Exact Ground States of Large Two-Dimensional Planar Ising Spin Glasses

Studying spin-glass physics through analyzing their ground-state properties has a long history. Although there exist polynomial-time algorithms for the two-dimensional planar case, where the problem of finding ground states is transformed to a minimum-weight perfect matching problem, the reachable system sizes have been limited both by the needed CPU time and by memory requirements. In this work, we present an algorithm for the calculation of exact ground states for two-dimensional Ising spin glasses with free boundary conditions in at least one direction. The algorithmic foundations of the method date back to the work of Kasteleyn from the 1960s for computing the complete partition function of the Ising model. Using Kasteleyn cities, we calculate exact ground states for huge two-dimensional planar Ising spin-glass lattices (up to 3000x3000 spins) within reasonable time. According to our knowledge, these are the largest sizes currently available. Kasteleyn cities were recently also used by Thomas and Middleton in the context of extended ground states on the torus. Moreover, they show that the method can also be used for computing ground states of planar graphs. Furthermore, we point out that the correctness of heuristically computed ground states can easily be verified. Finally, we evaluate the solution quality of heuristic variants of the Bieche et al. approach.Comment: 11 pages, 5 figures; shortened introduction, extended results; to appear in Physical Review E 7

The Tangled Nature model as an evolving quasi-species model

We show that the Tangled Nature model can be interpreted as a general formulation of the quasi-species model by Eigen et al. in a frequency dependent fitness landscape. We present a detailed theoretical derivation of the mutation threshold, consistent with the simulation results, that provides a valuable insight into how the microscopic dynamics of the model determine the observed macroscopic phenomena published previously. The dynamics of the Tangled Nature model is defined on the microevolutionary time scale via reproduction, with heredity, variation, and natural selection. Each organism reproduces with a rate that is linked to the individuals' genetic sequence and depends on the composition of the population in genotype space. Thus the microevolutionary dynamics of the fitness landscape is regulated by, and regulates, the evolution of the species by means of the mutual interactions. At low mutation rate, the macro evolutionary pattern mimics the fossil data: periods of stasis, where the population is concentrated in a network of coexisting species, is interrupted by bursts of activity. As the mutation rate increases, the duration and the frequency of bursts increases. Eventually, when the mutation rate reaches a certain threshold, the population is spread evenly throughout the genotype space showing that natural selection only leads to multiple distinct species if adaptation is allowed time to cause fixation.Comment: Paper submitted to Journal of Physics A. 13 pages, 4 figure

Depinning transition of a directed polymer by a periodic potential: a d-dimensional solution

We study the depinning phase transition of a directed polymer in a $d$-dimensional space by a periodic potential localized on a straight line. We give exact formulas in all dimensions for the critical pinning we need to localize the polymer. We show that a bounded state can still arise even if, in average, the potential layer is not attractive and for diverging values of the potential on the repulsive sites. The phase transition is of second order.Comment: 11 Pages in LaTeX. Figures available from the authors. [email protected] (e-mail address

Error threshold in the evolution of diploid organisms

The effects of error propagation in the reproduction of diploid organisms are studied within the populational genetics framework of the quasispecies model. The dependence of the error threshold on the dominance parameter is fully investigated. In particular, it is shown that dominance can protect the wild-type alleles from the error catastrophe. The analysis is restricted to a diploid analogue of the single-peaked landscape.Comment: 9 pages, 4 Postscript figures. Submitted to J. Phy. A: Mat. and Ge

Box representations of embedded graphs

A $d$-box is the cartesian product of $d$ intervals of $\mathbb{R}$ and a $d$-box representation of a graph $G$ is a representation of $G$ as the intersection graph of a set of $d$-boxes in $\mathbb{R}^d$. It was proved by Thomassen in 1986 that every planar graph has a 3-box representation. In this paper we prove that every graph embedded in a fixed orientable surface, without short non-contractible cycles, has a 5-box representation. This directly implies that there is a function $f$, such that in every graph of genus $g$, a set of at most $f(g)$ vertices can be removed so that the resulting graph has a 5-box representation. We show that such a function $f$ can be made linear in $g$. Finally, we prove that for any proper minor-closed class $\mathcal{F}$, there is a constant $c(\mathcal{F})$ such that every graph of $\mathcal{F}$ without cycles of length less than $c(\mathcal{F})$ has a 3-box representation, which is best possible.Comment: 16 pages, 6 figures - revised versio

