A hierarchical approach to the prediction of the quaternary structure of GCN4 and its mutants

First published in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 23 (1996) published by the American Mathematical Society.Presented at DIMACS Workshop on Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, March 20-21, 1995.A hierarchical approach to protein folding is employed to examine the folding pathway and predict the quaternary structure of the GCN4 leucine zipper. Structures comparable in quality to experiment have been predicted. In addition, the equilibrium between dimers, trimers and tetramers of a number of GCN4 mutants has been examined. In five out of eight cases, the simulation results are in accordance with the experimental studies of Harbury, et al

Online Sorting via Searching and Selection

In this paper, we present a framework based on a simple data structure and parameterized algorithms for the problems of finding items in an unsorted list of linearly ordered items based on their rank (selection) or value (search). As a side-effect of answering these online selection and search queries, we progressively sort the list. Our algorithms are based on Hoare's Quickselect, and are parameterized based on the pivot selection method. For example, if we choose the pivot as the last item in a subinterval, our framework yields algorithms that will answer q<=n unique selection and/or search queries in a total of O(n log q) average time. After q=\Omega(n) queries the list is sorted. Each repeated selection query takes constant time, and each repeated search query takes O(log n) time. The two query types can be interleaved freely. By plugging different pivot selection methods into our framework, these results can, for example, become randomized expected time or deterministic worst-case time. Our methods are easy to implement, and we show they perform well in practice

Successor-Invariant First-Order Logic on Graphs with Excluded Topological Subgraphs

We show that the model-checking problem for successor-invariant first-order logic is fixed-parameter tractable on graphs with excluded topological subgraphs when parameterised by both the size of the input formula and the size of the exluded topological subgraph. Furthermore, we show that model-checking for order-invariant first-order logic is tractable on coloured posets of bounded width, parameterised by both the size of the input formula and the width of the poset. Our result for successor-invariant FO extends previous results for this logic on planar graphs (Engelmann et al., LICS 2012) and graphs with excluded minors (Eickmeyer et al., LICS 2013), further narrowing the gap between what is known for FO and what is known for successor-invariant FO. The proof uses Grohe and Marx's structure theorem for graphs with excluded topological subgraphs. For order-invariant FO we show that Gajarsk\'y et al.'s recent result for FO carries over to order-invariant FO

On Brambles, Grid-Like Minors, and Parameterized Intractability of Monadic Second-Order Logic

Brambles were introduced as the dual notion to treewidth, one of the most central concepts of the graph minor theory of Robertson and Seymour. Recently, Grohe and Marx showed that there are graphs G, in which every bramble of order larger than the square root of the treewidth is of exponential size in |G|. On the positive side, they show the existence of polynomial-sized brambles of the order of the square root of the treewidth, up to log factors. We provide the first polynomial time algorithm to construct a bramble in general graphs and achieve this bound, up to log-factors. We use this algorithm to construct grid-like minors, a replacement structure for grid-minors recently introduced by Reed and Wood, in polynomial time. Using the grid-like minors, we introduce the notion of a perfect bramble and an algorithm to find one in polynomial time. Perfect brambles are brambles with a particularly simple structure and they also provide us with a subgraph that has bounded degree and still large treewidth; we use them to obtain a meta-theorem on deciding certain parameterized subgraph-closed problems on general graphs in time singly exponential in the parameter. The second part of our work deals with providing a lower bound to Courcelle's famous theorem, stating that every graph property that can be expressed by a sentence in monadic second-order logic (MSO), can be decided by a linear time algorithm on classes of graphs of bounded treewidth. Using our results from the first part of our work we establish a strong lower bound for tractability of MSO on classes of colored graphs

Testing for high-dimensional geometry in random graphs

We study the problem of detecting the presence of an underlying high-dimensional geometric structure in a random graph. Under the null hypothesis, the observed graph is a realization of an Erd\H{o}s-R\'enyi random graph $G(n,p)$. Under the alternative, the graph is generated from the $G(n,p,d)$ model, where each vertex corresponds to a latent independent random vector uniformly distributed on the sphere $\mathbb{S}^{d-1}$, and two vertices are connected if the corresponding latent vectors are close enough. In the dense regime (i.e., $p$ is a constant), we propose a near-optimal and computationally efficient testing procedure based on a new quantity which we call signed triangles. The proof of the detection lower bound is based on a new bound on the total variation distance between a Wishart matrix and an appropriately normalized GOE matrix. In the sparse regime, we make a conjecture for the optimal detection boundary. We conclude the paper with some preliminary steps on the problem of estimating the dimension in $G(n,p,d)$.Comment: 28 pages; v2 contains minor change

Connection Matrices and the Definability of Graph Parameters

In this paper we extend and prove in detail the Finite Rank Theorem for connection matrices of graph parameters definable in Monadic Second Order Logic with counting (CMSOL) from B. Godlin, T. Kotek and J.A. Makowsky (2008) and J.A. Makowsky (2009). We demonstrate its vast applicability in simplifying known and new non-definability results of graph properties and finding new non-definability results for graph parameters. We also prove a Feferman-Vaught Theorem for the logic CFOL, First Order Logic with the modular counting quantifiers