Inference of the genetic network regulating lateral root initiation in Arabidopsis thaliana

Regulation of gene expression is crucial for organism growth, and it is one of the challenges in Systems Biology to reconstruct the underlying regulatory biological networks from transcriptomic data. The formation of lateral roots in Arabidopsis thaliana is stimulated by a cascade of regulators of which only the interactions of its initial elements have been identified. Using simulated gene expression data with known network topology, we compare the performance of inference algorithms, based on different approaches, for which ready-to-use software is available. We show that their performance improves with the network size and the inclusion of mutants. We then analyse two sets of genes, whose activity is likely to be relevant to lateral root initiation in Arabidopsis, by integrating sequence analysis with the intersection of the results of the best performing methods on time series and mutants to infer their regulatory network. The methods applied capture known interactions between genes that are candidate regulators at early stages of development. The network inferred from genes significantly expressed during lateral root formation exhibits distinct scale-free, small world and hierarchical properties and the nodes with a high out-degree may warrant further investigation

Loop Groups and Discrete KdV Equations

A study is presented of fully discretized lattice equations associated with the KdV hierarchy. Loop group methods give a systematic way of constructing discretizations of the equations in the hierarchy. The lattice KdV system of Nijhoff et al. arises from the lowest order discretization of the trivial, lowest order equation in the hierarchy, b_t=b_x. Two new discretizations are also given, the lowest order discretization of the first nontrivial equation in the hierarchy, and a "second order" discretization of b_t=b_x. The former, which is given the name "full lattice KdV" has the (potential) KdV equation as a standard continuum limit. For each discretization a Backlund transformation is given and soliton content analyzed. The full lattice KdV system has, like KdV itself, solitons of all speeds, whereas both other discretizations studied have a limited range of speeds, being discretizations of an equation with solutions only of a fixed speed.Comment: LaTeX, 23 pages, 1 figur

QCD as a Quantum Link Model

QCD is constructed as a lattice gauge theory in which the elements of the link matrices are represented by non-commuting operators acting in a Hilbert space. The resulting quantum link model for QCD is formulated with a fifth Euclidean dimension, whose extent resembles the inverse gauge coupling of the resulting four-dimensional theory after dimensional reduction. The inclusion of quarks is natural in Shamir's variant of Kaplan's fermion method, which does not require fine-tuning to approach the chiral limit. A rishon representation in terms of fermionic constituents of the gluons is derived and the quantum link Hamiltonian for QCD with a U(N) gauge symmetry is expressed in terms of glueball, meson and constituent quark operators. The new formulation of QCD is promising both from an analytic and from a computational point of view.Comment: 27 pages, including three figures. ordinary LaTeX; Submitted to Nucl. Phys.

Universality in Turbulence: an Exactly Soluble Model

The present note contains the text of lectures discussing the problem of universality in fully developed turbulence. After a brief description of Kolmogorov's 1941 scaling theory of turbulence and a comparison between the statistical approach to turbulence and field theory, we discuss a simple model of turbulent advection which is exactly soluble but whose exact solution is still difficult to analyze. The model exhibits a restricted universality. Its correlation functions contain terms with universal but anomalous scaling but with non-universal amplitudes typically diverging with the growing size of the system. Strict universality applies only after such terms have been removed leaving renormalized correlators with normal scaling. We expect that the necessity of such an infrared renormalization is a characteristic feature of universality in turbulence.Comment: 31 pages, late

Effects of structure formation on the expansion rate of the Universe: An estimate from numerical simulations

General relativistic corrections to the expansion rate of the Universe arise when the Einstein equations are averaged over a spatial volume in a locally inhomogeneous cosmology. It has been suggested that they may contribute to the observed cosmic acceleration. In this paper, we propose a new scheme that utilizes numerical simulations to make a realistic estimate of the magnitude of these corrections for general inhomogeneities in (3+1) spacetime. We then quantitatively calculate the volume averaged expansion rate using N-body large-scale structure simulations and compare it with the expansion rate in a standard FRW cosmology. We find that in the weak gravitational field limit, the converged corrections are slightly larger than the previous claimed 10^{-5} level, but not large enough nor even of the correct sign to drive the current cosmic acceleration. Nevertheless, the question of whether the cumulative effect can significantly change the expansion history of the Universe needs to be further investigated with strong-field relativity.Comment: 13 pages, 6 figures, improved version published in Phys. Rev.

