Enumerating constrained elementary flux vectors of metabolic networks

The concept of elementary vector is generalised to the case where the steady-state space of the metabolic network is not a flux cone but is a general polyhedron due to further inhomogeneous constraints on the flows through some of the reactions. On one hand, this allows to selectively enumerate elementary modes which satisfy certain optimality criteria and this can yield a large computational gain compared with full enumeration. On the other hand, in contrast to the single optimum found by executing a linear program, this enables a comprehensive description of the set of alternate optima often encountered in flux balance analysis. The concepts are illustrated on a metabolic network model of human cardiac mitochondria.

Simulating the evolution of a clonal trait in plants with sexual and vegetative reproduction

Aims Phenotypic optimality models neglect genetics. However, especially when heterozygous genotypes ire fittest, evolving allele, genotype and phenotype frequencies may not correspond to predicted optima. This was not previously addressed for organisms with complex life histories. Methods Therefore, we modelled the evolution of a fitness-relevant trait of clonal plants, stolon internode length. We explored the likely case of air asymmetric unimodal fitness profile with three model types. In constant selection models (CSMs), which are gametic, but not spatially explicit, evolving allele frequencies in the one-locus and five-loci cases did not correspond to optimum stolon internode length predicted by the spatially explicit, but not gametic, phenotypic model. This deviation was due to the asymmetry of the fitness profile. Gametic, spatially explicit individual-based (SEIB) modeling allowed us relaxing the CSM assumptions of constant selection with exclusively sexual reproduction. Important findings For entirely vegetative or sexual reproduction, predictions. of the gametic SEIB model were close to the ones of spatially explicit CSMs gametic phenotypic models, hut for mixed modes of reproduction they appoximated those of gametic, not spatially explicit CSMs. Thus, in contrast to gametic SEIB models, phenotypic models and, especially for few loci, also CSMs can be very misleading. We conclude that the evolution of trails governed by few quantitative trait loci appears hardly predictable by simple models, that genetic algorithms aiming at technical optimization may actually, miss the optimum and that selection may lead to loci with smaller effects, in derived compared with ancestral lines.

Resource-allocation capabilities of commercial project management software. An experimental analysis

When project managers determine schedules for resource-constrained projects, they commonly use commercial project management software packages. Which resource-allocation methods are implemented in these packages is proprietary information. The resource-allocation problem is in general computationally difficult to solve to optimality. Hence, the question arises if and how various project management software packages differ in quality with respect to their resource-allocation capabilities. None of the few existing papers on this subject uses a sizeable data set and recent versions of common software packages. We experimentally analyze the resource-allocation capabilities of Acos Plus.1, AdeptTracker Professional, CS Project Professional, Microsoft Office Project 2007, Primavera P6, Sciforma PS8, and Turbo Project Professional. Our analysis is based on 1560 instances of the precedence- and resource-constrained project scheduling problem RCPSP. The experiment shows that using the resource-allocation feature of these packages may lead to a project duration increase of almost 115% above the best known feasible schedule. The increase gets larger with increasing resource scarcity and with increasing number of activities. We investigate the impact of different complexity scenarios and priority rules on the project duration obtained by the software packages. We provide a decision table to support managers in selecting a software package and a priority rule.

A continuous-time MILP model for short-term scheduling of make-and-pack production processes

In process industries, make-and-pack production is used to produce food and beverages, chemicals, and metal products, among others. This type of production process allows the fabrication of a wide range of products in relatively small amounts using the same equipment. In this article, we consider a real-world production process (cf. Honkomp et al. 2000. The curse of reality – why process scheduling optimization problems are diffcult in practice. Computers & Chemical Engineering, 24, 323–328.) comprising sequence-dependent changeover times, multipurpose storage units with limited capacities, quarantine times, batch splitting, partial equipment connectivity, and transfer times. The planning problem consists of computing a production schedule such that a given demand of packed products is fulfilled, all technological constraints are satisfied, and the production makespan is minimised. None of the models in the literature covers all of the technological constraints that occur in such make-and-pack production processes. To close this gap, we develop an efficient mixed-integer linear programming model that is based on a continuous time domain and general-precedence variables. We propose novel types of symmetry-breaking constraints and a preprocessing procedure to improve the model performance. In an experimental analysis, we show that small- and moderate-sized instances can be solved to optimality within short CPU times.

Egalitarianism under Earmark Constraints

Agents with single-peaked preferences share a resource coming from different suppliers; each agent is connected to only a subset of suppliers. Examples include workload balancing, sharing earmarked funds, and rationing utilities after a storm. Unlike in the one supplier model, in a Pareto optimal allocation agents who get more than their peak from underdemanded suppliers, coexist with agents who get less from overdemanded suppliers. Our Egalitarian solution is the Lorenz dominant Pareto optimal allocation. It treats agents with equal demands as equally as the connectivity constraints allow. Together, Strategyproofness, Pareto Optimality, and Equal Treatment of Equals, characterize our solution.

Guaranteed greedy routing in overlay networks

Greedy routing can be used in mobile ad-hoc networks as geographic routing protocol. This paper proposes to use greedy routing also in overlay networks by positioning overlay nodes into a multi-dimensional Euclidean space. Greedy routing can only be applied when a routing decision makes progress towards the final destination. Our proposed overlay network is built such that there will be always progress at each forwarding node. This is achieved by constructing at each node a so-called nearest neighbor convex set (NNCS). NNCSs can be used for various applications such as multicast routing, service discovery and Quality-of-Service routing. NNCS has been compared with Pastry, another topology-aware overlay network. NNCS has superior relative path stretches indicating the optimality of a path.

On an Application of Microsoft Excel’s Evolutionary Solver to the Resource-Constrained Project Scheduling Problem RCPSP

The Solver Add-in of Microsoft Excel is widely used in courses on Operations Research and in industrial applications. Since the 2010 version of Microsoft Excel, the Solver Add-in comprises a so-called evolutionary solver. We analyze how this metaheuristic can be applied to the resource-constrained project scheduling problem (RCPSP). We present an implementation of a schedule-generation scheme in a spreadsheet, which combined with the evolutionary solver can be used for devising good feasible schedules. Our computational results indicate that using this approach, non-trivial instances of the RCPSP can be (approximately) solved to optimality.

hp-DGFEM for second-order mixed elliptic problems polyhedra

We prove exponential rates of convergence of hp-version discontinuous Galerkin (dG) interior penalty finite element methods for second-order elliptic problems with mixed Dirichlet-Neumann boundary conditions in axiparallel polyhedra. The dG discretizations are based on axiparallel, σ-geometric anisotropic meshes of mapped hexahedra and anisotropic polynomial degree distributions of μ-bounded variation. We consider piecewise analytic solutions which belong to a larger analytic class than those for the pure Dirichlet problem considered in [11, 12]. For such solutions, we establish the exponential convergence of a nonconforming dG interpolant given by local L 2 -projections on elements away from corners and edges, and by suitable local low-order quasi-interpolants on elements at corners and edges. Due to the appearance of non-homogeneous, weighted norms in the analytic regularity class, new arguments are introduced to bound the dG consistency errors in elements abutting on Neumann edges. The non-homogeneous norms also entail some crucial modifications of the stability and quasi-optimality proofs, as well as of the analysis for the anisotropic interpolation operators. The exponential convergence bounds for the dG interpolant constructed in this paper generalize the results of [11, 12] for the pure Dirichlet case.