Computing Diffusion State Distance using Green's Function and Heat Kernel on Graphs

The diffusion state distance (DSD) was introduced by Cao-Zhang-Park-Daniels-Crovella-Cowen-Hescott [{\em PLoS ONE, 2013}] to capture functional similarity in protein-protein interaction networks. They proved the convergence of DSD for non-bipartite graphs. In this paper, we extend the DSD to bipartite graphs using lazy-random walks and consider the general $L_q$-version of DSD. We discovered the connection between the DSD $L_q$-distance and Green's function, which was studied by Chung and Yau [{\em J. Combinatorial Theory (A), 2000}]. Based on that, we computed the DSD $L_q$-distance for Paths, Cycles, Hypercubes, as well as random graphs $G(n,p)$ and $G(w_1,..., w_n)$. We also examined the DSD distances of two biological networks.Comment: Accepted by the 11th Workshop on Algorithms and Models for the Web Graph (WAW2014

Spatial Mixing of Coloring Random Graphs

We study the strong spatial mixing (decay of correlation) property of proper $q$-colorings of random graph $G(n, d/n)$ with a fixed $d$. The strong spatial mixing of coloring and related models have been extensively studied on graphs with bounded maximum degree. However, for typical classes of graphs with bounded average degree, such as $G(n, d/n)$, an easy counterexample shows that colorings do not exhibit strong spatial mixing with high probability. Nevertheless, we show that for $q\ge\alpha d+\beta$ with $\alpha>2$ and sufficiently large $\beta=O(1)$, with high probability proper $q$-colorings of random graph $G(n, d/n)$ exhibit strong spatial mixing with respect to an arbitrarily fixed vertex. This is the first strong spatial mixing result for colorings of graphs with unbounded maximum degree. Our analysis of strong spatial mixing establishes a block-wise correlation decay instead of the standard point-wise decay, which may be of interest by itself, especially for graphs with unbounded degree

A transition from river networks to scale-free networks

A spatial network is constructed on a two dimensional space where the nodes are geometrical points located at randomly distributed positions which are labeled sequentially in increasing order of one of their co-ordinates. Starting with $N$ such points the network is grown by including them one by one according to the serial number into the growing network. The $t$-th point is attached to the $i$-th node of the network using the probability: $\pi_i(t) \sim k_i(t)\ell_{ti}^{\alpha}$ where $k_i(t)$ is the degree of the $i$-th node and $\ell_{ti}$ is the Euclidean distance between the points $t$ and $i$. Here $\alpha$ is a continuously tunable parameter and while for $\alpha=0$ one gets the simple Barab\'asi-Albert network, the case for $\alpha \to -\infty$ corresponds to the spatially continuous version of the well known Scheidegger's river network problem. The modulating parameter $\alpha$ is tuned to study the transition between the two different critical behaviors at a specific value $\alpha_c$ which we numerically estimate to be -2.Comment: 5 pages, 5 figur

Scale free networks by preferential depletion

We show that not only preferential attachment but also preferential depletion leads to scale-free networks. The resulting degree distribution exponents is typically less than two (5/3) as opposed to the case of the growth models studied before where the exponents are larger. Our approach applies in particular to biological networks where in fact we find interesting agreement with experimental measurements. We investigate the most important properties characterizing these networks, as the cluster size distribution, the average shortest path and the clustering coefficient.Comment: 8 pages, 4 figure

Electromagnetic Form Factors of the Nucleon in an Improved Quark Model

Nucleon electromagnetic form factors are studied in the cloudy bag model (CBM) with center-of-mass and recoil corrections. This is the first presentation of a full set of nucleon form factors using the CBM. The center of mass motion is eliminated via several different momentum projection techniques and the results are compared. It is found that the shapes of these form factors are significantly improved with respect to the experimental data if the Lorentz contraction of the internal structure of the baryon is also appropriately taken into account.Comment: revtex, 28 pages, 8 ps figs include

Kaluza-Klein Induced Gravity Inflation

A D-dimensional induced gravity theory is studied carefully in a $4 + (D-4)$ dimensional Friedmann-Robertson-Walker space-time. We try to extract information of the symmetry breaking potential in search of an inflationary solution with non-expanding internal-space. We find that the induced gravity model imposes strong constraints on the form of symmetry breaking potential in order to generate an acceptable inflationary universe. These constraints are analyzed carefully in this paper.Comment: 10 pages, title changed, corrected some typos, two additional comments adde

