A Projection Argument for Differential Inclusions, with Applications to Persistence of Mass-Action Kinetics

Motivated by questions in mass-action kinetics, we introduce the notion of vertexical family of differential inclusions. Defined on open hypercubes, these families are characterized by particular good behavior under projection maps. The motivating examples are certain families of reaction networks -- including reversible, weakly reversible, endotactic, and strongly endotactic reaction networks -- that give rise to vertexical families of mass-action differential inclusions. We prove that vertexical families are amenable to structural induction. Consequently, a trajectory of a vertexical family approaches the boundary if and only if either the trajectory approaches a vertex of the hypercube, or a trajectory in a lower-dimensional member of the family approaches the boundary. With this technology, we make progress on the global attractor conjecture, a central open problem concerning mass-action kinetics systems. Additionally, we phrase mass-action kinetics as a functor on reaction networks with variable rates.Comment: v5: published version; v3 and v4: minor additional edits; v2: contains more general version of main theorem on vertexical families, including its accompanying corollaries -- some of them new; final section contains new results relating to prior and future research on persistence of mass-action systems; improved exposition throughou

Phase Diagram for Anderson Disorder: beyond Single-Parameter Scaling

The Anderson model for independent electrons in a disordered potential is transformed analytically and exactly to a basis of random extended states leading to a variant of augmented space. In addition to the widely-accepted phase diagrams in all physical dimensions, a plethora of additional, weaker Anderson transitions are found, characterized by the long-distance behavior of states. Critical disorders are found for Anderson transitions at which the asymptotically dominant sector of augmented space changes for all states at the same disorder. At fixed disorder, critical energies are also found at which the localization properties of states are singular. Under the approximation of single-parameter scaling, this phase diagram reduces to the widely-accepted one in 1, 2 and 3 dimensions. In two dimensions, in addition to the Anderson transition at infinitesimal disorder, there is a transition between two localized states, characterized by a change in the nature of wave function decay.Comment: 51 pages including 4 figures, revised 30 November 200

Heegaard Floer homology and integer surgeries on links

Let L be a link in an integral homology three-sphere. We give a description of the Heegaard Floer homology of integral surgeries on L in terms of some data associated to L, which we call a complete system of hyperboxes for L. Roughly, a complete systems of hyperboxes consists of chain complexes for (some versions of) the link Floer homology of L and all its sublinks, together with several chain maps between these complexes. Further, we introduce a way of presenting closed four-manifolds with b_2^+ > 1 by four-colored framed links in the three-sphere. Given a link presentation of this kind for a four-manifold X, we then describe the Ozsvath-Szabo mixed invariants of X in terms of a complete system of hyperboxes for the link. Finally, we explain how a grid diagram produces a particular complete system of hyperboxes for the corresponding link.Comment: 231 pages, 54 figures; major revision: we now work with one U variable for each w basepoint, rather than one per link component; we also added Section 4, with an overview of the main resul

Non-Perturbative Gravity and the Spin of the Lattice Graviton

The lattice formulation of quantum gravity provides a natural framework in which non-perturbative properties of the ground state can be studied in detail. In this paper we investigate how the lattice results relate to the continuum semiclassical expansion about smooth manifolds. As an example we give an explicit form for the lattice ground state wave functional for semiclassical geometries. We then do a detailed comparison between the more recent predictions from the lattice regularized theory, and results obtained in the continuum for the non-trivial ultraviolet fixed point of quantum gravity found using weak field and non-perturbative methods. In particular we focus on the derivative of the beta function at the fixed point and the related universal critical exponent $\nu$ for gravitation. Based on recently available lattice and continuum results we assess the evidence for the presence of a massless spin two particle in the continuum limit of the strongly coupled lattice theory. Finally we compare the lattice prediction for the vacuum-polarization induced weak scale dependence of the gravitational coupling with recent calculations in the continuum, finding similar effects.Comment: 46 pages, one figur

