No description available.

The transport of a biomolecule through a nanopore occurs in many biological functions such as, DNA or RNA transport across nuclear pores and the translocation of proteins across the eukaryotic endoplasmic reticulum. In addition to the biological processes, it has potential applications in technology such as, drug delivery, gene therapy, and single molecule sensing. The DNA translocation through a synthetic nanopore device is considered as the basis for cheap and fast sequencing technology. Motivated by the experimental advances, many theoretical models have been developed. In this thesis, we explore the dynamics of driven translocation of a semiflexible polymer through a nanopore in two dimensions (2D) using Langevin dynamics (LD) simulation. By carrying out extensive simulation as a function of different parameters such as, driving force, length and rigidity of the chain, viscosity of the solvent, and diameter of the nanopore, we provide a detailed description of the translocation process. Our studies are relevant for fundamental understanding of the translocation process which is essential for making accurate nano-pore based devices.

No description available.

L'objectif de cette thèse porte sur l'étude des phénomènes de blocage dans un flux particules à faible densité dans un canal. Le blocage est induit par la géométrie du canal. L'essentiel de mes travaux concerne la description des situations où le blocage est contrôlé par les limites en capacité d'un canal. Le paramètre pertinent pour ce phénomène est donné par le nombre de particules minimum, N, conduisant à l'interruption du flux de particules. Un modèle stochastique simple introduit par Gabrielli et al. (PRL. 110, 170601, 2013) illustre ce comportement: des particules arrivent aléatoirement selon une distribution de Poisson à l'entrée d'un canal unidimensionnel et le traversent avec un temps constant, noté t. Le blocage survient lorsque N particules sont simultanément sur le pont. Le travail de cette thèse à été d'étudier les extensions de ce modèle. Les observables du système sont la probabilité de survie, le flux sortant ainsi que la statistique sur les particules sorties avant le blocage. Les différentes études ont permis pour le cas N>2, pour une distribution homogène quelconque et inhomogène d'entrée, pour un système de multi-canaux ainsi que pour une durée finie de blocage d'obtenir des résultats analytiques exactes ainsi que des approximations à l'aide d'outils statistique. Le dernier projet de cette thèse porte sur l'étude microscopique des phénomènes de blocage. Le modèle simple que nous avons étudié est un système bidimensionnel de particules browniennes soumis à une force de traînée et se déplaçant dans un canal avec rétrécissement. La présence d'un obstacle au milieu du canal peut causer un colmatage selon les valeurs des différents paramètres du système. / This manuscript presents a study of blocking phenomenon in particulate streams flowing through anarrow channel. In particular, it examines situations in which blocking is controlled by the limitedcarrying capacity of the channel. It builds on a simple stochastic model, introduced by Gabrielli etal. (Phys. Rev. Lett. 110, 170601, 2013), in which particles arrive randomly according to a Poissondistribution at the entrance of a one-dimensional channel with an intensity λ and, unless interrupted,exit after a transit time, τ. Blocking occurs instantaneously when N=2 particles are simultaneouslypresent in the channel. The quantities of interest include the probability that the channel is still openat time t (survival probability) and the flux and total number of exiting particles. The thesisexamines a number of generalizations including when more than two particles must be present toinduce blockage, N>2, a time dependent intensity, a finite blocking time, and multi-channelsystems. We obtain exact and approximate analytical results using tools such as the masterequations describing the evolution of the n-particle partial probabilities, large deviation theory andqueuing theory. The theoretical results are validated by comparison with the results of numericalsimulations. The final chapter of the thesis uses a different approach, namely a brownian dynamics simulation of a two dimensional system of soft particles subjected to an external driving and dragforces. The presence of an obstacle in the middle of the channel can cause irreversible orintermittent clogging depending on the system geometry, temperature and particle stiffness.

This thesis consists of research work in the broad area of soft condensed matter theory with a focus on active matter. The study of long wavelength, low frequency collective behavior of active particles (bacterial suspensions, fish schools, motor-microtubule extracts, active gels) forms an interesting modification to liquid-crystal hydrodynamics, in which the constituent particles carry permanent stresses that stir the fluid. Activity introduces novel instabilities and many novel aspects emerge. Our works focus on the dynamics, order, fluctuations and instabilities in these systems. In particular, we investigated the dynamics, order and fluctuation properties emerging from effective hydrodynamic descriptions of translationally ordered active matter and also studied those in microwave-driven quantum Hall nematics. We also investigated the rheological properties of active suspensions subjected to an applied orienting field. A summary of the works carried out is as follows. Translationally ordered active phases – active smectics and active cholesterics: Active or self-propelled particles consume and dissipate energy generating permanent stresses that stir the fluid around them. The collective behavior of systems of active particles, in systems with translational order, pose interesting questions and possibilities of new physics that differ strikingly from those in systems at thermal equilibrium with the same spatial symmetry. We developed the hydrodynamic equations of motion for (a) an active system with spontaneously broken translational symmetry in one direction, i.e., smectic and (b) the simplest uniaxially ordered phase of active chiral objects, namely, an active cholesteric. We analyze the fluctuation properties as well as the nature of characteristic instabilities that these systems can display and make a number of predictions. For example, in the case of an active smectic, we show that active stresses generate an effective active layer tension which, if positive, sup-presses the Landau-Peierls effect, leading to long-range smectic order in dimension d =3 and quasi-long-range in d =2, in sharp contrast with thermal equilibrium systems. Negative active layer tension in bulk systems, however, lead to a spontaneous Helfrich-Hurault undulation instability of the layers, accompanied by spontaneous flow. Also, active smectics, unlike orientationally ordered active systems, normally have finite concentration fluctuations. Similarly, for the case of cholesterics we show that cholesteric elasticity intervenes to suppress some of the instabilities present in active nematics. xi Numerical simulation of active smectics: We present results from a Brownian Dynamics simulation, with no hydrodynamic interaction, of a system of apolar active particles form-ing translational liquid-crystalline order in a suspension. The particles interact through a prolate-ellipsoidal Gay-Berne potential. We model activity minimally through different noise temperatures for movement along and normal to the orientation axis of each particle. We present preliminary results on the disruptive effect of activity on smectic order for the parameter values investigated. Future work will test the predictions of our theory [1] on active smectics. Rheology of active suspensions near field-induced critical points : Shear induces orientation of active stresses in a suspension, through flow alignment. Depending on the sign, activity then either enhances or reduces the viscosity. The change in viscosity, in the zero frequency limit, is proportional to the product of the magnitude of active stress and the system relaxation time. A strong enough orienting field can make the system approach a critical point and the relaxation time diverges. We show that, this results in the divergence of viscosity at zero frequency making the system strongly viscoelastic. Depending on the sign, activity strengthens or reduces the effect of the field. We also investigate the rheological property of an active suspension with mixed polar and nematic oreder. Active quantum Hall systems: We construct the hydrodynamic theory for a 2d charged active nematic with 3d electrostatics. We have investigated the interplay of the Coulomb interaction and activity in these systems. We show that activity competes to enhance the charge density fluctuations normally suppressed by long-ranged Coulomb interactions. The charge structure factor Sq of the corresponding passive charged nematic goes to zero as q, whereas in charged active nematics, activity leads to a nonvanishing charge structure factor at small wavenumber. We also show how the effect of an applied magnetic field can be incorporated into the dynamics of the system and leave scope for further studies on these effects.