Operating a quantum pump in a closed circuit

During an adiabatic pumping cycle a conventional two barrier quantum device takes an electron from the left lead and ejects it to the right lead. Hence the pumped charge per cycle is naively expected to be $Q \le e$. This zero order adiabatic point of view is in fact misleading. For a closed device we can get ${Q > e}$ and even ${Q \gg e}$. In this paper a detailed analysis of the quantum pump operation is presented. Using the Kubo formula for the geometric conductance, and applying the Dirac chains picture, we derive practical estimates for~$Q$.Comment: 19 pages, 8 figs, minor textual corretions, to be published in JP

Quantum dynamics and transport in a double well system

The simplest one-dimensional model for the studying of non-trivial geometrical effects is a ring shaped device which is formed by joining two arms. We explore the possibility to model such a system as a two level system (TLS). Of particular interest is the analysis of quantum stirring, where it is not evident that the topology is properly reflected within the framework of the TLS modeling. On the technical side we provide a practical "neighboring level" approximation for the analysis of such quantum devices, which remains valid even if the TLS modeling does not apply.Comment: 10 pages, 4 figures, version to be published in PR

Disentangling Scaling Properties in Anisotropic Fracture

Structure functions of rough fracture surfaces in isotropic materials exhibit complicated scaling properties due to the broken isotropy in the fracture plane generated by a preferred propagation direction. Decomposing the structure functions into the even order irreducible representations of the SO(2) symmetry group (indexed by $m=0,2,4...$) results in a lucid and quickly convergent description. The scaling exponent of the isotropic sector ($m=0$) dominates at small length scales. One can reconstruct the anisotropic structure functions using only the isotropic and the first non vanishing anisotropic sector ($m=2$) (or at most the next one ($m=4$)). The scaling exponent of the isotropic sector should be observed in a proposed, yet unperformed, experiment.Comment: 5 pages, 8 figure

Quantum Stirring in low dimensional devices

A circulating current can be induced in the Fermi sea by displacing a scatterer, or more generally by integrating a quantum pump into a closed circuit. The induced current may have either the same or the opposite sense with respect to the "pushing" direction of the pump. We work out explicit expressions for the associated geometric conductance using the Kubo-Dirac monopoles picture, and illuminate the connection with the theory of adiabatic passage in multiple path geometry.Comment: 6 pages, 5 figures, improved versio

Nonspecific Transcription-Factor-DNA Binding Influences Nucleosome Occupancy in Yeast

AbstractQuantitative understanding of the principles regulating nucleosome occupancy on a genome-wide level is a central issue in eukaryotic genomics. Here, we address this question using budding yeast, Saccharomyces cerevisiae, as a model organism. We perform a genome-wide computational analysis of the nonspecific transcription factor (TF)-DNA binding free-energy landscape and compare this landscape with experimentally determined nucleosome-binding preferences. We show that DNA regions with enhanced nonspecific TF-DNA binding are statistically significantly depleted of nucleosomes. We suggest therefore that the competition between TFs with histones for nonspecific binding to genomic sequences might be an important mechanism influencing nucleosome-binding preferences in vivo. We also predict that poly(dA:dT) and poly(dC:dG) tracts represent genomic elements with the strongest propensity for nonspecific TF-DNA binding, thus allowing TFs to outcompete nucleosomes at these elements. Our results suggest that nonspecific TF-DNA binding might provide a barrier for statistical positioning of nucleosomes throughout the yeast genome. We predict that the strength of this barrier increases with the concentration of DNA binding proteins in a cell. We discuss the connection of the proposed mechanism with the recently discovered pathway of active nucleosome reconstitution

