Chvátal, V
2011-01-01
This book is a collection of six articles arising from the meeting of the NATO Advanced Study Institute (ASI) "Combinatorial Optimization: Methods and Applications," which was held at the University of Montreal in June 2006. This ASI consisted of seven series of five one-hour lectures and one series of four one-hour lectures. It was attended by some sixty students of graduate or postdoctoral level from fifteen countries worldwide. It includes topics such as: integer and mixed integer programming, facility location, branching on split disjunctions, convexity in combinatorial optimizat
Applications of combinatorial optimization
Paschos, Vangelis Th
2013-01-01
Combinatorial optimization is a multidisciplinary scientific area, lying in the interface of three major scientific domains: mathematics, theoretical computer science and management. The three volumes of the Combinatorial Optimization series aims to cover a wide range of topics in this area. These topics also deal with fundamental notions and approaches as with several classical applications of combinatorial optimization. "Applications of Combinatorial Optimization" is presenting a certain number among the most common and well-known applications of Combinatorial Optimization.
Concepts of combinatorial optimization
Paschos, Vangelis Th
2014-01-01
Combinatorial optimization is a multidisciplinary scientific area, lying in the interface of three major scientific domains: mathematics, theoretical computer science and management. The three volumes of the Combinatorial Optimization series aim to cover a wide range of topics in this area. These topics also deal with fundamental notions and approaches as with several classical applications of combinatorial optimization.Concepts of Combinatorial Optimization, is divided into three parts:- On the complexity of combinatorial optimization problems, presenting basics about worst-case and randomi
Integer and combinatorial optimization
Nemhauser, George L
1999-01-01
Rave reviews for INTEGER AND COMBINATORIAL OPTIMIZATION ""This book provides an excellent introduction and survey of traditional fields of combinatorial optimization . . . It is indeed one of the best and most complete texts on combinatorial optimization . . . available. [And] with more than 700 entries, [it] has quite an exhaustive reference list.""-Optima ""A unifying approach to optimization problems is to formulate them like linear programming problems, while restricting some or all of the variables to the integers. This book is an encyclopedic resource for such f
Polyhedral Techniques in Combinatorial Optimization
Aardal, K.I.; van Hoesel, S.
1995-01-01
Combinatorial optimization problems arise in several areas ranging from management to mathematics and graph theory. Most combinatorial optimization problems are compu- tationally hard due to the restriction that a subset of the variables have to take integral values. During the last two decades
Universally Balanced Combinatorial Optimization Games
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Xiaotie Deng
2010-09-01
Full Text Available This article surveys studies on universally balanced properties of cooperative games defined in a succinct form. In particular, we focus on combinatorial optimization games in which the values to coalitions are defined through linear optimization programs, possibly combinatorial, that is subject to integer constraints. In economic settings, the integer requirement reflects some forms of indivisibility. We are interested in the classes of games that guarantee a non-empty core no matter what are the admissible values assigned to the parameters defining these programs. We call such classes universally balanced. We present characterization and complexity results on the universally balancedness property for some classes of interesting combinatorial optimization games. In particular, we focus on the algorithmic properties for identifying universally balancedness for the games under discussion.
Combinatorial optimization theory and algorithms
Korte, Bernhard
2002-01-01
Combinatorial optimization is one of the youngest and most active areas of discrete mathematics, and is probably its driving force today. This book describes the most important ideas, theoretical results, and algorithms of this field. It is conceived as an advanced graduate text, and it can also be used as an up-to-date reference work for current research. The book includes the essential fundamentals of graph theory, linear and integer programming, and complexity theory. It covers classical topics in combinatorial optimization as well as very recent ones. The emphasis is on theoretical results and algorithms with provably good performance. Some applications and heuristics are mentioned, too.
Combinatorial optimization networks and matroids
Lawler, Eugene
2011-01-01
Perceptively written text examines optimization problems that can be formulated in terms of networks and algebraic structures called matroids. Chapters cover shortest paths, network flows, bipartite matching, nonbipartite matching, matroids and the greedy algorithm, matroid intersections, and the matroid parity problems. A suitable text or reference for courses in combinatorial computing and concrete computational complexity in departments of computer science and mathematics.
Some polyhedral results in combinatorial optimization
Xiao, Han; 肖汉
2016-01-01
Many combinatorial optimization problems can be conceived of as optimizing a linear function over a polyhedron. Investigating properties of the associated polyhedron has been evidenced to be a powerful schema for solving combinatorial optimization problems, especially for characterizing min-max relations. Three different topics in combinatorial optimization are explored in this thesis, which fall within a unified characterization: integrality of polyhedra. Various min-max relations in com...
Combinatorial Discovery and Optimization of New Materials
Institute of Scientific and Technical Information of China (English)
Gao Chen; Zhang Xinyi; Yan Dongsheng
2001-01-01
The concept of the combinatorial discovery and optimization of new materials, and its background,importance, and application, as well as its current status in the world, are briefly reviewed in this paper.
Combinatorial optimization tolerances calculated in linear time
Goldengorin, Boris; Sierksma, Gerard
2003-01-01
For a given optimal solution to a combinatorial optimization problem, we show, under very natural conditions, the equality of the minimal values of upper and lower tolerances, where the upper tolerances are calculated for the given optimal solution and the lower tolerances outside the optimal
Combinatorial optimization tolerances calculated in linear time
Goldengorin, Boris; Sierksma, Gerard
2003-01-01
For a given optimal solution to a combinatorial optimization problem, we show, under very natural conditions, the equality of the minimal values of upper and lower tolerances, where the upper tolerances are calculated for the given optimal solution and the lower tolerances outside the optimal soluti
Polyhredral techniques in combinatorial optimization I: theory
Aardal, K.; Hoesel, S. van
2001-01-01
Combinatorial optimization problems appear in many disciplines ranging from management and logistics to mathematics, physics, and chemistry. These problems are usually relatively easy to formulate mathematically, but most of them are computationally hard due to the restriction that a subset of the v
Dynamical System Approaches to Combinatorial Optimization
DEFF Research Database (Denmark)
Starke, Jens
2013-01-01
Several dynamical system approaches to combinatorial optimization problems are described and compared. These include dynamical systems derived from penalty methods; the approach of Hopfield and Tank; self-organizing maps, that is, Kohonen networks; coupled selection equations; and hybrid methods....... Many of them are investigated analytically, and the costs of the solutions are compared numerically with those of solutions obtained by simulated annealing and the costs of a global optimal solution. Using dynamical systems, a solution to the combinatorial optimization problem emerges in the limit...... of large times as an asymptotically stable point of the dynamics. The obtained solutions are often not globally optimal but good approximations of it. Dynamical system and neural network approaches are appropriate methods for distributed and parallel processing. Because of the parallelization...
Stochastic Combinatorial Optimization under Probabilistic Constraints
Agrawal, Shipra; Ye, Yinyu
2008-01-01
In this paper, we present approximation algorithms for combinatorial optimization problems under probabilistic constraints. Specifically, we focus on stochastic variants of two important combinatorial optimization problems: the k-center problem and the set cover problem, with uncertainty characterized by a probability distribution over set of points or elements to be covered. We consider these problems under adaptive and non-adaptive settings, and present efficient approximation algorithms for the case when underlying distribution is a product distribution. In contrast to the expected cost model prevalent in stochastic optimization literature, our problem definitions support restrictions on the probability distributions of the total costs, via incorporating constraints that bound the probability with which the incurred costs may exceed a given threshold.
Memetic firefly algorithm for combinatorial optimization
Fister, Iztok; Fister, Iztok; Brest, Janez
2012-01-01
Firefly algorithms belong to modern meta-heuristic algorithms inspired by nature that can be successfully applied to continuous optimization problems. In this paper, we have been applied the firefly algorithm, hybridized with local search heuristic, to combinatorial optimization problems, where we use graph 3-coloring problems as test benchmarks. The results of the proposed memetic firefly algorithm (MFFA) were compared with the results of the Hybrid Evolutionary Algorithm (HEA), Tabucol, and the evolutionary algorithm with SAW method (EA-SAW) by coloring the suite of medium-scaled random graphs (graphs with 500 vertices) generated using the Culberson random graph generator. The results of firefly algorithm were very promising and showed a potential that this algorithm could successfully be applied in near future to the other combinatorial optimization problems as well.
Gems of combinatorial optimization and graph algorithms
Skutella, Martin; Stiller, Sebastian; Wagner, Dorothea
2015-01-01
Are you looking for new lectures for your course on algorithms, combinatorial optimization, or algorithmic game theory? Maybe you need a convenient source of relevant, current topics for a graduate student or advanced undergraduate student seminar? Or perhaps you just want an enjoyable look at some beautiful mathematical and algorithmic results, ideas, proofs, concepts, and techniques in discrete mathematics and theoretical computer science? Gems of Combinatorial Optimization and Graph Algorithms is a handpicked collection of up-to-date articles, carefully prepared by a select group of international experts, who have contributed some of their most mathematically or algorithmically elegant ideas. Topics include longest tours and Steiner trees in geometric spaces, cartograms, resource buying games, congestion games, selfish routing, revenue equivalence and shortest paths, scheduling, linear structures in graphs, contraction hierarchies, budgeted matching problems, and motifs in networks. This ...
Combinatorial optimization with Boolean constraints
Energy Technology Data Exchange (ETDEWEB)
Hulme, B.L.; Worrell, R.B.
1983-02-01
This report shows how Boolean algebraic formula manipulation can be used to solve certain kinds of optimization problems. If the problem can be formulated in terms of 0 to 1 variables and if the feasible solutions can be described by a Boolean equation, then the method of this report can be used. The method generates feasible solutions algebraically as terms of a disjunctive normal form of a Boolean function. Many small sample problems are solved to illustrate the method and the practical situations in which these optimization problems arise.
Natural Dynamics for Combinatorial Optimization
Ovchinnikov, Igor V
2015-01-01
Stochastic and or natural dynamical systems (DSs) are dominated by sudden nonlinear processes such as neuroavalanches, gamma-ray bursts, solar flares, earthquakes etc. that exhibit scale-free statistics. These behaviors also occur in many nanosystems. On phase diagrams, these DSs belong to a finite-width phase that separates the phases of thermodynamic equilibrium and ordinary chaotic dynamics, and that is known under such names as intermittency, noise-induced chaos, and self-organized criticality. Within the recently formulated approximation-free cohomological theory of stochastic differential equations, the noise-induced chaos can be roughly interpreted as a noise-induced overlap between regular (integrable) and chaotic (non-integrable) deterministic dynamics so that DSs in this phase inherit the properties of the both. Here, we analyze this unique set of properties and conclude that such DSs must be the most efficient natural optimizers. Based on this understanding, we propose the method of the natural dyn...
Criticality and parallelism in combinatorial optimization
Energy Technology Data Exchange (ETDEWEB)
Macready, W.G.; Kauffman, S.A. [Santa Fe Institute, NM (United States); Siapas, A.G. [Massachusetts Institute of Technology, Cambridge, MA (United States)
1996-01-05
Local search methods constitute one of the most successful approaches to solving large-scale combinatorial optimization problems. As these methods are increasingly parallelized, optimization performance initially improves, but then abruptly degrades to no matter than that of random search beyond a certain point. The existence of this transition is demonstrated for a family of generalized spin-glass models and the traveling salesman problem. Finite-size scaling is used to characterize size-dependent effects near the transition, and analytical insight is obtained through a mean-field approximation. 17 refs., 5 figs.
Combinatorial Multiobjective Optimization Using Genetic Algorithms
Crossley, William A.; Martin. Eric T.
2002-01-01
The research proposed in this document investigated multiobjective optimization approaches based upon the Genetic Algorithm (GA). Several versions of the GA have been adopted for multiobjective design, but, prior to this research, there had not been significant comparisons of the most popular strategies. The research effort first generalized the two-branch tournament genetic algorithm in to an N-branch genetic algorithm, then the N-branch GA was compared with a version of the popular Multi-Objective Genetic Algorithm (MOGA). Because the genetic algorithm is well suited to combinatorial (mixed discrete / continuous) optimization problems, the GA can be used in the conceptual phase of design to combine selection (discrete variable) and sizing (continuous variable) tasks. Using a multiobjective formulation for the design of a 50-passenger aircraft to meet the competing objectives of minimizing takeoff gross weight and minimizing trip time, the GA generated a range of tradeoff designs that illustrate which aircraft features change from a low-weight, slow trip-time aircraft design to a heavy-weight, short trip-time aircraft design. Given the objective formulation and analysis methods used, the results of this study identify where turboprop-powered aircraft and turbofan-powered aircraft become more desirable for the 50 seat passenger application. This aircraft design application also begins to suggest how a combinatorial multiobjective optimization technique could be used to assist in the design of morphing aircraft.
Neural Meta-Memes Framework for Combinatorial Optimization
Song, Li Qin; Lim, Meng Hiot; Ong, Yew Soon
In this paper, we present a Neural Meta-Memes Framework (NMMF) for combinatorial optimization. NMMF is a framework which models basic optimization algorithms as memes and manages them dynamically when solving combinatorial problems. NMMF encompasses neural networks which serve as the overall planner/coordinator to balance the workload between memes. We show the efficacy of the proposed NMMF through empirical study on a class of combinatorial problem, the quadratic assignment problem (QAP).
Bioinspired computation in combinatorial optimization: algorithms and their computational complexity
DEFF Research Database (Denmark)
Neumann, Frank; Witt, Carsten
2012-01-01
Bioinspired computation methods, such as evolutionary algorithms and ant colony optimization, are being applied successfully to complex engineering and combinatorial optimization problems, and it is very important that we understand the computational complexity of these algorithms. This tutorials...
TARCMO: Theory and Algorithms for Robust, Combinatorial, Multicriteria Optimization
2016-11-28
magnitude in computational experiments on portfolio optimization problems. The research on this topic has been published as [CG15a], where details can...AFRL-AFOSR-UK-TR-2017-0001 TARCMO: Theory and Algorithms for Robust, Combinatorial, Multicriteria Optimization Horst Hamacher Technische Universität...To) 15 May 2013 to 12 May 2016 4. TITLE AND SUBTITLE TARCMO: Theory and Algorithms for Robust, Combinatorial, Multicriteria Optimization 5a. CONTRACT
Binary Cockroach Swarm Optimization for Combinatorial Optimization Problem
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Ibidun Christiana Obagbuwa
2016-09-01
Full Text Available The Cockroach Swarm Optimization (CSO algorithm is inspired by cockroach social behavior. It is a simple and efficient meta-heuristic algorithm and has been applied to solve global optimization problems successfully. The original CSO algorithm and its variants operate mainly in continuous search space and cannot solve binary-coded optimization problems directly. Many optimization problems have their decision variables in binary. Binary Cockroach Swarm Optimization (BCSO is proposed in this paper to tackle such problems and was evaluated on the popular Traveling Salesman Problem (TSP, which is considered to be an NP-hard Combinatorial Optimization Problem (COP. A transfer function was employed to map a continuous search space CSO to binary search space. The performance of the proposed algorithm was tested firstly on benchmark functions through simulation studies and compared with the performance of existing binary particle swarm optimization and continuous space versions of CSO. The proposed BCSO was adapted to TSP and applied to a set of benchmark instances of symmetric TSP from the TSP library. The results of the proposed Binary Cockroach Swarm Optimization (BCSO algorithm on TSP were compared to other meta-heuristic algorithms.
From combinatorial optimization to real algebraic geometry and back
Directory of Open Access Journals (Sweden)
Janez Povh
2014-12-01
Full Text Available In this paper, we explain the relations between combinatorial optimization and real algebraic geometry with a special focus to the quadratic assignment problem. We demonstrate how to write a quadratic optimization problem over discrete feasible set as a linear optimization problem over the cone of completely positive matrices. The latter formulation enables a hierarchy of approximations which rely on results from polynomial optimization, a sub-eld of real algebraic geometry.
On some interconnections between combinatorial optimization and extremal graph theory
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Cvetković Dragoš M.
2004-01-01
Full Text Available The uniting feature of combinatorial optimization and extremal graph theory is that in both areas one should find extrema of a function defined in most cases on a finite set. While in combinatorial optimization the point is in developing efficient algorithms and heuristics for solving specified types of problems, the extremal graph theory deals with finding bounds for various graph invariants under some constraints and with constructing extremal graphs. We analyze by examples some interconnections and interactions of the two theories and propose some conclusions.
Advances in bio-inspired computing for combinatorial optimization problems
Pintea, Camelia-Mihaela
2013-01-01
Advances in Bio-inspired Combinatorial Optimization Problems' illustrates several recent bio-inspired efficient algorithms for solving NP-hard problems.Theoretical bio-inspired concepts and models, in particular for agents, ants and virtual robots are described. Large-scale optimization problems, for example: the Generalized Traveling Salesman Problem and the Railway Traveling Salesman Problem, are solved and their results are discussed.Some of the main concepts and models described in this book are: inner rule to guide ant search - a recent model in ant optimization, heterogeneous sensitive a
View discovery in OLAP databases through statistical combinatorial optimization
Energy Technology Data Exchange (ETDEWEB)
Hengartner, Nick W [Los Alamos National Laboratory; Burke, John [PNNL; Critchlow, Terence [PNNL; Joslyn, Cliff [PNNL; Hogan, Emilie [PNNL
2009-01-01
OnLine Analytical Processing (OLAP) is a relational database technology providing users with rapid access to summary, aggregated views of a single large database, and is widely recognized for knowledge representation and discovery in high-dimensional relational databases. OLAP technologies provide intuitive and graphical access to the massively complex set of possible summary views available in large relational (SQL) structured data repositories. The capability of OLAP database software systems to handle data complexity comes at a high price for analysts, presenting them a combinatorially vast space of views of a relational database. We respond to the need to deploy technologies sufficient to allow users to guide themselves to areas of local structure by casting the space of 'views' of an OLAP database as a combinatorial object of all projections and subsets, and 'view discovery' as an search process over that lattice. We equip the view lattice with statistical information theoretical measures sufficient to support a combinatorial optimization process. We outline 'hop-chaining' as a particular view discovery algorithm over this object, wherein users are guided across a permutation of the dimensions by searching for successive two-dimensional views, pushing seen dimensions into an increasingly large background filter in a 'spiraling' search process. We illustrate this work in the context of data cubes recording summary statistics for radiation portal monitors at US ports.
PCB Drill Path Optimization by Combinatorial Cuckoo Search Algorithm
Directory of Open Access Journals (Sweden)
Wei Chen Esmonde Lim
2014-01-01
Full Text Available Optimization of drill path can lead to significant reduction in machining time which directly improves productivity of manufacturing systems. In a batch production of a large number of items to be drilled such as printed circuit boards (PCB, the travel time of the drilling device is a significant portion of the overall manufacturing process. To increase PCB manufacturing productivity and to reduce production costs, a good option is to minimize the drill path route using an optimization algorithm. This paper reports a combinatorial cuckoo search algorithm for solving drill path optimization problem. The performance of the proposed algorithm is tested and verified with three case studies from the literature. The computational experience conducted in this research indicates that the proposed algorithm is capable of efficiently finding the optimal path for PCB holes drilling process.
PCB drill path optimization by combinatorial cuckoo search algorithm.
Lim, Wei Chen Esmonde; Kanagaraj, G; Ponnambalam, S G
2014-01-01
Optimization of drill path can lead to significant reduction in machining time which directly improves productivity of manufacturing systems. In a batch production of a large number of items to be drilled such as printed circuit boards (PCB), the travel time of the drilling device is a significant portion of the overall manufacturing process. To increase PCB manufacturing productivity and to reduce production costs, a good option is to minimize the drill path route using an optimization algorithm. This paper reports a combinatorial cuckoo search algorithm for solving drill path optimization problem. The performance of the proposed algorithm is tested and verified with three case studies from the literature. The computational experience conducted in this research indicates that the proposed algorithm is capable of efficiently finding the optimal path for PCB holes drilling process.
Combinatorial particle swarm optimization for solving blocking flowshop scheduling problem
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Mansour Eddaly
2016-10-01
Full Text Available This paper addresses to the flowshop scheduling problem with blocking constraints. The objective is to minimize the makespan criterion. We propose a hybrid combinatorial particle swarm optimization algorithm (HCPSO as a resolution technique for solving this problem. At the initialization, different priority rules are exploited. Experimental study and statistical analysis were performed to select the most adapted one for this problem. Then, the swarm behavior is tested for solving a combinatorial optimization problem such as a sequencing problem under constraints. Finally, an iterated local search algorithm based on probabilistic perturbation is sequentially introduced to the particle swarm optimization algorithm for improving the quality of solution. The computational results show that our approach is able to improve several best known solutions of the literature. In fact, 76 solutions among 120 were improved. Moreover, HCPSO outperforms the compared methods in terms of quality of solutions in short time requirements. Also, the performance of the proposed approach is evaluated according to a real-world industrial problem.
Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort.
Jeschek, Markus; Gerngross, Daniel; Panke, Sven
2016-01-01
Rational flux design in metabolic engineering approaches remains difficult since important pathway information is frequently not available. Therefore empirical methods are applied that randomly change absolute and relative pathway enzyme levels and subsequently screen for variants with improved performance. However, screening is often limited on the analytical side, generating a strong incentive to construct small but smart libraries. Here we introduce RedLibs (Reduced Libraries), an algorithm that allows for the rational design of smart combinatorial libraries for pathway optimization thereby minimizing the use of experimental resources. We demonstrate the utility of RedLibs for the design of ribosome-binding site libraries by in silico and in vivo screening with fluorescent proteins and perform a simple two-step optimization of the product selectivity in the branched multistep pathway for violacein biosynthesis, indicating a general applicability for the algorithm and the proposed heuristics. We expect that RedLibs will substantially simplify the refactoring of synthetic metabolic pathways.
Combinatorial optimization problem solution based on improved genetic algorithm
Zhang, Peng
2017-08-01
Traveling salesman problem (TSP) is a classic combinatorial optimization problem. It is a simplified form of many complex problems. In the process of study and research, it is understood that the parameters that affect the performance of genetic algorithm mainly include the quality of initial population, the population size, and crossover probability and mutation probability values. As a result, an improved genetic algorithm for solving TSP problems is put forward. The population is graded according to individual similarity, and different operations are performed to different levels of individuals. In addition, elitist retention strategy is adopted at each level, and the crossover operator and mutation operator are improved. Several experiments are designed to verify the feasibility of the algorithm. Through the experimental results analysis, it is proved that the improved algorithm can improve the accuracy and efficiency of the solution.
