Phase Transitions in Lyotropic Nematic Gels

In this paper, we discuss the equilibrium phases and collapse transitions of a lyotropic nematic gel immersed in an isotropic solvent. A nematic gel consists of a cross-linked polymer network with rod-like molecules embedded in it. Upon decreasing the quality of the solvent, we find that a lyotropic nematic gel undergoes a discontinuous volume change accompanied by an isotropic-nematic transition. We also present phase diagrams that these systems may exhibit. In particular, we show that coexistence of two isotropic phases, of two nematic phases, or of an isotropic and a nematic phase can occur.Comment: 13 pages Revtex, 10 figures, submitted to EPJ

Fluctuations of a driven membrane in an electrolyte

We develop a model for a driven cell- or artificial membrane in an electrolyte. The system is kept far from equilibrium by the application of a DC electric field or by concentration gradients, which causes ions to flow through specific ion-conducting units (representing pumps, channels or natural pores). We consider the case of planar geometry and Debye-H\"{u}ckel regime, and obtain the membrane equation of motion within Stokes hydrodynamics. At steady state, the applied field causes an accumulation of charges close to the membrane, which, similarly to the equilibrium case, can be described with renormalized membrane tension and bending modulus. However, as opposed to the equilibrium situation, we find new terms in the membrane equation of motion, which arise specifically in the out-of-equilibrium case. We show that these terms lead in certain conditions to instabilities.Comment: 7 pages, 2 figures. submitted to Europhys. Let

Energy versus information based estimations of dissipation using a pair of magnetic colloidal particles

Using the framework of stochastic thermodynamics, we present an experimental study of a doublet of magnetic colloidal particles which is manipulated by a time-dependent magnetic field. Due to hydrodynamic interactions, each bead experiences a state-dependent friction, which we characterize using a hydrodynamic model. In this work, we compare two estimates of the dissipation in this system: the first one is energy based since it relies on the measured interaction potential, while the second one is information based since it uses only the information content of the trajectories. While the latter only offers a lower bound of the former, we find it to be simple to implement and of general applicability to more complex systems.Comment: Main text: 5 pages, 4 figures. Supplementary material: 5 pages, 5 figure

Gallavotti-Cohen-Type symmetry related to cycle decompositions for Markov chains and biochemical applications

We slightly extend the fluctuation theorem obtained in \cite{LS} for sums of generators, considering continuous-time Markov chains on a finite state space whose underlying graph has multiple edges and no loop. This extended frame is suited when analyzing chemical systems. As simple corollary we derive in a different method the fluctuation theorem of D. Andrieux and P. Gaspard for the fluxes along the chords associated to a fundamental set of oriented cycles \cite{AG2}. We associate to each random trajectory an oriented cycle on the graph and we decompose it in terms of a basis of oriented cycles. We prove a fluctuation theorem for the coefficients in this decomposition. The resulting fluctuation theorem involves the cycle affinities, which in many real systems correspond to the macroscopic forces. In addition, the above decomposition is useful when analyzing the large deviations of additive functionals of the Markov chain. As example of application, in a very general context we derive a fluctuation relation for the mechanical and chemical currents of a molecular motor moving along a periodic filament.Comment: 23 pages, 5 figures. Correction

Modified Fluctuation-dissipation theorem for non-equilibrium steady-states and applications to molecular motors

We present a theoretical framework to understand a modified fluctuation-dissipation theorem valid for systems close to non-equilibrium steady-states and obeying markovian dynamics. We discuss the interpretation of this result in terms of trajectory entropy excess. The framework is illustrated on a simple pedagogical example of a molecular motor. We also derive in this context generalized Green-Kubo relations similar to the ones derived recently by Seifert., Phys. Rev. Lett., 104, 138101 (2010) for more general networks of biomolecular states.Comment: 6 pages, 2 figures, submitted in EP

Coherent Backscattering of light in a magnetic field

This paper describes how coherent backscattering is altered by an external magnetic field. In the theory presented, magneto-optical effects occur inside Mie scatterers embedded in a non-magnetic medium. Unlike previous theories based on point-like scatterers, the decrease of coherent backscattering is obtained in leading order of the magnetic field using rigorous Mie theory. This decrease is strongly enhanced in the proximity of resonances, which cause the path length of the wave inside a scatterer to be increased. Also presented is a novel analysis of the shape of the backscattering cone in a magnetic field.Comment: 27 pages, 5 figures, Revtex, to appear in Phys. Rev.

