Non-degenerate solutions of universal Whitham hierarchy

The notion of non-degenerate solutions for the dispersionless Toda hierarchy is generalized to the universal Whitham hierarchy of genus zero with $M+1$ marked points. These solutions are characterized by a Riemann-Hilbert problem (generalized string equations) with respect to two-dimensional canonical transformations, and may be thought of as a kind of general solutions of the hierarchy. The Riemann-Hilbert problem contains $M$ arbitrary functions $H_a(z_0,z_a)$, $a = 1,...,M$, which play the role of generating functions of two-dimensional canonical transformations. The solution of the Riemann-Hilbert problem is described by period maps on the space of $(M+1)$-tuples $(z_\alpha(p) : \alpha = 0,1,...,M)$ of conformal maps from $M$ disks of the Riemann sphere and their complements to the Riemann sphere. The period maps are defined by an infinite number of contour integrals that generalize the notion of harmonic moments. The $F$-function (free energy) of these solutions is also shown to have a contour integral representation.Comment: latex2e, using amsmath, amssym and amsthm packages, 32 pages, no figur

GS2: an efficiently computable measure of GO-based similarity of gene sets

Motivation: The growing availability of genome-scale datasets has attracted increasing attention to the development of computational methods for automated inference of functional similarities among genes and their products. One class of such methods measures the functional similarity of genes based on their distance in the Gene Ontology (GO). To measure the functional relatedness of a gene set, these measures consider every pair of genes in the set, and the average of all pairwise distances is calculated. However, as more data becomes available and gene sets used for analysis become larger, such pair-based calculation becomes prohibitive

Flexible construction of hierarchical scale-free networks with general exponent

Extensive studies have been done to understand the principles behind architectures of real networks. Recently, evidences for hierarchical organization in many real networks have also been reported. Here, we present a new hierarchical model which reproduces the main experimental properties observed in real networks: scale-free of degree distribution $P(k)$ (frequency of the nodes that are connected to $k$ other nodes decays as a power-law $P(k)\sim k^{-\gamma}$) and power-law scaling of the clustering coefficient $C(k)\sim k^{-1}$. The major novelties of our model can be summarized as follows: {\it (a)} The model generates networks with scale-free distribution for the degree of nodes with general exponent $\gamma > 2$, and arbitrarily close to any specified value, being able to reproduce most of the observed hierarchical scale-free topologies. In contrast, previous models can not obtain values of $\gamma > 2.58$. {\it (b)} Our model has structural flexibility because {\it (i)} it can incorporate various types of basic building blocks (e.g., triangles, tetrahedrons and, in general, fully connected clusters of $n$ nodes) and {\it (ii)} it allows a large variety of configurations (i.e., the model can use more than $n-1$ copies of basic blocks of $n$ nodes). The structural features of our proposed model might lead to a better understanding of architectures of biological and non-biological networks.Comment: RevTeX, 5 pages, 4 figure

MACiE: a database of enzyme reaction mechanisms.

SUMMARY: MACiE (mechanism, annotation and classification in enzymes) is a publicly available web-based database, held in CMLReact (an XML application), that aims to help our understanding of the evolution of enzyme catalytic mechanisms and also to create a classification system which reflects the actual chemical mechanism (catalytic steps) of an enzyme reaction, not only the overall reaction. AVAILABILITY: http://www-mitchell.ch.cam.ac.uk/macie/.EPSRC (G.L.H. and J.B.O.M.), the BBSRC (G.J.B. and J.M.T.—CASE studentship in association with Roche Products Ltd; N.M.O.B. and J.B.O.M.—grant BB/C51320X/1), the Chilean Government’s Ministerio de Planificacio´n y Cooperacio´n and Cambridge Overseas Trust (D.E.A.) for funding and Unilever for supporting the Centre for Molecular Science Informatics.application note restricted to 2 printed pages web site: http://www-mitchell.ch.cam.ac.uk/macie

