641 research outputs found
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
-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 -box is the cartesian product of intervals of and a
-box representation of a graph is a representation of as the
intersection graph of a set of -boxes in . 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 , such that in every graph of genus , a
set of at most vertices can be removed so that the resulting graph has a
5-box representation. We show that such a function can be made linear in
. Finally, we prove that for any proper minor-closed class ,
there is a constant such that every graph of
without cycles of length less than has a 3-box representation,
which is best possible.Comment: 16 pages, 6 figures - revised versio
Subextensive singularity in the 2D Ising spin glass
The statistics of low energy states of the 2D Ising spin glass with +1 and -1
bonds are studied for square lattices with , and =
0.5, where 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 , in order to obtain
the low temperature behavior of the model. For large finite there is a
range of in which the heat capacity is proportional to .
The range of in which this behavior occurs scales slowly to as
increases. Similar results are found for = 0.25. Our results indicate that
this model probably obeys the ordinary hyperscaling relation , even though . 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 (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
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