Numerical Diagonalisation Study of the Trimer Deposition-Evaporation Model in One Dimension

We study the model of deposition-evaporation of trimers on a line recently introduced by Barma, Grynberg and Stinchcombe. The stochastic matrix of the model can be written in the form of the Hamiltonian of a quantum spin-1/2 chain with three-spin couplings given by H= \sum\displaylimits_i [(1 - \sigma_i^-\sigma_{i+1}^-\sigma_{i+2}^-) \sigma_i^+\sigma_{i+1}^+\sigma_{i+2}^+ + h.c]. We study by exact numerical diagonalization of $H$ the variation of the gap in the eigenvalue spectrum with the system size for rings of size up to 30. For the sector corresponding to the initial condition in which all sites are empty, we find that the gap vanishes as $L^{-z}$ where the gap exponent $z$ is approximately $2.55\pm 0.15$. This model is equivalent to an interfacial roughening model where the dynamical variables at each site are matrices. From our estimate for the gap exponent we conclude that the model belongs to a new universality class, distinct from that studied by Kardar, Parisi and Zhang.Comment: 11 pages, 2 figures (included

Nonequilibrium Phase Transitions in a Driven Sandpile Model

We construct a driven sandpile slope model and study it by numerical simulations in one dimension. The model is specified by a threshold slope \sigma_c\/, a parameter \alpha\/, governing the local current-slope relation (beyond threshold), and $j_{\rm in}$, the mean input current of sand. A nonequilibrium phase diagram is obtained in the \alpha\, -\, j_{\rm in}\/ plane. We find an infinity of phases, characterized by different mean slopes and separated by continuous or first-order boundaries, some of which we obtain analytically. Extensions to two dimensions are discussed.Comment: 11 pages, RevTeX (preprint format), 4 figures available upon requs

The Irreducible String and an Infinity of Additional Constants of Motion in a Deposition-Evaporation Model on a Line

We study a model of stochastic deposition-evaporation with recombination, of three species of dimers on a line. This model is a generalization of the model recently introduced by Barma {\it et. al.} (1993 {\it Phys. Rev. Lett.} {\bf 70} 1033) to $q\ge 3$ states per site. It has an infinite number of constants of motion, in addition to the infinity of conservation laws of the original model which are encoded as the conservation of the irreducible string. We determine the number of dynamically disconnected sectors and their sizes in this model exactly. Using the additional symmetry we construct a class of exact eigenvectors of the stochastic matrix. The autocorrelation function decays with different powers of $t$ in different sectors. We find that the spatial correlation function has an algebraic decay with exponent 3/2, in the sector corresponding to the initial state in which all sites are in the same state. The dynamical exponent is nontrivial in this sector, and we estimate it numerically by exact diagonalization of the stochastic matrix for small sizes. We find that in this case $z=2.39\pm0.05$.Comment: Some minor errors in the first version has been correcte

Heat conduction in disordered harmonic lattices with energy conserving noise

We study heat conduction in a harmonic crystal whose bulk dynamics is supplemented by random reversals (flips) of the velocity of each particle at a rate $\lambda$. The system is maintained in a nonequilibrium stationary state(NESS) by contacts with Langevin reservoirs at different temperatures. We show that the one-body and pair correlations in this system are the same (after an appropriate mapping of parameters) as those obtained for a model with self-consistent reservoirs. This is true both for the case of equal and random(quenched) masses. While the heat conductivity in the NESS of the ordered system is known explicitly, much less is known about the random mass case. Here we investigate the random system, with velocity flips. We improve the bounds on the Green-Kubo conductivity obtained by C.Bernardin. The conductivity of the 1D system is then studied both numerically and analytically. This sheds some light on the effect of noise on the transport properties of systems with localized states caused by quenched disorder.Comment: 19 pages, 8 figure

Multiple interfaces between a serine recombinase and an enhancer control site-specific DNA inversion.

Serine recombinases are often tightly controlled by elaborate, topologically-defined, nucleoprotein complexes. Hin is a member of the DNA invertase subclass of serine recombinases that are regulated by a remote recombinational enhancer element containing two binding sites for the protein Fis. Two Hin dimers bound to specific recombination sites associate with the Fis-bound enhancer by DNA looping where they are remodeled into a synaptic tetramer competent for DNA chemistry and exchange. Here we show that the flexible beta-hairpin arms of the Fis dimers contact the DNA binding domain of one subunit of each Hin dimer. These contacts sandwich the Hin dimers to promote remodeling into the tetramer. A basic region on the Hin catalytic domain then contacts enhancer DNA to complete assembly of the active Hin tetramer. Our results reveal how the enhancer generates the recombination complex that specifies DNA inversion and regulates DNA exchange by the subunit rotation mechanism. DOI:http://dx.doi.org/10.7554/eLife.01211.001

Dynamic Response of Ising System to a Pulsed Field

The dynamical response to a pulsed magnetic field has been studied here both using Monte Carlo simulation and by solving numerically the meanfield dynamical equation of motion for the Ising model. The ratio R_p of the response magnetisation half-width to the width of the external field pulse has been observed to diverge and pulse susceptibility \chi_p (ratio of the response magnetisation peak height and the pulse height) gives a peak near the order-disorder transition temperature T_c (for the unperturbed system). The Monte Carlo results for Ising system on square lattice show that R_p diverges at T_c, with the exponent $\nu z \cong 2.0$, while \chi_p shows a peak at $T_c^e$, which is a function of the field pulse width $\delta t$. A finite size (in time) scaling analysis shows that $T_c^e = T_c + C (\delta t)^{-1/x}$, with $x = \nu z \cong 2.0$. The meanfield results show that both the divergence of R and the peak in \chi_p occur at the meanfield transition temperature, while the peak height in $\chi_p \sim (\delta t)^y$, $y \cong 1$ for small values of $\delta t$. These results also compare well with an approximate analytical solution of the meanfield equation of motion.Comment: Revtex, Eight encapsulated postscript figures, submitted to Phys. Rev.

Non-perturbative corrections to mean-field behavior: spherical model on spider-web graph

We consider the spherical model on a spider-web graph. This graph is effectively infinite-dimensional, similar to the Bethe lattice, but has loops. We show that these lead to non-trivial corrections to the simple mean-field behavior. We first determine all normal modes of the coupled springs problem on this graph, using its large symmetry group. In the thermodynamic limit, the spectrum is a set of $\delta$-functions, and all the modes are localized. The fractional number of modes with frequency less than $\omega$ varies as $\exp (-C/\omega)$ for $\omega$ tending to zero, where $C$ is a constant. For an unbiased random walk on the vertices of this graph, this implies that the probability of return to the origin at time $t$ varies as $\exp(- C' t^{1/3})$, for large $t$, where $C'$ is a constant. For the spherical model, we show that while the critical exponents take the values expected from the mean-field theory, the free-energy per site at temperature $T$, near and above the critical temperature $T_c$, also has an essential singularity of the type $\exp[ -K {(T - T_c)}^{-1/2}]$.Comment: substantially revised, a section adde