Extracting the hierarchical organization of complex systems

Extracting understanding from the growing ``sea'' of biological and socio-economic data is one of the most pressing scientific challenges facing us. Here, we introduce and validate an unsupervised method that is able to accurately extract the hierarchical organization of complex biological, social, and technological networks. We define an ensemble of hierarchically nested random graphs, which we use to validate the method. We then apply our method to real-world networks, including the air-transportation network, an electronic circuit, an email exchange network, and metabolic networks. We find that our method enables us to obtain an accurate multi-scale descriptions of a complex system.Comment: Figures in screen resolution. Version with full resolution figures available at http://amaral.chem-eng.northwestern.edu/Publications/Papers/sales-pardo-2007.pd

qq-analogue of modified KP hierarchy and its quasi-classical limit

A $q$-analogue of the tau function of the modified KP hierarchy is defined by a change of independent variables. This tau function satisfies a system of bilinear $q$-difference equations. These bilinear equations are translated to the language of wave functions, which turn out to satisfy a system of linear $q$-difference equations. These linear $q$-difference equations are used to formulate the Lax formalism and the description of quasi-classical limit. These results can be generalized to a $q$-analogue of the Toda hierarchy. The results on the $q$-analogue of the Toda hierarchy might have an application to the random partition calculus in gauge theories and topological strings.Comment: latex2e, a4 paper 15 pages, no figure; (v2) a few references are adde

Melting Crystal, Quantum Torus and Toda Hierarchy

Searching for the integrable structures of supersymmetric gauge theories and topological strings, we study melting crystal, which is known as random plane partition, from the viewpoint of integrable systems. We show that a series of partition functions of melting crystals gives rise to a tau function of the one-dimensional Toda hierarchy, where the models are defined by adding suitable potentials, endowed with a series of coupling constants, to the standard statistical weight. These potentials can be converted to a commutative sub-algebra of quantum torus Lie algebra. This perspective reveals a remarkable connection between random plane partition and quantum torus Lie algebra, and substantially enables to prove the statement. Based on the result, we briefly argue the integrable structures of five-dimensional $\mathcal{N}=1$ supersymmetric gauge theories and $A$-model topological strings. The aforementioned potentials correspond to gauge theory observables analogous to the Wilson loops, and thereby the partition functions are translated in the gauge theory to generating functions of their correlators. In topological strings, we particularly comment on a possibility of topology change caused by condensation of these observables, giving a simple example.Comment: Final version to be published in Commun. Math. Phys. . A new section is added and devoted to Conclusion and discussion, where, in particular, a possible relation with the generating function of the absolute Gromov-Witten invariants on CP^1 is commented. Two references are added. Typos are corrected. 32 pages. 4 figure

Widespread sex differences in gene expression and splicing in the adult human brain

There is strong evidence to show that men and women differ in terms of neurodevelopment, neurochemistry and susceptibility to neurodegenerative and neuropsychiatric disease. The molecular basis of these differences remains unclear. Progress in this field has been hampered by the lack of genome-wide information on sex differences in gene expression and in particular splicing in the human brain. Here we address this issue by using post-mortem adult human brain and spinal cord samples originating from 137 neuropathologically confirmed control individuals to study whole-genome gene expression and splicing in 12 CNS regions. We show that sex differences in gene expression and splicing are widespread in adult human brain, being detectable in all major brain regions and involving 2.5% of all expressed genes. We give examples of genes where sex-biased expression is both disease-relevant and likely to have functional consequences, and provide evidence suggesting that sex biases in expression may reflect sex-biased gene regulatory structures

Thermodynamic limit of random partitions and dispersionless Toda hierarchy

We study the thermodynamic limit of random partition models for the instanton sum of 4D and 5D supersymmetric U(1) gauge theories deformed by some physical observables. The physical observables correspond to external potentials in the statistical model. The partition function is reformulated in terms of the density function of Maya diagrams. The thermodynamic limit is governed by a limit shape of Young diagrams associated with dominant terms in the partition function. The limit shape is characterized by a variational problem, which is further converted to a scalar-valued Riemann-Hilbert problem. This Riemann-Hilbert problem is solved with the aid of a complex curve, which may be thought of as the Seiberg-Witten curve of the deformed U(1) gauge theory. This solution of the Riemann-Hilbert problem is identified with a special solution of the dispersionless Toda hierarchy that satisfies a pair of generalized string equations. The generalized string equations for the 5D gauge theory are shown to be related to hidden symmetries of the statistical model. The prepotential and the Seiberg-Witten differential are also considered.Comment: latex2e using amsmath,amssymb,amsthm packages, 55 pages, no figure; (v2) typos correcte

Complex networks theory for analyzing metabolic networks

One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of the organism, while networks are appropriate abstract description of all kinds of interactions. In the past few years, great achievement has been made in developing theory of complex networks for revealing the organizing principles that govern the formation and evolution of various complex biological, technological and social networks. This paper reviews the accomplishments in constructing genome-based metabolic networks and describes how the theory of complex networks is applied to analyze metabolic networks.Comment: 13 pages, 2 figure