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

Edge-Fault Tolerance of Hypercube-like Networks

This paper considers a kind of generalized measure $\lambda_s^{(h)}$ of fault tolerance in a hypercube-like graph $G_n$ which contain several well-known interconnection networks such as hypercubes, varietal hypercubes, twisted cubes, crossed cubes and M\"obius cubes, and proves $\lambda_s^{(h)}(G_n)= 2^h(n-h)$ for any $h$ with $0\leqslant h\leqslant n-1$ by the induction on $n$ and a new technique. This result shows that at least $2^h(n-h)$ edges of $G_n$ have to be removed to get a disconnected graph that contains no vertices of degree less than $h$. Compared with previous results, this result enhances fault-tolerant ability of the above-mentioned networks theoretically

A general analytical model of adaptive wormhole routing in k-ary n-cubes

Several analytical models of fully adaptive routing have recently been proposed for k-ary n-cubes and hypercube networks under the uniform traffic pattern. Although,hypercube is a special case of k-ary n-cubes topology, the modeling approach for hypercube is more accurate than karyn-cubes due to its simpler structure. This paper proposes a general analytical model to predict message latency in wormhole-routed k-ary n-cubes with fully adaptive routing that uses a similar modeling approach to hypercube. The analysis focuses Duato's fully adaptive routing algorithm [12], which is widely accepted as the most general algorithm for achieving adaptivity in wormhole-routed networks while allowing for an efficient router implementation. The proposed model is general enough that it can be used for hypercube and other fully adaptive routing algorithms

Canalization and Symmetry in Boolean Models for Genetic Regulatory Networks

Canalization of genetic regulatory networks has been argued to be favored by evolutionary processes due to the stability that it can confer to phenotype expression. We explore whether a significant amount of canalization and partial canalization can arise in purely random networks in the absence of evolutionary pressures. We use a mapping of the Boolean functions in the Kauffman N-K model for genetic regulatory networks onto a k-dimensional Ising hypercube to show that the functions can be divided into different classes strictly due to geometrical constraints. The classes can be counted and their properties determined using results from group theory and isomer chemistry. We demonstrate that partially canalized functions completely dominate all possible Boolean functions, particularly for higher k. This indicates that partial canalization is extremely common, even in randomly chosen networks, and has implications for how much information can be obtained in experiments on native state genetic regulatory networks.Comment: 14 pages, 4 figures; version to appear in J. Phys.

Optimal Networks from Error Correcting Codes

To address growth challenges facing large Data Centers and supercomputing clusters a new construction is presented for scalable, high throughput, low latency networks. The resulting networks require 1.5-5 times fewer switches, 2-6 times fewer cables, have 1.2-2 times lower latency and correspondingly lower congestion and packet losses than the best present or proposed networks providing the same number of ports at the same total bisection. These advantage ratios increase with network size. The key new ingredient is the exact equivalence discovered between the problem of maximizing network bisection for large classes of practically interesting Cayley graphs and the problem of maximizing codeword distance for linear error correcting codes. Resulting translation recipe converts existent optimal error correcting codes into optimal throughput networks.Comment: 14 pages, accepted at ANCS 2013 conferenc