Dynamics of Molecular Motors and Polymer Translocation with Sequence Heterogeneity

The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or DNA is biased due to the different chemical environments on the two sides of the membrane, while the molecular motor motion is biased through a coupling to chemical energy. An externally applied force can oppose these biases. For both systems we solve lattice models exactly both with and without disorder. The models incorporate explicitly the coupling to the different chemical environments for polymer translocation and the coupling to the chemical energy (as well as nucleotide pairing energies) for molecular motors. Using the exact solutions and general arguments we show that the heterogeneity leads to anomalous dynamics. Most notably, over a range of forces around the stall force (or stall tension for DNA polymerase/exonuclease systems) the displacement grows sublinearly as t^\mu with \mu<1. The range over which this behavior can be observed experimentally is estimated for several systems and argued to be detectable for appropriate forces and buffers. Similar sequence heterogeneity effects may arise in the packing of viral DNA.Comment: 42 pages, 12 figure

Unzipping flux lines from extended defects in type-II superconductors

With magnetic force microscopy in mind, we study the unbinding transition of individual flux lines from extended defects like columnar pins and twin planes in type II superconductors. In the presence of point disorder, the transition is universal with an exponent which depends only on the dimensionality of the extended defect. We also consider the unbinding transition of a single vortex line from a twin plane occupied by other vortices. We show that the critical properties of this transition depend strongly on the Luttinger liquid parameter which describes the long distance physics of the two-dimensional flux line array.Comment: 5 pages, 4 figure

Slow Coarsening in a Class of Driven Systems

The coarsening process in a class of driven systems is studied. These systems have previously been shown to exhibit phase separation and slow coarsening in one dimension. We consider generalizations of this class of models to higher dimensions. In particular we study a system of three types of particles that diffuse under local conserving dynamics in two dimensions. Arguments and numerical studies are presented indicating that the coarsening process in any number of dimensions is logarithmically slow in time. A key feature of this behavior is that the interfaces separating the various growing domains are smooth (well approximated by a Fermi function). This implies that the coarsening mechanism in one dimension is readily extendible to higher dimensions.Comment: submitted to EPJB, 13 page

Phase transition in a non-conserving driven diffusive system

An asymmetric exclusion process comprising positive particles, negative particles and vacancies is introduced. The model is defined on a ring and the dynamics does not conserve the number of particles. We solve the steady state exactly and show that it can exhibit a continuous phase transition in which the density of vacancies decreases to zero. The model has no absorbing state and furnishes an example of a one-dimensional phase transition in a homogeneous non-conserving system which does not belong to the absorbing state universality classes

Quantum interface between an electrical circuit and a single atom

We show how to bridge the divide between atomic systems and electronic devices by engineering a coupling between the motion of a single ion and the quantized electric field of a resonant circuit. Our method can be used to couple the internal state of an ion to the quantized circuit with the same speed as the internal-state coupling between two ions. All the well-known quantum information protocols linking ion internal and motional states can be converted to protocols between circuit photons and ion internal states. Our results enable quantum interfaces between solid state qubits, atomic qubits, and light, and lay the groundwork for a direct quantum connection between electrical and atomic metrology standards.Comment: Supplemental material available on reques