How to Tackle Underdeterminacy in Metabolic Flux Analysis? A Tutorial and Critical Review

Metabolic flux analysis is often (not to say almost always) faced with system underdeterminacy. Indeed, the linear algebraic system formed by the steady-state mass balance equations around the intracellular metabolites and the equality constraints related to the measurements of extracellular fluxes do not define a unique solution for the distribution of intracellular fluxes, but instead a set of solutions belonging to a convex polytope. Various methods have been proposed to tackle this underdeterminacy, including flux pathway analysis, flux balance analysis, flux variability analysis and sampling. These approaches are reviewed in this article and a toy example supports the discussion with illustrative numerical results.

On Hamilton-Connectivity and Detour Index of Certain Families of Convex Polytopes

A convex polytope is the convex hull of a finite set of points in the Euclidean space ℝ n . By preserving the adjacency-incidence relation between vertices of a polytope, its structural graph is constructed. A graph is called Hamilton-connected if there exists at least one Hamiltonian path between any of its two vertices. The detour index is defined to be the sum of the lengths of longest distances, i.e., detours between vertices in a graph. Hamiltonian and Hamilton-connected graphs have diverse applications in computer science and electrical engineering, whereas the detour index has important applications in chemistry. Checking whether a graph is Hamilton-connected and computing the detour index of an arbitrary graph are both NP-complete problems. In this paper, we study these problems simultaneously for certain families of convex polytopes. We construct two infinite families of Hamilton-connected convex polytopes. Hamilton-connectivity is shown by constructing Hamiltonian paths between any pair of vertices. We then use the Hamilton-connectivity to compute the detour index of these families. A family of non-Hamilton-connected convex polytopes has also been constructed to show that not all convex polytope families are Hamilton-connected.

Projective toric codes

Any integral convex polytope [Formula: see text] in [Formula: see text] provides an [Formula: see text]-dimensional toric variety [Formula: see text] and an ample divisor [Formula: see text] on this variety. This paper gives an explicit construction of the algebraic geometric error-correcting code on [Formula: see text], obtained by evaluating global section of the line bundle corresponding to [Formula: see text] on every rational point of [Formula: see text]. This work presents an extension of toric codes analogous to the one of Reed–Muller codes into projective ones, by evaluating on the whole variety instead of considering only points with nonzero coordinates. The dimension of the code is given in terms of the number of integral points in the polytope [Formula: see text] and an algorithmic technique to get a lower bound on the minimum distance is described.

Tetrahedral cages for unit discs

A cage is the 1-skeleton of a convex polytope in ℝ3. A cage is said to hold a set if the set cannot be continuously moved to a distant location, remaining congruent to itself and disjoint from the cage. In how many positions can (compact 2-dimensional) unit discs be held by a tetrahedral cage? We completely answer this question for all tetrahedra.

On the total irregularity strength of convex polytope graphs

A vertex (edge) irregular total k-labeling ? of a graph G is a labeling of the vertices and edges of G with labels from the set {1,2,...,k} in such a way that any two different vertices (edges) have distinct weights. Here, the weight of a vertex x in G is the sum of the label of x and the labels of all edges incident with the vertex x, whereas the weight of an edge is the sum of label of the edge and the vertices incident to that edge. The minimum k for which the graph G has a vertex (edge) irregular total k-labeling is called the total vertex (edge) irregularity strength of G. In this paper, we are dealing with infinite classes of convex polytopes generated by prism graph and antiprism graph. We have determined the exact value of their total vertex irregularity strength and total edge irregularity strength.

On convex holes in d-dimensional point sets

Given a finite set $A \subseteq \mathbb{R}^d$ , points $a_1,a_2,\dotsc,a_{\ell} \in A$ form an $\ell$ -hole in A if they are the vertices of a convex polytope, which contains no points of A in its interior. We construct arbitrarily large point sets in general position in $\mathbb{R}^d$ having no holes of size $O(4^dd\log d)$ or more. This improves the previously known upper bound of order $d^{d+o(d)}$ due to Valtr. The basic version of our construction uses a certain type of equidistributed point sets, originating from numerical analysis, known as (t,m,s)-nets or (t,s)-sequences, yielding a bound of $2^{7d}$ . The better bound is obtained using a variant of (t,m,s)-nets, obeying a relaxed equidistribution condition.

Geometry of Multiprimary Display Colors II: Metameric Control Sets and Gamut Tiling Color Control Functions

<div>For multiprimary displays that have four or more primaries, a color may be reproduced using multiple alternative control vectors. We provide a complete characterization of the Metameric Control Set (MCS), i.e., the set of control vectors that reproduce a given color on the display. Specifically, we show that MCS is a convex polytope whose vertices are control vectors obtained from (parallelepiped) tilings of the gamut, i.e., the range of colors that the display can produce. The mathematical framework that we develop: (a) characterizes gamut tilings in terms of fundamental building blocks called facet spans, (b) establishes that the vertices of the MCS are fully characterized by the tilings of the gamut, and (c) introduces a methodology for the efficient enumeration of gamut tilings. The framework reveals the fundamental inter-relations between the geometry of the MCS and the geometry of the gamut developed in a companion Part I paper, and provides insight into alternative strategies for color control. Our characterization of tilings and the strategy for their enumeration also advance knowledge in geometry, providing new approaches and computational results for the enumeration of tilings for a broad class of zonotopes in R³.</div>

Geometry of Multiprimary Display Colors I: Gamut and Color Control

<div>Displays that render colors using combinations of more than three lights are referred to as multiprimary displays. For multiprimary displays, the gamut, i.e., the range of colors that can be rendered using additive combinations of an arbitrary number of light sources (primaries) with modulated intensities, is known to be a zonotope, which is a specific type of convex polytope. Under the specific three-dimensional setting relevant for color representation and the constraint of physically meaningful nonnegative primaries, we develop a complete, cohesive, and directly usable mathematical characterization of the geometry of the multiprimary gamut zonotope that immediately identifies the surface facets, edges, and vertices and provides a parallelepiped tiling of the gamut. We relate the parallelepiped tilings of the gamut, that arise naturally in our characterization, to the flexibility in color control afforded by displays with more than four primaries, a relation that is further analyzed and completed in a Part II companion paper. We demonstrate several applications of the geometric representations we develop and highlight how the paper advances theory required for multiprimary display modeling, design, and color management and provides an integrated view of past work on on these topics. Additionally, we highlight how our work on gamut representations connects with and furthers the study of three-dimensional zonotopes in geometry.</div>