Translocation of structured polynucleotides through nanopores

We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic barriers for the translocation process. We show that this circumstance may be exploited to determine the full basepairing pattern of polynucleotides, including RNA pseudoknots. The crucial requirement is that the translocation dynamics (i.e., the length of the translocated molecular segment) needs to be recorded as a function of time with a spatial resolution of a few nucleotides. This could be achieved, for instance, by applying a mechanical driving force for translocation and recording force-extension curves (FEC's) with a device such as an atomic force microscope or optical tweezers. Our analysis suggests that with this added spatial resolution, nanopores could be transformed into a powerful experimental tool to study the folding of nucleic acids.Comment: 9 pages, 5 figure

Charmonium suppression from purely geometrical effects

The extend to which geometrical effects contribute to the production and suppression of the $J/\psi$ and $q\bar{q}$ minijet pairs in general is investigated for high energy heavy ion collisions at SPS, RHIC and LHC energies. For the energy range under investigation, the geometrical effects referred to are shadowing and anti-shadowing, respectively. Due to those effects, the parton distributions in nuclei deviate from the naive extrapolation from the free nucleon result; $f_{A}\neq A f_{N}$. The strength of the shadowing/anti-shadowing effect increases with the mass number. The consequences of gluonic shadowing effects for the $x_F$ distribution of $J/\psi$'s at $\sqrt s =20$ GeV, $\sqrt s =200$ GeV and $\sqrt s =6$ TeV are calculated for some relevant combinations of nuclei, as well as the $p_T$ distribution of minijets at midrapidity for $N_f=4$ in the final state.Comment: corrected some typos, improved shadowing ratio

Single Cell Kinetics of Phenotypic Switching in the Arabinose Utilization System of E. coli

Inducible switching between phenotypes is a common strategy of bacteria to adapt to fluctuating environments. Here, we analyze the switching kinetics of a paradigmatic inducible system, the arabinose utilization system in E. coli. Using time-lapse fluorescence microscopy of microcolonies in a microfluidic chamber, which permits sudden up-and down-shifts in the inducer arabinose, we characterize the single-cell gene expression dynamics of the araBAD operon responsible for arabinose degradation. While there is significant, inducer-dependent cell-to-cell variation in the timing of the on-switching, the off-switching triggered by sudden removal of arabinose is homogeneous and rapid. We find that rapid off-switching does not depend on internal arabinose degradation. Because the system is regulated via the internal arabinose level sensed by AraC, internal arabinose must be rapidly depleted by leakage or export from the cell, or by degradation via a non-canonical pathway. We explored whether the poorly characterized membrane protein AraJ, which is part of the arabinose regulon and has been annotated as a possible arabinose efflux protein, is responsible for rapid depletion. However, we find that AraJ is not essential for rapid switching to the off-state. We develop a mathematical model for the arabinose system, which quantitatively describes both the heterogeneous on-switching and the homogeneous off-switching. The model also predicts that mutations which disrupt the positive feedback of internal arabinose on the production of arabinose uptake proteins change the heterogeneous on-switching behavior into a homogeneous, graded response. We construct such a mutant and confirm the graded response experimentally. Taken together, our results indicate that the physiological switching behavior of this sugar utilization system is asymmetric, such that off-switching is always rapid and homogeneous, while on-switching is slow and heterogeneously timed at sub-saturating inducer levels

Fano effect of a strongly interacting quantum dot in contact with superconductor

The physics of a system consisting of an Aharonov Bohm (AB) interferometer containing a single level interacting quantum dot (QD) on one of its arms, and attached to normal (N) and superconducting (S) leads is studied and elucidated. Here the focus is directed mainly on N-AB-S junctions but the theory is capable of studying S-AB-S junctions as well. The interesting physics comes into play under the conditions that both the Kondo effect in the QD and the the Fano effect are equally important.It is found the conductance of the junction is suppressed as the Fano effect becomes more dominant.Comment: 4 pages, Talk to be given at the NATO Conference MQO, Bled, Slovenia 7-10 September 200

