeler. On each of these three levels recent work has been able to provide crucial insights which add new twists to this exciting and unfinished story, which we highlight in this perspective

A fluctuation-corrected functional of convex Poisson–Boltzmann theory

International audiencePoisson-Boltzmann theory allows to study soft matter and biophysical systems involving point-like charges of low valencies. The inclusion of fluctuation corrections beyond the mean-field approach typically requires the application of loop expansions around a mean-field solution for the electrostatic potential φ(r), or sophisticated variational approaches. Recently, Poisson-Boltzmann theory has been recast, via a Legendre transform, as a mean-field theory involving the dielectric displacement field D(r). In this paper we consider the path integral formulation of this dual theory. Exploiting the transformation between φ and D, we formulate a dual Sine-Gordon field theory in terms of the displacement field and provide a strategy for precise numerical computations of free energies beyond the leading order

Chromatin remodelers as active Brownian dimers

International audienceChromatin remodelers are molecular motors which actively displace nucleosomes on chromatin. Recent results on the structural properties of these motors indicate that the displacement of nucleosomal DNA corresponds to an inchworm motion induced by the generation and propagation of twist defects. Here we show that this basic action mechanism can be described by a coarse-grained active Brownian dimer (ABD) model, thereby quantitatively rationalizing the notion of inchworm motion. The model allows for extensions to more microscopic as well towards more macroscopic descriptions of chromatin hydrodynamics

Compositionality, stochasticity and cooperativity in dynamic models of gene regulation

We present an approach for constructing dynamic models for the simulation of gene regulatory networks from simple computational elements. Each element is called a ``gene gate'' and defines an input/output-relationship corresponding to the binding and production of transcription factors. The proposed reaction kinetics of the gene gates can be mapped onto stochastic processes and the standard ode-description. While the ode-approach requires fixing the system's topology before its correct implementation, expressing them in stochastic pi-calculus leads to a fully compositional scheme: network elements become autonomous and only the input/output relationships fix their wiring. The modularity of our approach allows to pass easily from a basic first-level description to refined models which capture more details of the biological system. As an illustrative application we present the stochastic repressilator, an artificial cellular clock, which oscillates readily without any cooperative effects.Comment: 15 pages, 8 figures. Accepted by the HFSP journal (13/09/07

A statistical procedure to adjust for time-interval mismatch in forensic voice comparison

The present paper describes a statistical modeling procedure that was developed to account for the fact that, in a forensic voice comparison analysis conducted for a particular case, there was a long time interval between when the questioned- and known-speaker recordings were made (six years), but in the sample of the relevant population used for training and testing the forensic voice comparison system there was a short interval (hours to days) between when each of multiple recordings of each speaker was made. The present paper also includes results of empirical validation of the procedure. Although based on a particular case, the procedure has potential for wider application given that relatively long time intervals between the recording of questioned and known speakers are not uncommon in casework