Development of Combinatorial Methods for Alloy Design and Optimization
Energy Technology Data Exchange (ETDEWEB)
Pharr, George M.; George, Easo P.; Santella, Michael L
2005-07-01
The primary goal of this research was to develop a comprehensive methodology for designing and optimizing metallic alloys by combinatorial principles. Because conventional techniques for alloy preparation are unavoidably restrictive in the range of alloy composition that can be examined, combinatorial methods promise to significantly reduce the time, energy, and expense needed for alloy design. Combinatorial methods can be developed not only to optimize existing alloys, but to explore and develop new ones as well. The scientific approach involved fabricating an alloy specimen with a continuous distribution of binary and ternary alloy compositions across its surface--an ''alloy library''--and then using spatially resolved probing techniques to characterize its structure, composition, and relevant properties. The three specific objectives of the project were: (1) to devise means by which simple test specimens with a library of alloy compositions spanning the range interest can be produced; (2) to assess how well the properties of the combinatorial specimen reproduce those of the conventionally processed alloys; and (3) to devise screening tools which can be used to rapidly assess the important properties of the alloys. As proof of principle, the methodology was applied to the Fe-Ni-Cr ternary alloy system that constitutes many commercially important materials such as stainless steels and the H-series and C-series heat and corrosion resistant casting alloys. Three different techniques were developed for making alloy libraries: (1) vapor deposition of discrete thin films on an appropriate substrate and then alloying them together by solid-state diffusion; (2) co-deposition of the alloying elements from three separate magnetron sputtering sources onto an inert substrate; and (3) localized melting of thin films with a focused electron-beam welding system. Each of the techniques was found to have its own advantages and disadvantages. A new and very
Trajectory and Population Metaheuristics applied to Combinatorial Optimization Problems
Directory of Open Access Journals (Sweden)
Natalia Alancay
2016-04-01
Full Text Available In the world there are a multitude of everyday problems that require a solution that meets a set of requirements in the most appropriate way maximizing or minimizing a certain value. However, finding an optimal solution for certain optimization problems can be an incredibly difficult or an impossible task. This is because when a problem becomes large enough, we have to look through a huge number of possible solutions, the most efficient solution, that is, the one that has the lower cost. The ways to treat feasible solutions for their practical application are varied. One of the strategy that has gained a great acceptance and that has been getting an important formal body are the metaheuristics since it is established strategies to cross and explore the space of solutions of the problem usually generated in a random and iterative way. The main advantage of this technique is their flexibility and robustness, which allows them to be applied to a wide range of problems. In this work we focus on a metaheuristic based on Simulated Annealing trajectory and a population - based Cellular Genetic Algorithm with the objective of carrying out a study and comparison of the results obtained in its application for the resolution of a set of academic problems of combinatorial optimization.
AN ADAPTIVE MEMBRANE ALGORITHM FOR SOLVING COMBINATORIAL OPTIMIZATION PROBLEMS
Institute of Scientific and Technical Information of China (English)
Juanjuan HE; Jianhua XIAO; Zehui SHAO
2014-01-01
Membrane algorithms (MAs), which inherit from P systems, constitute a new parallel and distribute framework for approximate computation. In the paper, a membrane algorithm is proposed with the improvement that the involved parameters can be adaptively chosen. In the algorithm, some membranes can evolve dynamically during the computing process to specify the values of the requested parameters. The new algorithm is tested on a well-known combinatorial optimization problem, the travelling salesman problem. The em-pirical evidence suggests that the proposed approach is efficient and reliable when dealing with 11 benchmark instances, particularly obtaining the best of the known solutions in eight instances. Compared with the genetic algorithm, simulated annealing algorithm, neural net-work and a fine-tuned non-adaptive membrane algorithm, our algorithm performs better than them. In practice, to design the airline network that minimize the total routing cost on the CAB data with twenty-five US cities, we can quickly obtain high quality solutions using our algorithm.
Hartmann, Alexander K
2005-01-01
A concise, comprehensive introduction to the topic of statistical physics of combinatorial optimization, bringing together theoretical concepts and algorithms from computer science with analytical methods from physics. The result bridges the gap between statistical physics and combinatorial optimization, investigating problems taken from theoretical computing, such as the vertex-cover problem, with the concepts and methods of theoretical physics. The authors cover rapid developments and analytical methods that are both extremely complex and spread by word-of-mouth, providing all the necessary
Zhang, Gexiang; Rong, Haina; Neri, Ferrante; Pérez-Jiménez, Mario J
2014-08-01
Membrane systems (also called P systems) refer to the computing models abstracted from the structure and the functioning of the living cell as well as from the cooperation of cells in tissues, organs, and other populations of cells. Spiking neural P systems (SNPS) are a class of distributed and parallel computing models that incorporate the idea of spiking neurons into P systems. To attain the solution of optimization problems, P systems are used to properly organize evolutionary operators of heuristic approaches, which are named as membrane-inspired evolutionary algorithms (MIEAs). This paper proposes a novel way to design a P system for directly obtaining the approximate solutions of combinatorial optimization problems without the aid of evolutionary operators like in the case of MIEAs. To this aim, an extended spiking neural P system (ESNPS) has been proposed by introducing the probabilistic selection of evolution rules and multi-neurons output and a family of ESNPS, called optimization spiking neural P system (OSNPS), are further designed through introducing a guider to adaptively adjust rule probabilities to approximately solve combinatorial optimization problems. Extensive experiments on knapsack problems have been reported to experimentally prove the viability and effectiveness of the proposed neural system.
Combinatorial Clustering Algorithm of Quantum-Behaved Particle Swarm Optimization and Cloud Model
Directory of Open Access Journals (Sweden)
Mi-Yuan Shan
2013-01-01
Full Text Available We propose a combinatorial clustering algorithm of cloud model and quantum-behaved particle swarm optimization (COCQPSO to solve the stochastic problem. The algorithm employs a novel probability model as well as a permutation-based local search method. We are setting the parameters of COCQPSO based on the design of experiment. In the comprehensive computational study, we scrutinize the performance of COCQPSO on a set of widely used benchmark instances. By benchmarking combinatorial clustering algorithm with state-of-the-art algorithms, we can show that its performance compares very favorably. The fuzzy combinatorial optimization algorithm of cloud model and quantum-behaved particle swarm optimization (FCOCQPSO in vague sets (IVSs is more expressive than the other fuzzy sets. Finally, numerical examples show the clustering effectiveness of COCQPSO and FCOCQPSO clustering algorithms which are extremely remarkable.
New Meta-Heuristic for Combinatorial Optimization Problems:Intersection Based Scaling
Institute of Scientific and Technical Information of China (English)
Peng Zou; Zhi Zhou; Ying-Yu Wan; Guo-Liang Chen; Jun Gu
2004-01-01
Combinatorial optimization problems are found in many application fields such as computer science, engineering and economy. In this paper, a new efficient meta-heuristic, Intersection-Based Scaling (IBS for abbreviation),is proposed and it can be applied to the combinatorial optimization problems. The main idea of IBS is to scale the size of the instance based on the intersection of some local optima, and to simplify the search space by extracting the intersection from the instance, which makes the search more efficient. The combination of IBS with some local search heuristics of different combinatorial optimization problems such as Traveling Salesman Problem (TSP) and Graph Partitioning Problem (GPP) is studied, and comparisons are made with some of the best heuristic algorithms and meta-heuristic algorithms. It is found that it has significantly improved the performance of existing local search heuristics and significantly outperforms the known best algorithms.
An Optimal Multi-Unit Combinatorial Procurement Auction with Single Minded Bidders
Gujar, Sujit
2009-01-01
The current art in optimal combinatorial auctions is limited to handling the case of single units of multiple items, with each bidder bidding on exactly one bundle (single minded bidders). This paper extends the current art by proposing an optimal auction for procuring multiple units of multiple items when the bidders are single minded. The auction minimizes the cost of procurement while satisfying Bayesian incentive compatibility and interim individual rationality. Under appropriate regularity conditions, this optimal auction also satisfies dominant strategy incentive compatibility.
Combinatorial Optimization of Transparent Conducting Oxides (TCOS) for PV
Energy Technology Data Exchange (ETDEWEB)
Perkins, J. D.; Taylor, M. P.; van Hest, M.F.A.M.; Teplin, C. W.; Alleman, J. L.; Dabney, M. S.; Gedvilas, L. M.; Keyes, B. M.; To, B.; Readey, D. W.; Delahoy, A. E.; Guo, S.; Ginley, D. S.
2005-02-01
Transparent conducting oxides (TCOs) can serve a variety of important functions in thin-film photovoltaics such as transparent electrical contacts, antireflection coatings, and chemical barriers. Two areas of particular interest are TCOs that can be deposited at low temperatures and TCOs with high carrier mobilities. We have employed combinatorial high-throughput approaches to investigate both these areas. Conductivities of s = 2500 W-1-cm-1 have been obtained for In-Zn-O (IZO) films deposited at 100 C and s > 5000 W-1-cm-1 for In-Ti-O (ITiO) and In-Mo-O (IMO) films deposited at 550 C. The highest mobility obtained was 83 cm2/V-s for ITiO deposited at 550 C.
Warners, J.P.
1997-01-01
We show how a large class of combinatorial optimization problems can be reformulated as a nonconvex minimization problem over the unit hyper cube with continuous variables. No additional constraints are required; all constraints are incorporated in the n onconvex objective function, which is a polyn
Chang, Yuchao; Tang, Hongying; Cheng, Yongbo; Zhao, Qin; Yuan, Baoqing Li andXiaobing
2017-07-19
Routing protocols based on topology control are significantly important for improving network longevity in wireless sensor networks (WSNs). Traditionally, some WSN routing protocols distribute uneven network traffic load to sensor nodes, which is not optimal for improving network longevity. Differently to conventional WSN routing protocols, we propose a dynamic hierarchical protocol based on combinatorial optimization (DHCO) to balance energy consumption of sensor nodes and to improve WSN longevity. For each sensor node, the DHCO algorithm obtains the optimal route by establishing a feasible routing set instead of selecting the cluster head or the next hop node. The process of obtaining the optimal route can be formulated as a combinatorial optimization problem. Specifically, the DHCO algorithm is carried out by the following procedures. It employs a hierarchy-based connection mechanism to construct a hierarchical network structure in which each sensor node is assigned to a special hierarchical subset; it utilizes the combinatorial optimization theory to establish the feasible routing set for each sensor node, and takes advantage of the maximum-minimum criterion to obtain their optimal routes to the base station. Various results of simulation experiments show effectiveness and superiority of the DHCO algorithm in comparison with state-of-the-art WSN routing algorithms, including low-energy adaptive clustering hierarchy (LEACH), hybrid energy-efficient distributed clustering (HEED), genetic protocol-based self-organizing network clustering (GASONeC), and double cost function-based routing (DCFR) algorithms.
Optimal weighted combinatorial forecasting model of QT dispersion of ECGs in Chinese adults.
Wen, Zhang; Miao, Ge; Xinlei, Liu; Minyi, Cen
2016-07-01
This study aims to provide a scientific basis for unifying the reference value standard of QT dispersion of ECGs in Chinese adults. Three predictive models including regression model, principal component model, and artificial neural network model are combined to establish the optimal weighted combination model. The optimal weighted combination model and single model are verified and compared. Optimal weighted combinatorial model can reduce predicting risk of single model and improve the predicting precision. The reference value of geographical distribution of Chinese adults' QT dispersion was precisely made by using kriging methods. When geographical factors of a particular area are obtained, the reference value of QT dispersion of Chinese adults in this area can be estimated by using optimal weighted combinatorial model and reference value of the QT dispersion of Chinese adults anywhere in China can be obtained by using geographical distribution figure as well.
DEFF Research Database (Denmark)
Moghadasi, Amirhasan; Sarwat, Arif; Guerrero, Josep M.
2016-01-01
on the extreme load reduction is effectively demonstrated. A large WPP has a complicated structure using several components, and the inclusion of RSFCL composes this layout more problematic for optimal performance of the system. Hence, the most-widely decision-making technique based on the analytic hierarchy...... process (AHP) is proposed for the optimal design of the combinatorial RSFCL and 50MW WPP to compute the three-dimensional alignment in Pareto front at the end of the optimization run. The numerical simulations verify effectiveness of the proposed approach, using the Pareto optimality concept....
Optimization Query Process of Mediators Interrogation Based On Combinatorial Storage
Directory of Open Access Journals (Sweden)
L. Cherrat
2013-05-01
Full Text Available In the distributed environment where a query involves several heterogeneous sources, communication costs must be taken into consideration. In this paper we describe a query optimization approach using dynamic programming technique for set integrated heterogeneous sources. The objective of the optimization is to minimize the total processing time including load processing, request rewriting and communication costs, to facilitate communication inter-sites and to optimize the time of data transfer from site to others. Moreover, the ability to store data in more than one centre site provides more flexibility in terms of Security/Safety and overload of the network. In contrast to optimizers which are considered a restricted search space, the proposed optimizer searches the closed subsets of sources and independency relationship which may be deep laniary or hierarchical trees. Especially the execution of the queries can start traversal anywhere over any subset and not only from a specific source.
Wanneng Shu
2009-01-01
Quantum-inspired genetic algorithm (QGA) is applied to simulated annealing (SA) to develop a class of quantum-inspired simulated annealing genetic algorithm (QSAGA) for combinatorial optimization. With the condition of preserving QGA advantages, QSAGA takes advantage of the SA algorithm so as to avoid premature convergence. To demonstrate its effectiveness and applicability, experiments are carried out on the knapsack problem. The results show that QSAGA performs well, without premature conve...
Juan, Angel A.; Javier Faulin; Scott E. Grasman; Markus Rabe; Gonçalo Figueira
2015-01-01
Many combinatorial optimization problems (COPs) encountered in real-world logistics, transportation, production, healthcare, financial, telecommunication, and computing applications are NP-hard in nature. These real-life COPs are frequently characterized by their large-scale sizes and the need for obtaining high-quality solutions in short computing times, thus requiring the use of metaheuristic algorithms. Metaheuristics benefit from different random-search and parallelization paradigms, but ...
Scheduling Internal Audit Activities: A Stochastic Combinatorial Optimization Problem
Rossi, R.; Tarim, S.A.; Hnich, B.; Prestwich, S.; Karacaer, S.
2010-01-01
The problem of finding the optimal timing of audit activities within an organisation has been addressed by many researchers. We propose a stochastic programming formulation with Mixed Integer Linear Programming (MILP) and Constraint Programming (CP) certainty-equivalent models. In experiments neithe
Scheduling Internal Audit Activities: A Stochastic Combinatorial Optimization Problem
Rossi, R.; Tarim, S.A.; Hnich, B.; Prestwich, S.; Karacaer, S.
2010-01-01
The problem of finding the optimal timing of audit activities within an organisation has been addressed by many researchers. We propose a stochastic programming formulation with Mixed Integer Linear Programming (MILP) and Constraint Programming (CP) certainty-equivalent models. In experiments
Directory of Open Access Journals (Sweden)
Fushing Hsieh
2016-11-01
Full Text Available Discrete combinatorial optimization problems in real world are typically defined via an ensemble of potentially high dimensional measurements pertaining to all subjects of a system under study. We point out that such a data ensemble in fact embeds with system's information content that is not directly used in defining the combinatorial optimization problems. Can machine learning algorithms extract such information content and make combinatorial optimizing tasks more efficient? Would such algorithmic computations bring new perspectives into this classic topic of Applied Mathematics and Theoretical Computer Science? We show that answers to both questions are positive. One key reason is due to permutation invariance. That is, the data ensemble of subjects' measurement vectors is permutation invariant when it is represented through a subject-vs-measurement matrix. An unsupervised machine learning algorithm, called Data Mechanics (DM, is applied to find optimal permutations on row and column axes such that the permuted matrix reveals coupled deterministic and stochastic structures as the system's information content. The deterministic structures are shown to facilitate geometry-based divide-and-conquer scheme that helps optimizing task, while stochastic structures are used to generate an ensemble of mimicries retaining the deterministic structures, and then reveal the robustness pertaining to the original version of optimal solution. Two simulated systems, Assignment problem and Traveling Salesman problem, are considered. Beyond demonstrating computational advantages and intrinsic robustness in the two systems, we propose brand new robust optimal solutions. We believe such robust versions of optimal solutions are potentially more realistic and practical in real world settings.
A methodology to find the elementary landscape decomposition of combinatorial optimization problems.
Chicano, Francisco; Whitley, L Darrell; Alba, Enrique
2011-01-01
A small number of combinatorial optimization problems have search spaces that correspond to elementary landscapes, where the objective function f is an eigenfunction of the Laplacian that describes the neighborhood structure of the search space. Many problems are not elementary; however, the objective function of a combinatorial optimization problem can always be expressed as a superposition of multiple elementary landscapes if the underlying neighborhood used is symmetric. This paper presents theoretical results that provide the foundation for algebraic methods that can be used to decompose the objective function of an arbitrary combinatorial optimization problem into a sum of subfunctions, where each subfunction is an elementary landscape. Many steps of this process can be automated, and indeed a software tool could be developed that assists the researcher in finding a landscape decomposition. This methodology is then used to show that the subset sum problem is a superposition of two elementary landscapes, and to show that the quadratic assignment problem is a superposition of three elementary landscapes.
Adaptive Uncertainty Resolution in Bayesian Combinatorial Optimization Problems
Guha, Sudipto
2008-01-01
In several applications such as databases, planning, and sensor networks, parameters such as selectivity, load, or sensed values are known only with some associated uncertainty. The performance of such a system (as captured by some objective function over the parameters) is significantly improved if some of these parameters can be probed or observed. In a resource constrained situation, deciding which parameters to observe in order to optimize system performance itself becomes an interesting and important optimization problem. This general problem is the focus of this paper. One of the most important considerations in this framework is whether adaptivity is required for the observations. Adaptive observations introduce blocking or sequential operations in the system whereas non-adaptive observations can be performed in parallel. One of the important questions in this regard is to characterize the benefit of adaptivity for probes and observation. We present general techniques for designing constant factor appr...
Smooth Constrained Heuristic Optimization of a Combinatorial Chemical Space
2015-05-01
CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7...Advances in computational protein design. Curr Opin Struct Biol. 2004;14(4):487–494. 4. Mang NG, Zeng C. Reference energy extremal optimization: A
Algorithms and theoretical topics on selected combinatorial optimization problems
Kaveh, Arman
2010-01-01
We study the Quadratic Assignment Problem (QAP), Three Dimensional Assignment Problem (3AP) and Quadratic Three Dimensional Assignment Problem (Q3AP), which combines aspects of both QAP and 3AP. The three problems are known to be NP-hard. We propose new algorithms for obtaining near optimal solutions of QAP and 3AP and present computational results. Our algorithms obtain improved solutions in some benchmark instances of QAP and 3AP. We also discuss theoretical results on 3AP and Q3AP such as ...
Theory of Randomized Search Heuristics in Combinatorial Optimization
DEFF Research Database (Denmark)
The rigorous mathematical analysis of randomized search heuristics(RSHs) with respect to their expected runtime is a growing research area where many results have been obtained in recent years. This class of heuristics includes well-known approaches such as Randomized Local Search (RLS), the Metr......The rigorous mathematical analysis of randomized search heuristics(RSHs) with respect to their expected runtime is a growing research area where many results have been obtained in recent years. This class of heuristics includes well-known approaches such as Randomized Local Search (RLS...... analysis of randomized algorithms to RSHs. Mostly, the expected runtime of RSHs on selected problems is analzyed. Thereby, we understand why and when RSHs are efficient optimizers and, conversely, when they cannot be efficient. The tutorial will give an overview on the analysis of RSHs for solving...
Igeta, Hideki; Hasegawa, Mikio
Chaotic dynamics have been effectively applied to improve various heuristic algorithms for combinatorial optimization problems in many studies. Currently, the most used chaotic optimization scheme is to drive heuristic solution search algorithms applicable to large-scale problems by chaotic neurodynamics including the tabu effect of the tabu search. Alternatively, meta-heuristic algorithms are used for combinatorial optimization by combining a neighboring solution search algorithm, such as tabu, gradient, or other search method, with a global search algorithm, such as genetic algorithms (GA), ant colony optimization (ACO), or others. In these hybrid approaches, the ACO has effectively optimized the solution of many benchmark problems in the quadratic assignment problem library. In this paper, we propose a novel hybrid method that combines the effective chaotic search algorithm that has better performance than the tabu search and global search algorithms such as ACO and GA. Our results show that the proposed chaotic hybrid algorithm has better performance than the conventional chaotic search and conventional hybrid algorithms. In addition, we show that chaotic search algorithm combined with ACO has better performance than when combined with GA.
The application of combinatorial approach to the optimization of dielectric/ferroelectric materials
Chang, Hauyee
Combinatorial approaches are methods developed to facilitate the rapid discovery and optimization of materials by the simultaneous synthesis and screening of a large number of compounds within a short period of time. This work describes its application to dielectric and ferroelectric thin film materials, in particular, (Ba,SrCa)TiO3. New methods and instruments for thin film fabrication and measurement are developed to handle the synthesis and analysis of up to thousands of samples simultaneously. Thin films are fabricated with a novel multilayer precursor method. Precursors of the various elemental components within the target compound, such as BaF 2 and TiO2 for BaTiO3, are deposited at room temperature as separate layers. These multilayers are thermally processed under a two step procedure. A low temperature treatment over a period of days interdiffuses the layers to form a homogeneous amorphous intermediate. This is followed by a high temperature crystallization step, which forms the final crystalline product. Effects of dopants on the dielectric constant and loss of (BaSr)TiO 3 are studied with the discrete combinatorial approach, where up to thousands of discrete thin film samples are fabricated on an individual single crystal substrate. A continuous combinatorial sample resembling a ternary phase diagram of (Ba,Sr,Ca)TiO3 is also fabricated in search of the lowest loss compositions that are useful for various applications such as the storage node capacitors in dynamic random access memories. These combinatorial samples of (BaSr,Ca)TiO3 are measured with the newly developed scanning evanescent microwave microscope (SEMM). This instrument is capable of rapid and accurate non-contact characterization of the thin film dielectric constants and losses. The measured results show good agreement with results from more conventional methods such as the interdigital electrodes measurements. Various issues concerning the combinatorial approach in materials science are
Shim, Yong; Jaiswal, Akhilesh; Roy, Kaushik
2017-05-01
Ising spin model is considered as an efficient computing method to solve combinatorial optimization problems based on its natural tendency of convergence towards low energy state. The underlying basic functions facilitating the Ising model can be categorized into two parts, "Annealing and Majority vote." In this paper, we propose an Ising cell based on Spin Hall Effect (SHE) induced magnetization switching in a Magnetic Tunnel Junction (MTJ). The stochasticity of our proposed Ising cell based on SHE induced MTJ switching can implement the natural annealing process by preventing the system from being stuck in solutions with local minima. Further, by controlling the current through the Heavy-Metal (HM) underlying the MTJ, we can mimic the majority vote function which determines the next state of the individual spins. By solving coupled Landau-Lifshitz-Gilbert equations, we demonstrate that our Ising cell can be replicated to map certain combinatorial problems. We present results for two representative problems—Maximum-cut and Graph coloring—to illustrate the feasibility of the proposed device-circuit configuration in solving combinatorial problems. Our proposed solution using a HM based MTJ device can be exploited to implement compact, fast, and energy efficient Ising spin model.
Combinatorial optimization using dynamical phase transitions in driven-dissipative systems
Leleu, Timothée; Yamamoto, Yoshihisa; Utsunomiya, Shoko; Aihara, Kazuyuki
2017-02-01
The dynamics of driven-dissipative systems is shown to be well-fitted for achieving efficient combinatorial optimization. The proposed method can be applied to solve any combinatorial optimization problem that is equivalent to minimizing an Ising Hamiltonian. Moreover, the dynamics considered can be implemented using various physical systems as it is based on generic dynamics—the normal form of the supercritical pitchfork bifurcation. The computational principle of the proposed method relies on an hybrid analog-digital representation of the binary Ising spins by considering the gradient descent of a Lyapunov function that is the sum of an analog Ising Hamiltonian and archetypal single or double-well potentials. By gradually changing the shape of the latter potentials from a single to double well shape, it can be shown that the first nonzero steady states to become stable are associated with global minima of the Ising Hamiltonian, under the approximation that all analog spins have the same amplitude. In the more general case, the heterogeneity in amplitude between analog spins induces the stabilization of local minima, which reduces the quality of solutions to combinatorial optimization problems. However, we show that the heterogeneity in amplitude can be reduced by setting the parameters of the driving signal near a regime, called the dynamic phase transition, where the analog spins' DC components map more accurately the global minima of the Ising Hamiltonian which, in turn, increases the quality of solutions found. Last, we discuss the possibility of a physical implementation of the proposed method using networks of degenerate optical parametric oscillators.