Subquadratic-Time Algorithm for the Diameter and All Eccentricities on Median Graphs

On sparse graphs, Roditty and Williams [2013] proved that no O(n^{2-?})-time algorithm achieves an approximation factor smaller than 3/2 for the diameter problem unless SETH fails. We answer here an open question formulated in the literature: can we use the structural properties of median graphs to break this global quadratic barrier? We propose the first combinatorial algorithm computing exactly all eccentricities of a median graph in truly subquadratic time. Median graphs constitute the family of graphs which is the most studied in metric graph theory because their structure represents many other discrete and geometric concepts, such as CAT(0) cube complexes. Our result generalizes a recent one, stating that there is a linear-time algorithm for computing all eccentricities in median graphs with bounded dimension d, i.e. the dimension of the largest induced hypercube (note that 1-dimensional median graphs are exactly the forests). This prerequisite on d is not necessarily anymore to determine all eccentricities in subquadratic time. The execution time of our algorithm is O(n^{1.6456}log^{O(1)} n)

Subquadratic-time algorithm for the diameter and all eccentricities on median graphs

On sparse graphs, Roditty and Williams [2013] proved that no $O(n^{2-\varepsilon})$-time algorithm achieves an approximation factor smaller than $\frac{3}{2}$ for the diameter problem unless SETH fails. In this article, we solve an open question formulated in the literature: can we use the structural properties of median graphs to break this global quadratic barrier? We propose the first combinatiorial algorithm computing exactly all eccentricities of a median graph in truly subquadratic time. Median graphs constitute the family of graphs which is the most studied in metric graph theory because their structure represents many other discrete and geometric concepts, such as CAT(0) cube complexes. Our result generalizes a recent one, stating that there is a linear-time algorithm for all eccentricities in median graphs with bounded dimension $d$, i.e. the dimension of the largest induced hypercube. This prerequisite on $d$ is not necessarily anymore to determine all eccentricities in subquadratic time. The execution time of our algorithm is $O(n^{1.6408}\log^{O(1)} n)$. We provide also some satellite outcomes related to this general result. In particular, restricted to simplex graphs, this algorithm enumerates all eccentricities with a quasilinear running time. Moreover, an algorithm is proposed to compute exactly all reach centralities in time $O(2^{3d}n\log^{O(1)}n)$.Comment: 43 pages, extended abstract in STACS 202

Rational Orthogonal versus Real Orthogonal

The main question we raise here is the following one: given a real orthogonal n by n matrix X, is it true that there exists a rational orthogonal matrix Y having the same zero-pattern? We conjecture that this is the case and prove it for n<=5. We also consider the related problem for symmetric orthogonal matrices.Comment: 23 page

Rational Design of DNA Sequences with Non-Orthogonal Binding Interactions

Molecular computation involving promiscuous, or non-orthogonal, binding interactions between system components is found commonly in natural biological systems, as well as some proposed human-made molecular computers. Such systems are characterized by the fact that each computational unit, such as a domain within a DNA strand, may bind to several different partners with distinct, prescribed binding strengths. Unfortunately, implementing systems of molecular computation that incorporate non-orthogonal binding is difficult, because researchers lack a robust, general-purpose method for designing molecules with this type of behavior. In this work, we describe and demonstrate a process for the rational design of DNA sequences with prescribed non-orthogonal binding behavior. This process makes use of a model that represents large sets of non-orthogonal DNA sequences using fixed-length binary strings, and estimates the differential binding affinity between pairs of sequences through the Hamming distance between their corresponding binary strings. The real-world applicability of this model is supported by simulations and some experimental data. We then select two previously described systems of molecular computation involving non-orthogonal interactions, and apply our sequence design process to implement them using DNA strand displacement. Our simulated results on these two systems demonstrate both digital and analog computation. We hope that this work motivates the development and implementation of new computational paradigms based on non-orthogonal binding