Inflationary Universe in Higher Derivative Induced Gravity

In an induced-gravity model, the stability condition of an inflationary slow-rollover solution is shown to be $\phi_0 \partial_{\phi_0}V(\phi_0)=4V(\phi_0)$. The presence of higher derivative terms will, however, act against the stability of this expanding solution unless further constraints on the field parameters are imposed. We find that these models will acquire a non-vanishing cosmological constant at the end of inflation. Some models are analyzed for their implication to the early universe.Comment: 6 pages, two typos correcte

Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire

Idiosyncratic adverse drug reactions are unpredictable, dose independent and potentially life threatening; this makes them a major factor contributing to the cost and uncertainty of drug development. Clinical data suggest that many such reactions involve immune mechanisms, and genetic association studies have identified strong linkage between drug hypersensitivity reactions to several drugs and specific HLA alleles. One of the strongest such genetic associations found has been for the antiviral drug abacavir, which causes severe adverse reactions exclusively in patients expressing the HLA molecular variant B*57:01. Abacavir adverse reactions were recently shown to be driven by drug-specific activation of cytokine-producing, cytotoxic CD8+ T cells that required HLA-B*57:01 molecules for their function. However, the mechanism by which abacavir induces this pathologic T cell response remains unclear. Here we show that abacavir can bind within the F-pocket of the peptide-binding groove of HLA-B*57:01 thereby altering its specificity. This supports a novel explanation for HLA-linked idiosyncratic adverse drug reactions; namely that drugs can alter the repertoire of self-peptides presented to T cells thus causing the equivalent of an alloreactive T cell response. Indeed, we identified specific self-peptides that are presented only in the presence of abacavir, and that were recognized by T cells of hypersensitive patients. The assays we have established can be applied to test additional compounds with suspected HLA linked hypersensitivities in vitro. Where successful, these assays could speed up the discovery and mechanistic understanding of HLA linked hypersensitivities as well as guide the development of safer drugs

Analysis of a large-scale weighted network of one-to-one human communication

We construct a connected network of 3.9 million nodes from mobile phone call records, which can be regarded as a proxy for the underlying human communication network at the societal level. We assign two weights on each edge to reflect the strength of social interaction, which are the aggregate call duration and the cumulative number of calls placed between the individuals over a period of 18 weeks. We present a detailed analysis of this weighted network by examining its degree, strength, and weight distributions, as well as its topological assortativity and weighted assortativity, clustering and weighted clustering, together with correlations between these quantities. We give an account of motif intensity and coherence distributions and compare them to a randomized reference system. We also use the concept of link overlap to measure the number of common neighbors any two adjacent nodes have, which serves as a useful local measure for identifying the interconnectedness of communities. We report a positive correlation between the overlap and weight of a link, thus providing strong quantitative evidence for the weak ties hypothesis, a central concept in social network analysis. The percolation properties of the network are found to depend on the type and order of removed links, and they can help understand how the local structure of the network manifests itself at the global level. We hope that our results will contribute to modeling weighted large-scale social networks, and believe that the systematic approach followed here can be adopted to study other weighted networks.Comment: 25 pages, 17 figures, 2 table

Is backreaction really small within concordance cosmology?

Smoothing over structures in general relativity leads to a renormalisation of the background, and potentially many other effects which are poorly understood. Observables such as the distance-redshift relation when averaged on the sky do not necessarily yield the same smooth model which arises when performing spatial averages. These issues are thought to be of technical interest only in the standard model of cosmology, giving only tiny corrections. However, when we try to calculate observable quantities such as the all-sky average of the distance-redshift relation, we find that perturbation theory delivers divergent answers in the UV and corrections to the background of order unity. There are further problems. Second-order perturbations are the same size as first-order, and fourth-order at least the same as second, and possibly much larger, owing to the divergences. Much hinges on a coincidental balance of 2 numbers: the primordial power, and the ratio between the comoving Hubble scales at matter-radiation equality and today. Consequently, it is far from obvious that backreaction is irrelevant even in the concordance model, however natural it intuitively seems.Comment: 28 pages. Invited contribution to Classical and Quantum Gravity special issue "Inhomogeneous Cosmological Models and Averaging in Cosmology