The combinatorial construction for a class of optimal optical orthogonal codes
Institute of Scientific and Technical Information of China (English)
唐煜; 殷剑兴
2002-01-01
Optical orthogonal code (OOC) has good correlation properties. It has many important appli-cations in a fiber-optic code-division multiple access channel. In this paper, a combinatorial construction foroptimal (15p, 5, 1) optical orthogonal codes with p congruent to 1 modulo 4 and greater than 5 is given byapplying Weil's Theorem. From this, when v is a product of primes congruent to 1 modulo 4 and greater than5, an optimal (15v, 5, 1)-OOC can be obtained by applying a known recursive construction.
Tsuchiya, Kazuo; Nishiyama, Takehiro; Tsujita, Katsuyoshi
2001-02-01
We have proposed an optimization method for a combinatorial optimization problem using replicator equations. To improve the solution further, a deterministic annealing algorithm may be applied. During the annealing process, bifurcations of equilibrium solutions will occur and affect the performance of the deterministic annealing algorithm. In this paper, the bifurcation structure of the proposed model is analyzed in detail. It is shown that only pitchfork bifurcations occur in the annealing process, and the solution obtained by the annealing is the branch uniquely connected with the uniform solution. It is also shown experimentally that in many cases, this solution corresponds to a good approximate solution of the optimization problem. Based on the results, a deterministic annealing algorithm is proposed and applied to the quadratic assignment problem to verify its performance.
Extensions of Dynamic Programming: Decision Trees, Combinatorial Optimization, and Data Mining
Hussain, Shahid
2016-07-10
This thesis is devoted to the development of extensions of dynamic programming to the study of decision trees. The considered extensions allow us to make multi-stage optimization of decision trees relative to a sequence of cost functions, to count the number of optimal trees, and to study relationships: cost vs cost and cost vs uncertainty for decision trees by construction of the set of Pareto-optimal points for the corresponding bi-criteria optimization problem. The applications include study of totally optimal (simultaneously optimal relative to a number of cost functions) decision trees for Boolean functions, improvement of bounds on complexity of decision trees for diagnosis of circuits, study of time and memory trade-off for corner point detection, study of decision rules derived from decision trees, creation of new procedure (multi-pruning) for construction of classifiers, and comparison of heuristics for decision tree construction. Part of these extensions (multi-stage optimization) was generalized to well-known combinatorial optimization problems: matrix chain multiplication, binary search trees, global sequence alignment, and optimal paths in directed graphs.
Yu, Jun-Han; Zhu, Li-Wen; Xia, Shi-Tao; Li, Hong-Mei; Tang, Ya-Ling; Liang, Xin-Hua; Chen, Tao; Tang, Ya-Jie
2016-07-01
To balance the flux of an engineered metabolic pathway to achieve high yield of target product is a major challenge in metabolic engineering. In previous work, the collaborative regulation of CO2 transport and fixation was investigated with co-overexpressing exogenous genes regulating both CO2 transport (sbtA and bicA) and PEP carboxylation (phosphoenolpyruvate (PEP) carboxylase (ppc) and carboxykinase (pck)) under trc promoter in Escherichia coli for succinate biosynthesis. For balancing metabolic flux to maximize succinate titer, a combinatorial optimization strategy to fine-tuning CO2 transport and fixation process was implemented by promoter engineering in this study. Firstly, based on the energy matrix a synthetic promoter library containing 20 rationally designed promoters with strengths ranging from 0.8% to 100% compared with the widely used trc promoter was generated. Evaluations of rfp and cat reporter genes provided evidence that the synthetic promoters were stably and had certain applicability. Secondly, four designed promoters with different strengths were used for combinatorial assembly of single CO2 transport gene (sbtA or bicA) and single CO2 fixation gene (ppc or pck) expression. Three combinations, such as Tang1519 (P4 -bicA + pP19 -pck), Tang1522 (P4 -sbtA + P4 -ppc), Tang1523 (P4 -sbtA + P17 -ppc) with a more than 10% increase in succinate production were screened in bioreactor. Finally, based on the above results, co-expression of the four transport and fixation genes were further investigated. Co-expression of sbtA, bicA, and ppc with weak promoter P4 and pck with strong promoter P19 (AFP111/pT-P4 -bicA-P4 -sbtA + pACYC-P19 -pck-P4 -ppc) provided the best succinate production among all the combinations. The highest succinate production of 89.4 g/L was 37.5% higher than that obtained with empty vector control. This work significantly enhanced succinate production through combinatorial optimization of CO2 transport and fixation
Combinatorial pathway engineering for optimized production of the anti-malarial FR900098.
Freestone, Todd S; Zhao, Huimin
2016-02-01
As resistance to current anti-malarial therapeutics spreads, new compounds to treat malaria are increasingly needed. One promising compound is FR900098, a naturally occurring phosphonate. Due to limitations in both chemical synthesis and biosynthetic methods for FR900098 production, this potential therapeutic has yet to see widespread implementation. Here we applied a combinatorial pathway engineering strategy to improve the production of FR900098 in Escherichia coli by modulating each of the pathway's nine genes with four promoters of different strengths. Due to the large size of the library and the low screening throughput, it was necessary to develop a novel screening strategy that significantly reduced the sample size needed to find an optimal strain. This was done by using biased libraries that localize searching around top hits and home in on high-producing strains. By incorporating this strategy, a significantly improved strain was found after screening less than 3% of the entire library. When coupled with culturing optimization, a strain was found to produce 96 mg/L, a 16-fold improvement over the original strain. We believe the enriched library method developed here can be used on other large pathways that may be difficult to engineer by combinatorial methods due to low screening throughput.
De Vincenzo, Ilario; Carbone, Giuseppe
2016-01-01
A large number of optimization algorithms have been developed by researchers to solve a variety of complex problems in operations management area. We present a novel optimization algorithm belonging to the class of swarm intelligence optimization methods. The algorithm mimics the decision making process of human groups and exploits the dynamics of this process as an optimization tool for combinatorial problems. In order to achieve this aim, a continuous-time Markov process is proposed to describe the behavior of a population of socially interacting agents, modelling how humans in a group modify their opinions driven by self-interest and consensus seeking. As in the case of a collection of spins, the dynamics of such a system is characterized by a phase transition from low to high values of the overall consenus (magnetization). We recognize this phase transition as being associated with the emergence of a collective superior intelligence of the population. While this state being active, a cooling schedule is a...
A review of three decades of research on some combinatorial optimization problems
Directory of Open Access Journals (Sweden)
Horacio Hideki Yanasse
2013-04-01
Full Text Available This paper presents an overview of our research in combinatorial optimization problems. Over the last three decades, our team has been studying mostly optimization problems that arise in industrial environments through the elaboration and solution of mathematical decision models. In addition to elaborating innovative models, we have improved upon existing solutions to complex problems, helping decision makers and researchers to better understand complex industrial systems. Our work has focused on the development of computationally more efficient algorithms that improve on existing methods by improving the solution quality or reducing the computation effort to obtain good solutions. While some of our earlier work became less necessary with the speed up of the computational facilities, the search for improved solution quality and reduced computational effort continues. After reviewing our findings on lot sizing, production scheduling, cutting problems, pattern sequencing, tool switches in flexible manufacturing machines and integrated cutting and sequencing problems, we propose topics for future study.
Optimal Length Scale for a Turbulent Dynamo.
Sadek, Mira; Alexakis, Alexandros; Fauve, Stephan
2016-02-19
We demonstrate that there is an optimal forcing length scale for low Prandtl number dynamo flows that can significantly reduce the required energy injection rate. The investigation is based on simulations of the induction equation in a periodic box of size 2πL. The flows considered are the laminar and turbulent ABC flows forced at different forcing wave numbers k_{f}, where the turbulent case is simulated using a subgrid turbulence model. At the smallest allowed forcing wave number k_{f}=k_{min}=1/L the laminar critical magnetic Reynolds number Rm_{c}^{lam} is more than an order of magnitude smaller than the turbulent critical magnetic Reynolds number Rm_{c}^{turb} due to the hindering effect of turbulent fluctuations. We show that this hindering effect is almost suppressed when the forcing wave number k_{f} is increased above an optimum wave number k_{f}L≃4 for which Rm_{c}^{turb} is minimum. At this optimal wave number, Rm_{c}^{turb} is smaller by more than a factor of 10 than the case forced in k_{f}=1. This leads to a reduction of the energy injection rate by 3 orders of magnitude when compared to the case where the system is forced at the largest scales and thus provides a new strategy for the design of a fully turbulent experimental dynamo.
Zheng, Wei; Friedman, Alan M; Bailey-Kellogg, Chris
2009-08-01
In engineering protein variants by constructing and screening combinatorial libraries of chimeric proteins, two complementary and competing goals are desired: the new proteins must be similar enough to the evolutionarily-selected wild-type proteins to be stably folded, and they must be different enough to display functional variation. We present here the first method, Staversity, to simultaneously optimize stability and diversity in selecting sets of breakpoint locations for site-directed recombination. Our goal is to uncover all "undominated" breakpoint sets, for which no other breakpoint set is better in both factors. Our first algorithm finds the undominated sets serving as the vertices of the lower envelope of the two-dimensional (stability and diversity) convex hull containing all possible breakpoint sets. Our second algorithm identifies additional breakpoint sets in the concavities that are either undominated or dominated only by undiscovered breakpoint sets within a distance bound computed by the algorithm. Both algorithms are efficient, requiring only time polynomial in the numbers of residues and breakpoints, while characterizing a space defined by an exponential number of possible breakpoint sets. We applied Staversity to identify 2-10 breakpoint plans for different sets of parent proteins taken from the purE family, as well as for parent proteins TEM-1 and PSE-4 from the beta-lactamase family. The average normalized distance between our plans and the lower bound for optimal plans is around 2%. Our plans dominate most (60-90% on average for each parent set) of the plans found by other possible approaches, random sampling or explicit optimization for stability with implicit optimization for diversity. The identified breakpoint sets provide a compact representation of good plans, enabling a protein engineer to understand and account for the trade-offs between two key considerations in combinatorial chimeragenesis.
Woodhouse, Michael; Parkinson, B A
2009-01-01
The cost effective generation of hydrogen with sunlight via water photoelectrolysis is the critical breakthrough needed to transition the world to a renewable energy based hydrogen economy. A semiconductor based photoelectrolysis system may have cost advantages over using either a photovoltaic cell coupled to an electrolyzer or solar thermochemical cycles for water splitting. Unfortunately there is no known semiconducting material or combination of materials with the electronic properties and stability needed to efficiently photoelectrolyze water. Semiconducting oxides can have the required stability but present theoretical methods are insufficient to a priori identify materials with the required properties. Most likely, the discovered material will be a complex oxide containing many elements whereby each contributes to the required material properties such as light absorption across the solar spectrum, stability and electrocatalytic activity. The large number of possible multicomponent metal oxides, even if only ternary or quaternary materials are considered, points to the use of high-throughput combinatorial methods to discover and optimize candidate materials. In this critical review, we will cover some techniques for the combinatorial production and screening of metal oxides for their ability to efficiently split water with sunlight (88 references).
Multi-Objective Combinatorial Optimization of Trigeneration Plants Based on Metaheuristics
Directory of Open Access Journals (Sweden)
Mirko M. Stojiljković
2014-12-01
Full Text Available In this paper, a methodology for multi-objective optimization of trigeneration plants is presented. It is primarily applicable to the systems for buildings’ energy supply characterized by high load variations on daily, weekly and annual bases, as well as the components applicable for flexible operation. The idea is that this approach should enable high accuracy and flexibility in mathematical modeling, while remaining efficient enough. The optimization problem is structurally decomposed into two new problems. The main problem of synthesis and design optimization is combinatorial and solved with different metaheuristic methods. For each examined combination of the synthesis and design variables, when calculating the values of the objective functions, the inner, mixed integer linear programming operation optimization problem is solved with the branch-and-cut method. The applicability of the exploited metaheuristic methods is demonstrated. This approach is compared with the alternative, superstructure-based approach. The potential for combining them is also examined. The methodology is applied for multi-objective optimization of a trigeneration plant that could be used for the energy supply of a real residential settlement in Niš, Serbia. Here, two objectives are considered: annual total costs and primary energy consumption. Results are obtained in the form of a Pareto chart using the epsilon-constraint method.
Gunnels, John
2010-06-01
We provide a first demonstration of the idea that matrix-based algorithms for nonlinear combinatorial optimization problems can be efficiently implemented. Such algorithms were mainly conceived by theoretical computer scientists for proving efficiency. We are able to demonstrate the practicality of our approach by developing an implementation on a massively parallel architecture, and exploiting scalable and efficient parallel implementations of algorithms for ultra high-precision linear algebra. Additionally, we have delineated and implemented the necessary algorithmic and coding changes required in order to address problems several orders of magnitude larger, dealing with the limits of scalability from memory footprint, computational efficiency, reliability, and interconnect perspectives. © Springer and Mathematical Programming Society 2010.
A Structure-Based Design Protocol for Optimizing Combinatorial Protein Libraries.
Lunt, Mark W; Snow, Christopher D
2016-01-01
Protein variant libraries created via site-directed mutagenesis are a powerful approach to engineer improved proteins for numerous applications such as altering enzyme substrate specificity. Conventional libraries commonly use a brute force approach: saturation mutagenesis via degenerate codons that encode all 20 natural amino acids. In contrast, this chapter describes a protocol for designing "smarter" degenerate codon libraries via direct combinatorial optimization in "library space." Several case studies illustrate how it is possible to design degenerate codon libraries that are highly enriched for favorable, low-energy sequences as assessed using a standard all-atom scoring function. There is much to gain for experimental protein engineering laboratories willing to think beyond site saturation mutagenesis. In the common case that the exact experimental screening budget is not fixed, it is particularly helpful to perform a Pareto analysis to inspect favorable libraries at a range of possible library sizes.
Mehrotra, Shakti; Prakash, O; Khan, Feroz; Kukreja, A K
2013-02-01
KEY MESSAGE : ANN-based combinatorial model is proposed and its efficiency is assessed for the prediction of optimal culture conditions to achieve maximum productivity in a bioprocess in terms of high biomass. A neural network approach is utilized in combination with Hidden Markov concept to assess the optimal values of different environmental factors that result in maximum biomass productivity of cultured tissues after definite culture duration. Five hidden Markov models (HMMs) were derived for five test culture conditions, i.e. pH of liquid growth medium, volume of medium per culture vessel, sucrose concentration (%w/v) in growth medium, nitrate concentration (g/l) in the medium and finally the density of initial inoculum (g fresh weight) per culture vessel and their corresponding fresh weight biomass. The artificial neural network (ANN) model was represented as the function of these five Markov models, and the overall simulation of fresh weight biomass was done with this combinatorial ANN-HMM. The empirical results of Rauwolfia serpentina hairy roots were taken as model and compared with simulated results obtained from pure ANN and ANN-HMMs. The stochastic testing and Cronbach's α-value of pure and combinatorial model revealed more internal consistency and skewed character (0.4635) in histogram of ANN-HMM compared to pure ANN (0.3804). The simulated results for optimal conditions of maximum fresh weight production obtained from ANN-HMM and ANN model closely resemble the experimentally optimized culture conditions based on which highest fresh weight was obtained. However, only 2.99 % deviation from the experimental values could be observed in the values obtained from combinatorial model when compared to the pure ANN model (5.44 %). This comparison showed 45 % better potential of combinatorial model for the prediction of optimal culture conditions for the best growth of hairy root cultures.
Directory of Open Access Journals (Sweden)
Angel A. Juan
2015-12-01
Full Text Available Many combinatorial optimization problems (COPs encountered in real-world logistics, transportation, production, healthcare, financial, telecommunication, and computing applications are NP-hard in nature. These real-life COPs are frequently characterized by their large-scale sizes and the need for obtaining high-quality solutions in short computing times, thus requiring the use of metaheuristic algorithms. Metaheuristics benefit from different random-search and parallelization paradigms, but they frequently assume that the problem inputs, the underlying objective function, and the set of optimization constraints are deterministic. However, uncertainty is all around us, which often makes deterministic models oversimplified versions of real-life systems. After completing an extensive review of related work, this paper describes a general methodology that allows for extending metaheuristics through simulation to solve stochastic COPs. ‘Simheuristics’ allow modelers for dealing with real-life uncertainty in a natural way by integrating simulation (in any of its variants into a metaheuristic-driven framework. These optimization-driven algorithms rely on the fact that efficient metaheuristics already exist for the deterministic version of the corresponding COP. Simheuristics also facilitate the introduction of risk and/or reliability analysis criteria during the assessment of alternative high-quality solutions to stochastic COPs. Several examples of applications in different fields illustrate the potential of the proposed methodology.
Directory of Open Access Journals (Sweden)
Chefi Triki
2016-08-01
Full Text Available We address in this paper a periodic petroleum station replenishment problem (PPSRP that aims to plan the delivery of petroleum products to a set of geographically dispatched stations. It is assumed that each station is characterized by its weekly demand and by its frequency of service. The main objective of the delivery process is to minimize the total travelled distance by the vailable trucks over an extended planning horizon. The problem configuration is described through a set of trucks with several compartments each and a set of stations with demands and prefixed delivery frequencies. Given such input data, the minimization of the total distance is subject to assignment and routing constraints that express the capacity limitations of each truck's compartment in terms of the frequency and the pathways' restrictions. In this paper, we develop and solve the full space mathematical formulation for the PPSRP with application to the Omani context. Our ultimate aim is to include such a model into an integrated framework having the objective of advising petroleum distribution companies on how to prepare bids in case of participation in combinatorial auctions of the transportation procurement.
Combinatorial Algorithms for Portfolio Optimization Problems - Case of Risk Moderate Investor
Juarna, A.
2017-03-01
Portfolio optimization problem is a problem of finding optimal combination of n stocks from N ≥ n available stocks that gives maximal aggregate return and minimal aggregate risk. In this paper given N = 43 from the IDX (Indonesia Stock Exchange) group of the 45 most-traded stocks, known as the LQ45, with p = 24 data of monthly returns for each stock, spanned over interval 2013-2014. This problem actually is a combinatorial one where its algorithm is constructed based on two considerations: risk moderate type of investor and maximum allowed correlation coefficient between every two eligible stocks. The main outputs resulted from implementation of the algorithms is a multiple curve of three portfolio’s attributes, e.g. the size, the ratio of return to risk, and the percentage of negative correlation coefficient for every two chosen stocks, as function of maximum allowed correlation coefficient between each two stocks. The output curve shows that the portfolio contains three stocks with ratio of return to risk at 14.57 if the maximum allowed correlation coefficient between every two eligible stocks is negative and contains 19 stocks with maximum allowed correlation coefficient 0.17 to get maximum ratio of return to risk at 25.48.
Optimality Of Variable-Length Codes
Yeh, Pen-Shu; Miller, Warner H.; Rice, Robert F.
1994-01-01
Report presents analysis of performances of conceptual Rice universal noiseless coders designed to provide efficient compression of data over wide range of source-data entropies. Includes predictive preprocessor that maps source data into sequence of nonnegative integers and variable-length-coding processor, which adapts to varying entropy of source data by selecting whichever one of number of optional codes yields shortest codeword.
Minimum length scale in topology optimization by geometric constraints
DEFF Research Database (Denmark)
Zhou, Mingdong; Lazarov, Boyan Stefanov; Wang, Fengwen
2015-01-01
A density-based topology optimization approach is proposed to design structures with strict minimum length scale. The idea is based on using a filtering-threshold topology optimization scheme and computationally cheap geometric constraints. The constraints are defined over the underlying structural...... geometry represented by the filtered and physical fields. Satisfying the constraints leads to a design that possesses user-specified minimum length scale. Conventional topology optimization problems can be augmented with the proposed constraints to achieve minimum length scale on the final design....... No additional finite element analysis is required for the constrained optimization. Several benchmark examples are presented to show the effectiveness of this approach....
Time Complexity of Evolutionary Algorithms for Combinatorial Optimization: A Decade of Results
Institute of Scientific and Technical Information of China (English)
Pietro S. Oliveto; Jun He; Xin Yao
2007-01-01
Computational time complexity analyzes of evolutionary algorithms (EAs) have been performed since the mid-nineties. The first results were related to very simple algorithms, such as the (1+1)-EA, on toy problems. These efforts produced a deeper understanding of how EAs perform on different kinds of fitness landscapes and general mathematical tools that may be extended to the analysis of more complicated EAs on more realistic problems. In fact, in recent years, it has been possible to analyze the (1+1)-EA on combinatorial optimization problems with practical applications and more realistic population-based EAs on structured toy problems. This paper presents a survey of the results obtained in the last decade along these two research lines. The most common mathematical techniques are introduced, the basic ideas behind them are discussed and their elective applications are highlighted. Solved problems that were still open are enumerated as are those still awaiting for a solution. New questions and problems arisen in the meantime are also considered.
Wei, Qinhua; Wan, Jieqiong; Liu, Guanghui; Zhou, Zhenzhen; Yang, Hua; Wang, Jiacheng; Liu, Qian
2015-04-13
A combinatorial method was employed to rapidly screen the effects of La, Ce-co-doping on the luminescent properties of Gd2Si2O7 pyrosilicate using an 8 × 8 library. The candidate formulations (Gd1-x-yLax)2Si2O7:Ce2y were evaluated by luminescence pictures under ultraviolet excitation. The optimal composition was found to be (Gd0.89La0.1)2Si2O7:Ce0.02 after scaled-up preparation and detailed characterization of powder samples, which shows an excellent light output under both ultraviolet and X-ray excitation (about 5.43 times of commercial YAG:Ce powders). The XRD results indicate that the phase structure sequence is tetragonal-orthorhombic-triclinic for different calcination temperatures and doping ions. The (Gd0.89La0.1)2Si2O7:Ce0.02 powder sample also demonstrated excellent temperature stability of luminescence up to 200 °C and a short decay time of several tens of nanoseconds, suggesting that this may represent a new kind of scintillation material, such as single crystals, ceramics, glass, or phosphors.
Kanazawa, Takahiko; Yasuda, Keiichiro
Metaheuristics is a new paradigm that aims to obtain an approximate solution within a feasible computation time. To design the effective metaheuristics, strategies of intensification and diversification are essential. This paper proposes an algorithm that has long term policy for realizing intensification and diversification based on higher level structure in solution space. In order to verify the performance, the proposed algorithm is applied to some traveling salesman problems which are typical combinatorial optimization problems.
Directory of Open Access Journals (Sweden)
E. Osaba
2014-01-01
Full Text Available Since their first formulation, genetic algorithms (GAs have been one of the most widely used techniques to solve combinatorial optimization problems. The basic structure of the GAs is known by the scientific community, and thanks to their easy application and good performance, GAs are the focus of a lot of research works annually. Although throughout history there have been many studies analyzing various concepts of GAs, in the literature there are few studies that analyze objectively the influence of using blind crossover operators for combinatorial optimization problems. For this reason, in this paper a deep study on the influence of using them is conducted. The study is based on a comparison of nine techniques applied to four well-known combinatorial optimization problems. Six of the techniques are GAs with different configurations, and the remaining three are evolutionary algorithms that focus exclusively on the mutation process. Finally, to perform a reliable comparison of these results, a statistical study of them is made, performing the normal distribution z-test.