Evolution with hole doping of the electronic excitation spectrum in the cuprate superconductors

The recent scanning tunnelling results of Alldredge et al on Bi-2212 and of Hanaguri et al on Na-CCOC are examined from the perspective of the BCS/BEC boson-fermion resonant crossover model for the mixed-valent HTSC cuprates. The model specifies the two energy scales controlling the development of HTSC behaviour and the dichotomy often now alluded to between nodal and antinodal phenomena in the HTSC cuprates. Indication is extracted from the data as to how the choice of the particular HTSC system sees these two basic energy scales (cursive-U, the local pair binding energy and, Delta-sc, the nodal BCS-like gap parameter) evolve with doping and change in degree of metallization of the structurally and electronically perturbed mixed-valent environment.Comment: 19 pages, 5 figure

Developments in the negative-U modelling of the cuprate HTSC systems

The paper deals with the many stands that go into creating the unique and complex nature of the HTSC cuprates above Tc as below. Like its predecessors it treats charge, not spin or lattice, as prime mover, but thus taken in the context of the chemical bonding relevant to these copper oxides. The crucial shell filling, negative-U, double-loading fluctuations possible there require accessing at high valent local environment as prevails within the mixed valent, inhomogeneous two sub-system circumstance of the HTSC materials. Close attention is paid to the recent results from Corson, Demsar, Li, Johnson, Norman, Varma, Gyorffy and colleagues.Comment: 44 pages:200+ references. Submitted to J.Phys.:Condensed Matter, Sept 7 200

On the Convergence of the Expansion of Renormalization Group Flow Equation

We compare and discuss the dependence of a polynomial truncation of the effective potential used to solve exact renormalization group flow equation for a model with fermionic interaction (linear sigma model) with a grid solution. The sensitivity of the results on the underlying cutoff function is discussed. We explore the validity of the expansion method for second and first-order phase transitions.Comment: 12 pages with 10 EPS figures included; revised versio

Phase Transitions in SO(3) Lattice Gauge Theory

The phase diagram of SO(3) lattice gauge theory is investigated by Monte Carlo techniques on both symmetric and asymmetric lattices with a view (i) to understanding the relationship between the bulk transition and the deconfinement transition, and (ii) to resolving the current ambiguity about the nature of the high temperature phase. A number of tests, including an introduction of a magnetic field and measurement of different correlation functions in the phases with positive and negative values for the adjoint Polyakov line, lead to the conclusion that the two phases correspond to the same physical state. Studies on lattices of different sizes reveal only one phase transition for this theory on all of them and it appears to have a deconfining nature.Comment: Latex 19 pages, 9 figures. Minor changes in introduction and summary sections. The version that appeared in journa

Z2 Monopoles, Vortices, and the Deconfinement Transition in Mixed Action SU(2) Gauge Theory

Adding separate chemical potentials lambda and gamma for Z2 monopoles and vortices respectively in the Villain form of the mixed fundamental-adjoint action for the SU(2) lattice gauge theory, we investigate their role in the interplay between the deconfinement and bulk phase transitions using Monte Carlo techniques. Setting lambda to be nonzero, we find that the line of deconfinement transitions is shifted in the coupling plane but it behaves curiously also like the bulk transition line for large enough adjoint coupling, as for lambda=0. In a narrow range of couplings, however, we find separate deconfinement and bulk phase transitions on the same lattice for nonzero and large lambda, suggesting the two to be indeed coincident in the region where a first order deconfinement phase transition is seen. In the limit of large lambda and gamma, we obtain only lines of second order deconfinement phase transitions, as expected from universality.Comment: 18 pages, 10 figures include