Coexistence of excited states in confined Ising systems

Using the density-matrix renormalization-group method we study the two-dimensional Ising model in strip geometry. This renormalization scheme enables us to consider the system up to the size 300 x infinity and study the influence of the bulk magnetic field on the system at full range of temperature. We have found out the crossover in the behavior of the correlation length on the line of coexistence of the excited states. A detailed study of scaling of this line is performed. Our numerical results support and specify previous conclusions by Abraham, Parry, and Upton based on the related bubble model.Comment: 4 Pages RevTeX and 4 PostScript figures included; the paper has been rewritten without including new result

Fixed Point of the Finite System DMRG

The density matrix renormalization group (DMRG) is a numerical method that optimizes a variational state expressed by a tensor product. We show that the ground state is not fully optimized as far as we use the standard finite system algorithm, that uses the block structure B**B. This is because the tensors are not improved directly. We overcome this problem by using the simpler block structure B*B for the final several sweeps in the finite iteration process. It is possible to increase the numerical precision of the finite system algorithm without increasing the computational effort.Comment: 6 pages, 4 figure

Effective affinities in microarray data

In the past couple of years several studies have shown that hybridization in Affymetrix DNA microarrays can be rather well understood on the basis of simple models of physical chemistry. In the majority of the cases a Langmuir isotherm was used to fit experimental data. Although there is a general consensus about this approach, some discrepancies between different studies are evident. For instance, some authors have fitted the hybridization affinities from the microarray fluorescent intensities, while others used affinities obtained from melting experiments in solution. The former approach yields fitted affinities that at first sight are only partially consistent with solution values. In this paper we show that this discrepancy exists only superficially: a sufficiently complete model provides effective affinities which are fully consistent with those fitted to experimental data. This link provides new insight on the relevant processes underlying the functioning of DNA microarrays.Comment: 8 pages, 6 figure

Stability domains of actin genes and genomic evolution

In eukaryotic genes the protein coding sequence is split into several fragments, the exons, separated by non-coding DNA stretches, the introns. Prokaryotes do not have introns in their genome. We report the calculations of stability domains of actin genes for various organisms in the animal, plant and fungi kingdoms. Actin genes have been chosen because they have been highly conserved during evolution. In these genes all introns were removed so as to mimic ancient genes at the time of the early eukaryotic development, i.e. before introns insertion. Common stability boundaries are found in evolutionary distant organisms, which implies that these boundaries date from the early origin of eukaryotes. In general boundaries correspond with introns positions of vertebrates and other animals actins, but not much for plants and fungi. The sharpest boundary is found in a locus where fungi, algae and animals have introns in positions separated by one nucleotide only, which identifies a hot-spot for insertion. These results suggest that some introns may have been incorporated into the genomes through a thermodynamic driven mechanism, in agreement with previous observations on human genes. They also suggest a different mechanism for introns insertion in plants and animals.Comment: 9 Pages, 7 figures. Phys. Rev. E in pres

Numerical Latent Heat Observation of the q=5 Potts Model

Site energy of the five-state ferromagnetic Potts model is numerically calculated at the first-order transition temperature using corner transfer matrix renormalization group (CTMRG) method. The calculated energy of the disordered phase $U^{+}$ is clearly different from that of the ordered phase $U^{-}$. The obtained latent heat $L = U^{-} - U^{+}$ is 0.027, which quantitatively agrees with the exact solution.Comment: 2 pages, Latex(JPSJ style files are included), 2 ps figures, submitted to J. Phys. Soc. Jpn.(short note

The Density Matrix Renormalization Group technique with periodic boundary conditions

The Density Matrix Renormalization Group (DMRG) method with periodic boundary conditions is introduced for two dimensional classical spin models. It is shown that this method is more suitable for derivation of the properties of infinite 2D systems than the DMRG with open boundary conditions despite the latter describes much better strips of finite width. For calculation at criticality, phenomenological renormalization at finite strips is used together with a criterion for optimum strip width for a given order of approximation. For this width the critical temperature of 2D Ising model is estimated with seven-digit accuracy for not too large order of approximation. Similar precision is reached for critical indices. These results exceed the accuracy of similar calculations for DMRG with open boundary conditions by several orders of magnitude.Comment: REVTeX format contains 8 pages and 6 figures, submitted to Phys. Rev.