Osaba, E; Carballedo, R; Diaz, F; Onieva, E; de la Iglesia, I; Perallos, A
2014-01-01
Since their first formulation, genetic algorithms (GAs) have been one of the most widely used techniques to solve combinatorial optimization problems. The basic structure of the GAs is known by the scientific community, and thanks to their easy application and good performance, GAs are the focus of a lot of research works annually. Although throughout history there have been many studies analyzing various concepts of GAs, in the literature there are few studies that analyze objectively the influence of using blind crossover operators for combinatorial optimization problems. For this reason, in this paper a deep study on the influence of using them is conducted. The study is based on a comparison of nine techniques applied to four well-known combinatorial optimization problems. Six of the techniques are GAs with different configurations, and the remaining three are evolutionary algorithms that focus exclusively on the mutation process. Finally, to perform a reliable comparison of these results, a statistical study of them is made, performing the normal distribution z-test.
Osaba, E.; Carballedo, R.; Diaz, F.; Onieva, E.; de la Iglesia, I.; Perallos, A.
2014-01-01
Since their first formulation, genetic algorithms (GAs) have been one of the most widely used techniques to solve combinatorial optimization problems. The basic structure of the GAs is known by the scientific community, and thanks to their easy application and good performance, GAs are the focus of a lot of research works annually. Although throughout history there have been many studies analyzing various concepts of GAs, in the literature there are few studies that analyze objectively the influence of using blind crossover operators for combinatorial optimization problems. For this reason, in this paper a deep study on the influence of using them is conducted. The study is based on a comparison of nine techniques applied to four well-known combinatorial optimization problems. Six of the techniques are GAs with different configurations, and the remaining three are evolutionary algorithms that focus exclusively on the mutation process. Finally, to perform a reliable comparison of these results, a statistical study of them is made, performing the normal distribution z-test. PMID:25165731
Optimal recombination in genetic algorithms for combinatorial optimization problems: Part II
Directory of Open Access Journals (Sweden)
Eremeev Anton V.
2014-01-01
Full Text Available This paper surveys results on complexity of the optimal recombination problem (ORP, which consists in finding the best possible offspring as a result of a recombination operator in a genetic algorithm, given two parent solutions. In Part II, we consider the computational complexity of ORPs arising in genetic algorithms for problems on permutations: the Travelling Salesman Problem, the Shortest Hamilton Path Problem and the Makespan Minimization on Single Machine and some other related problems. The analysis indicates that the corresponding ORPs are NP-hard, but solvable by faster algorithms, compared to the problems they are derived from.
Sabar, Nasser R; Ayob, Masri; Kendall, Graham; Qu, Rong
2015-02-01
Hyper-heuristics are search methodologies that aim to provide high-quality solutions across a wide variety of problem domains, rather than developing tailor-made methodologies for each problem instance/domain. A traditional hyper-heuristic framework has two levels, namely, the high level strategy (heuristic selection mechanism and the acceptance criterion) and low level heuristics (a set of problem specific heuristics). Due to the different landscape structures of different problem instances, the high level strategy plays an important role in the design of a hyper-heuristic framework. In this paper, we propose a new high level strategy for a hyper-heuristic framework. The proposed high-level strategy utilizes a dynamic multiarmed bandit-extreme value-based reward as an online heuristic selection mechanism to select the appropriate heuristic to be applied at each iteration. In addition, we propose a gene expression programming framework to automatically generate the acceptance criterion for each problem instance, instead of using human-designed criteria. Two well-known, and very different, combinatorial optimization problems, one static (exam timetabling) and one dynamic (dynamic vehicle routing) are used to demonstrate the generality of the proposed framework. Compared with state-of-the-art hyper-heuristics and other bespoke methods, empirical results demonstrate that the proposed framework is able to generalize well across both domains. We obtain competitive, if not better results, when compared to the best known results obtained from other methods that have been presented in the scientific literature. We also compare our approach against the recently released hyper-heuristic competition test suite. We again demonstrate the generality of our approach when we compare against other methods that have utilized the same six benchmark datasets from this test suite.
Optimized Reaction Conditions for Amide Bond Formation in DNA-Encoded Combinatorial Libraries.
Li, Yizhou; Gabriele, Elena; Samain, Florent; Favalli, Nicholas; Sladojevich, Filippo; Scheuermann, Jörg; Neri, Dario
2016-08-08
DNA-encoded combinatorial libraries are increasingly being used as tools for the discovery of small organic binding molecules to proteins of biological or pharmaceutical interest. In the majority of cases, synthetic procedures for the formation of DNA-encoded combinatorial libraries incorporate at least one step of amide bond formation between amino-modified DNA and a carboxylic acid. We investigated reaction conditions and established a methodology by using 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide, 1-hydroxy-7-azabenzotriazole and N,N'-diisopropylethylamine (EDC/HOAt/DIPEA) in combination, which provided conversions greater than 75% for 423/543 (78%) of the carboxylic acids tested. These reaction conditions were efficient with a variety of primary and secondary amines, as well as with various types of amino-modified oligonucleotides. The reaction conditions, which also worked efficiently over a broad range of DNA concentrations and reaction scales, should facilitate the synthesis of novel DNA-encoded combinatorial libraries.
Maximum length scale in density based topology optimization
DEFF Research Database (Denmark)
Lazarov, Boyan Stefanov; Wang, Fengwen
2017-01-01
The focus of this work is on two new techniques for imposing maximum length scale in topology optimization. Restrictions on the maximum length scale provide designers with full control over the optimized structure and open possibilities to tailor the optimized design for broader range...... of manufacturing processes by fulfilling the associated technological constraints. One of the proposed methods is based on combination of several filters and builds on top of the classical density filtering which can be viewed as a low pass filter applied to the design parametrization. The main idea...
Directory of Open Access Journals (Sweden)
Nelson Maculan
2003-01-01
Full Text Available We present integer linear models with a polynomial number of variables and constraints for combinatorial optimization problems in graphs: optimum elementary cycles, optimum elementary paths and optimum tree problems.Apresentamos modelos lineares inteiros com um número polinomial de variáveis e restrições para problemas de otimização combinatória em grafos: ciclos elementares ótimos, caminhos elementares ótimos e problemas em árvores ótimas.
Directory of Open Access Journals (Sweden)
Oscar Montiel
2015-01-01
Full Text Available Nowadays, solving optimally combinatorial problems is an open problem. Determining the best arrangement of elements proves being a very complex task that becomes critical when the problem size increases. Researchers have proposed various algorithms for solving Combinatorial Optimization Problems (COPs that take into account the scalability; however, issues are still presented with larger COPs concerning hardware limitations such as memory and CPU speed. It has been shown that the Reduce-Optimize-Expand (ROE method can solve COPs faster with the same resources; in this methodology, the reduction step is the most important procedure since inappropriate reductions, applied to the problem, will produce suboptimal results on the subsequent stages. In this work, an algorithm to improve the reduction step is proposed. It is based on a fuzzy inference system to classify portions of the problem and remove them, allowing COPs solving algorithms to utilize better the hardware resources by dealing with smaller problem sizes, and the use of metadata and adaptive heuristics. The Travelling Salesman Problem has been used as a case of study; instances that range from 343 to 3056 cities were used to prove that the fuzzy logic approach produces a higher percentage of successful reductions.
Podlewska, Sabina; Czarnecki, Wojciech M; Kafel, Rafał; Bojarski, Andrzej J
2017-02-15
The growing computational abilities of various tools that are applied in the broadly understood field of computer-aided drug design have led to the extreme popularity of virtual screening in the search for new biologically active compounds. Most often, the source of such molecules consists of commercially available compound databases, but they can also be searched for within the libraries of structures generated in silico from existing ligands. Various computational combinatorial approaches are based solely on the chemical structure of compounds, using different types of substitutions for new molecules formation. In this study, the starting point for combinatorial library generation was the fingerprint referring to the optimal substructural composition in terms of the activity toward a considered target, which was obtained using a machine learning-based optimization procedure. The systematic enumeration of all possible connections between preferred substructures resulted in the formation of target-focused libraries of new potential ligands. The compounds were initially assessed by machine learning methods using a hashed fingerprint to represent molecules; the distribution of their physicochemical properties was also investigated, as well as their synthetic accessibility. The examination of various fingerprints and machine learning algorithms indicated that the Klekota-Roth fingerprint and support vector machine were an optimal combination for such experiments. This study was performed for 8 protein targets, and the obtained compound sets and their characterization are publically available at http://skandal.if-pan.krakow.pl/comb_lib/ .
DEFF Research Database (Denmark)
Nielsen, John
1994-01-01
An overview of combinatorial chemistry is presented. Combinatorial chemistry, sometimes referred to as `irrational drug design,' involves the generation of molecular diversity. The resulting chemical library is then screened for biologically active compounds.......An overview of combinatorial chemistry is presented. Combinatorial chemistry, sometimes referred to as `irrational drug design,' involves the generation of molecular diversity. The resulting chemical library is then screened for biologically active compounds....
DEFF Research Database (Denmark)
Nielsen, John
1994-01-01
An overview of combinatorial chemistry is presented. Combinatorial chemistry, sometimes referred to as `irrational drug design,' involves the generation of molecular diversity. The resulting chemical library is then screened for biologically active compounds.......An overview of combinatorial chemistry is presented. Combinatorial chemistry, sometimes referred to as `irrational drug design,' involves the generation of molecular diversity. The resulting chemical library is then screened for biologically active compounds....
Effective Length Design of Humanoid Robot Fingers Using Biomimetic Optimization
Directory of Open Access Journals (Sweden)
Byoung-Ho Kim
2015-10-01
Full Text Available In this study, we propose an effective design method for the phalangeal parameters and the total size of humanoid robot fingers based on a biomimetic optimization. For the optimization, an interphalangeal joint coordination parameter and the length constraints inherent in human fingers are considered from a biomimetic perspective. A reasonable grasp formulation is also taken into account from the viewpoint of power grasping, where the grasp space of a humanoid robot finger is importantly considered to determine the phalangeal length parameters. The usefulness of the devised biomimetic optimization method is shown through the design examples of various humanoid robot fingers. In fact, the optimization-based finger design method enables us to determine effectively the proper phalangeal size of humanoid robot fingers for human-like object handling tasks. In addition, we discuss its contribution to the structural configuration and coordinated motion of a humanoid robot finger, and address its practical availability in terms of effective finger design.
Energy Technology Data Exchange (ETDEWEB)
Costa, Wagner Emanoel; Gouvea, Elizabeth Ferreira; Goldbarg, Marco Cesar [Rio Grande do Norte Univ., Natal, RN (Brazil). Dept. de Informatica e Matematica Aplicada]. E-mail: wemano@digi.com.br; beth@dimap.ufrn.br; gold@dimap.ufrn.br
2003-07-01
Brazil is in a excellent context for the development of natural gas as energy source. The responsibility of design a network to deliver gas increases with the new investments made every day. However the computer aided design (CAD) technologies for gas network design were poor developed because in EUA and Europe have their gas networks from long time ago, in such that only a little of the potential of computer had been explored for the gas network design. This work studies the use of combinatorial optimization techniques and others techniques from evolutionary computing to find layouts to create and expand a network and make the pipeline optimization looking for costs minimizations and respecting all demands of pressures and flow. (author)
In vivo myograph measurement of muscle contraction at optimal length
Directory of Open Access Journals (Sweden)
Ahmed Aminul
2007-01-01
Full Text Available Abstract Background Current devices for measuring muscle contraction in vivo have limited accuracy in establishing and re-establishing the optimum muscle length. They are variable in the reproducibility to determine the muscle contraction at this length, and often do not maintain precise conditions during the examination. Consequently, for clinical testing only semi-quantitative methods have been used. Methods We present a newly developed myograph, an accurate measuring device for muscle contraction, consisting of three elements. Firstly, an element for adjusting the axle of the device and the physiological axis of muscle contraction; secondly, an element to accurately position and reposition the extremity of the muscle; and thirdly, an element for the progressive pre-stretching and isometric locking of the target muscle. Thus it is possible to examine individual in vivo muscles in every pre-stretched, specified position, to maintain constant muscle-length conditions, and to accurately re-establish the conditions of the measurement process at later sessions. Results In a sequence of experiments the force of contraction of the muscle at differing stretching lengths were recorded and the forces determined. The optimum muscle length for maximal force of contraction was established. In a following sequence of experiments with smaller graduations around this optimal stretching length an increasingly accurate optimum muscle length for maximal force of contraction was determined. This optimum length was also accurately re-established at later sessions. Conclusion We have introduced a new technical solution for valid, reproducible in vivo force measurements on every possible point of the stretching curve. Thus it should be possible to study the muscle contraction in vivo to the same level of accuracy as is achieved in tests with in vitro organ preparations.
Optimization of inhibitory decision rules relative to length and coverage
Alsolami, Fawaz
2012-01-01
The paper is devoted to the study of algorithms for optimization of inhibitory rules relative to the length and coverage. In contrast with usual rules that have on the right-hand side a relation "attribute ≠ value", inhibitory rules have a relation "attribute = value" on the right-hand side. The considered algorithms are based on extensions of dynamic programming. © 2012 Springer-Verlag.
Energy Technology Data Exchange (ETDEWEB)
Machado, Marcelo Dornellas; Schirru, Roberto [Universidade Federal, Rio de Janeiro, RJ (Brazil). Coordenacao dos Programas de Pos-graduacao de Engenharia. Programa de Engenharia Nuclear
2000-07-01
Genetic algorithms are biologically motivated adaptive systems which have been used, with good results, for combinatorial problems optimization. In this work, a new learning mode, to be used by the population-based incremental learning algorithm, has the aim to build a new evolutionary algorithm to be used in optimization of numerical problems and combinatorial problems. This new learning mode uses a variable learning rate during the optimization process, constituting a process known as proportional reward. The development of this new algorithm aims its application in the optimization of reload problem of PWR nuclear reactors, in order to increase the useful life of the nuclear fuel. For the test, two classes of problems are used: numerical problems and combinatorial problems. Due to the fact that the reload problem is a combinatorial problem, the major interest relies on the last class. The results achieved with the tests indicate the applicability of the new learning mode, showing its potential as a developing tool in the solution of reload problem. (author)
Hybrid Nested Partitions and Math Programming Framework for Large-scale Combinatorial Optimization
2010-03-31
optimization problems: 1) exact algorithms and 2) metaheuristic algorithms. This project will integrate concepts from these two technologies to develop...generic optimization frameworks to find provably good solutions to large-scale discrete optimization problems often encountered in many real applications...integer programming decomposition approaches, such as Dantzig Wolfe decomposition and Lagrangian relaxation, and metaheuristics such as the Nested
Directory of Open Access Journals (Sweden)
Jinye WANG
Full Text Available The automatic stereo warehouse system is a storage system with multi-storey warehouse, by which the automation access and integrated automation management are realized in the computer's direct control and management. The emerging, bypass automatic stereo warehouse has gained more and more application in rapid access. The stacker's working time directly affects the efficiency of the warehouse. To improve the bypass automatic warehouse efficiency and analyze the stacker route, an integrated optimization model considering the export selection and the path picking is established. The model aims to the picking task cycle and develops the population's generating method of genetic algorithm, then solves the optimization model. The last section in this stage is the initial point of the next optimization stage, using the nearest neighbor method to find the optimal export location. Simulation and practical application show that the model and the algorithm are feasible and effective.
Lv, Xiaomei; Gu, Jiali; Wang, Fan; Xie, Wenping; Liu, Min; Ye, Lidan; Yu, Hongwei
2016-12-01
Metabolic engineering of microorganisms for heterologous biosynthesis is a promising route to sustainable chemical production which attracts increasing research and industrial interest. However, the efficiency of microbial biosynthesis is often restricted by insufficient activity of pathway enzymes and unbalanced utilization of metabolic intermediates. This work presents a combinatorial strategy integrating modification of multiple rate-limiting enzymes and modular pathway engineering to simultaneously improve intra- and inter-pathway balance, which might be applicable for a range of products, using isoprene as an example product. For intra-module engineering within the methylerythritol-phosphate (MEP) pathway, directed co-evolution of DXS/DXR/IDI was performed adopting a lycopene-indicated high-throughput screening method developed herein, leading to 60% improvement of isoprene production. In addition, inter-module engineering between the upstream MEP pathway and the downstream isoprene-forming pathway was conducted via promoter manipulation, which further increased isoprene production by 2.94-fold compared to the recombinant strain with solely protein engineering and 4.7-fold compared to the control strain containing wild-type enzymes. These results demonstrated the potential of pathway optimization in isoprene overproduction as well as the effectiveness of combining metabolic regulation and protein engineering in improvement of microbial biosynthesis. Biotechnol. Bioeng. 2016;113: 2661-2669. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
DEFF Research Database (Denmark)
1997-01-01
The invention provides a method for the production of a combinatorial library of compound of general formula (I) using solid phase methodologies. The cleavage of the array of immobilised compounds of the phthalimido type from the solid support matrix is accomplished by using an array of dinucleop......The invention provides a method for the production of a combinatorial library of compound of general formula (I) using solid phase methodologies. The cleavage of the array of immobilised compounds of the phthalimido type from the solid support matrix is accomplished by using an array...... of dinucleophiles, e.g. hydrazines (hydrazinolysis) or N-hydroxylamines, whereby a combinatorial dimension is introduced in the cleavage step. The invention also provides a compound library....
Takabe, Satoshi; Hukushima, Koji
2016-05-01
Typical behavior of the linear programming (LP) problem is studied as a relaxation of the minimum vertex cover (min-VC), a type of integer programming (IP) problem. A lattice-gas model on the Erdös-Rényi random graphs of α -uniform hyperedges is proposed to express both the LP and IP problems of the min-VC in the common statistical mechanical model with a one-parameter family. Statistical mechanical analyses reveal for α =2 that the LP optimal solution is typically equal to that given by the IP below the critical average degree c =e in the thermodynamic limit. The critical threshold for good accuracy of the relaxation extends the mathematical result c =1 and coincides with the replica symmetry-breaking threshold of the IP. The LP relaxation for the minimum hitting sets with α ≥3 , minimum vertex covers on α -uniform random graphs, is also studied. Analytic and numerical results strongly suggest that the LP relaxation fails to estimate optimal values above the critical average degree c =e /(α -1 ) where the replica symmetry is broken.
Sudhölter, S.; Krüger, J.; Reuter, M. A.
1996-12-01
The demands placed on the environmental and social acceptability of metallurgical processing technology are rising steadily. Of particular importance are the production techniques, products, and disposal of residues. These aspects are affected by the varying compositions of the primary and secondary raw materials processed in the plants and the rapidly changing market situations in the metallurgical industry. Metallurgical engineers have to select “optimal” processes from a vast number of existing technologies for the primary production of zinc and for the processing of zinc containing residues. To enable the engineer to compare these techniques and to choose the right combination of unit operations, a process design methodology is presented here, which has been adapted from methodologies developed in chemical engineering and minerals processing. In a previous article by the authors, a structural parameter approach was introduced, that implements a synthesis model, which includes all unit operations currently implemented in zinc metallurgy. At the basis of this model is a data base containing the details of the unit operations included in the model. In this article, this methodology is expanded to incorporate an unlimited quantity of different components by introducing the simulated annealing optimization technique to generate optimal flow sheets for the production of zinc under varying constraints which include operation costs, metal prices, environmental costs, and split factors for Zn, Pb, Ag, and Fe. Case studies demonstrate the functionality of this metallurgical tool for the hydrometallurgical recovery of zinc including numerous unit operations for the processing of by-products and residues. It will also be demonstrated how this model can be extended to a “waste management” tool that generates processing routes not only for the residues from the zinc industry but also for zinc containing residues from other processes, e.g., EAF dusts.
组合优化调度问题求解方法%The Approach to Solving Combinatorial Optimization Schedule Problems
Institute of Scientific and Technical Information of China (English)
张居阳; 孙吉贵
2003-01-01
Optimization schedule problem is this kind of problem that people often meet in the field of industrial manufacture,transportation and traffic. A good schedule scheme can improve the efficiency of production and reduce the cost of production. So scholars in all of the related fields have high regard for schedule problem at all times. This paper describes the method and technology about combinatorial optimization schedule problems. The research state and advances in this field are reviewed and surveyed. At the end of the paper an approach to solving Job Shop problem,a representative paradigm in schedule problem ,is introduced and discussed concretely.
Combinatorial optimization of (Y(x)Lu(1-x-y))(3)Al(5)O(12):Ce(3y) green-yellow phosphors.
Zhang, Kong; Liu, Qingfeng; Liu, Qian; Shi, Yun; Pan, Yubai
2010-07-12
A combinatorial chemistry method was used to synthesize and screen (Y(x)Lu(1-x-y))(3)Al(5)O(12):Ce(3y) green-yellow phosphors. The material libraries were obtained using an inkjet delivery system and screened for their fluorescence under an ultraviolet light of 365 nm. The optimized composition was identified to be (Y(0.2)Lu(0.788))(3)Al(5)O(12):Ce(3+)(0.036). Scale-up experiments confirmed that the optimized composition of the phosphor showed the highest luminescence intensity and an excellent scintillation performance with a short decay time (scintillators.
Sagnol, Guillaume
2010-01-01
The theory of "optimal experimental design" explains how to best select experiments in order to estimate a set of parameters. The quality of the estimation can be measured by the confidence ellipsoids of a certain estimator. This leads to concave maximization problems in which the objective function is nondecreasing with respect to the L\\"owner ordering of symmetric matrices, and is applied to the "information matrix" describing the structure of these confidence ellipsoids. In a number of real-world applications, the variables controlling the experimental design are discrete, or binary. This paper provides approximability bounds for this NP-hard problem. In particular, we establish a matrix inequality which shows that the objective function is submodular, from which it follows that the greedy approach, which has often been used for this problem, always gives a design within $1-1/e$ of the optimum. We next study the design found by rounding the solution of the continuous relaxed problem, an approach which has ...
Kodali, Anuradha
In this thesis, we develop dynamic multiple fault diagnosis (DMFD) algorithms to diagnose faults that are sporadic and coupled. Firstly, we formulate a coupled factorial hidden Markov model-based (CFHMM) framework to diagnose dependent faults occurring over time (dynamic case). Here, we implement a mixed memory Markov coupling model to determine the most likely sequence of (dependent) fault states, the one that best explains the observed test outcomes over time. An iterative Gauss-Seidel coordinate ascent optimization method is proposed for solving the problem. A soft Viterbi algorithm is also implemented within the framework for decoding dependent fault states over time. We demonstrate the algorithm on simulated and real-world systems with coupled faults; the results show that this approach improves the correct isolation rate as compared to the formulation where independent fault states are assumed. Secondly, we formulate a generalization of set-covering, termed dynamic set-covering (DSC), which involves a series of coupled set-covering problems over time. The objective of the DSC problem is to infer the most probable time sequence of a parsimonious set of failure sources that explains the observed test outcomes over time. The DSC problem is NP-hard and intractable due to the fault-test dependency matrix that couples the failed tests and faults via the constraint matrix, and the temporal dependence of failure sources over time. Here, the DSC problem is motivated from the viewpoint of a dynamic multiple fault diagnosis problem, but it has wide applications in operations research, for e.g., facility location problem. Thus, we also formulated the DSC problem in the context of a dynamically evolving facility location problem. Here, a facility can be opened, closed, or can be temporarily unavailable at any time for a given requirement of demand points. These activities are associated with costs or penalties, viz., phase-in or phase-out for the opening or closing of a
Dieleman, Peter; Waitukaitis, Scott; van Hecke, Martin
To design rigidly foldable quadrilateral meshes one generally needs to solve a complicated set of constraints. Here we present a systematic, combinatorial approach to create rigidly foldable quadrilateral meshes with a limited number of different vertices. The number of discrete, 1 degree-of-freedom folding branches for some of these meshes scales exponentially with the number of vertices on the edge, whilst other meshes generated this way only have two discrete folding branches, regardless of mesh size. We show how these two different behaviours both emerge from the two folding branches present in a single generic 4-vertex. Furthermore, we model generic 4-vertices as a spherical linkage and exploit a previously overlooked symmetry to create non-developable origami patterns using the same combinatorial framework.