Anomalous decay of a prepared state due to non-Ohmic coupling to the continuum

We study the decay of a prepared state $E_0$ into a continuum {E_k} in the case of non-Ohmic models. This means that the coupling is $|V_{k,0}| \propto |E_k-E_0|^{s-1}$ with $s \ne 1$. We find that irrespective of model details there is a universal generalized Wigner time $t_0$ that characterizes the evolution of the survival probability $P_0(t)$. The generic decay behavior which is implied by rate equation phenomenology is a slowing down stretched exponential, reflecting the gradual resolution of the bandprofile. But depending on non-universal features of the model a power-law decay might take over: it is only for an Ohmic coupling to the continuum that we get a robust exponential decay that is insensitive to the nature of the intra-continuum couplings. The analysis highlights the co-existence of perturbative and non-perturbative features in the dynamics. It turns out that there are special circumstances in which $t_0$ is reflected in the spreading process and not only in the survival probability, contrary to the naive linear response theory expectation.Comment: 13 pages, 11 figure

Quantum anomalies and linear response theory

The analysis of diffusive energy spreading in quantized chaotic driven systems, leads to a universal paradigm for the emergence of a quantum anomaly. In the classical approximation a driven chaotic system exhibits stochastic-like diffusion in energy space with a coefficient $D$ that is proportional to the intensity $\epsilon^2$ of the driving. In the corresponding quantized problem the coherent transitions are characterized by a generalized Wigner time $t_{\epsilon}$, and a self-generated (intrinsic) dephasing process leads to non-linear dependence of $D$ on $\epsilon^2$.Comment: 8 pages, 2 figures, textual improvements (as in published version

Quantum decay into a non-flat continuum

We study the decay of a prepared state into non-flat continuum. We find that the survival probability $P(t)$ might exhibit either stretched-exponential or power-law decay, depending on non-universal features of the model. Still there is a universal characteristic time $t_0$ that does not depend on the functional form. It is only for a flat continuum that we get a robust exponential decay that is insensitive to the nature of the intra-continuum couplings. The analysis highlights the co-existence of perturbative and non-perturbative features in the local density of states, and the non-linear dependence of $1/t_0$ on the strength of the coupling.Comment: 10 pages, 4 figure

DNA sequence correlations shape nonspecific transcription factor-DNA binding affinity

Transcription factors (TFs) are regulatory proteins that bind DNA in promoter regions of the genome and either promote or repress gene expression. Here we predict analytically that enhanced homo-oligonucleotide sequence correlations, such as poly(dA:dT) and poly(dC:dG) tracts, statistically enhance non-specific TF-DNA binding affinity. This prediction is generic and qualitatively independent of microscopic parameters of the model. We show that non-specific TF binding affinity is universally controlled by the strength and symmetry of DNA sequence correlations. We perform correlation analysis of the yeast genome and show that DNA regions highly occupied by TFs exhibit stronger homo-oligonucleotide sequence correlations, and thus higher propensity for non-specific binding, as compared with poorly occupied regions. We suggest that this effect plays the role of an effective localization potential enhancing the quasi-one-dimensional diffusion of TFs in the vicinity of DNA, speeding up the stochastic search process for specific TF binding sites. The predicted effect also imposes an upper bound on the size of TF-DNA binding motifs

Statistical Physics of Fracture Surfaces Morphology

Experiments on fracture surface morphologies offer increasing amounts of data that can be analyzed using methods of statistical physics. One finds scaling exponents associated with correlation and structure functions, indicating a rich phenomenology of anomalous scaling. We argue that traditional models of fracture fail to reproduce this rich phenomenology and new ideas and concepts are called for. We present some recent models that introduce the effects of deviations from homogeneous linear elasticity theory on the morphology of fracture surfaces, succeeding to reproduce the multiscaling phenomenology at least in 1+1 dimensions. For surfaces in 2+1 dimensions we introduce novel methods of analysis based on projecting the data on the irreducible representations of the SO(2) symmetry group. It appears that this approach organizes effectively the rich scaling properties. We end up with the proposition of new experiments in which the rotational symmetry is not broken, such that the scaling properties should be particularly simple.Comment: A review paper submitted to J. Stat. Phy