Numerical Method for Accessing the Universal Scaling Function for a Multi-Particle Discrete Time Asymmetric Exclusion Process

In the universality class of the one dimensional Kardar-Parisi-Zhang surface growth, Derrida and Lebowitz conjectured the universality of not only the scaling exponents, but of an entire scaling function. Since Derrida and Lebowitz's original publication [PRL 80 209 (1998)] this universality has been verified for a variety of continuous time, periodic boundary systems in the KPZ universality class. Here, we present a numerical method for directly examining the entire particle flux of the asymmetric exclusion process (ASEP), thus providing an alternative to more difficult cumulant ratios studies. Using this method, we find that the Derrida-Lebowitz scaling function (DLSF) properly characterizes the large system size limit (N-->infty) of a single particle discrete time system, even in the case of very small system sizes (N <= 22). This fact allows us to not only verify that the DLSF properly characterizes multiple particle discrete-time asymmetric exclusion processes, but also provides a way to numerically solve for quantities of interest, such as the particle hopping flux. This method can thus serve to further increase the ease and accessibility of studies involving even more challenging dynamics, such as the open boundary ASEP

Analytical description of finite size effects for RNA secondary structures

The ensemble of RNA secondary structures of uniform sequences is studied analytically. We calculate the partition function for very long sequences and discuss how the cross-over length, beyond which asymptotic scaling laws apply, depends on thermodynamic parameters. For realistic choices of parameters this length can be much longer than natural RNA molecules. This has to be taken into account when applying asymptotic theory to interpret experiments or numerical results.Comment: 10 pages, 13 figures, published in Phys. Rev.

Arsenic in the Iberoamerican region. The IBEROARSEN Network and a possible economic solution for arsenic removal in isolated rural zones

In this work, a short description of the problematic of arsenic in Iberoamerica will be given, indicating the affected geographical regions and their incidence on the quality of life of the populations. In Argentina, Chile, Bolivia, Peru, Ecuador and Mexico, at least 4 million people depend on water sources with toxic concentrations of arsenic. While in these countries the problem is known since decades, in Uruguay, Brazil, Nicaragua, Honduras and El Salvador, the problem has been detected or investigated only in last years, and, in other Latinamerican countries, the studies began only recently. In Spain and Portugal the problem of As is becoming increasingly important. The presence of As in drinking waters, together with poverty and malnutrition, causes the incidence of CERHA (chronic endemic regional hydroarsenicism, HACRE in Spanish), an illness that provokes serious problems like skin lesions and even cancer. The activities of the IBEROARSEN Network of the CYTED Program, an Iberoamerican project that aims at the interconnection of groups devoted to arsenic R&D, trying to find solutions to this problem in the region, will be described. In addition, results of evaluation of the efficiency of two very simple low-cost methods for As removal in plastic bottles using solar light, one of them using heterogeneous photocatalysis with TiO2 immobilized on the walls followed by iron addition, and another one based on the use of zerovalent iron, which employs very cheap materials, are presented. The study was performed with synthetic and natural waters of rural, isolated, poor populations, not connected to the drinking water network of the provinces of Tucumán and Santiago del Estero, Argentina. For HP tests, synthetic as well as natural samples containing arsenic placed in bottles internally covered by a TiO2 layer and exposed to solar or artificial UV light followed by an addition of an iron source resulted in As concentration well below the national standards. For ZVI tests, iron wool demonstrated to be a better iron source than packing wire for As removal. Solar irradiation, in synthetic as well as in natural samples, seems to definitively improve As removal, avoiding the use of high amounts of iron. Although both HP and ZVI gave similar results, the use of the first one could be superior due to the ability of removing simultaneously As, organic matter, toxic metals and microbiological contamination

Statistical mechanics of RNA folding: a lattice approach

We propose a lattice model for RNA based on a self-interacting two-tolerant trail. Self-avoidance and elements of tertiary structure are taken into account. We investigate a simple version of the model in which the native state of RNA consists of just one hairpin. Using exact arguments and Monte Carlo simulations we determine the phase diagram for this case. We show that the denaturation transition is first order and can either occur directly or through an intermediate molten phase.Comment: 8 pages, 9 figure