Lewis, Jared C.
2010-11-24
Made for each other: Combinatorial alanine substitution of active site residues in a thermostable cytochrome P450BM3 variant was used to generate an enzyme that is active with large substrates. Selective hydroxylation of methoxymethylated monosaccharides, alkaloids, and steroids was thus made possible (see Scheme). This approach could be useful for improving the activity of enzymes that show only limited activity with larger substrates. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Combinatorial materials synthesis
Directory of Open Access Journals (Sweden)
Ichiro Takeuchi
2005-10-01
Full Text Available The pace at which major technological changes take place is often dictated by the rate at which new materials are discovered, and the timely arrival of new materials has always played a key role in bringing advances to our society. It is no wonder then that the so-called combinatorial or high-throughput strategy has been embraced by practitioners of materials science in virtually every field. High-throughput experimentation allows simultaneous synthesis and screening of large arrays of different materials. Pioneered by the pharmaceutical industry, the combinatorial method is now widely considered to be a watershed in accelerating the discovery and optimization of new materials1–5.
Tap-length optimization of adaptive filters used in stereophonic acoustic echo cancellation
DEFF Research Database (Denmark)
Kar, Asutosh; Swamy, M.N.S.
2017-01-01
of acoustic echo paths. The tap-length optimization is applied to a single long adaptive filter with thousands of coefficients to decrease the total number of weights, which in turn reduces the computational load. To further increase the convergence rate, the proposed tap-length-optimization algorithm...
Length scale and manufacturability in density-based topology optimization
DEFF Research Database (Denmark)
Lazarov, Boyan Stefanov; Wang, Fengwen; Sigmund, Ole
2016-01-01
Since its original introduction in structural design, density-based topology optimization has been applied to a number of other fields such as microelectromechanical systems, photonics, acoustics and fluid mechanics. The methodology has been well accepted in industrial design processes where it c......, well-defined designs with robust performances. The overview discusses the limitations, the advantages and the associated computational costs. The review is completed with optimized designs for minimum compliance, mechanism design and heat transfer.......Since its original introduction in structural design, density-based topology optimization has been applied to a number of other fields such as microelectromechanical systems, photonics, acoustics and fluid mechanics. The methodology has been well accepted in industrial design processes where it can...
Directory of Open Access Journals (Sweden)
Ali Kadhim
2016-01-01
Full Text Available A combinatorial pulsed laser deposition system was developed by integrating a computer controlled scanning sample stage in order to rapidly screen processing conditions relevant to CdTe/CdS thin-film solar cells. Using this system, the thickness of the CdTe absorber layer is varied across a single sample from 1.5 μm to 0.75 μm. The effects of thickness on CdTe grain morphology, crystal orientation, and cell efficiency were investigated with respect to different postprocessing conditions. It is shown that the thinner CdTe layer of 0.75 μm obtained the best power conversion efficiency up to 5.3%. The results of this work shows the importance that CdTe grain size/morphology relative to CdTe thickness has on device performance and quantitatively exhibits what those values should be to obtain efficient thin-film CdTe/CdS solar cells fabricated with pulsed laser deposition. Further development of this combinatorial approach could enable high-throughput exploration and optimization of CdTe/CdS solar cells.
FINDING THE OPTIMAL LENGTH OF DATA FRAME IN PLC COMPUTER NETWORK
Institute of Scientific and Technical Information of China (English)
HuangRonghui; Zhoumingtian
2003-01-01
The length of data frame is an important parameter in Medium Access Control (MAC) layer protocol.A method of finding the optimal length of data frame when impulsive disturdance is inuolved in PowerLine Communications (PLC) is proposed.Having analyzed the characteristics of impulsive disturbance in powerline and the collision mechanism between the disturbance and data frame,this letter gives the function of the network channel utilization with the length of data frame in MAC layer and the impulsive disurbance.Our stochastic process simulation shows that it is feasible to get the optimal length of data frame.
FINDING THE OPTIMAL LENGTH OF DATA FRAME IN PLC COMPUTER NETWORK
Institute of Scientific and Technical Information of China (English)
Huang Ronghui; Zhou Mingtian; She Kun
2003-01-01
The length of data frame is an important parameter in Medium Access Control(MAC) layer protocol. A method of finding the optimal length of data frame when impulsive disturbance is involved in PowerLine Communications (PLC) is proposed. Having analyzed the characteristics of impulsive disturbance in powerline and the collision mechanism between the disturbance and data frame, this letter gives the function of the network channel utilization with the length of data frame in MAC layer and the impulsive disturbance. Our stochastic process simulation shows that it is feasible to get the optimal length of data frame.
Su, Xiaobin; Zhang, Kong; Liu, Qian; Zhong, Hongmei; Shi, Yun; Pan, Yubai
2011-01-10
A combinatorial chemistry method was employed to screen the yellow phosphors of (Lu₁₋(x)Gd(x))₃Al₅O₁₂:Ce₃(y) as luminescent materials. An array of 81 compositions was synthesized by inkjetting nitrate solutions into microreactor wells and sintering at high temperature. The candidate formulations were evaluated by luminescence pictures, and the optimal composition was determined to be Lu(2.7)Gd(0.3)Al(5)O(12):Ce(0.045) after scale-up and detailed characterization. Lu₂.₇Gd₀.₃Al₅O₁₂:Ce₀.₀₄₅ was also found to have a short decay time (≤53.97 ns). These results demonstrate the great potential of the Lu₂.₇Gd₀.₃Al₅O₁₂:Ce₀.₀₄₅ as a component of ceramic scintillators.
Hansson-Sandsten, Maria
2010-05-01
The purpose of this paper is to present the optimal number of windows and window lengths using multiple window spectrogram for estimation of non-stationary processes with shorter or longer duration. Such processes could start in the EEG as a result of a stimuli, e.g., steady-state visual evoked potentials (SSVEP). In many applications, the Welch method is used with standard set-ups for window lengths and number of averaged spectra/spectrograms. This paper optimizes the window lengths and number of windows of the Welch method and other more recent, so called, multiple window or multitaper methods and compares the mean squared errors of these methods. Approximative formulas for the choice of optimal number of windows and window lengths are also given. Examples of spectrogram estimation of SSVEP are shown.
Energy Technology Data Exchange (ETDEWEB)
Parkinson, Bruce A. [Univ. of Wyoming, Laramie, WY (United States); Jianghua, He [Univ. of Wyoming, Laramie, WY (United States)
2015-01-06
The increasing need for carbon free energy has focused renewed attention on solar energy conversion. Although photovoltaic cells excel at directly converting of solar energy to electricity, they do not directly produce stored energy or fuels that account for more than 75% of current energy use. Direct photoelectrolysis of water has the advantage of converting solar energy directly to hydrogen, an ideal non-carbon and nonpolluting energy carrier, by replacing both a photovoltaic array and an electrolysis unit with one potentially inexpensive device. Unfortunately no materials are currently known to efficiently photoelectrolyze water that are, efficient, inexpensive and stable under illumination in electrolytes for many years. Nanostructured semiconducting metal oxides could potentially fulfill these requirements, making them the most promising materials for solar water photoelectrolysis, however no oxide semiconductor has yet been discovered with all the required properties. We have developed a simple, high-throughput combinatorial approach to prepare and screen many multi component metal oxides for water photoelectrolysis activity. The approach uses ink jet printing of overlapping patterns of soluble metal oxide precursors onto conductive glass substrates. Subsequent pyrolysis produces metal oxide phases that are screened for photoelectrolysis activity by measuring photocurrents produced by scanning a laser over the printed patterns in aqueous electrolytes. Several promising and unexpected compositions have been identified.
Optimization of element length for imaging small volumetric reflectors with linear ultrasonic arrays
Barber, T. S.; Wilcox, P. D.; Nixon, A. D.
2016-02-01
A 3D ultrasonic simulation study is presented, aimed at understanding the effect of element length for imaging small volumetric flaws with linear arrays in ultrasonically noisy materials. The geometry of a linear array can be described by the width, pitch and total number of the elements along with the length perpendicular to imaging plane. This paper is concerned with the latter parameter, which tends to be ignored in array optimization studies and is often chosen arbitrarily for industrial array inspections. A 3D analytical model based on imaging a point target is described, validated and used to make calculations of relative Signal-to-Noise Ratio (SNR) as a function of element length. SNR is found to be highly sensitive to element length with a 12dB variation observed over the length range investigated. It is then demonstrated that the optimal length can be predicted directly from the Point Spread Function (PSF) of the imaging system as well as the natural focal point of the array element from 2D beam profiles perpendicular to the imaging plane. This result suggests that the optimal length for any imaging position can be predicted without the need for a full 3D model and is independent of element pitch and the number of elements. Array element design guidelines are then described with respect to wavelength and extensions of these results are discussed for application to realistically-sized defects and coarse-grained materials.
Optimal length of capacitive-discharge and glow-discharge excilamps
Boichenko, A. M.; Erofeev, M. V.; Sosnin, E. A.; Tarasenko, V. F.; Yakovlenko, S. I.
2007-06-01
The optimal tube length of capacitive-discharge and glow-discharge excimer lamps with ring and circular electrodes of equal radii is considered. It is demonstrated that, at the same potential difference between electrodes and their radii, the ratio of the optimal lengths of the tubes with circular and ring electrodes depends on width L of the ring electrodes. The ratio of the lengths decreases with decreasing L. A relationship between the tube length and radius, the width of ring electrodes, and the minimum voltage at the tube that provide for an approximately uniform glow of the discharge column in the presence of voltage pulses with opposite polarities at the electrodes is derived.
Offset Optimization Based on Queue Length Constraint for Saturated Arterial Intersections
Directory of Open Access Journals (Sweden)
Xianmin Song
2012-01-01
Full Text Available Offset optimization is of critical importance to the traffic control system, especially when spillovers appear. In order to avoid vehicle queue spillovers, an arterial offset optimization model was presented in saturated arterial intersections based on minimizing the queue length over the whole duration of the saturated traffic environment. The paper uses the shockwave theory to analyze the queue evolution process of the intersection approach under the saturated traffic environment. Then through establishing and analyzing a function relationship between offset and the maximum queue length per cycle, a mapping model of offset and maximum queue length was established in the saturated condition. The validity and sensitivity of this model were tested by the VISSIM simulation environment. Finally, results showed that when volumes ratios are 0.525–0.6, adjusting offset reasonably under the saturated condition could decrease the queue length and effectively improve the vehicle operating efficiency.
An explicit combinatorial design
Ma, Xiongfeng
2011-01-01
A combinatorial design is a family of sets that are almost disjoint, which is applied in pseudo random number generations and randomness extractions. The parameter, $\\rho$, quantifying the overlap between the sets within the family, is directly related to the length of a random seed needed and the efficiency of an extractor. Nisan and Wigderson proposed an explicit construction of designs in 1994. Later in 2003, Hartman and Raz proved a bound of $\\rho\\le e^2$ for the Nisan-Wigderson construction. In this work, we prove a tighter bound of $\\rho
Optimization of element length for imaging small volumetric reflectors with linear ultrasonic arrays
Barber, T. S.; Wilcox, P. D.; Nixon, A. D.
2016-01-01
A 3D ultrasonic simulation study is presented, aimed at understanding the effect of element length for imaging small volumetric flaws with linear arrays in ultrasonically noisy materials. The geometry of a linear array can be described by the width, pitch and total number of the elements along with the length perpendicular to imaging plane. This paper is concerned with the latter parameter, which tends to be ignored in array optimization studies and is often chosen arbitrarily for industrial ...
An actuator line model simulation with optimal body force projection length scales
Martinez-Tossas, Luis; Churchfield, Matthew J.; Meneveau, Charles
2016-11-01
In recent work (Martínez-Tossas et al. "Optimal smoothing length scale for actuator line models of wind turbine blades", preprint), an optimal body force projection length-scale for an actuator line model has been obtained. This optimization is based on 2-D aerodynamics and is done by comparing an analytical solution of inviscid linearized flow over a Gaussian body force to the potential flow solution of flow over a Joukowski airfoil. The optimization provides a non-dimensional optimal scale ɛ / c for different Joukowski airfoils, where ɛ is the width of the Gaussian kernel and c is the chord. A Gaussian kernel with different widths in the chord and thickness directions can further reduce the error. The 2-D theory developed is extended by simulating a full scale rotor using the optimal body force projection length scales. Using these values, the tip losses are captured by the LES and thus, no additional explicit tip-loss correction is needed for the actuator line model. The simulation with the optimal values provides excellent agreement with Blade Element Momentum Theory. This research is supported by the National Science Foundation (Grant OISE-1243482, the WINDINSPIRE project).
Directory of Open Access Journals (Sweden)
Imed Hadj Kacem
2008-01-01
Full Text Available We consider the problem of optimization of the training sequence length when a turbo-detector composed of a maximum a posteriori (MAP equalizer and a MAP decoder is used. At each iteration of the receiver, the channel is estimated using the hard decisions on the transmitted symbols at the output of the decoder. The optimal length of the training sequence is found by maximizing an effective signal-to-noise ratio (SNR taking into account the data throughput loss due to the use of pilot symbols.
DYNAMIC OPTIMIZATION OF OVERLAPAND-ADD LENGTH OVER MBOFDM SYSTEM BASED ON SNR AND CIR ESTIMATE
Directory of Open Access Journals (Sweden)
Nouri Naziha
2014-12-01
Full Text Available An important role performed by Zero Padding (ZP in multi-band OFDM (MB-OFDM System. This role show for low-complexity in résistance against multipath interference by reducing inter-carrier interference (ICI and eliminating the inter-symbol interference (ISI Also, zeropadded suffix can be used to eliminate ripples in the power spectral density in order to conform to FCC requirements. At the receiver of MB-OFDM system needs to use of a technique called as overlap-and-add (OLA. Which maintain the circular convolution property and take the multipath energy of the channel. In this paper, we proposed a method of performing overlap-and-add length for zero padded suffixes. Then, we studied the effect of this method, dynamic optimization of overlap-and-add (OLA equalization, on the performance of MBOFDM system on Bit Error Rate (BER with AWGN channel and Saleh-Valenzuela (S-V Multipath channel Model. In the dynamic optimization OLA, the Length of ZP depends on length of channel impulse response (CIR. These measures, based on SNR, insert the ZP according to the measurement. Dynamic optimization of length of ZP improves the Performance of MBOFDM system. In fact we developed a technique to select the length of ZP as function of SNR and CIR estimate(repetition. In our simulation this technique improve to 3 dB at BER=10-2 with a multipath channels CM4.
Alsolami, Fawaz
2013-01-01
This paper is devoted to the study of algorithms for sequential optimization of approximate inhibitory rules relative to the length, coverage and number of misclassifications. Theses algorithms are based on extensions of dynamic programming approach. The results of experiments for decision tables from UCI Machine Learning Repository are discussed. © 2013 Springer-Verlag.
Mardirossian, Narbe; Head-Gordon, Martin
2016-06-01
A combinatorially optimized, range-separated hybrid, meta-GGA density functional with VV10 nonlocal correlation is presented. The final 12-parameter functional form is selected from approximately 10 × 109 candidate fits that are trained on a training set of 870 data points and tested on a primary test set of 2964 data points. The resulting density functional, ωB97M-V, is further tested for transferability on a secondary test set of 1152 data points. For comparison, ωB97M-V is benchmarked against 11 leading density functionals including M06-2X, ωB97X-D, M08-HX, M11, ωM05-D, ωB97X-V, and MN15. Encouragingly, the overall performance of ωB97M-V on nearly 5000 data points clearly surpasses that of all of the tested density functionals. In order to facilitate the use of ωB97M-V, its basis set dependence and integration grid sensitivity are thoroughly assessed, and recommendations that take into account both efficiency and accuracy are provided.
Energy Technology Data Exchange (ETDEWEB)
Krumke, S.O.; Rambau, J. [Zuse-Institut Berlin, Berlin (Germany)
2002-07-01
The automation of in-house logistic systems requires - beyond the physical control of the machinery - an efficient organization of transport requests: a field of combinatorial optimization. With the help of three concrete applications, this article illustrates the online-issues (incomplete knowledge) and the real-time issues (short time frame for computations) frequently occuring in logistic systems. We give an overview over general purpose methods to construct online-algorithms and over analysis methods which help to decide which algorithms are suitable for a particular problem setting. (orig.) [German] Die Automatisierung von innerbetrieblicher Logistik erfordert - ueber die physikalische Steuerung von Geraeten hinaus - auch eine effiziente Organisation der Transporte: ein Aufgabenfeld der kombinatorischen Optimierung. Dieser Artikel illustriert anhand von konkreten Aufgabenstellungen die Online-Problematik (unvollstaendiges Wissen) sowie die Echtzeit-Problematik (beschraenkte Rechenzeit), auf die man in der innerbetrieblichen Logistik trifft. Der Text gibt einen Ueberblick ueber allgemeine Konstruktionsprinzipien fuer Online-Algorithmen und Bewertungsmethoden, die bei der Entscheidung helfen, welche Algorithmen fuer eine vorliegende Problemstellung geeignet sind. (orig.)
Institute of Scientific and Technical Information of China (English)
吴俊; 胡协和; 陈生; 褚健
2003-01-01
The closed-loop stability issue of finite-precision realizations was investigated for digital controllers implemented in block-floating-point format. The controller coefficient perturbation was analyzed resulting from using finite word length (FWL) block-floating-point representation scheme. A block-floating-point FWL closed-loop stability measure was derived which considers both the dynamic range and precision. To facilitate the design of optimal finite-precision controller realizations, a computationally tractable block-floating-point FWL closed-loop stability measure was then introduced and the method of computing the value of this measure for a given controller realization was developed. The optimal controller realization is defined as the solution that maximizes the corresponding measure, and a numerical optimization approach was adopted to solve the resulting optimal realization problem. A numerical example was used to illustrate the design procedure and to compare the optimal controller realization with the initial realization.
Institute of Scientific and Technical Information of China (English)
吴俊; 胡协和; 陈生; 褚健
2003-01-01
The closed-loop stability issue of finite-precision realizations was investigated for digital control-lers implemented in block-floating-point format. The controller coefficient perturbation was analyzed resultingfrom using finite word length (FWL) block-floating-point representation scheme. A block-floating-point FWL closed-loop stability measure was derived which considers both the dynamic range and precision. To facilitate the design of optimal finite-precision controller realizations, a computationally tractable block-floating-point FWL closed-loop stability measure was then introduced and the method of computing the value of this measure for a given controller realization was developed. The optimal controller realization is defined as the solution that maximizes the corresponding measure, and a numerical optimization approach was adopted to solve the resulting optimal realization problem. A numerical example was used to illustrate the design procedure and to compare the optimal controller realization with the initial realization.
Weninger, Astrid; Hatzl, Anna-Maria; Schmid, Christian; Vogl, Thomas; Glieder, Anton
2016-10-10
The methylotrophic yeast Pichia pastoris (Komagataella phaffii) is one of the most commonly used expression systems for heterologous protein production. However the recombination machinery in P. pastoris is less effective in contrast to Saccharomyces cerevisiae, where efficient homologous recombination naturally facilitates genetic modifications. The lack of simple and efficient methods for gene disruption and specifically integrating cassettes has remained a bottleneck for strain engineering in P. pastoris. Therefore tools and methods for targeted genome modifications are of great interest. Here we report the establishment of CRISPR/Cas9 technologies for P. pastoris and demonstrate targeting efficiencies approaching 100%. However there appeared to be a narrow window of optimal conditions required for efficient CRISPR/Cas9 function for this host. We systematically tested combinations of various codon optimized DNA sequences of CAS9, different gRNA sequences, RNA Polymerase III and RNA Polymerase II promoters in combination with ribozymes for the expression of the gRNAs and RNA Polymerase II promoters for the expression of CAS9. Only 6 out of 95 constructs were functional for efficient genome editing. We used this optimized CRISPR/Cas9 system for gene disruption studies, to introduce multiplexed gene deletions and to test the targeted integration of homologous DNA cassettes. This system allows rapid, marker-less genome engineering in P. pastoris enabling unprecedented strain and metabolic engineering applications.
Choi, Dong-Won; Sohng, Kyeoung-Yae; Kim, Bum-Soo
2010-12-01
This study was conducted to assess optimal needle length for gluteal intramuscular injections (IM) via simple skinfold thickness (SFT). For this study, 190 healthy adults were recruited and grouped into eight groups according to gender and body mass index (BMI) (kg/m²). The Korean Society for the Study of Obesity criteria defines a BMI under 20 as underweight, 20.1-22.9 as normal, 23-24.9 as overweight and over 25 as obese. For each participant, the SFT of dorsoguteal (DG) and ventrogluteal (VG) sites were measured using a caliper. Subcutaneous tissue thickness was acquired through ultrasonic images. For men in the overweight and obese groups at the DG site, for the obese group at the VG site, and for women in the normal weight, overweight and obese groups at both sites, the mean subcutaneous tissue thickness exceeded 1.84 cm, the minimal length for a 1 inch needle used for IM. At the DG site, optimal intramuscular needle length (OINL) was 1.4 times in women and 1.0 times in men compared to SFT. At the VG site, OINL was 1.3 times in women and 0.9 times in men compared to SFT. The results of this study suggest that SFT is a reliable index to determine optimal needle length with minimal effort prior to IM.
Werfel, Thomas A; Jackson, Meredith A; Kavanaugh, Taylor E; Kirkbride, Kellye C; Miteva, Martina; Giorgio, Todd D; Duvall, Craig
2017-03-30
A rationally-designed library of ternary siRNA polyplexes was developed and screened for gene silencing efficacy in vitro and in vivo with the goal of overcoming both cell-level and systemic delivery barriers. [2-(dimethylamino)ethyl methacrylate] (DMAEMA) was homopolymerized or colpolymerized (50mol% each) with butyl methacrylate (BMA) from a reversible addition - fragmentation chain transfer (RAFT) chain transfer agent, with and without pre-conjugation to polyethylene glycol (PEG). Both single block polymers were tested as core-forming units, and both PEGylated, diblock polymers were screened as corona-forming units. Ternary siRNA polyplexes were assembled with varied amounts and ratios of core-forming polymers to PEGylated corona-forming polymers. The impact of polymer composition/ratio, hydrophobe (BMA) placement, and surface PEGylation density was correlated to important outcomes such as polyplex size, stability, pH-dependent membrane disruptive activity, biocompatibility, and gene silencing efficiency. The lead formulation, DB4-PDB12, was optimally PEGylated not only to ensure colloidal stability (no change in size by DLS between 0 and 24h) and neutral surface charge (0.139mV) but also to maintain higher cell uptake (>90% positive cells) than the most densely PEGylated particles. The DB4-PDB12 polyplexes also incorporated BMA in both the polyplex core- and corona-forming polymers, resulting in robust endosomolysis and in vitro siRNA silencing (~85% protein level knockdown) of the model gene luciferase across multiple cell types. Further, the DB4-PDB12 polyplexes exhibited greater stability, increased blood circulation time, reduced renal clearance, increased tumor biodistribution, and greater silencing of luciferase compared to our previously-optimized, binary parent formulation following intravenous (i.v.) delivery. This polyplex library approach enabled concomitant optimization of the composition and ratio of core- and corona-forming polymers (indirectly
Accessing Specific Peptide Recognition by Combinatorial Chemistry
DEFF Research Database (Denmark)
Li, Ming
Peptide Recognition by Combinatorial Chemistry”. Molecular recognition is a specific interaction between two or more molecules through noncovalent bonding, such as hydrogen bonding, metal coordination, van der Waals forces, π−π, hydrophobic, or electrostatic interactions. The association involves kinetic....... Combinatorial chemistry was invented in 1980s based on observation of functional aspects of the adaptive immune system. It was employed for drug development and optimization in conjunction with high-throughput synthesis and screening. (chapter 2) Combinatorial chemistry is able to rapidly produce many thousands...... was studied with this hook peptide library via the beadbead adhesion screening approach. The recognition pairs interlocked and formed a complex. (chapter 8) During accessing peptide molecular recognition by combinatorial chemistry, we faced several problems, which were solved by a range of analytical...
