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

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

Exoskeleton master controller with force-reflecting telepresence

A thorough understanding of the requirements for successful master-slave robotic systems is becoming increasingly desirable. Such systems can aid in the accomplishment of tasks that are hazardous or inaccessible to humans. Although a history of use has proven master-slave systems to be viable, system requirements and the impact of specifications on the human factors side of system performance are not well known. In support of the next phase of teleoperation research being conducted at the Armstrong Research Laboratory, a force-reflecting, seven degree of freedom exoskeleton for master-slave teleoperation has been concepted, and is presently being developed. The exoskeleton has a unique kinematic structure that complements the structure of the human arm. It provides a natural means for teleoperating a dexterous, possibly redundant manipulator. It allows ease of use without operator fatigue and faithfully follows human arm and wrist motions. Reflected forces and moments are remotely transmitted to the operator hand grip using a cable transmission scheme. This paper presents the exoskeleton concept and development results to date. Conceptual design, hardware, algorithms, computer architecture, and software are covered

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

Competition and cooperation in one-dimensional stepping stone models

Cooperative mutualism is a major force driving evolution and sustaining ecosystems. Although the importance of spatial degrees of freedom and number fluctuations is well-known, their effects on mutualism are not fully understood. With range expansions of microbes in mind, we show that, even when mutualism confers a distinct selective advantage, it persists only in populations with high density and frequent migrations. When these parameters are reduced, mutualism is generically lost via a directed percolation process, with a phase diagram strongly influenced by an exceptional DP2 transition.Comment: 8 pages, 4 figure

Thermodynamics and the Global Optimization of Lennard-Jones clusters

Theoretical design of global optimization algorithms can profitably utilize recent statistical mechanical treatments of potential energy surfaces (PES's). Here we analyze the basin-hopping algorithm to explain its success in locating the global minima of Lennard-Jones (LJ) clusters, even those such as \LJ{38} for which the PES has a multiple-funnel topography, where trapping in local minima with different morphologies is expected. We find that a key factor in overcoming trapping is the transformation applied to the PES which broadens the thermodynamic transitions. The global minimum then has a significant probability of occupation at temperatures where the free energy barriers between funnels are surmountable.Comment: 13 pages, 13 figures, revte

The double-funnel energy landscape of the 38-atom Lennard-Jones cluster

The 38-atom Lennard-Jones cluster has a paradigmatic double-funnel energy landscape. One funnel ends in the global minimum, a face-centred-cubic (fcc) truncated octahedron. At the bottom of the other funnel is the second lowest energy minimum which is an incomplete Mackay icosahedron. We characterize the energy landscape in two ways. Firstly, from a large sample of minima and transition states we construct a disconnectivity tree showing which minima are connected below certain energy thresholds. Secondly we compute the free energy as a function of a bond-order parameter. The free energy profile has two minima, one which corresponds to the fcc funnel and the other which at low temperature corresponds to the icosahedral funnel and at higher temperatures to the liquid-like state. These two approaches show that the greater width of the icosahedral funnel, and the greater structural similarity between the icosahedral structures and those associated with the liquid-like state, are the cause of the smaller free energy barrier for entering the icosahedral funnel from the liquid-like state and therefore of the cluster's preferential entry into this funnel on relaxation down the energy landscape. Furthermore, the large free energy barrier between the fcc and icosahedral funnels, which is energetic in origin, causes the cluster to be trapped in one of the funnels at low temperature. These results explain in detail the link between the double-funnel energy landscape and the difficulty of global optimization for this cluster.Comment: 12 pages, 11 figures, revte

Inelastic and reactive scattering of hyperthermal atomic oxygen from amorphous carbon

The reaction of hyperthermal oxygen atoms with an amorphous carbon-13 surface was studied using a modified universal crossed molecular beams apparatus. Time-of-flight distributions of inelastically scattered O-atoms and reactively scattered CO-13 and CO2-13 were measured with a rotatable mass spectrometer detector. Two inelastic scattering channels were observed, corresponding to a direct inelastic process in which the scattered O-atoms retain 20 to 30 percent of their initial kinetic energy and to a trapping desorption process whereby O-atoms emerge from the surface at thermal velocities. Reactive scattering data imply the formation of two kinds of CO products, slow products whose translational energies are determined by the surface temperature and hyperthermal (Approx. 3 eV) products with translational energies comprising roughly 30 percent of the total available energy (E sub avl), where E sub avl is the sum of the collision energy and the reaction exothermicity. Angular data show that the hyperthermal CO is scattered preferentially in the specular direction. CO2 product was also observed, but at much lower intensities than CO and with only thermal velocities