Bounds for graph regularity and removal lemmas

We show, for any positive integer k, that there exists a graph in which any equitable partition of its vertices into k parts has at least ck^2/\log^* k pairs of parts which are not \epsilon-regular, where c,\epsilon>0 are absolute constants. This bound is tight up to the constant c and addresses a question of Gowers on the number of irregular pairs in Szemer\'edi's regularity lemma. In order to gain some control over irregular pairs, another regularity lemma, known as the strong regularity lemma, was developed by Alon, Fischer, Krivelevich, and Szegedy. For this lemma, we prove a lower bound of wowzer-type, which is one level higher in the Ackermann hierarchy than the tower function, on the number of parts in the strong regularity lemma, essentially matching the upper bound. On the other hand, for the induced graph removal lemma, the standard application of the strong regularity lemma, we find a different proof which yields a tower-type bound. We also discuss bounds on several related regularity lemmas, including the weak regularity lemma of Frieze and Kannan and the recently established regular approximation theorem. In particular, we show that a weak partition with approximation parameter \epsilon may require as many as 2^{\Omega(\epsilon^{-2})} parts. This is tight up to the implied constant and solves a problem studied by Lov\'asz and Szegedy.Comment: 62 page

Theory of continuum percolation II. Mean field theory

I use a previously introduced mapping between the continuum percolation model and the Potts fluid to derive a mean field theory of continuum percolation systems. This is done by introducing a new variational principle, the basis of which has to be taken, for now, as heuristic. The critical exponents obtained are $\beta= 1$, $\gamma= 1$ and $\nu = 0.5$, which are identical with the mean field exponents of lattice percolation. The critical density in this approximation is \rho_c = 1/\ve where \ve = \int d \x \, p(\x) \{ \exp [- v(\x)/kT] - 1 \}. p(\x) is the binding probability of two particles separated by \x and v(\x) is their interaction potential.Comment: 25 pages, Late

Boolean versus continuous dynamics on simple two-gene modules

We investigate the dynamical behavior of simple modules composed of two genes with two or three regulating connections. Continuous dynamics for mRNA and protein concentrations is compared to a Boolean model for gene activity. Using a generalized method, we study within a single framework different continuous models and different types of regulatory functions, and establish conditions under which the system can display stable oscillations. These conditions concern the time scales, the degree of cooperativity of the regulating interactions, and the signs of the interactions. Not all models that show oscillations under Boolean dynamics can have oscillations under continuous dynamics, and vice versa.Comment: 8 pages, 10 figure

A new method for constructing small-bias spaces from Hermitian codes

We propose a new method for constructing small-bias spaces through a combination of Hermitian codes. For a class of parameters our multisets are much faster to construct than what can be achieved by use of the traditional algebraic geometric code construction. So, if speed is important, our construction is competitive with all other known constructions in that region. And if speed is not a matter of interest the small-bias spaces of the present paper still perform better than the ones related to norm-trace codes reported in [12]

Comparing the reliability of networks by spectral analysis

We provide a method for the ranking of the reliability of two networks with the same connectance. Our method is based on the Cheeger constant linking the topological property of a network with its spectrum. We first analyze a set of twisted rings with the same connectance and degree distribution, and obtain the ranking of their reliability using their eigenvalue gaps. The results are generalized to general networks using the method of rewiring. The success of our ranking method is verified numerically for the IEEE57, the Erd\H{o}s-R\'enyi, and the Small-World networks.Comment: 7 pages, 3 figure

Beyond Worst-Case Analysis for Joins with Minesweeper

We describe a new algorithm, Minesweeper, that is able to satisfy stronger runtime guarantees than previous join algorithms (colloquially, `beyond worst-case guarantees') for data in indexed search trees. Our first contribution is developing a framework to measure this stronger notion of complexity, which we call {\it certificate complexity}, that extends notions of Barbay et al. and Demaine et al.; a certificate is a set of propositional formulae that certifies that the output is correct. This notion captures a natural class of join algorithms. In addition, the certificate allows us to define a strictly stronger notion of runtime complexity than traditional worst-case guarantees. Our second contribution is to develop a dichotomy theorem for the certificate-based notion of complexity. Roughly, we show that Minesweeper evaluates $\beta$-acyclic queries in time linear in the certificate plus the output size, while for any $\beta$-cyclic query there is some instance that takes superlinear time in the certificate (and for which the output is no larger than the certificate size). We also extend our certificate-complexity analysis to queries with bounded treewidth and the triangle query.Comment: [This is the full version of our PODS'2014 paper.

Non-equilibrium dynamics of gene expression and the Jarzynski equality

In order to express specific genes at the right time, the transcription of genes is regulated by the presence and absence of transcription factor molecules. With transcription factor concentrations undergoing constant changes, gene transcription takes place out of equilibrium. In this paper we discuss a simple mapping between dynamic models of gene expression and stochastic systems driven out of equilibrium. Using this mapping, results of nonequilibrium statistical mechanics such as the Jarzynski equality and the fluctuation theorem are demonstrated for gene expression dynamics. Applications of this approach include the determination of regulatory interactions between genes from experimental gene expression data

Harmonic generation by atoms in circularly polarized two-color laser fields with coplanar polarizations and commensurate frequencies

The generation of harmonics by atoms or ions in a two-color, coplanar field configuration with commensurate frequencies is investigated through both, an analytical calculation based on the Lewenstein model and the numerical ab initio solution of the time-dependent Schroedinger equation of a two-dimensional model ion. Through the analytical model, selection rules for the harmonic orders in this field configuration, a generalized cut-off for the harmonic spectra, and an integral expression for the harmonic dipole strength is provided. The numerical results are employed to test the predictions of the analytical model. The scaling of the cut-off as a function of both, one of the laser intensities and frequency ratio $\eta$, as well as entire spectra for different $\eta$ and laser intensities are presented and analyzed. The theoretical cut-off is found to be an upper limit for the numerical results. Other discrepancies between analytical model and numerical results are clarified by taking into account the probabilities of the absorption processes involved.Comment: 8 figure