Statistical mechanics of combinatorial auctions
Galla, Tobias; Leone, Michele; Marsili, Matteo; Sellitto, Mauro; Weigt, Martin; Zecchina, Riccardo
2006-05-01
Combinatorial auctions are formulated as frustrated lattice gases on sparse random graphs, allowing the determination of the optimal revenue by methods of statistical physics. Transitions between computationally easy and hard regimes are found and interpreted in terms of the geometric structure of the space of solutions. We introduce an iterative algorithm to solve intermediate and large instances, and discuss competing states of optimal revenue and maximal number of satisfied bidders. The algorithm can be generalized to the hard phase and to more sophisticated auction protocols.
Fairness in Combinatorial Auctioning Systems
Saini, Megha
2008-01-01
One of the Multi-Agent Systems that is widely used by various government agencies, buyers and sellers in a market economy, in such a manner so as to attain optimized resource allocation, is the Combinatorial Auctioning System (CAS). We study another important aspect of resource allocations in CAS, namely fairness. We present two important notions of fairness in CAS, extended fairness and basic fairness. We give an algorithm that works by incorporating a metric to ensure fairness in a CAS that uses the Vickrey-Clark-Groves (VCG) mechanism, and uses an algorithm of Sandholm to achieve optimality. Mathematical formulations are given to represent measures of extended fairness and basic fairness.
Optimal Limb Length Ratio of Quadruped Robot Minimising Joint Torque on Slopes
Directory of Open Access Journals (Sweden)
Tadayoshi Aoyama
2009-01-01
Full Text Available This paper aims to determine an optimal structure for a quadruped robot, which will allow the robot’s joint torque sum to be minimised. An animal’s characteristic limb length ratio is a vital part of its overall morphology and the one that enables it to travel easily through its environment. For the same reason, a robot’s structure needs to be suitably designed for locomotion in its working environment. Joint torques are necessary to maintain the posture of the robot and to accelerate joint angles during walking motion, hence, minimisation of joint torques reduces energy consumption. We performed a numerical simulation in which we analysed the joint torques for various limb lengths and slope angles in order to determine the optimal structure of a robot walking on a slope. Our investigation determines that the optimal Ratio of Rear Leg Length (RRL can be derived by the use of a simulation designed to determine the physical structure of quadruped robot. Our analysis suggests that joint torque will increase as the slope angle becomes steeper if the rear legs of the robot are shorter than its forelegs, and that joint torque will decrease as the slope angle declines if the robot’s forelegs are shorter than its rear legs. Finally, experimental results validated our simulation analysis.
Biophysical constraints on optimal patch lengths for settlement of a reef-building bivalve.
Directory of Open Access Journals (Sweden)
Heidi L Fuchs
Full Text Available Reef-building species form discrete patches atop soft sediments, and reef restoration often involves depositing solid material as a substrate for larval settlement and growth. There have been few theoretical efforts to optimize the physical characteristics of a restored reef patch to achieve high recruitment rates. The delivery of competent larvae to a reef patch is influenced by larval behavior and by physical habitat characteristics such as substrate roughness, patch length, current speed, and water depth. We used a spatial model, the "hitting-distance" model, to identify habitat characteristics that will jointly maximize both the settlement probability and the density of recruits on an oyster reef (Crassostrea virginica. Modeled larval behaviors were based on laboratory observations and included turbulence-induced diving, turbulence-induced passive sinking, and neutral buoyancy. Profiles of currents and turbulence were based on velocity profiles measured in coastal Virginia over four different substrates: natural oyster reefs, mud, and deposited oyster and whelk shell. Settlement probabilities were higher on larger patches, whereas average settler densities were higher on smaller patches. Larvae settled most successfully and had the smallest optimal patch length when diving over rough substrates in shallow water. Water depth was the greatest source of variability, followed by larval behavior, substrate roughness, and tidal current speed. This result suggests that the best way to maximize settlement on restored reefs is to construct patches of optimal length for the water depth, whereas substrate type is less important than expected. Although physical patch characteristics are easy to measure, uncertainty about larval behavior remains an obstacle for predicting settlement patterns. The mechanistic approach presented here could be combined with a spatially explicit metapopulation model to optimize the arrangement of reef patches in an estuary
Probabilistic methods in combinatorial analysis
Sachkov, Vladimir N
2014-01-01
This 1997 work explores the role of probabilistic methods for solving combinatorial problems. These methods not only provide the means of efficiently using such notions as characteristic and generating functions, the moment method and so on but also let us use the powerful technique of limit theorems. The basic objects under investigation are nonnegative matrices, partitions and mappings of finite sets, with special emphasis on permutations and graphs, and equivalence classes specified on sequences of finite length consisting of elements of partially ordered sets; these specify the probabilist
Effect of calibration data length on performance and optimal parameters of hydrological model
Directory of Open Access Journals (Sweden)
Chuan-Zhe LI
2010-12-01
Full Text Available In order to assess the effects of calibration data length on the performance and optimal parameter values of hydrological model in ungauged or data limited catchments (actually, data are non-continuous and fragmental in some catchments, we choose to use non-continuous calibration periods to have more independent streamflow data for SIMHYD model calibration. Nash-Sutcliffe efficiency (NSE and percentage water balance error (WBE are used as performance measures. The Particle Swarm Optimization (PSO method is used to calibrate the rainfall-runoff models. Different length of data range from 1 year to 10 years randomly sampled used for study on impact of calibration data length. 55 relatively unimpaired catchments all over Australia with daily precipitation, potential evapotranspiration (PET, and streamflow data are tested to obtain more general conclusions. The results show that, longer calibration data does not necessarily result in better model performance. In general, 8 years data are sufficient to obtain steady estimates of model performance and parameters for SIMHYD model. It is also show that most humid catchments require fewer calibration data to get good performance and stable parameter values. The model performs better in humid and semi-humid catchments than arid catchments. Our results may have useful and interesting implications in the efficiency of limited observation data used for hydrological model calibration in different climatic catchments.
Axial Region Optimization for Cycle Length Extension of Small Modular PWR
Energy Technology Data Exchange (ETDEWEB)
Choe, Ji Won [UNIST, Ulsan (Korea, Republic of); Shin, Ho Cheol; Jung, Ji Eun [KHNP CRI, Daejeon (Korea, Republic of); Zheng, Youqi; Tak, Tae Woo; Lee, Deok Jung [UNIST, Ulsan (Korea, Republic of)
2016-05-15
This paper studied axial region sensitivity test in SMPWR to extend the cycle length. Zr- {sup 167}Er, Zr-B and Zr-Gd are used for BA material, the height of cutback and axial region has been changed. The cycle length of the reference core is 798 EFPD (26.6 EFPM), and there is no cutback and only {sup 167}Er-Zr is used in R-BA.Soluble boron-free small modular pressurized water reactor (SMPWR) can be a transportable size core due to the absence of the chemical volume control system (CVCS) and the amount of liquid radioactive waste, and further remove the corrosion problem caused by boric acid. The SMPWR needs large amount of burnable absorber (BA) instead of soluble boron, but the more the amount of BA is, the shorter the fuel cycle length is. Therefore, this paper studies axial region sensitivity test to make fuel cycle length of SMWPR longer. The procedure of axial region sensitivity test is as follows: cutback sensitivity tests, material and height sensitivity tests in the axial's reactor core design code system, has been used for these simulation. The optimal BA for cutback region is 10 cm of cutback with natural Gd 10 % in Zr-Gd, and the cycle length increases to 942 EFPD (31.4 months). Through the axial region sensitivity test, the cycle length becomes 1026 EFPD (34.2 months), but the peaking factors were not satisfied their limits. The 4.8-month increases compared with the reference core through the cutback sensitivity test. The possibility to excess reactivity with control rods in this core should verify.
The Influence of Added Mass on Optimal Step Length in Running.
Reenalda, Jasper; Maas, Maurice T F; de Koning, Jos J
2016-10-01
To examine the influence of induced changes in the morphology of the leg by adding mass on the optimal step length (OSL) in experienced runners to get more insight into parameters that influence preferred step length (PSL) and OSL. Thirteen experienced male runners (mean age 26.9 ± 6.1 y, height 183.7 ± 7.1 cm, mass 71.8 ± 5.9 kg) ran on a treadmill in 3 different conditions: unloaded (UL), loaded with 2 kg mass at the ankles (MA), and loaded with 2 kg mass at the hips (MH) at 7 different step lengths (SLs). SL deviations were expressed as deviations in relative leg length (%LL) from the individual PSL: 0%LL, ±5%LL, ±10%LL, and ±15%LL. Trials lasted 8 min, and 8 min of rest was given between trials. Oxygen uptake (V̇O2) was expressed as a fraction of V̇O2 at PSL + 0%LL in the unloaded condition (%V̇O2). The %SL with the lowest value of %V̇O2 was considered the OSL for this group of participants. OSL at the UL condition was 6% shorter than PSL. The MA condition resulted in a 7%LL larger OSL than at UL and MH (P distribution of the leg is a determinant of the OSL. As a consequence of the added mass to the ankles, OSL was 7%LL longer. Morphological characteristics of the leg might therefore play an important role in determining the runner's individual optimal SL.
Ground-up circular Higgs Factory ring design and cell length optimization
Talman, Richard
2017-02-01
A “ground-up” Higgs Factory design methodology is described. For concreteness, numerical parameter choices are drawn primarily from CEPC, the Circular Electron Positron Collider. The goals are to find: (i) optimal parameters, (ii) improved understanding , (iii) a tentative lattice design. As illustration of the method, six chromaticity-corrected lattices, with cell lengths ranging from 45 m to 280 m, all with identical βy = 2 mm or βy = 10 mm intersection region optics, are designed and their properties compared. For simplicity only a single “toy ring,” circumference (76 km), with one interaction point, and a single beam energy (120 GeV) is considered. For the cell-length optimization a figure of merit FOM (essentially integrated luminosity) is maximized consistent with a dimensionless “fine tuning penalty function” or figure of demerit FOD not being allowed to exceed a conservatively chosen upper limit. The tentative recommendation from this investigation is that the optimal CEPC route is (except for obvious changes) to simply copy LEP: 80 m cell length and two-in-one single-ring operation. The main luminosity-increasing improvements are increased radius and power, top-off-full-energy-injection, noninterleaved sextupoles, more than 100 beam bunch operation, and improved intersection region design. Local chromaticity compensation (with its inevitable intense hard X-rays incident on the detectors) is found to be unnecessary. With these changes luminosity in excess of 1034cm‑2s‑1 is projected to be achievable.
Industrialised application of combinatorial optimization
DEFF Research Database (Denmark)
Hansen, Jesper
2003-01-01
This thesis is one of the results of CIAMM (Center for Industrialised Application of Mathematical Modelling). The center is composed of industrial companies e.g. Odense Steel Shipyard (OSS), Bang & Olufsen (B&O), Danish Technological Institute and 4 departments from 3 universities including...
Chen, Yi-Lang; Liu, Yi-Nan
2014-07-01
This study examined body posture, subjective discomfort, and stability, requiring the participants to ride a stationary bicycle for 20 min (cadence: 60 rpm; workrate: 120 W), using various combinations of two handle heights and five seat-protruding node lengths (PNLs). The results indicated that bicycle handle height significantly influenced body posture, and that seat PNL caused differences in the riders' subjective discomfort and stability scores. The various PNLs affected only the trunk angle (approximately 6°), but had significantly positive (r = 0.994, p optimal reference for bicycle seat designs.
Optimal Heavy-Traffic Queue Length Scaling in an Incompletely Saturated Switch
Maguluri, Siva Theja; Burle, Sai Kiran; Srikant, R.
2016-01-01
We consider an input queued switch operating under the MaxWeight scheduling algorithm. This system is interesting to study because it is a model for Internet routers and data center networks. Recently, it was shown that the MaxWeight algorithm has optimal heavy-traffic queue length scaling when all ports are uniformly saturated. Here we consider the case when an arbitrary number of ports are saturated (which we call the incompletely saturated case), and each port is allowed to saturate at a d...
The variance of length of stay and the optimal DRG outlier payments.
Felder, Stefan
2009-09-01
Prospective payment schemes in health care often include supply-side insurance for cost outliers. In hospital reimbursement, prospective payments for patient discharges, based on their classification into diagnosis related group (DRGs), are complemented by outlier payments for long stay patients. The outlier scheme fixes the length of stay (LOS) threshold, constraining the profit risk of the hospitals. In most DRG systems, this threshold increases with the standard deviation of the LOS distribution. The present paper addresses the adequacy of this DRG outlier threshold rule for risk-averse hospitals with preferences depending on the expected value and the variance of profits. It first shows that the optimal threshold solves the hospital's tradeoff between higher profit risk and lower premium loading payments. It then demonstrates for normally distributed truncated LOS that the optimal outlier threshold indeed decreases with an increase in the standard deviation.
Directory of Open Access Journals (Sweden)
Wilhelm F. Maier
2004-10-01
Full Text Available Two recently published books examine combinatorial materials synthesis, high-throughput screening of libraries, and the design of successful experiments. Both are a must for those interested in materials development and discovery, says Wilhelm F. Maier
de Silva, Vin; Salamon, Dietmar
2012-01-01
We define combinatorial Floer homology of a transverse pair of noncontractibe nonisotopic embedded loops in an oriented 2-manifold without boundary, prove that it is invariant under isotopy, and prove that it is isomorphic to the original Lagrangian Floer homology.
Normal Order: Combinatorial Graphs
Solomon, A I; Blasiak, P; Horzela, A; Penson, K A; Solomon, Allan I.; Duchamp, Gerard; Blasiak, Pawel; Horzela, Andrzej; Penson, Karol A.
2004-01-01
A conventional context for supersymmetric problems arises when we consider systems containing both boson and fermion operators. In this note we consider the normal ordering problem for a string of such operators. In the general case, upon which we touch briefly, this problem leads to combinatorial numbers, the so-called Rook numbers. Since we assume that the two species, bosons and fermions, commute, we subsequently restrict ourselves to consideration of a single species, single-mode boson monomials. This problem leads to elegant generalisations of well-known combinatorial numbers, specifically Bell and Stirling numbers. We explicitly give the generating functions for some classes of these numbers. In this note we concentrate on the combinatorial graph approach, showing how some important classical results of graph theory lead to transparent representations of the combinatorial numbers associated with the boson normal ordering problem.
Microbatteries for Combinatorial Studies of Conventional Lithium-Ion Batteries
West, William; Whitacre, Jay; Bugga, Ratnakumar
2003-01-01
Integrated arrays of microscopic solid-state batteries have been demonstrated in a continuing effort to develop microscopic sources of power and of voltage reference circuits to be incorporated into low-power integrated circuits. Perhaps even more importantly, arrays of microscopic batteries can be fabricated and tested in combinatorial experiments directed toward optimization and discovery of battery materials. The value of the combinatorial approach to optimization and discovery has been proven in the optoelectronic, pharmaceutical, and bioengineering industries. Depending on the specific application, the combinatorial approach can involve the investigation of hundreds or even thousands of different combinations; hence, it is time-consuming and expensive to attempt to implement the combinatorial approach by building and testing full-size, discrete cells and batteries. The conception of microbattery arrays makes it practical to bring the advantages of the combinatorial approach to the development of batteries.
Accessing Specific Peptide Recognition by Combinatorial Chemistry
DEFF Research Database (Denmark)
Li, Ming
Molecular recognition is at the basis of all processes for life, and plays a central role in many biological processes, such as protein folding, the structural organization of cells and organelles, signal transduction, and the immune response. Hence, my PhD project is entitled “Accessing Specific...... Peptide Recognition by Combinatorial Chemistry”. Molecular recognition is a specific interaction between two or more molecules through noncovalent bonding, such as hydrogen bonding, metal coordination, van der Waals forces, π−π, hydrophobic, or electrostatic interactions. The association involves kinetic....... Combinatorial chemistry was invented in 1980s based on observation of functional aspects of the adaptive immune system. It was employed for drug development and optimization in conjunction with high-throughput synthesis and screening. (chapter 2) Combinatorial chemistry is able to rapidly produce many thousands...
Institute of Scientific and Technical Information of China (English)
周荣喜; 王晓光; 余湄
2014-01-01
针对单个静态利率期限结构模型在拟合收益率曲线时的不足，本文引入组合预测的方法，在绝对误差和与方差和最小准则下，分别建立了静态利率期限结构组合优化模型，并给出了模型的遗传算法求解过程。然后将上海证券交易所2004～2009年的国债每日交易数据分为样本内数据和样本外数据，对多项式样条、指数样条、NS、SV和组合优化模型进行实证比较。结果表明：无论是对于样本内数据的拟合，还是对于样本外数据的预测，组合优化模型的统计特征指标几乎都要优于其他单一模型，并且具有良好的适应性和稳健性，适用于拟合我国国债利率期限结构。%For the weakness in fitting the yield curve of certain term structure of interest rates model , this paper introduces the combinatorial forecast method , and develops respectively the combinatorial term structure of inter-est rates models based on the principle of the minimization variance and the minimization absolute error criterion , and presents the process of genetic algorithms for the models .The data of Shanghai Stock Exchange from 2004 to 2009 are divided into in-sample and out-of-sample data for the empirical research .The comparisons of empirical results of the five models including polynomial spline , exponential spline , Nelson-Siegel , Svensson and the com-binatorial optimization show that combinatorial optimization model outperforms other models in most of the statisti -cal indicators , and has good adaptability and robustness .It can be applied to fitting the static term structure of interest rates in the bond market of China .
Optimal forming zone length in continuous extrusion of lead-clad glass fiber wire
Institute of Scientific and Technical Information of China (English)
李霞; 唐景林; 王丽薇; 高明
2008-01-01
Forming zone length (FZL) is a key parameter of the lead-clad glass fiber extrusion dies, and an unsuitable FZL will lead to breakage of the glass fiber and/or unacceptable geometric and metallographic qualities of the product. The optimal FZL was determined theoretically based on a mathematical model established by upper bound method, and accepted Pb-GF wire was actually obtained experimentally by symmetric side-feed extrusion at a much lower temperature than that published before. The wire has features of fine grains, uniform diameter, good coaxiality and satisfied mechanical property. The results and conclusions obtained in the research can be used to design the forming tools for lead-clad glass fiber extrusion and have significance to further research on the extrusion of other complex wires of metal-clad brittle core.
DEFF Research Database (Denmark)
Larsen, Jesper Abildgaard; Wisniewski, Rafal; Grunnet, Jacob Deleuran
2008-01-01
As initially suggested by E. Sontag, it is possible to approximate an arbitrary nonlinear system by a set of piecewise linear systems. In this work we concentrate on how to control a system given by a set of piecewise linear systems defined on simplices. By using the results of L. Habets and J. van...... Schuppen, it is possible to find a controller for the system on each of the simplices thus guaranteeing that the system flow on the simplex only will leave the simplex through a subset of its faces. Motivated by R. Forman, on the triangulated state space we define a combinatorial vector field, which...... indicates for a given face the future simplex. In the suggested definition we allow nondeterminacy in form of splitting and merging of solution trajectories. The combinatorial vector field gives rise to combinatorial counterparts of most concepts from dynamical systems, such as duals to vector fields, flow...
Chen, Lei; Luo, Anqi; Zhang, Yao; Liu, Fayong; Jiang, Yang; Xu, Qingsheng; Chen, Xinhui; Hu, Qingzhuo; Chen, Shi-Fu; Chen, Kuo-Ju; Kuo, Hao-Chung
2012-12-10
The best performance of the phosphor Li(2)SrSiO(4): Eu(2+), Ce(3+) in terms of luminescence efficiency (LE), color rendering index (CRI) and color temperature (Tc) for light-emitting diode application was optimized with combinatorial approach. The combinatorial libraries were synthesized with solution-based method and the scale-up samples were synthesized with conventional solid-reaction method. Crystal structure was investigated by using the X-ray diffraction spectrometer. The emission spectra of each sample in combinatorial libraries were measured in situ by using a fiber optic spectrometer. Fluorescence spectrometers were used to record excitation and emission spectra of bulk samples. White light generation was tuned up by tailoring Eu(2+) and Ce(3+) concentrations in the single-phased host of Li(2)SrSiO(4) under near-ultraviolet excitation, but it exhibited low efficiency of luminescence and poor color rendering index. The effects of each level of the Eu(2+) and Ce(3+) concentrations on LE, CRI, and Tc were evaluated with the Taguchi method. The optimum levels of the interaction pairs between Eu(2+) and Ce(3+) concentration on LE, CRI, and Tc were [2, 1] (0.006 M, 0.003 M), [1, 2] (0.003 M, 0.006 M), and [3, 1] (0.009 M, 0.00 3M), respectively. The thermal stability of luminescence, the external quantum efficiency (QE), luminance, chromaticity coordinates, correlated color temperature, color purity including the composition ratio of RGB in white light, and color rendering index of the white light emission of phosphor were evaluated comprehensively from a bulk sample.
Introduction to combinatorial designs
Wallis, WD
2007-01-01
Combinatorial theory is one of the fastest growing areas of modern mathematics. Focusing on a major part of this subject, Introduction to Combinatorial Designs, Second Edition provides a solid foundation in the classical areas of design theory as well as in more contemporary designs based on applications in a variety of fields. After an overview of basic concepts, the text introduces balanced designs and finite geometries. The author then delves into balanced incomplete block designs, covering difference methods, residual and derived designs, and resolvability. Following a chapter on the e
Ali Kadhim; Paul Harrison; Jake Meeth; Alaa Al-Mebir; Guanggen Zeng; Judy Wu
2016-01-01
A combinatorial pulsed laser deposition system was developed by integrating a computer controlled scanning sample stage in order to rapidly screen processing conditions relevant to CdTe/CdS thin-film solar cells. Using this system, the thickness of the CdTe absorber layer is varied across a single sample from 1.5 μm to 0.75 μm. The effects of thickness on CdTe grain morphology, crystal orientation, and cell efficiency were investigated with respect to different postprocessing conditions. It i...
Manipulating Combinatorial Structures.