Subextensive singularity in the 2D ±J\pm J Ising spin glass

The statistics of low energy states of the 2D Ising spin glass with +1 and -1 bonds are studied for $L \times L$ square lattices with $L \le 48$, and $p$ = 0.5, where $p$ is the fraction of negative bonds, using periodic and/or antiperiodic boundary conditions. The behavior of the density of states near the ground state energy is analyzed as a function of $L$, in order to obtain the low temperature behavior of the model. For large finite $L$ there is a range of $T$ in which the heat capacity is proportional to $T^{5.33 \pm 0.12}$. The range of $T$ in which this behavior occurs scales slowly to $T = 0$ as $L$ increases. Similar results are found for $p$ = 0.25. Our results indicate that this model probably obeys the ordinary hyperscaling relation $d \nu = 2 - \alpha$, even though $T_c = 0$. The existence of the subextensive behavior is attributed to long-range correlations between zero-energy domain walls, and evidence of such correlations is presented.Comment: 13 pages, 7 figures; final version, to appear in J. Stat. Phy

Fermions and Loops on Graphs. II. Monomer-Dimer Model as Series of Determinants

We continue the discussion of the fermion models on graphs that started in the first paper of the series. Here we introduce a Graphical Gauge Model (GGM) and show that : (a) it can be stated as an average/sum of a determinant defined on the graph over $\mathbb{Z}_{2}$ (binary) gauge field; (b) it is equivalent to the Monomer-Dimer (MD) model on the graph; (c) the partition function of the model allows an explicit expression in terms of a series over disjoint directed cycles, where each term is a product of local contributions along the cycle and the determinant of a matrix defined on the remainder of the graph (excluding the cycle). We also establish a relation between the MD model on the graph and the determinant series, discussed in the first paper, however, considered using simple non-Belief-Propagation choice of the gauge. We conclude with a discussion of possible analytic and algorithmic consequences of these results, as well as related questions and challenges.Comment: 11 pages, 2 figures; misprints correcte

Novel insights into the transport mechanism of the human amino acid transporter LAT1 (SLC7A5) : probing critical residues for substrate translocation

BACKGROUND: LAT1 (SLC7A5) is the transport competent unit of the heterodimer formed with the glycoprotein CD98 (SLC3A2). It catalyzes antiport of His and some neutral amino acids such as Ile, Leu, Val, Cys, Met, Gln and Phe thus being involved in amino acid metabolism. Interestingly, LAT1 is over-expressed in many human cancers that are characterized by increased demand of amino acids. Therefore LAT1 was recently acknowledged as a novel target for cancer therapy. However, knowledge on molecular mechanism of LAT1 transport is still scarce. METHODS: Combined approaches of bioinformatics, site-directed mutagenesis, chemical modification, and transport assay in proteoliposomes, have been adopted to unravel dark sides of human LAT1 structure/function relationships. RESULTS: It has been demonstrated that residues F252, S342, C335 are crucial for substrate recognition and C407 plays a minor role. C335 and C407 cannot be targeted by SH reagents. The transporter has a preferential dimeric structure and catalyzes an antiport reaction which follows a simultaneous random mechanism. CONCLUSIONS: Critical residues of the substrate binding site of LAT1 have been probed. This site is not freely accessible by molecules other than substrate. Similarly to LeuT, K+ has some regulatory properties on LAT1. GENERAL SIGNIFICANCE: The collected data represent a solid basis for deciphering molecular mechanism underlying LAT1 function

On the potentials of object group localization in the internet of things

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