Complex-linear invariants of biochemical networks

The nonlinearities found in molecular networks usually prevent mathematical analysis of network behaviour, which has largely been studied by numerical simulation. This can lead to difficult problems of parameter determination. However, molecular networks give rise, through mass-action kinetics, to polynomial dynamical systems, whose steady states are zeros of a set of polynomial equations. These equations may be analysed by algebraic methods, in which parameters are treated as symbolic expressions whose numerical values do not have to be known in advance. For instance, an "invariant" of a network is a polynomial expression on selected state variables that vanishes in any steady state. Invariants have been found that encode key network properties and that discriminate between different network structures. Although invariants may be calculated by computational algebraic methods, such as Gr\"obner bases, these become computationally infeasible for biologically realistic networks. Here, we exploit Chemical Reaction Network Theory (CRNT) to develop an efficient procedure for calculating invariants that are linear combinations of "complexes", or the monomials coming from mass action. We show how this procedure can be used in proving earlier results of Horn and Jackson and of Shinar and Feinberg for networks of deficiency at most one. We then apply our method to enzyme bifunctionality, including the bacterial EnvZ/OmpR osmolarity regulator and the mammalian 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase glycolytic regulator, whose networks have deficiencies up to four. We show that bifunctionality leads to different forms of concentration control that are robust to changes in initial conditions or total amounts. Finally, we outline a systematic procedure for using complex-linear invariants to analyse molecular networks of any deficiency.Comment: 36 pages, 6 figure

Edge Intersection Graphs of L-Shaped Paths in Grids

In this paper we continue the study of the edge intersection graphs of one (or zero) bend paths on a rectangular grid. That is, the edge intersection graphs where each vertex is represented by one of the following shapes: $\llcorner$,$\ulcorner$, $\urcorner$, $\lrcorner$, and we consider zero bend paths (i.e., | and $-$) to be degenerate $\llcorner$s. These graphs, called $B_1$-EPG graphs, were first introduced by Golumbic et al (2009). We consider the natural subclasses of $B_1$-EPG formed by the subsets of the four single bend shapes (i.e., {$\llcorner$}, {$\llcorner$,$\ulcorner$}, {$\llcorner$,$\urcorner$}, and {$\llcorner$,$\ulcorner$,$\urcorner$}) and we denote the classes by [$\llcorner$], [$\llcorner$,$\ulcorner$], [$\llcorner$,$\urcorner$], and [$\llcorner$,$\ulcorner$,$\urcorner$] respectively. Note: all other subsets are isomorphic to these up to 90 degree rotation. We show that testing for membership in each of these classes is NP-complete and observe the expected strict inclusions and incomparability (i.e., [$\llcorner$] $\subsetneq$ [$\llcorner$,$\ulcorner$], [$\llcorner$,$\urcorner$] $\subsetneq$ [$\llcorner$,$\ulcorner$,$\urcorner$] $\subsetneq$ $B_1$-EPG; also, [$\llcorner$,$\ulcorner$] is incomparable with [$\llcorner$,$\urcorner$]). Additionally, we give characterizations and polytime recognition algorithms for special subclasses of Split $\cap$ [$\llcorner$].Comment: 14 pages, to appear in DAM special issue for LAGOS'1

Finite automata with advice tapes

We define a model of advised computation by finite automata where the advice is provided on a separate tape. We consider several variants of the model where the advice is deterministic or randomized, the input tape head is allowed real-time, one-way, or two-way access, and the automaton is classical or quantum. We prove several separation results among these variants, demonstrate an infinite hierarchy of language classes recognized by automata with increasing advice lengths, and establish the relationships between this and the previously studied ways of providing advice to finite automata.Comment: Corrected typo

Phosphorus-Containing Food Additives in the Food Supply-An Audit of Products on Supermarket Shelves