Labelle, Gilbert
This set of transparencies shows how the manipulation of combinatorial structures in the context of modern combinatorics can easily lead to interesting teaching and learning activities at every level of education from elementary school to university. The transparencies describe: (1) the importance and relations of combinatorics to science and…
Optimizing x-ray mirror thermal performance using variable length cooling for second generation FELs
Hardin, Corey L.; Srinivasan, Venkat N.; Amores, Lope; Kelez, Nicholas M.; Morton, Daniel S.; Stefan, Peter M.; Nicolas, Josep; Zhang, Lin; Cocco, Daniele
2016-09-01
The success of the LCLS led to an interest across a number of disciplines in the scientific community including physics, chemistry, biology, and material science. Fueled by this success, SLAC National Accelerator Laboratory is developing a new high repetition rate free electron laser, LCLS-II, a superconducting linear accelerator capable of a repetition rate up to 1 MHz. Undulators will be optimized for 200 to 1300 eV soft X-rays, and for 1000 to 5000 eV hard X-rays. To absorb spontaneous radiation, higher harmonic energies and deflect the x-ray beam to various end stations, the transport and diagnostics system includes grazing incidence plane mirrors on both the soft and Hard X-ray beamline. To deliver the FEL beam with minimal power loss and wavefront distortion, we need mirrors of height errors below 1nm rms in operational conditions. We need to mitigate the thermal load effects due to the high repetition rate. The absorbed thermal profile is highly dependent on the beam divergence, and this is a function of the photon energy. To address this complexity, we developed a mirror cradle with variable length cooling and first order curve correction. Mirror figure error is minimized using variable length water-cooling through a gallium-indium eutectic bath. Curve correction is achieved with an off-axis bender that will be described in details. We present the design features, mechanical analysis and results from optical and mechanical tests of a prototype assembly, with particular regards to the figure sensitivity to bender corrections.
Analysis on effective reservoirs and length optimization of horizontal wells in the Sulige Gasfield
Directory of Open Access Journals (Sweden)
Chao Luo
2016-05-01
Full Text Available By virtue of unique technical and economical advantages, horizontal well development has become a key technology in the high-efficiency development of tight gas reservoirs, however, this has worked unsatisfactorily in unstratified gas reservoirs. In this paper, the orientation and coverage of gas-bearing sand bodies (in isolated distribution of Member 8 of Permian Lower Shihezi Fm in the Sulige Gasfield were analyzed by means of outcrop analogy, geostatistical analysis and pilot tests of dense well patterns. Then, four gas-bearing sand distribution patterns suitable for the deployment of horizontal wells in Member 8 were proposed according to the precise geological anatomy results of dense well patterns. These patterns include thick massive isolated pattern, vertically superimposed pattern with physical interlayers, vertically superimposed pattern with argillaceous interlayers and lateral sugar-coated haw string pattern. Based on the statistics on gas-bearing sand bodies drilled by horizontal well drilling, the drilled gas-bearing sand bodies are 670–1300 m long. Based on production data correction, numerical simulation and economic evaluation, the length of rational horizontal sections were optimized by performing a case study of the vertically superimposed reservoirs with physical interlayers in the typical well group SuX-18-36 of Su-X Block. It is indicated that the rational horizontal well length within 1200 m in the Sulige Gasfield under current economic and technical conditions. This paper provides a technical support for the high-efficiency development of the Sulige Gasfield in the future.
Research on universal combinatorial coding.
Lu, Jun; Zhang, Zhuo; Mo, Juan
2014-01-01
The conception of universal combinatorial coding is proposed. Relations exist more or less in many coding methods. It means that a kind of universal coding method is objectively existent. It can be a bridge connecting many coding methods. Universal combinatorial coding is lossless and it is based on the combinatorics theory. The combinational and exhaustive property make it closely related with the existing code methods. Universal combinatorial coding does not depend on the probability statistic characteristic of information source, and it has the characteristics across three coding branches. It has analyzed the relationship between the universal combinatorial coding and the variety of coding method and has researched many applications technologies of this coding method. In addition, the efficiency of universal combinatorial coding is analyzed theoretically. The multicharacteristic and multiapplication of universal combinatorial coding are unique in the existing coding methods. Universal combinatorial coding has theoretical research and practical application value.
Analysis and design of algorithms for combinatorial problems
Ausiello, G
1985-01-01
Combinatorial problems have been from the very beginning part of the history of mathematics. By the Sixties, the main classes of combinatorial problems had been defined. During that decade, a great number of research contributions in graph theory had been produced, which laid the foundations for most of the research in graph optimization in the following years. During the Seventies, a large number of special purpose models were developed. The impressive growth of this field since has been strongly determined by the demand of applications and influenced by the technological increases in computing power and the availability of data and software. The availability of such basic tools has led to the feasibility of the exact or well approximate solution of large scale realistic combinatorial optimization problems and has created a number of new combinatorial problems.
Combinatorial Reciprocity Theorems
Beck, Matthias
2012-01-01
A common theme of enumerative combinatorics is formed by counting functions that are polynomials evaluated at positive integers. In this expository paper, we focus on four families of such counting functions connected to hyperplane arrangements, lattice points in polyhedra, proper colorings of graphs, and $P$-partitions. We will see that in each instance we get interesting information out of a counting function when we evaluate it at a \\emph{negative} integer (and so, a priori the counting function does not make sense at this number). Our goals are to convey some of the charm these "alternative" evaluations of counting functions exhibit, and to weave a unifying thread through various combinatorial reciprocity theorems by looking at them through the lens of geometry, which will include some scenic detours through other combinatorial concepts.
Pseudorandomness and Combinatorial Constructions
2006-01-01
In combinatorics, the probabilistic method is a very powerful tool to prove the existence of combinatorial objects with interesting and useful properties. Explicit constructions of objects with such properties are often very difficult, or unknown. In computer science, probabilistic algorithms are sometimes simpler and more efficient than the best known deterministic algorithms for the same problem. Despite this evidence for the power of random choices, the computational theory of pseudorandom...
Lyndon, Roger C
2001-01-01
From the reviews: "This book (...) defines the boundaries of the subject now called combinatorial group theory. (...)it is a considerable achievement to have concentrated a survey of the subject into 339 pages. This includes a substantial and useful bibliography; (over 1100 ÄitemsÜ). ...the book is a valuable and welcome addition to the literature, containing many results not previously available in a book. It will undoubtedly become a standard reference." Mathematical Reviews, AMS, 1979.
Trugenberger, Carlo A
2016-01-01
In a recently developed approach, geometry is modelled as an emergent property of random networks. Here I show that one of these models I proposed is exactly quantum gravity defined in terms of the combinatorial Ricci curvature recently derived by Ollivier. Geometry in the weak (classical) gravity regime arises in a phase transition driven by the condensation of short graph cycles. The strong (quantum) gravity regime corresponds to "small world" random graphs with logarithmic distance scaling.
A combinatorial approach to metamaterials discovery
Plum, E; Chen, W T; Fedotov, V A; Tsai, D P; Zheludev, N I
2010-01-01
We report a high through-put combinatorial approach to photonic metamaterial optimization. The new approach is based on parallel synthesis and consecutive optical characterization of large numbers of spatially addressable nano-fabricated metamaterial samples (libraries) with quasi-continuous variation of design parameters under real manufacturing conditions. We illustrate this method for Fano-resonance plasmonic nanostructures arriving at explicit recipes for high quality factors needed for switching and sensing applications.
The Combinatorial Retention Auction Mechanism (CRAM)
Coughlan, Peter; Gates, William (Bill); Myung, Noah
2013-01-01
Approved for public release; distribution is unlimited. Revised version We propose a reverse uniform price auction called Combinatorial Retention Auction Mechanism (CRAM) that integrates both monetary and non-monetary incentives (NMIs). CRAM computes the cash bonus and NMIs to a single cost parameter, retains the lowest cost employees and provides them with compensation equal to the cost of the first excluded employee. CRAM is dominant strategy incentive compatible. We provide optimal b...
Combinatorial auctions for electronic business
Indian Academy of Sciences (India)
Y Narahari; Pankaj Dayama
2005-04-01
Combinatorial auctions (CAs) have recently generated signiﬁcant interest as an automated mechanism for buying and selling bundles of goods. They are proving to be extremely useful in numerous e-business applications such as eselling, e-procurement, e-logistics, and B2B exchanges. In this article, we introduce combinatorial auctions and bring out important issues in the design of combinatorial auctions. We also highlight important contributions in current research in this area. This survey emphasizes combinatorial auctions as applied to electronic business situations.
The Yoccoz Combinatorial Analytic Invariant
DEFF Research Database (Denmark)
Petersen, Carsten Lunde; Roesch, Pascale
2008-01-01
In this paper we develop a combinatorial analytic encoding of the Mandelbrot set M. The encoding is implicit in Yoccoz' proof of local connectivity of M at any Yoccoz parameter, i.e. any at most finitely renormalizable parameter for which all periodic orbits are repelling. Using this encoding we...... define an explicit combinatorial analytic modelspace, which is sufficiently abstract that it can serve as a go-between for proving that other sets such as the parabolic Mandelbrot set M1 has the same combinatorial structure as M. As an immediate application we use here the combinatorial-analytic model...
Directory of Open Access Journals (Sweden)
Wei Lin Teoh
Full Text Available Designs of the double sampling (DS X chart are traditionally based on the average run length (ARL criterion. However, the shape of the run length distribution changes with the process mean shifts, ranging from highly skewed when the process is in-control to almost symmetric when the mean shift is large. Therefore, we show that the ARL is a complicated performance measure and that the median run length (MRL is a more meaningful measure to depend on. This is because the MRL provides an intuitive and a fair representation of the central tendency, especially for the rightly skewed run length distribution. Since the DS X chart can effectively reduce the sample size without reducing the statistical efficiency, this paper proposes two optimal designs of the MRL-based DS X chart, for minimizing (i the in-control average sample size (ASS and (ii both the in-control and out-of-control ASSs. Comparisons with the optimal MRL-based EWMA X and Shewhart X charts demonstrate the superiority of the proposed optimal MRL-based DS X chart, as the latter requires a smaller sample size on the average while maintaining the same detection speed as the two former charts. An example involving the added potassium sorbate in a yoghurt manufacturing process is used to illustrate the effectiveness of the proposed MRL-based DS X chart in reducing the sample size needed.
Directory of Open Access Journals (Sweden)
Wataru eTeramoto
2016-02-01
Full Text Available The present study investigated whether word width and length affect the optimal character size for reading of horizontally scrolling Japanese words, using reading speed as a measure. In Experiment 1, three Japanese words, each consisting of 4 Hiragana characters, sequentially scrolled on a display screen from right to left. Participants, all Japanese native speakers, were instructed to read the words aloud as accurately as possible, irrespective of their order within the sequence. To quantitatively measure their reading performance, we used rapid serial visual presentation paradigm, where the scrolling rate was increased until the participants began to make mistakes. Thus, the highest scrolling rate at which the participants’ performance exceeded 88.9% correct rate was calculated for each character size (0.3, 0.6, 1.0, and 3.0° and scroll window size (5 or 10 character spaces. Results showed that the reading performance was highest in the range of 0.6° to 1.0°, irrespective of the scroll window size. Experiment 2 investigated whether the optimal character size observed in Experiment 1 was applicable for any word width and word length (i.e., the number of characters in a word. Results showed that reading speeds were slower for longer than shorter words and the word width of 3.6° was optimal among the word lengths tested (3, 4, and 6 character words. Considering that character size varied depending on word width and word length in the present study, this means that the optimal character size can be changed by word width and word length.
Combinatorial and high-throughput screening approaches for strain engineering.
Liu, Wenshan; Jiang, Rongrong
2015-03-01
Microbes have long been used in the industry to produce valuable biochemicals. Combinatorial engineering approaches, new strain engineering tools derived from inverse metabolic engineering, have started to attract attention in recent years, including genome shuffling, error-prone DNA polymerase, global transcription machinery engineering (gTME), random knockout/overexpression libraries, ribosome engineering, multiplex automated genome engineering (MAGE), customized optimization of metabolic pathways by combinatorial transcriptional engineering (COMPACTER), and library construction of "tunable intergenic regions" (TIGR). Since combinatorial approaches and high-throughput screening methods are fundamentally interconnected, color/fluorescence-based, growth-based, and biosensor-based high-throughput screening methods have been reviewed. We believe that with the help of metabolic engineering tools and new combinatorial approaches, plus effective high-throughput screening methods, researchers will be able to achieve better results on improving microorganism performance under stress or enhancing biochemical yield.
Introduction to combinatorial analysis
Riordan, John
2002-01-01
This introduction to combinatorial analysis defines the subject as ""the number of ways there are of doing some well-defined operation."" Chapter 1 surveys that part of the theory of permutations and combinations that finds a place in books on elementary algebra, which leads to the extended treatment of generation functions in Chapter 2, where an important result is the introduction of a set of multivariable polynomials.Chapter 3 contains an extended treatment of the principle of inclusion and exclusion which is indispensable to the enumeration of permutations with restricted position given
Infinitary Combinatory Reduction Systems
DEFF Research Database (Denmark)
Ketema, Jeroen; Simonsen, Jakob Grue
2011-01-01
We define infinitary Combinatory Reduction Systems (iCRSs), thus providing the first notion of infinitary higher-order rewriting. The systems defined are sufficiently general that ordinary infinitary term rewriting and infinitary ¿-calculus are special cases. Furthermore,we generalise a number...... of knownresults fromfirst-order infinitary rewriting and infinitary ¿-calculus to iCRSs. In particular, for fully-extended, left-linear iCRSs we prove the well-known compression property, and for orthogonal iCRSs we prove that (1) if a set of redexes U has a complete development, then all complete developments...
Dynamic Combinatorial Chemistry
DEFF Research Database (Denmark)
Lisbjerg, Micke
This thesis is divided into seven chapters, which can all be read individually. The first chapter, however, contains a general introduction to the chemistry used in the remaining six chapters, and it is therefore recommended to read chapter one before reading the other chapters. Chapter 1...... is a general introductory chapter for the whole thesis. The history and concepts of dynamic combinatorial chemistry are described, as are some of the new and intriguing results recently obtained. Finally, the properties of a broad range of hexameric macrocycles are described in detail. Chapter 2 gives...
Dynamic Combinatorial Chemistry
DEFF Research Database (Denmark)
Lisbjerg, Micke
This thesis is divided into seven chapters, which can all be read individually. The first chapter, however, contains a general introduction to the chemistry used in the remaining six chapters, and it is therefore recommended to read chapter one before reading the other chapters. Chapter 1...... is a general introductory chapter for the whole thesis. The history and concepts of dynamic combinatorial chemistry are described, as are some of the new and intriguing results recently obtained. Finally, the properties of a broad range of hexameric macrocycles are described in detail. Chapter 2 gives...
Blenkinsop, Georgina; Mossadegh, Somayyeh; Ballard, Mark; Parker, Paul
2015-01-01
Significant lessons to inform best practice in trauma care should be learned from the last decade of conflict in Afghanistan and Iraq. This study used radiological data collated in the UK Military Hospital in Camp Bastion, Afghanistan, to investigate the most appropriate device length for needle chest decompression of tension pneumothorax (TP). We reviewed the optimal length of device and site needed for needle decompression of a tension pneumothorax in a UK military population and found no significant difference between sites for needle chest decompression (NCD). As a result, we do not recommend use of devices longer than 60mm for UK service personnel. 2015.
Simple Combinatorial Optimisation Cost Games
van Velzen, S.
2005-01-01
In this paper we introduce the class of simple combinatorial optimisation cost games, which are games associated to {0, 1}-matrices.A coalitional value of a combinatorial optimisation game is determined by solving an integer program associated with this matrix and the characteristic vector of the
Directory of Open Access Journals (Sweden)
Jorge Perdomo
2013-12-01
Full Text Available The sports scheduling problem has been center of attention in the Operational Research community due to their variety of models, and computational complexity of solutions (see for example Ribeiro (2010. In a Round Robin tournament, the schedule is proposed by assigning a “home" or “away" labels to a preestablished itinerary, in a such way that the total distance traveled by the teams during the tournament is minimized. In terms of operation research, the problem is modeled as a binary quadratic programming problem with linear constraints. In Suzuka y cols. (2005 the problem is treated as a MIN-RES-CUT. In this work we study the structure of the home-away assignment problem, and propose a simplification of the combinatorial formulation. We solve exactly small instances of the problem with an exhaustive search, and also approximately solve larger instances with a random search. // RESUMEN El problema de elaboración de calendarios deportivos ha centrado la atención de la comunidad de investigación de operaciones por la variedad de modelos y la complejidad computacional de las soluciones (ver por ejemplo Ribeiro (2010. En torneos tipo Round Robin de ida y vuelta el calendario se propone asignando la etiqueta de local o visitante a cada equipo, en un itinerario preestablecido de manera que se minimice el recorrido total de los equipos durante el torneo. En términos de investigación de operaciones lo modelamos como un problema de optimización cuadrática binaria con restricciones lineales. Suzuka, Miyashiro, Yoshise, y Matsui (2005 lo tratan como uno de encontrar el corte mínimo con restricciones (Min-Res-Cut en un grafo no dirigido, proporcionando una formulación de optimización combinatoria. En el presente trabajo estudiamos la estructura del problema de asignación local-visitante, y proponemos una simplificación de la formulación de optimización combinatoria. Resolvemos de forma exacta con una búsqueda exhaustiva instancias peque
Energy Technology Data Exchange (ETDEWEB)
Papp, D; Unkelbach, J [Massachusetts General Hospital, Boston, MA (United States)
2014-06-01
Purpose: Non-uniform fractionation, i.e. delivering distinct dose distributions in two subsequent fractions, can potentially improve outcomes by increasing biological dose to the target without increasing dose to healthy tissues. This is possible if both fractions deliver a similar dose to normal tissues (exploit the fractionation effect) but high single fraction doses to subvolumes of the target (hypofractionation). Optimization of such treatment plans can be formulated using biological equivalent dose (BED), but leads to intractable nonconvex optimization problems. We introduce a novel optimization approach to address this challenge. Methods: We first optimize a reference IMPT plan using standard techniques that delivers a homogeneous target dose in both fractions. The method then divides the pencil beams into two sets, which are assigned to either fraction one or fraction two. The total intensity of each pencil beam, and therefore the physical dose, remains unchanged compared to the reference plan. The objectives are to maximize the mean BED in the target and to minimize the mean BED in normal tissues, which is a quadratic function of the pencil beam weights. The optimal reassignment of pencil beams to one of the two fractions is formulated as a binary quadratic optimization problem. A near-optimal solution to this problem can be obtained by convex relaxation and randomized rounding. Results: The method is demonstrated for a large arteriovenous malformation (AVM) case treated in two fractions. The algorithm yields a treatment plan, which delivers a high dose to parts of the AVM in one of the fractions, but similar doses in both fractions to the normal brain tissue adjacent to the AVM. Using the approach, the mean BED in the target was increased by approximately 10% compared to what would have been possible with a uniform reference plan for the same normal tissue mean BED.
Three-dimensional suction flow control and suction jet length optimization of NACA 0012 wing
Yousefi, Kianoosh; Saleh, Reza
2015-01-01
A three-dimensional suction flow control study was performed to investigate the aerodynamic characteristics of a rectangular wing with a NACA 0012 airfoil section. In addition, the optimum suction jet length was determined. In this study, the Reynolds-averaged Navier–Stokes equations were employed in conjunction with a k–ω SST turbulent model. Perpendicular suction was applied at the leading edge of the wing's upper surface, with two different types of slot distributions: i.e., center suction...
Directory of Open Access Journals (Sweden)
Avnish Chandra Suman
2016-09-01
Full Text Available In the last few years it has been seen that many software vendors have started delivering projects incrementally with very short release cycles. Best examples of success of this approach has been Ubuntu Operating system that has a 6 months release cycle and popular web browsers such as Google Chrome, Opera, Mozilla Firefox. However there is very little knowledge available to the project managers to validate the chosen release cycle length. We propose a decision support system that helps to validate and estimate release cycle length in the early development phase by assuming that release cycle length is directly affected by three factors, (i choosing right requirements for current cycle, (ii estimating proximal time for each requirement, (iii requirement wise feedback from last iteration based on product reception, model accuracy and failed requirements. We have altered and used the EVOLVE technique proposed by G. Ruhe to select best requirements for current cycle and map it to time domain using UCP (Use Case Points based estimation and feedback factors. The model has been evaluated on both in-house as well as industry projects.
Combinatorial Maps with Normalized Knot
Zeps, Dainis
2010-01-01
We consider combinatorial maps with fixed combinatorial knot numbered with augmenting numeration called normalized knot. We show that knot's normalization doesn't affect combinatorial map what concerns its generality. Knot's normalization leads to more concise numeration of corners in maps, e.g., odd or even corners allow easy to follow distinguished cycles in map caused by the fixation of the knot. Knot's normalization may be applied to edge structuring knot too. If both are normalized then one is fully and other partially normalized mutually.
Combinatorial fractal Brownian motion model
Institute of Scientific and Technical Information of China (English)
朱炬波; 梁甸农
2000-01-01
To solve the problem of how to determine the non-scaled interval when processing radar clutter using fractal Brownian motion (FBM) model, a concept of combinatorial FBM model is presented. Since the earth (or sea) surface varies diversely with space, a radar clutter contains several fractal structures, which coexist on all scales. Taking the combination of two FBMs into account, via theoretical derivation we establish a combinatorial FBM model and present a method to estimate its fractal parameters. The correctness of the model and the method is proved by simulation experiments and computation of practial data. Furthermore, we obtain the relationship between fractal parameters when processing combinatorial model with a single FBM model. Meanwhile, by theoretical analysis it is concluded that when combinatorial model is observed on different scales, one of the fractal structures is more obvious.
Combinatorial designs constructions and analysis
Stinson, Douglas R
2004-01-01
Created to teach students many of the most important techniques used for constructing combinatorial designs, this is an ideal textbook for advanced undergraduate and graduate courses in combinatorial design theory. The text features clear explanations of basic designs, such as Steiner and Kirkman triple systems, mutual orthogonal Latin squares, finite projective and affine planes, and Steiner quadruple systems. In these settings, the student will master various construction techniques, both classic and modern, and will be well-prepared to construct a vast array of combinatorial designs. Design theory offers a progressive approach to the subject, with carefully ordered results. It begins with simple constructions that gradually increase in complexity. Each design has a construction that contains new ideas or that reinforces and builds upon similar ideas previously introduced. A new text/reference covering all apsects of modern combinatorial design theory. Graduates and professionals in computer science, applie...
Automatic generation of combinatorial test data
Zhang, Jian; Ma, Feifei
2014-01-01
This book reviews the state-of-the-art in combinatorial testing, with particular emphasis on the automatic generation of test data. It describes the most commonly used approaches in this area - including algebraic construction, greedy methods, evolutionary computation, constraint solving and optimization - and explains major algorithms with examples. In addition, the book lists a number of test generation tools, as well as benchmarks and applications. Addressing a multidisciplinary topic, it will be of particular interest to researchers and professionals in the areas of software testing, combi
Stochastic integrals: a combinatorial approach
Rota, Gian-Carlo; Wallstrom, Timothy C.
1997-01-01
A combinatorial definition of multiple stochastic integrals is given in the setting of random measures. It is shown that some properties of such stochastic integrals, formerly known to hold in special cases, are instances of combinatorial identities on the lattice of partitions of a set. The notion of stochastic sequences of binomial type is introduced as a generalization of special polynomial sequences occuring in stochastic integration, such as Hermite, Poisson–Charlier an...
Combinatorial methods with computer applications
Gross, Jonathan L
2007-01-01
Combinatorial Methods with Computer Applications provides in-depth coverage of recurrences, generating functions, partitions, and permutations, along with some of the most interesting graph and network topics, design constructions, and finite geometries. Requiring only a foundation in discrete mathematics, it can serve as the textbook in a combinatorial methods course or in a combined graph theory and combinatorics course.After an introduction to combinatorics, the book explores six systematic approaches within a comprehensive framework: sequences, solving recurrences, evaluating summation exp
Combinatorial chemistry in the agrosciences.