Construction of a matrix product stationary state from solutions of finite size system

Stationary states of stochastic models, which have $N$ states per site, in matrix product form are considered. First we give a necessary condition for the existence of a finite $M$-dimensional matrix product state for any ${N,M}$. Second, we give a method to construct the matrices from the stationary states of small size system when the above condition and $N\le M$ are satisfied. Third, the method by which one can check that the obtained matrices are valid for any system size is presented for the case where $M=N$ is satisfied. The application of our methods is explained using three examples: the asymmetric exclusion process, a model studied in [F. H. Jafarpour: J. Phys. A: Math. Gen. 36 (2003) 7497] and a hybrid of both of the models.Comment: 22 pages, no figure. Major changes: sec.3 was shortened; the list of references were changed. This is the final version, which will appear in J.Phys.

Critical Behavior of the Random Potts Chain

We study the critical behavior of the random q-state Potts quantum chain by density matrix renormalization techniques. Critical exponents are calculated by scaling analysis of finite lattice data of short chains ($L \leq 16$) averaging over all possible realizations of disorder configurations chosen according to a binary distribution. Our numerical results show that the critical properties of the model are independent of q in agreement with a renormalization group analysis of Senthil and Majumdar (Phys. Rev. Lett.{\bf 76}, 3001 (1996)). We show how an accurate analysis of moments of the distribution of magnetizations allows a precise determination of critical exponents, circumventing some problems related to binary disorder. Multiscaling properties of the model and dynamical correlation functions are also investigated.Comment: LaTeX2e file with Revtex, 9 pages, 8 eps figures, 4 tables; typos correcte

Nonequilibrium effects in DNA microarrays: a multiplatform study

It has recently been shown that in some DNA microarrays the time needed to reach thermal equilibrium may largely exceed the typical experimental time, which is about 15h in standard protocols (Hooyberghs et al. Phys. Rev. E 81, 012901 (2010)). In this paper we discuss how this breakdown of thermodynamic equilibrium could be detected in microarray experiments without resorting to real time hybridization data, which are difficult to implement in standard experimental conditions. The method is based on the analysis of the distribution of fluorescence intensities I from different spots for probes carrying base mismatches. In thermal equilibrium and at sufficiently low concentrations, log I is expected to be linearly related to the hybridization free energy $\Delta G$ with a slope equal to $1/RT_{exp}$, where $T_{exp}$ is the experimental temperature and R is the gas constant. The breakdown of equilibrium results in the deviation from this law. A model for hybridization kinetics explaining the observed experimental behavior is discussed, the so-called 3-state model. It predicts that deviations from equilibrium yield a proportionality of $\log I$ to $\Delta G/RT_{eff}$. Here, $T_{eff}$ is an effective temperature, higher than the experimental one. This behavior is indeed observed in some experiments on Agilent arrays. We analyze experimental data from two other microarray platforms and discuss, on the basis of the results, the attainment of equilibrium in these cases. Interestingly, the same 3-state model predicts a (dynamical) saturation of the signal at values below the expected one at equilibrium.Comment: 27 pages, 9 figures, 1 tabl

Density-Matrix Renormalization-Group Analysis of Quantum Critical Points: I. Quantum Spin Chains

We present a simple method, combining the density-matrix renormalization-group (DMRG) algorithm with finite-size scaling, which permits the study of critical behavior in quantum spin chains. Spin moments and dimerization are induced by boundary conditions at the chain ends and these exhibit power-law decay at critical points. Results are presented for the spin-1/2 Heisenberg antiferromagnet; an analytic calculation shows that logarithmic corrections to scaling can sometimes be avoided. We also examine the spin-1 chain at the critical point separating the Haldane gap and dimerized phases. Exponents for the dimer-dimer and the spin-spin correlation functions are consistent with results obtained from bosonization.Comment: 21 pages, 12 figures, new results and added references, to appear in PR