Objectives: Phosphorus (P)-containing food additives pose a risk for chronic kidney disease (CKD) patients. We aimed to investigate the prevalence of P-containing additives in the Finnish food supply across different food categories to evaluate their burden in CKD, reflecting the situation in Europe. Methods: The dataset of 6,176 products was obtained in June-August 2019 from the foodie.fi website, which contains all foodstuffs sold in the grocery stores of the S Group (46% of the Finnish market share in 2019). The food category, full product name, type of P additive (inorganic, organic, and natural P-containing), and reporting methods (name or E number) of P additives were recorded. Duplicates and products lacking ingredient information were excluded. Results: The prevalence of P additives was 36% in the final sample (n 5 5,149). Among food categories, the prevalence varied from 4% in dairy-based snacks to 67% in meat products. Altogether 17 different P additives were observed. Inorganic P additives were the most common P additive type, present in 20% of foodstuffs. Natural P-containing additives were observed in 19% and organic P additives in 2% of foodstuffs. The most commonly used P additives were lecithin (E 322), pyrophosphate (E 450), and triphosphate (E 451). E number was used as a reporting method in 49% of foodstuffs, and full name in 44% of foodstuffs. Reporting by E number was particularly common in the products containing inorganic P. Conclusions: The use of P additives is common in the Finnish food supply, indicating the situation in Europe. The high prevalence of inorganic, that is, the most absorbable and potentially most harmful P additives in particular food groups, and their usual reporting only by E numbers can create challenges in CKD dietary counseling. (c) 2021 The Authors. Published by Elsevier Inc. on behalf of the National Kidney Foundation, Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).Peer reviewe

Dynamic Range Majority Data Structures

Given a set $P$ of coloured points on the real line, we study the problem of answering range $\alpha$-majority (or "heavy hitter") queries on $P$. More specifically, for a query range $Q$, we want to return each colour that is assigned to more than an $\alpha$-fraction of the points contained in $Q$. We present a new data structure for answering range $\alpha$-majority queries on a dynamic set of points, where $\alpha \in (0,1)$. Our data structure uses O(n) space, supports queries in $O((\lg n) / \alpha)$ time, and updates in $O((\lg n) / \alpha)$ amortized time. If the coordinates of the points are integers, then the query time can be improved to $O(\lg n / (\alpha \lg \lg n) + (\lg(1/\alpha))/\alpha))$. For constant values of $\alpha$, this improved query time matches an existing lower bound, for any data structure with polylogarithmic update time. We also generalize our data structure to handle sets of points in d-dimensions, for $d \ge 2$, as well as dynamic arrays, in which each entry is a colour.Comment: 16 pages, Preliminary version appeared in ISAAC 201

Percolation of satisfiability in finite dimensions

The satisfiability and optimization of finite-dimensional Boolean formulas are studied using percolation theory, rare region arguments, and boundary effects. In contrast with mean-field results, there is no satisfiability transition, though there is a logical connectivity transition. In part of the disconnected phase, rare regions lead to a divergent running time for optimization algorithms. The thermodynamic ground state for the NP-hard two-dimensional maximum-satisfiability problem is typically unique. These results have implications for the computational study of disordered materials.Comment: 4 pages, 4 fig

Convex Independence in Permutation Graphs

A set C of vertices of a graph is P_3-convex if every vertex outside C has at most one neighbor in C. The convex hull \sigma(A) of a set A is the smallest P_3-convex set that contains A. A set M is convexly independent if for every vertex x \in M, x \notin \sigma(M-x). We show that the maximal number of vertices that a convexly independent set in a permutation graph can have, can be computed in polynomial time

Sparse stretching for solving sparse-dense linear least-squares problems

Large-scale linear least-squares problems arise in a wide range of practical applications. In some cases, the system matrix contains a small number of dense rows. These make the problem significantly harder to solve because their presence limits the direct applicability of sparse matrix techniques. In particular, the normal matrix is (close to) dense, so that forming it is impractical. One way to help overcome the dense row problem is to employ matrix stretching. Stretching is a sparse matrix technique that improves sparsity by making the least-squares problem larger. We show that standard stretching can still result in the normal matrix for the stretched problem having an unacceptably large amount of fill. This motivates us to propose a new sparse stretching strategy that performs the stretching so as to limit the fill in the normal matrix and its Cholesky factor. Numerical examples from real problems are used to illustrate the potential gains

Routing Games over Time with FIFO policy

We study atomic routing games where every agent travels both along its decided edges and through time. The agents arriving on an edge are first lined up in a \emph{first-in-first-out} queue and may wait: an edge is associated with a capacity, which defines how many agents-per-time-step can pop from the queue's head and enter the edge, to transit for a fixed delay. We show that the best-response optimization problem is not approximable, and that deciding the existence of a Nash equilibrium is complete for the second level of the polynomial hierarchy. Then, we drop the rationality assumption, introduce a behavioral concept based on GPS navigation, and study its worst-case efficiency ratio to coordination.Comment: Submission to WINE-2017 Deadline was August 2nd AoE, 201