Statistical mechanics of RNA folding: importance of alphabet size

We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two kinds of bases, there are many alternate folding configurations, yielding thermodynamically stable ground-states only for a small set of structures of high designability, i.e., total number of associated sequences. In contrast, sequences made from four bases, as found in nature, or six bases have far fewer competing folding configurations, resulting in a much greater average stability of the ground state.Comment: 7 figures; uses revtex

Localization-delocalization transition of disordered d-wave superconductors in class CI

A lattice model for disordered d-wave superconductors in class CI is reconsidered. Near the band-center, the lattice model can be described by Dirac fermions with several species, each of which yields WZW term for an effective action of the Goldstone mode. The WZW terms cancel out each other because of the four-fold symmetry of the model, which suggests that the quasiparticle states are localized. If the lattice model has, however, symmetry breaking terms which generate mass for any species of the Dirac fermions, remaining WZW term which avoids the cancellation can derive the system to a delocalized strong-coupling fixed point.Comment: 4 pages, revte

RNA denaturation: excluded volume, pseudoknots and transition scenarios

A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous transition. Otherwise a smooth crossover occurs from the swollen linear polymer behavior to highly ramified, almost compact conformations with secondary structures. In the latter scenario, which is appropriate when these structures are much more stable than pseudoknot links, probability distributions for the lengths of both loops and main branches obey scaling with nonclassical exponents.Comment: 4 pages 3 figure

Superconductors with Magnetic Impurities: Instantons and Sub-gap States

When subject to a weak magnetic impurity potential, the order parameter and quasi-particle energy gap of a bulk singlet superconductor are suppressed. According to the conventional mean-field theory of Abrikosov and Gor'kov, the integrity of the energy gap is maintained up to a critical concentration of magnetic impurities. In this paper, a field theoretic approach is developed to critically analyze the validity of the mean field theory. Using the supersymmetry technique we find a spatially homogeneous saddle-point that reproduces the Abrikosov-Gor'kov theory, and identify instanton contributions to the density of states that render the quasi-particle energy gap soft at any non-zero magnetic impurity concentration. The sub-gap states are associated with supersymmetry broken field configurations of the action. An analysis of fluctuations around these configurations shows how the underlying supersymmetry of the action is restored by zero modes. An estimate of the density of states is given for all dimensionalities. To illustrate the universality of the present scheme we apply the same method to study `gap fluctuations' in a normal quantum dot coupled to a superconducting terminal. Using the same instanton approach, we recover the universal result recently proposed by Vavilov et al. Finally, we emphasize the universality of the present scheme for the description of gap fluctuations in d-dimensional superconducting/normal structures.Comment: 18 pages, 9 eps figure

Statistical mechanics of secondary structures formed by random RNA sequences

The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical studies. First, a two-replica calculation is performed. By mapping the two-replica problem to the denaturation of a single homogeneous RNA in 6-dimensional embedding space, we show that sequence disorder is perturbatively irrelevant, i.e., an RNA molecule with weak sequence disorder is in a molten phase where many secondary structures with comparable total energy coexist. A numerical study of various models at high temperature reproduces behaviors characteristic of the molten phase. On the other hand, a scaling argument based on the extremal statistics of rare regions can be constructed to show that the low temperature phase is unstable to sequence disorder. We performed a detailed numerical study of the low temperature phase using the droplet theory as a guide, and characterized the statistics of large-scale, low-energy excitations of the secondary structures from the ground state structure. We find the excitation energy to grow very slowly (i.e., logarithmically) with the length scale of the excitation, suggesting the existence of a marginal glass phase. The transition between the low temperature glass phase and the high temperature molten phase is also characterized numerically. It is revealed by a change in the coefficient of the logarithmic excitation energy, from being disorder dominated to entropy dominated.Comment: 24 pages, 16 figure

Localization and delocalization in dirty superconducting wires

We present Fokker-Planck equations that describe transport of heat and spin in dirty unconventional superconducting quantum wires. Four symmetry classes are distinguished, depending on the presence or absence of time-reversal and spin rotation invariance. In the absence of spin-rotation symmetry, heat transport is anomalous in that the mean conductance decays like $1/\sqrt{L}$ instead of exponentially fast for large enough length $L$ of the wire. The Fokker-Planck equations in the presence of time-reversal symmetry are solved exactly and the mean conductance for quasiparticle transport is calculated for the crossover from the diffusive to the localized regime.Comment: 4 pages, RevTe