Driven Polymer Translocation Through a Narrow Pore

Motivated by experiments in which a polynucleotide is driven through a proteinaceous pore by an electric field, we study the diffusive motion of a polymer threaded through a narrow channel with which it may have strong interactions. We show that there is a range of polymer lengths in which the system is approximately translationally invariant, and we develop a coarse-grained description of this regime. From this description, general features of the distribution of times for the polymer to pass through the pore may be deduced. We also introduce a more microscopic model. This model provides a physically reasonable scenario in which, as in experiments, the polymer's speed depends sensitively on its chemical composition, and even on its orientation in the channel. Finally, we point out that the experimental distribution of times for the polymer to pass through the pore is much broader than expected from simple estimates, and speculate on why this might be.Comment: 16 pages, 8 figures, RevTex and harvard citation style, submitted to Biophysical Journa

Caddo Ceramics on the Red River in North Central Texas

Caddo ceramics manufactured after A.D. 900 were widely traded in Texas, being found in some quantity on North Central, East Central, Central, and inland Southeast Texas archeological sites. They were also traded with prehistoric peoples in the Midwest (as far north as Iowa and Illinois) and the Southeastern U.S. While archeologists have known this for some time, much of the ceramic evidence for prehistoric Caddoan trade and exchange with other Native Americans has not been systematically compiled and studied, as became apparent during a recent review of the prehistoric and historic aboriginal pottery in Texas. Consequently, Caddoan archeologists are not yet in the position to confidently discuss the scope, timing, or direction of trade/exchange between Caddoan groups and surrounding non-Caddoan communities, or explore changes in the nature of social and economic relationships between particular Caddo groups and other prehistoric peoples. This paper represents part of our initial efforts to begin systematically compiling archeological information on the distribution and character of Caddo ceramic sherds and vessels outside what is considered the southern Caddoan archaeological area. In it, we report on Early and Late Caddo ceramics found by Dr. Ernest R. Martin at two sites along the Red River in North Central Texas, some 130 km or more west of the westernmost Caddo settlements on the Red River in Northeast Texas

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

Randomized benchmarking of atomic qubits in an optical lattice

We perform randomized benchmarking on neutral atomic quantum bits (qubits) confined in an optical lattice. Single qubit gates are implemented using microwaves, resulting in a measured error per randomized computational gate of 1.4(1) x 10^-4 that is dominated by the system T2 relaxation time. The results demonstrate the robustness of the system, and its viability for more advanced quantum information protocols.Comment: 11 pages, 4 figure

Self-Consistent Screening Approximation for Flexible Membranes: Application to Graphene

Crystalline membranes at finite temperatures have an anomalous behavior of the bending rigidity that makes them more rigid in the long wavelength limit. This issue is particularly relevant for applications of graphene in nano- and micro-electromechanical systems. We calculate numerically the height-height correlation function $G(q)$ of crystalline two-dimensional membranes, determining the renormalized bending rigidity, in the range of wavevectors $q$ from $10^{-7}$ \AA$^{-1}$ till 10 \AA$^{-1}$ in the self-consistent screening approximation (SCSA). For parameters appropriate to graphene, the calculated correlation function agrees reasonably with the results of atomistic Monte Carlo simulations for this material within the range of $q$ from $10^{-2}$ \AA$^{-1}$ till 1 \AA$^{-1}$. In the limit $q\rightarrow 0$ our data for the exponent $\eta$ of the renormalized bending rigidity $\kappa_R(q)\propto q^{-\eta}$ is compatible with the previously known analytical results for the SCSA $\eta\simeq 0.82$. However, this limit appears to be reached only for $q<10^{-5}$ \AA$^{-1}$ whereas at intermediate $q$ the behavior of $G(q)$ cannot be described by a single exponent.Comment: 5 pages, 4 figure

Radial honeycomb core

Core alleviates many limitations of conventional nacelle construction methods. Radical core, made of metals or nonmetals, is fabricated either by joining nodes and then expanding, or by performing each layer and then joining nodes. Core may also be produced from ribbons or strips with joined nodes or ribbons oriented in longitudinal planes

Quantum geometry from 2+1 AdS quantum gravity on the torus

Wilson observables for 2+1 quantum gravity with negative cosmological constant, when the spatial manifold is a torus, exhibit several novel features: signed area phases relate the observables assigned to homotopic loops, and their commutators describe loop intersections, with properties that are not yet fully understood. We describe progress in our study of this bracket, which can be interpreted as a q-deformed Goldman bracket, and provide a geometrical interpretation in terms of a quantum version of Pick's formula for the area of a polygon with integer vertices.Comment: 19 pages, 11 figures, revised with more explanations, improved figures and extra figures. To appear GER

Transverse Meissner Physics of Planar Superconductors with Columnar Pins

The statistical mechanics of thermally excited vortex lines with columnar defects can be mapped onto the physics of interacting quantum particles with quenched random disorder in one less dimension. The destruction of the Bose glass phase in Type II superconductors, when the external magnetic field is tilted sufficiently far from the column direction, is described by a poorly understood non-Hermitian quantum phase transition. We present here exact results for this transition in (1+1)-dimensions, obtained by mapping the problem in the hard core limit onto one-dimensional fermions described by a non-Hermitian tight binding model. Both site randomness and the relatively unexplored case of bond randomness are considered. Analysis near the mobility edge and near the band center in the latter case is facilitated by a real space renormalization group procedure used previously for Hermitian quantum problems with quenched randomness in one dimension.Comment: 23 pages, 22 figure