The Numerical Renormalization Group Method for correlated electrons

The Numerical Renormalization Group method (NRG) has been developed by Wilson in the 1970's to investigate the Kondo problem. The NRG allows the non-perturbative calculation of static and dynamic properties for a variety of impurity models. In addition, this method has been recently generalized to lattice models within the Dynamical Mean Field Theory. This paper gives a brief historical overview of the development of the NRG and discusses its application to the Hubbard model; in particular the results for the Mott metal-insulator transition at low temperatures.Comment: 14 pages, 7 eps-figures include

Spectral Statistics and Dynamical Localization: sharp transition in a generalized Sinai billiard

We consider a Sinai billiard where the usual hard disk scatterer is replaced by a repulsive potential with $V(r)\sim\lambda r^{-\alpha}$ close to the origin. Using periodic orbit theory and numerical evidence we show that its spectral statistics tends to Poisson statistics for large energies when $\alpha2$, while for $\alpha=2$ it is independent of energy, but depends on $\lambda$. We apply the approach of Altshuler and Levitov [Phys. Rep. {\bf 288}, 487 (1997)] to show that the transition in the spectral statistics is accompanied by a dynamical localization-delocalization transition. This behaviour is reminiscent of a metal-insulator transition in disordered electronic systems.Comment: 8 pages, 2 figures, accepted for publication in Phys. Rev. Let

Aharonov-Bohm interferometry with quantum dots: scattering approach versus tunneling picture

We address the question of how to model electron transport through closed Aharonov-Bohm interferometers which contain quantum dots. By explicitly studying interferometers with one and two quantum dots, we establish the connection between a tunneling-Hamiltonian formulation on the one hand and a scattering-matrix approach on the other hand. We prove that, under certain circumstances, both approaches are equivalent, i.e., both types of models can describe the same experimental setups. Furthermore, we analyze how the interplay of the Aharonov-Bohm phase and the orbital phase associated with the lengths of the interferometers' arms affect transport properties.Comment: 8 pages, 8 figures, published versio

Fano and Kondo resonance in electronic current through nanodevices

Electronic transport through a quantum dot strongly coupled to electrodes is studied within a model with two conduction channels. It is shown that multiple scattering and interference of transmitted waves through both channels lead to Fano resonance associated with Kondo resonance. Interference effects are also pronouncedly seen in transport through the Aharonov-Bohm ring with the Kondo dot, where the current characteristics continuously evolve with the magnetic flux.Comment: 4 pages, 3 figures,a typing error has been correcte

Mutation, selection, and ancestry in branching models: a variational approach

We consider the evolution of populations under the joint action of mutation and differential reproduction, or selection. The population is modelled as a finite-type Markov branching process in continuous time, and the associated genealogical tree is viewed both in the forward and the backward direction of time. The stationary type distribution of the reversed process, the so-called ancestral distribution, turns out as a key for the study of mutation-selection balance. This balance can be expressed in the form of a variational principle that quantifies the respective roles of reproduction and mutation for any possible type distribution. It shows that the mean growth rate of the population results from a competition for a maximal long-term growth rate, as given by the difference between the current mean reproduction rate, and an asymptotic decay rate related to the mutation process; this tradeoff is won by the ancestral distribution. Our main application is the quasispecies model of sequence evolution with mutation coupled to reproduction but independent across sites, and a fitness function that is invariant under permutation of sites. Here, the variational principle is worked out in detail and yields a simple, explicit result.Comment: 45 pages,8 figure

Correlation effects on electronic transport through dots and wires

We investigate how two-particle interactions affect the electronic transport through meso- and nanoscopic systems of two different types: quantum dots with local Coulomb correlations and quasi one-dimensional quantum wires of interacting electrons. A recently developed functional renormalization group scheme is used that allows to investigate systems of complex geometry. Considering simple setups we show that the method includes the essential aspects of Luttinger liquid physics (one-dimensional wires) as well as of the physics of local correlations, with the Kondo effect being an important example. For more complex systems of coupled dots and Y-junctions of interacting wires we find surprising new correlation effects.Comment: to appear in "Advances in Solid State Physics" Volume 46, Ed. R. Haug (Springer, 2006