An Improved Multi-parametric Programming Algorithm for Flux Balance Analysis of Metabolic Networks

Flux balance analysis has proven an effective tool for analyzing metabolic networks. In flux balance analysis, reaction rates and optimal pathways are ascertained by solving a linear program, in which the growth rate is maximized subject to mass-balance constraints. A variety of cell functions in response to environmental stimuli can be quantified using flux balance analysis by parameterizing the linear program with respect to extracellular conditions. However, for most large, genome-scale metabolic networks of practical interest, the resulting parametric problem has multiple and highly degenerate optimal solutions, which are computationally challenging to handle. An improved multi-parametric programming algorithm based on active-set methods is introduced in this paper to overcome these computational difficulties. Degeneracy and multiplicity are handled, respectively, by introducing generalized inverses and auxiliary objective functions into the formulation of the optimality conditions. These improvements are especially effective for metabolic networks because their stoichiometry matrices are generally sparse; thus, fast and efficient algorithms from sparse linear algebra can be leveraged to compute generalized inverses and null-space bases. We illustrate the application of our algorithm to flux balance analysis of metabolic networks by studying a reduced metabolic model of Corynebacterium glutamicum and a genome-scale model of Escherichia coli. We then demonstrate how the critical regions resulting from these studies can be associated with optimal metabolic modes and discuss the physical relevance of optimal pathways arising from various auxiliary objective functions. Achieving more than fivefold improvement in computational speed over existing multi-parametric programming tools, the proposed algorithm proves promising in handling genome-scale metabolic models.     

On asymptotic properties of matrix semigroups with an invariant cone

Recently, several research efforts showed that the analysis of joint spectral characteristics of sets of matrices can be simplified when these matrices share an invariant cone. We prove new results in this direction.We prove that the joint spectral subradius is continuous in the neighborhood of sets of matrices that leave an embedded pair of cones invariant.We show that both the averaged maximal spectral radius, as well as the maximal trace, where the maximum is taken on all the products of the same length t, converge towards the joint spectral radius when t increases, provided that the matrices share an invariant cone, and additionally one of them is primitive.     

Generalized tangent cone and an optimization problem in a normed space

Most abstract multiplier rules in the literature are based on the tangential approximation at a point to some set in a Banach space. The present paper is concerned with the study of a generalized tangent cone, which is a tangential approximation to that set at a common point of two sets. The new notion of tangent cone generalizes previous concepts of tangent cones. This generalized tangent cone is used to characterize the optimality conditions for a simultaneous maximization and minimization problem. The paper is of theoretical character; practical applications are not found so far.     

Application of homotopy analysis method for natural convection of Darcian fluid about a vertical full cone embedded in pours media prescribed surface heat flux

In this paper, a powerful analytical method, called homotopy analysis method (HAM) is used to obtain the analytical solution for a nonlinear ordinary deferential equation that often appear in boundary layers problems arising in heat and mass transfer which these kinds of the equations contain infinity boundary condition. The boundary layer approximations of fluid flow and heat transfer of vertical full cone embedded in porous media give us the similarity solution for full cone subjected to surface heat flux boundary conditions. Nonlinear ODE which is obtained by similarity solution has been solved through homotopy analysis method (HAM). The main objective is to propose alternative methods of solution, which do not require small parameters and avoid linearization and physically unrealistic assumptions. The obtained analytical solution in comparison with the numerical ones represents a remarkable accuracy. The results also indicate that HAM can provide us with a convenient way to control and adjust the convergence region.     

A metric approach to asymptotic analysis

We introduce a notion of “firm” (or uniform) asymptotic cone to an unbounded subset of a normed space. We relate this notion to a concept of “firm” asymptotic function. We use these notions to study boundedness properties which can be applied to continuity questions for some operations on sets and functions. Such questions arise in stability analysis of Hamilton-Jacobi equations. We present some other applications such as an extension of a theorem of Dieudonné and existence results in optimization and fixed point theory.     

A method for constructing the polar cone of a polyhedral cone,with applications to linear multicriteria decision problems

The necessary and sufficient conditions for solution sets of linear multicriteria decision problems are given in the first part of this paper. In order to find the solution sets by applying the theorem describing the conditions, the constructions of the open polar cone and the semi-open polar cone of a given polyhedral cone are required.A method of construction of the polar cone, open polar cone, and semi-open polar cone is presented. For this purpose, edge vectors of the polar cone are introduced and characterized in terms of the generating vectors of a given polyhedral cone. It is shown that these polar cones are represented by the edge vectors.Numerical examples of linear multicriteria decision problems are solved to illustrate the construction of the polar cones and to explain the application of the theorem to obtain the solution sets.The author is grateful to Professor P. L. Yu for helpful comments concerning the development of Theorem 2.1.     

一类非凸区域的拟法锥构造方法及其在非凸规划求解中的应用

本文给出基于球形的一类满足拟法锥条件区域的拟法锥构造方法,基于该可行域的拟法锥,建立求解在该类非凸区域上的规划问题的K-K-T点的部分凝聚同伦组合方程,并证明了该同伦内点法的整体收敛性,给出实现同伦内点法的具体数值跟踪算法步骤,并通过数值例子证明算法是可行的和有效的．     

A combinatorial proof of a fixed point property

A class of finite simplicial complexes, called pseudo cones, is developed that has a number of useful combinatorial properties. A partially ordered set is a pseudo cone if its order complex is a pseudo cone. Pseudo cones can be constructed from other pseudo cones in a number of ways. Pseudo cone ordered sets include finite dismantlable ordered sets and finite truncated noncomplemented lattices. The main result of the paper is a combinatorial proof of the fixed simplex property for finite pseudo cones in which a combinatorial structure is constructed that relates fixed simplices to one another. This gives combinatorial proofs of some well known non-constructive results in the fixed point theory of finite partially ordered sets.     

Nonlinear instability of hypersonic flow over a cone

This study investigates the nonlinear stability of hypersonicviscous flow over a sharp slender cone. The attached shock andthe effects of curvature are taken into account. Asymptoticmethods are used for large Reynolds number and large Mach numberto examine the viscous modes of instability, which may be describedby a triple-deck structure. A weakly nonlinear analysis is carriedout allowing an equation for the amplitude of disturbances tobe derived. The coefficients of the terms in the amplitude equationare evaluated for axisymmetric and non-axisymmetric disturbances.Thus, the effects of the shock and curvature on the nonlinearstability of the flow may be deduced.     

On merit functions for <Emphasis Type="Italic">p</Emphasis>-order cone complementarity problem

Merit function approach is a popular method to deal with complementarity problems, in which the complementarity problem is recast as an unconstrained minimization via merit function or complementarity function. In this paper, for the complementarity problem associated with p-order cone, which is a type of nonsymmetric cone complementarity problem, we show the readers how to construct merit functions for solving p-order cone complementarity problem. In addition, we study the conditions under which the level sets of the corresponding merit functions are bounded, and we also assert that these merit functions provide an error bound for the p-order cone complementarity problem. These results build up a theoretical basis for the merit method for solving p-order cone complementarity problem.