Stochastic model for nucleosome sliding in the presence of DNA ligands

Heat-induced mobility of nucleosomes along DNA is an experimentally well-studied phenomenon. A recent experiment shows that the repositioning is modified in the presence of minor-groove binding DNA ligands. We present here a stochastic three-state model for the diffusion of a nucleosome along DNA in the presence of such ligands. It allows us to describe the dynamics and the steady state of such a motion analytically. The analytical results are in excellent agreement with numerical simulations of this stochastic process.With this model, we study the response of a nucleosome to an external force and how it is affected by the presence of ligands.Comment: 10 pages, 8 figures, submitted to Eur. Phys. J.

Electrostatic and electrokinetic contributions to the elastic moduli of a driven membrane

We discuss the electrostatic contribution to the elastic moduli of a cell or artificial membrane placed in an electrolyte and driven by a DC electric field. The field drives ion currents across the membrane, through specific channels, pumps or natural pores. In steady state, charges accumulate in the Debye layers close to the membrane, modifying the membrane elastic moduli. We first study a model of a membrane of zero thickness, later generalizing this treatment to allow for a finite thickness and finite dielectric constant. Our results clarify and extend the results presented in [D. Lacoste, M. Cosentino Lagomarsino, and J. F. Joanny, Europhys. Lett., {\bf 77}, 18006 (2007)], by providing a physical explanation for a destabilizing term proportional to \kps^3 in the fluctuation spectrum, which we relate to a nonlinear ($E^2$) electro-kinetic effect called induced-charge electro-osmosis (ICEO). Recent studies of ICEO have focused on electrodes and polarizable particles, where an applied bulk field is perturbed by capacitive charging of the double layer and drives flow along the field axis toward surface protrusions; in contrast, we predict "reverse" ICEO flows around driven membranes, due to curvature-induced tangential fields within a non-equilibrium double layer, which hydrodynamically enhance protrusions. We also consider the effect of incorporating the dynamics of a spatially dependent concentration field for the ion channels.Comment: 22 pages, 10 figures. Under review for EPJ

Modulating spin transfer torque switching dynamics with two orthogonal spin-polarizers by varying the cell aspect ratio

We study in-plane magnetic tunnel junctions with additional perpendicular polarizer for subnanosecond-current-induced switching memories. The spin-transfer-torque switching dynamics was studied as a function of the cell aspect ratio both experimentally and by numerical simulations using the macrospin model. We show that the anisotropy field plays a significant role in the dynamics, along with the relative amplitude of the two spin-torque contributions. This was confirmed by micromagnetic simulations. Real-time measurements of the reversal were performed with samples of low and high aspect ratio. For low aspect ratios, a precessional motion of the magnetization was observed and the effect of temperature on the precession coherence was studied. For high aspect ratios, we observed magnetization reversals in less than 1 ns for high enough current densities, the final state being controlled by the current direction in the magnetic tunnel junction cell.Comment: 6 pages, 7 figure

Fluctuation theorem and large deviation function for a solvable model of a molecular motor

We study a discrete stochastic model of a molecular motor. This discrete model can be viewed as a \emph{minimal} ratchet model. We extend our previous work on this model, by further investigating the constraints imposed by the Fluctuation Theorem on the operation of a molecular motor far from equilibrium. In this work, we show the connections between different formulations of the Fluctuation Theorem. One formulation concerns the generating function of the currents while another one concerns the corresponding large deviation function, which we have calculated exactly for this model. A third formulation of FT concerns the ratio of the probability of making one forward step to the probability of making one backward step. The predictions of this last formulation of the Fluctuation Theorem adapted to our model are in very good agreement with the data of Carter and Cross [Nature, {\bf 435}, 308 (2005)] on single molecule measurements with kinesin. Finally, we show that all the formulations of FT can be understood from the notion of entropy production.Comment: 15 pages, 9 figure