Networks, (K)nots, Nucleotides, and Nanostructures

Designing self-assembling DNA nanostructures often requires the identification of a route for a scaffolding strand of DNA through the target structure. When the target structure is modeled as a graph, these scaffolding routes correspond to Eulerian circuits subject to turning restrictions imposed by physical constraints on the strands of DNA. Existence of such Eulerian circuits is an NP-hard problem, which can be approached by adapting solutions to a version of the Traveling Salesperson Problem. However, the author and collaborators have demonstrated that even Eulerian circuits obeying these turning restrictions are not necessarily feasible as scaffolding routes by giving examples of nontrivially knotted circuits which cannot be traced by the unknotted scaffolding strand. Often, targets of DNA nanostructure self-assembly are modeled as graphs embedded on surfaces in space. In this case, Eulerian circuits obeying the turning restrictions correspond to A-trails, circuits which turn immediately left or right at each vertex. In any graph embedded on the sphere, all A-trails are unknotted regardless of the embedding of the sphere in space. We show that this does not hold in general for graphs on the torus. However, we show this property does hold for checkerboard-colorable graphs on the torus, that is, those graphs whose faces can be properly 2-colored, and provide a partial converse to this result. As a consequence, we characterize (with one exceptional family) regular triangulations of the torus containing unknotted A-trails. By developing a theory of sums of A-trails, we lift constructions from the torus to arbitrary n-tori, and by generalizing our work on A-trails to smooth circuit decompositions, we construct all torus links and certain sums of torus links from circuit decompositions of rectangular torus grids. Graphs embedded on surfaces are equivalent to ribbon graphs, which are particularly well-suited to modeling DNA nanostructures, as their boundary components correspond to strands of DNA and their twisted ribbons correspond to double-helices. Every ribbon graph has a corresponding delta-matroid, a combinatorial object encoding the structure of the ribbon-graph\u27s spanning quasi-trees (substructures having exactly one boundary component). We show that interlacement with respect to quasi-trees can be generalized to delta-matroids, and use the resulting structure on delta-matroids to provide feasible-set expansions for a family of delta-matroid polynomials, both recovering well-known expansions of this type (such as the spanning-tree expansion of the Tutte polynnomial) as well as providing several previously unknown expansions. Among these are expansions for the transition polynomial, a version of which has been used to study DNA nanostructure self-assembly, and the interlace polynomial, which solves a problem in DNA recombination

Adaptive cluster expansion for the inverse Ising problem: convergence, algorithm and tests

We present a procedure to solve the inverse Ising problem, that is to find the interactions between a set of binary variables from the measure of their equilibrium correlations. The method consists in constructing and selecting specific clusters of variables, based on their contributions to the cross-entropy of the Ising model. Small contributions are discarded to avoid overfitting and to make the computation tractable. The properties of the cluster expansion and its performances on synthetic data are studied. To make the implementation easier we give the pseudo-code of the algorithm.Comment: Paper submitted to Journal of Statistical Physic

Algorithmic Problems Arising in Posets and Permutations

Partially ordered sets and permutations are combinatorial structures having vast applications in theoretical computer science. In this thesis, we study various computational and algorithmic problems related to these structures. The first chapter of the thesis contains discussion about randomized fully polynomial approximation schemes obtained by employing Markov chain Monte Carlo. In this chapter we study various Markov chains that we call: the gladiator chain, the interval chain, and cube shuffling. Our objective is to identify some conditions that assure rapid mixing; and we obtain partial results. The gladiator chain is a biased random walk on the set of permutations. This chain is related to self organizing lists, and various versions of it have been studied. The interval chain is a random walk on the set of points in $\mathbb{R}^n$ whose coordinates respect a partial order. Since the sample space of the interval chain is continuous, many mixing techniques for discrete chains are not applicable to it. The cube shuffle chain is a generalization of H\r{a}stad\u27s square shuffle. The importance of this chain is that it mixes in constant number of steps. In the second chapter, we are interested in calculating expected value of real valued function $f:S\rightarrow \mathbb{R}$ on a set of combinatorial structures $S$, given a probability distribution on it. We first suggest a Markov chain Monte Carlo approach to this problem. We identify the conditions under which our proposed solution will be efficient, and present examples where it fails. Then, we study homomesy. Homomesy is a phenomenon introduced by Jim Propp and Tom Roby. We say the triple $\langle S, \tau,f\rangle$ ($\tau$ is a permutation mapping $S$ to itself) exhibits homomesy, if the average of $f$ along all $\tau$-orbits of $S$ is a constant only depending on $f$ and $S$. We study homomesy and obtain some results when $S$ is the set of ideals in a class of simply described lattices

Geometric and Topological Combinatorics

The 2007 Oberwolfach meeting “Geometric and Topological Combinatorics” presented a great variety of investigations where topological and algebraic methods are brought into play to solve combinatorial and geometric problems, but also where geometric and combinatorial ideas are applied to topological questions