Transport on a Lattice with Dynamical Defects

Many transport processes in nature take place on substrates, often considered as unidimensional lanes. These unidimensional substrates are typically non-static: affected by a fluctuating environment, they can undergo conformational changes. This is particularly true in biological cells, where the state of the substrate is often coupled to the active motion of macromolecular complexes, such as motor proteins on microtubules or ribosomes on mRNAs, causing new interesting phenomena. Inspired by biological processes such as protein synthesis by ribosomes and motor protein transport, we introduce the concept of localized dynamical sites coupled to a driven lattice gas dynamics. We investigate the phenomenology of transport in the presence of dynamical defects and find a novel regime characterized by an intermittent current and subject to severe finite-size effects. Our results demonstrate the impact of the regulatory role of the dynamical defects in transport, not only in biology but also in more general contexts

Correlated percolation models of structured habitat in ecology

Percolation offers acknowledged models of random media when the relevant medium characteristics can be described as a binary feature. However, when considering habitat modeling in ecology, a natural constraint comes from nearest-neighbor correlations between the suitable/unsuitable states of the spatial units forming the habitat. Such constraints are also relevant in the physics of aggregation where underlying processes may lead to a form of correlated percolation. However, in ecology, the processes leading to habitat correlations are in general not known or very complex. As proposed by Hiebeler [Ecology {\bf 81}, 1629 (2000)], these correlations can be captured in a lattice model by an observable aggregation parameter $q$, supplementing the density $p$ of suitable sites. We investigate this model as an instance of correlated percolation. We analyze the phase diagram of the percolation transition and compute the cluster size distribution, the pair-connectedness function $C(r)$ and the correlation function $g(r)$. We find that while $g(r)$ displays a power-law decrease associated with long-range correlations in a wide domain of parameter values, critical properties are compatible with the universality class of uncorrelated percolation. We contrast the correlation structures obtained respectively for the correlated percolation model and for the Ising model, and show that the diversity of habitat configurations generated by the Hiebeler model is richer than the archetypal Ising model. We also find that emergent structural properties are peculiar to the implemented algorithm, leading to questioning the notion of a well-defined model of aggregated habitat. We conclude that the choice of model and algorithm have strong consequences on what insights ecological studies can get using such models of species habitat

Collapse Dynamics of a Homopolymer: Theory and Simulation

We present a scaling theory describing the collapse of a homopolymer chain in poor solvent. At time t after the beginning of the collapse, the original Gaussian chain of length N is streamlined to form N/g segments of length R(t), each containing g ~ t monomers. These segments are statistical quantities representing cylinders of length R ~ t^{1/2} and diameter d ~ t^{1/4}, but structured out of stretched arrays of spherical globules. This prescription incorporates the capillary instability. We compare the time-dependent structure factor derived for our theory with that obtained from ultra-large-scale molecular dynamics simulation with explicit solvent. This is the first time such a detailed comparison of theoretical and simulation predictions of collapsing chain structure has been attempted. The favorable agreement between the theoretical and computed structure factors supports the picture of the coarse-graining process during polymer collapse.Comment: 4 pages, 3 figure

Tumor transfection after systemic injection of DNA lipid nanocapsules

With the goal of generating an efficient vector for systemic gene delivery, a new kind of nanocarrier consisting of lipid nanocapsules encapsulating DOTAP/DOPE lipoplexes (DNA LNCs) was pegylated by the post-insertion of amphiphilic and flexible polymers. The aim of this surface modification was to create a long-circulating vector, able to circulate in the blood stream and efficient in transfecting tumoral cells after passive targeting by enhanced permeability and retention effect (EPR effect). PEG conformation, electrostatic features, and hydrophylicity are known to be important factors able to influence the pharmacokinetic behaviour of vectors. In this context, the surface structure characteristics of the newly pegylated DNA LNCs were studied by measuring electrophoretic mobility as a function of ionic strength in order to establish a correlation between surface properties and in vivo performance of the vector. Finally, thanks to this PEGylation, gene expression was measured up to 84-fold higher in tumor compared to other tested organs after intravenous injection. The present results indicate that PEGylated DNA LNCs are promising carriers for an efficient cancer gene therapy

Injected Power Fluctuations in 1D Dissipative Systems

Using fermionic techniques, we compute exactly the large deviation function (ldf) of the time-integrated injected power in several one-dimensional dissipative systems of classical spins. The dynamics are T=0 Glauber dynamics supplemented by an injection mechanism, which is taken as a Poissonian flipping of one particular spin. We discuss the physical content of the results, specifically the influence of the rate of the Poisson process on the properties of the ldf.Comment: 18 pages, 8 figure

Folding and unfolding kinetics of a single semiflexible polymer

We theoretically investigate the kinetics of the folding transition of a single semiflexible polymer. In the folding transition, the growth rate decrease with an increase in the number of monomers in a collapsed domain, suggesting that the main contribution to dissipation is from the motion of the domain. In the unfolding transition, dynamic scaling exponents, 1/8 and 1/4, were determined for disentanglement and relaxation steps, respectively. We performed Langevin dynamics simulations to test our theory. It is found that our theory is in good agreement with simulations. We also propose the kinetics of the transitions in the presence of the hydrodynamic interaction.Comment: 12 pages, 10 figure

Critical behavior of a fluid in a disordered porous matrix: An Ornstein-Zernike approach

Using a liquid-state approach based on Ornstein-Zernike equations, we study the behavior of a fluid inside a porous disordered matrix near the liquid-gas critical point.The results obtained within various standard approximation schemes such as lowest-order $\gamma$-ordering and the mean-spherical approximation suggest that the critical behavior is closely related to that of the random-field Ising model (RFIM).Comment: 10 pages, revtex, to appear in Physical Review Letter

Structure factor of polymers interacting via a short range repulsive potential: application to hairy wormlike micelles

We use the Random Phase Approximation (RPA) to compute the structure factor, S(q), of a solution of chains interacting through a soft and short range repulsive potential V. Above a threshold polymer concentration, whose magnitude is essentially controlled by the range of the potential, S(q) exhibits a peak whose position depends on the concentration. We take advantage of the close analogy between polymers and wormlike micelles and apply our model, using a Gaussian function for V, to quantitatively analyze experimental small angle neutron scattering profiles of semi-dilute solutions of hairy wormlike micelles. These samples, which consist in surfactant self-assembled flexible cylinders decorated by amphiphilic copolymer, provide indeed an appropriate experimental model system to study the structure of sterically interacting polymer solutions

Capillary condensation in disordered porous materials: hysteresis versus equilibrium behavior

We study the interplay between hysteresis and equilibrium behavior in capillary condensation of fluids in mesoporous disordered materials via a mean-field density functional theory of a disordered lattice-gas model. The approach reproduces all major features observed experimentally. We show that the simple van der Waals picture of metastability fails due to the appearance of a complex free-energy landscape with a large number of metastable states. In particular, hysteresis can occur both with and without an underlying equilibrium transition, thermodynamic consistency is not satisfied along the hysteresis loop, and out-of-equilibrium phase transitions are possible.Comment: 4 pages, 4 figure