Lindell, Stephen D; Pattenden, Lisa C; Shannon, Jonathan
2009-06-15
Combinatorial chemistry and high throughput screening have had a profound effect upon the way in which agrochemical companies conduct their lead discovery research. The article reviews recent applications of combinatorial synthesis in the lead discovery process for new fungicides, herbicides and insecticides. The role and importance of bioavailability guidelines, natural products, privileged structures, virtual screening and X-ray crystallographic protein structures on the design of solid- and solution-phase compound libraries is discussed and illustrated.
Islam, Md Rafiqul; Mahmud, Abdullah Al; Islam, Md Saiful; Babu, Hafiz Md Hasan
2010-01-01
This paper describes an integrated framework for SOC test automation. This framework is based on a new approach for Wrapper/TAM co-optimization based on rectangle packing considering the diagonal length of the rectangles to emphasize on both TAM widths required by a core and its corresponding testing time. In this paper, we propose an efficient algorithm to construct wrappers that reduce testing time for cores. We then use rectangle packing to develop an integrated scheduling algorithm that incorporates power constraints in the test schedule. The test power consumption is important to consider since exceeding the system's power limit might damage the system.
Relativity in Combinatorial Gravitational Fields
Directory of Open Access Journals (Sweden)
Mao Linfan
2010-04-01
Full Text Available A combinatorial spacetime $(mathscr{C}_G| uboverline{t}$ is a smoothly combinatorial manifold $mathscr{C}$ underlying a graph $G$ evolving on a time vector $overline{t}$. As we known, Einstein's general relativity is suitable for use only in one spacetime. What is its disguise in a combinatorial spacetime? Applying combinatorial Riemannian geometry enables us to present a combinatorial spacetime model for the Universe and suggest a generalized Einstein gravitational equation in such model. Forfinding its solutions, a generalized relativity principle, called projective principle is proposed, i.e., a physics law ina combinatorial spacetime is invariant under a projection on its a subspace and then a spherically symmetric multi-solutions ofgeneralized Einstein gravitational equations in vacuum or charged body are found. We also consider the geometrical structure in such solutions with physical formations, and conclude that an ultimate theory for the Universe maybe established if all such spacetimes in ${f R}^3$. Otherwise, our theory is only an approximate theory and endless forever.
Algorithmic Strategies in Combinatorial Chemistry
Energy Technology Data Exchange (ETDEWEB)
GOLDMAN,DEBORAH; ISTRAIL,SORIN; LANCIA,GIUSEPPE; PICCOLBONI,ANTONIO; WALENZ,BRIAN
2000-08-01
Combinatorial Chemistry is a powerful new technology in drug design and molecular recognition. It is a wet-laboratory methodology aimed at ``massively parallel'' screening of chemical compounds for the discovery of compounds that have a certain biological activity. The power of the method comes from the interaction between experimental design and computational modeling. Principles of ``rational'' drug design are used in the construction of combinatorial libraries to speed up the discovery of lead compounds with the desired biological activity. This paper presents algorithms, software development and computational complexity analysis for problems arising in the design of combinatorial libraries for drug discovery. The authors provide exact polynomial time algorithms and intractability results for several Inverse Problems-formulated as (chemical) graph reconstruction problems-related to the design of combinatorial libraries. These are the first rigorous algorithmic results in the literature. The authors also present results provided by the combinatorial chemistry software package OCOTILLO for combinatorial peptide design using real data libraries. The package provides exact solutions for general inverse problems based on shortest-path topological indices. The results are superior both in accuracy and computing time to the best software reports published in the literature. For 5-peptoid design, the computation is rigorously reduced to an exhaustive search of about 2% of the search space; the exact solutions are found in a few minutes.
Length optimization of an S-shaped transition between offset optical waveguides.
Marcuse, D
1978-03-01
We derive expressions for the radiation loss of an S-shaped waveguide transition used to connect two straight integrated optics waveguides that are offset with respect to each other. It is assumed that the diffused integrated optics waveguides are produced with the help of an electron beam machine that allows beam positioning in the y direction only in discrete steps. We thus must consider staircase approximations to the desired smooth S-shaped curves. A waveguide whose axis consists of a staircase suffers radiation losses due to the quasi-periodic deformation of its axis. A second loss contribution comes from the S-shape of the waveguide axis. The sum of these loss contributions assumes a minimum that defines the optimum length of the transition waveguide.
Mapping Optimal Charge Density and Length of ROMP-Based PTDMs for siRNA Internalization.
Caffrey, Leah M; deRonde, Brittany M; Minter, Lisa M; Tew, Gregory N
2016-10-10
A fundamental understanding of how polymer structure impacts internalization and delivery of biologically relevant cargoes, particularly small interfering ribonucleic acid (siRNA), is of critical importance to the successful design of improved delivery reagents. Herein we report the use of ring-opening metathesis polymerization (ROMP) methods to synthesize two series of guanidinium-rich protein transduction domain mimics (PTDMs): one based on an imide scaffold that contains one guanidinium moiety per repeat unit, and another based on a diester scaffold that contains two guanidinium moieties per repeat unit. By varying both the degree of polymerization and, in effect, the relative number of cationic charges in each PTDM, the performances of the two ROMP backbones for siRNA internalization were evaluated and compared. Internalization of fluorescently labeled siRNA into Jurkat T cells demonstrated that fluorescein isothiocyanate (FITC)-siRNA internalization had a charge content dependence, with PTDMs containing approximately 40 to 60 cationic charges facilitating the most internalization. Despite this charge content dependence, the imide scaffold yielded much lower viabilities in Jurkat T cells than the corresponding diester PTDMs with similar numbers of cationic charges, suggesting that the diester scaffold is preferred for siRNA internalization and delivery applications. These developments will not only improve our understanding of the structural factors necessary for optimal siRNA internalization, but will also guide the future development of optimized PTDMs for siRNA internalization and delivery.
Directory of Open Access Journals (Sweden)
Banani Basu
2010-06-01
Full Text Available A method based on constricted Particle Swarm Optimization (CPSO algorithm to design a non-uniformly spaced collinear array of thin dipole antennas of unequal height is proposed. This paper presents a method for computing the appropriate excitation and geometry of individual array elements to generate a pencil beam in the vertical plane with minimum Standing Wave Ratio (SWR and fixed Side Lobe Level (SLL. Coupling effect between any two collinear center-fed thin dipole antennas having sinusoidal current distributions is analyzed using induced EMF method and minimized in terms of SWR. DRR of excitation distribution is fixed at a lower value for further mitigation of the coupling effect. Phase distribution for all the elements is kept at zero degree for broadside array. Optimization results show the effectiveness of the algorithm for the design of the array. Moreover method seems very conducive for estimating the mutual impedance between any two collinear center-fed thin dipole antennas having sinusoidal current distributions.
Institute of Scientific and Technical Information of China (English)
林培群; 徐建闽
2012-01-01
针对国内外许多城市的BRT专用道仅有1个车道、车辆进站排队容易造成通道阻塞的情况,首先以最小化排队概率为目标,推导出车站组的停靠线路组合优化模型,然后定义上游交叉口的累积效应系数以使模型适应车辆间歇性批量到站的情况,随后针对模型的求解,给出了一种n进制数编码的新的遗传算法.算例以广州市某典型BRT车站组为例进行停靠线路配置优化,并利用VISSIM软件对原始方案及优化方案进行多次仿真和对比,结果表明所提出的方法能有效地缓解公交车辆的进站排队现象,并降低泊位占有率,减少停车次数和行程时间.%Queuing in the bus station often causes traffic jam owing to the fact that BRT system in many cities contains only one lane. In order to relieve this crunch, firstly, a combinatorial optimization model of bus stop in BRT station group was put forward to minimize the queuing probability, then by defining the intersection vehicle cumulative effect coefficient, the optimization model was improved to adapt to intermittent bus batch arrivals caused by the upstream intersection. Furthermore, a genetic algorithm with n-based number encoding was put forward to solve the optimization model. Finally, several bus stop optimization programs of a typical station group in Guangzhou BRT system were obtained in the example, and the simulated results of the original and the new programs from VISSIM software showed that the proposed method could reduce the queuing situation effectively, and decrease the berth occupation rate, bus stop times and travel time simultaneously.
Combinatorial conditions for low rank solutions in semidefinite programming
Varvitsiotis, A.
2013-01-01
In this thesis we investigate combinatorial conditions that guarantee the existence of low-rank optimal solutions to semidefinite programs. Results of this type are important for approximation algorithms and for the study of geometric representations of graphs. The structure of the thesis is as
Combinatorial conditions for low rank solutions in semidefinite programming
A. Varvitsiotis (Antonios)
2013-01-01
htmlabstractIn this thesis we investigate combinatorial conditions that guarantee the existence of low-rank optimal solutions to semidefinite programs. Results of this type are important for approximation algorithms and for the study of geometric representations of graphs. The structure of the
Combinatorial Model Involving Stochastic Choices of Destination, Mode and Route
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
Traffic assignment models are one of the basic tools for the analysis and design of transportation systems. However, the existing models have some defects. Considering the characteristics of Chinese urban mixed traffic and the randomness of transportation information, the author develops a combinatorial model involving stochastic choices of destination, mode and route. Its uniqueness and equivalance are also proved by the optimization theory.
Combinatorial conditions for low rank solutions in semidefinite programming
Varvitsiotis, A.
2013-01-01
In this thesis we investigate combinatorial conditions that guarantee the existence of low-rank optimal solutions to semidefinite programs. Results of this type are important for approximation algorithms and for the study of geometric representations of graphs. The structure of the thesis is as foll
Directory of Open Access Journals (Sweden)
Boyan Grigorov
Full Text Available BACKGROUND: Measles virus (MV is a member of the Paramyxoviridae family and an important human pathogen causing strong immunosuppression in affected individuals and a considerable number of deaths worldwide. Currently, measles is a re-emerging disease in developed countries. MV is usually quantified in infectious units as determined by limiting dilution and counting of plaque forming unit either directly (PFU method or indirectly from random distribution in microwells (TCID50 method. Both methods are time-consuming (up to several days, cumbersome and, in the case of the PFU assay, possibly operator dependent. METHODS/FINDINGS: A rapid, optimized, accurate, and reliable technique for titration of measles virus was developed based on the detection of virus infected cells by flow cytometry, single round of infection and titer calculation according to the Poisson's law. The kinetics follow up of the number of infected cells after infection with serial dilutions of a virus allowed estimation of the duration of the replication cycle, and consequently, the optimal infection time. The assay was set up to quantify measles virus, vesicular stomatitis virus (VSV, and human immunodeficiency virus type 1 (HIV-1 using antibody labeling of viral glycoprotein, virus encoded fluorescent reporter protein and an inducible fluorescent-reporter cell line, respectively. CONCLUSION: Overall, performing the assay takes only 24-30 hours for MV strains, 12 hours for VSV, and 52 hours for HIV-1. The step-by-step procedure we have set up can be, in principle, applicable to accurately quantify any virus including lentiviral vectors, provided that a virus encoded gene product can be detected by flow cytometry.
Optimal smoothing length scale for actuator line models of lifting surfaces
Martinez-Tossas, Luis A
2015-01-01
The actuator line model (ALM) is a commonly used method to represent lifting surfaces such as wind turbine blades within Large-Eddy Simulations (LES). In ALM the lift and drag forces are replaced by an imposed body force which is typically smoothed over several grid points using a Gaussian kernel with some prescribed smoothing width $\\epsilon$. To date, the choice of $\\epsilon$ has most often been based on numerical considerations mostly related to the grid spacing used in LES. However, especially for finely resolved LES with grid spacings on the order or smaller than the chord-length of the blade, the best choice of $\\epsilon$ is not known. Focusing first on the lift force, here we find $\\epsilon$ and the force center location that minimize the square difference between the velocity fields obtained from solving 2D potential flow over Joukowski airfoils and solving the Euler equations including the imposed body force. The latter solution is found for the linearized problem, and is valid for small angles of at...
Sun, Di; Guo, Chao; Zhang, Ziyang; Han, Tongshuai; Liu, Jin
2016-10-01
The blood hemoglobin concentration's (BHC) measurement using Photoplethysmography (PPG), which gets blood absorption to near infrared light from the instantaneous pulse of transmitted light intensity, has not been applied to the clinical use due to the non-enough precision. The main challenge might be caused of the non-enough stable pulse signal when it's very weak and it often varies in different human bodies or in the same body with different physiological states. We evaluated the detection limit of BHC using PPG as the measurement precision level, which can be considered as a best precision result because we got the relative stable subject's pulse signals recorded by using a spectrometer with high signal-to-noise ratio (SNR) level, which is about 30000:1 in short term. Moreover, we optimized the used pathlength using the theory based on optimum pathlength to get a better sensitivity to the absorption variation in blood. The best detection limit was evaluated as about 1 g/L for BHC, and the best SNR of pulse for in vivo measurement was about 2000:1 at 1130 and 1250 nm. Meanwhile, we conclude that the SNR of pulse signal should be better than 400:1 when the required detection limit is set to 5 g/L. Our result would be a good reference to the BHC measurement to get a desired BHC measurement precision of real application.
Combinatorial Evolution and Forecasting of Communication Protocol ZigBee
Levin, Mark Sh; Kistler, Rolf; Klapproth, Alexander
2012-01-01
The article addresses combinatorial evolution and forecasting of communication protocol for wireless sensor networks (ZigBee). Morphological tree structure (a version of and-or tree) is used as a hierarchical model for the protocol. Three generations of ZigBee protocol are examined. A set of protocol change operations is generated and described. The change operations are used as items for forecasting based on combinatorial problems (e.g., clustering, knapsack problem, multiple choice knapsack problem). Two kinds of preliminary forecasts for the examined communication protocol are considered: (i) direct expert (expert judgment) based forecast, (ii) computation of the forecast(s) (usage of multicriteria decision making and combinatorial optimization problems). Finally, aggregation of the obtained preliminary forecasts is considered (two aggregation strategies are used).
Beck, M.; Lowry, C.
2016-12-01
The exchange of surface water and groundwater in the hyporheic zone encourages biogeochemical reactions that naturally attenuate nutrients in streams. Stream restoration efforts often include instream, dam-like structures that increase hyporheic exchange, with the goal of enhancing natural attenuation. The effectiveness of these structures on improving stream quality has been widely researched, however the ideal installation location for these structures along a stream reach to achieve maximum hyporheic exchange must be optimized based on physical and temporal changes in bed forms and hydrologic drivers. Through the use of the finite difference model MODFLOW and particle tracking code MODPATH, the optimal location for emplacement of these stream barriers to maximize the spatial extent of the hyporheic zone was explored. In addition, impacts of seasonal changes in stream stage were also evaluated based on hyporheic zone path lengths. A total of sixteen realizations were created to vary the location of the stream barrier relative to a pool and riffle sequence. Once the ideal location of the barrier was determined, a region of variable groundwater discharge was prescribed to determine the effect of focused discharge. Using MODPATH, imaginary particles identify areas of maximized hyporheic exchange. The results show that the optimal location of the stream restoration structure changes based on stream stage and groundwater discharge zones. The spatial location of the instream barrier relative to zones of concentrated groundwater discharge as well as the location along a pool and riffle sequence has a significant effect on the extent of the hyporheic zone.
Institute of Scientific and Technical Information of China (English)
陈晓青; 刘莉; 焦飞鹏; 王珍
2012-01-01
In order to obtain a better enantioselectivity of phenylalanine enantiomers and establish the optimal chiral ex- traction conditions, the distribution behavior was investigated in aqueous two-phase systems which were composed of polyethylene glycol and ammonium sulfate containing combinatorial chiral selector： β-cyclodextrin and HP-β-cyclodextrin. The influence of the molar concentration ratio of combinatorial chiral selectors, the total molar concentration of combinatorial chiral selectors, pH value, buffer type and its concentration were thoroughly studied, respectively. The results show that the enantioselectivity reaches 1.53 under the optimal chiral extraction conditions This extraction is a potential economical and effective way for chiral resolution.
Stoletzki, Nina
2011-04-11
Surprisingly, in several multi-cellular eukaryotes optimal codon use correlates negatively with gene length. This contrasts with the expectation under selection for translational accuracy. While suggested explanations focus on variation in strength and efficiency of translational selection, it has rarely been noticed that the negative correlation is reported only in organisms whose optimal codons are biased towards codons that end with G or C (-GC). This raises the question whether forces that affect base composition--such as GC-biased gene conversion--contribute to the negative correlation between optimal codon use and gene length. Yeast is a good organism to study this as equal numbers of optimal codons end in -GC and -AT and one may hence compare frequencies of optimal GC- with optimal AT-ending codons to disentangle the forces. Results of this study demonstrate in yeast frequencies of GC-ending (optimal AND non-optimal) codons decrease with gene length and increase with recombination. A decrease of GC-ending codons along genes contributes to the negative correlation with gene length. Correlations with recombination and gene expression differentiate between GC-ending and optimal codons, and also substitution patterns support effects of GC-biased gene conversion. While the general effect of GC-biased gene conversion is well known, the negative correlation of optimal codon use with gene length has not been considered in this context before. Initiation of gene conversion events in promoter regions and the presence of a gene conversion gradient most likely explain the observed decrease of GC-ending codons with gene length and gene position.
Structure-based design of combinatorial mutagenesis libraries.
Verma, Deeptak; Grigoryan, Gevorg; Bailey-Kellogg, Chris
2015-05-01
The development of protein variants with improved properties (thermostability, binding affinity, catalytic activity, etc.) has greatly benefited from the application of high-throughput screens evaluating large, diverse combinatorial libraries. At the same time, since only a very limited portion of sequence space can be experimentally constructed and tested, an attractive possibility is to use computational protein design to focus libraries on a productive portion of the space. We present a general-purpose method, called "Structure-based Optimization of Combinatorial Mutagenesis" (SOCoM), which can optimize arbitrarily large combinatorial mutagenesis libraries directly based on structural energies of their constituents. SOCoM chooses both positions and substitutions, employing a combinatorial optimization framework based on library-averaged energy potentials in order to avoid explicitly modeling every variant in every possible library. In case study applications to green fluorescent protein, β-lactamase, and lipase A, SOCoM optimizes relatively small, focused libraries whose variants achieve energies comparable to or better than previous library design efforts, as well as larger libraries (previously not designable by structure-based methods) whose variants cover greater diversity while still maintaining substantially better energies than would be achieved by representative random library approaches. By allowing the creation of large-scale combinatorial libraries based on structural calculations, SOCoM promises to increase the scope of applicability of computational protein design and improve the hit rate of discovering beneficial variants. While designs presented here focus on variant stability (predicted by total energy), SOCoM can readily incorporate other structure-based assessments, such as the energy gap between alternative conformational or bound states.
Combinatorial synthesis of natural products
DEFF Research Database (Denmark)
Nielsen, John
2002-01-01
for preparation of combinatorial libraries. In other examples, natural products or intermediates have served as building blocks or scaffolds in the synthesis of complex natural products, bioactive analogues or designed hybrid molecules. Finally, structural motifs from the biologically active parent molecule have......Combinatorial syntheses allow production of compound libraries in an expeditious and organized manner immediately applicable for high-throughput screening. Natural products possess a pedigree to justify quality and appreciation in drug discovery and development. Currently, we are seeing a rapid...
Institute of Scientific and Technical Information of China (English)
祝效华; 石昌帅; 童华
2015-01-01
In order to meet the high temperature environment requirement of deep and superdeep well exploitation, a technology of large length-to-diameter ratio metal stator screw lining meshing with rotor is presented. Based on the elastic-plasticity theory, and under the consideration of the effect of tube size, material mechanical parameters, friction coefficient and loading paths, the external pressure plastic forming mechanical model of metal stator screw lining is established, to study the optimal loading path of metal stator lining tube hydroforming process. The results show that wall thickness reduction of the external pressure tube hydroforming (THF) is about 4%, and three evaluation criteria of metal stator screw lining forming quality are presented: fillet stick mold coefficient, thickness relative error and forming quality coefficient. The smaller the three criteria are, the better the forming quality is. Each indicator has a trend of increase with the loading rate reducing, and the adjustment laws of die arc transition zone equidistance profile curve are acquired for improving tube forming quality. Hence, the research results prove the feasibility of external pressure THF used for processing high-accuracy large length-to-diameter ratio metal stator screw lining, and provide theoretical basis for designing new kind of stator structure which has better performance and longer service life.
Directory of Open Access Journals (Sweden)
Dhriti Sundar Maity
2015-02-01
Full Text Available This paper represents The Ant Colony Optimization for MTSP and Swarm Inspired Multipath Data Transmission with Congestion Control in MANET using Total Queue Length based on the behavioral nature in the biological ants. We consider the problem of congestion control for multicast traffic in wireless networks. MANET is multi hop wireless network in which the network components such as PC, mobile phones are mobile in nature. The components can communicate with each other without going through its server. One kind of agent (salesman is engaged in routing. One is Routing agent (salesman, who collects the information about network congestion as well as link failure and same is message agent (salesman that uses this information to get his destination nodes. Though a number of routing protocols exists, which aim to provide effecting routing but few provide a plausible solution to overall network congestion. We attempt to explore the property of the pheromone deposition by the real ant for MTSP. The proposed algorithm using path pheromone scents constantly updates the goodness of choosing a particular path and measuring the congestion in the network using total queue length and Hop-distance.
On an Extension of a Combinatorial Identity
Indian Academy of Sciences (India)
M Rana; A K Agarwal
2009-02-01
Using Frobenius partitions we extend the main results of [4]. This leads to an infinite family of 4-way combinatorial identities. In some particular cases we get even 5-way combinatorial identities which give us four new combinatorial versions of Göllnitz–Gordon identities.
Rachev, Alexander; Greenwald, Stephen; Shazly, Tarek
2013-08-01
It is well-documented that the geometrical dimensions, the longitudinal stretch ratio in situ, certain structural mechanical descriptors such as compliance and pressure-diameter moduli, as well as the mass fractions of structural constituents, vary along the length of the descending aorta. The origins of and possible interrelations among these observed variations remain open questions. The central premise of this study is that having considered the variation of the deformed inner diameter, axial stretch ratio, and area compliance along the aorta to be governed by the systemic requirements for flow distribution and reduction of cardiac preload, the zero-stress state geometry and mass fractions of the basic structural constituents of aortic tissue meet a principle of optimal mechanical operation. The principle manifests as a uniform distribution of the circumferential stress in the aortic wall that ensures effective bearing of the physiological load and a favorable mechanical environment for mechanosensitive vascular smooth muscle cells. A mathematical model is proposed and inverse boundary value problems are solved for the equations that follow from finite elasticity, structure-based constitutive modeling within constrained mixture theory, and stress-induced control of aortic homeostasis, mediated by the synthetic activity of vascular smooth muscle cells. Published experimental data are used to illustrate the predictive power of the proposed model. The results obtained are in agreement with published experimental data and support the proposed principle of optimal mechanical operation for the descending aorta.
Cryptographic Combinatorial Clock-Proxy Auctions
Parkes, David C.; Rabin, Michael O.; Thorpe, Christopher
We present a cryptographic protocol for conducting efficient, provably correct and secrecy-preserving combinatorial clock-proxy auctions. The “clock phase” functions as a trusted auction despite price discovery: bidders submit encrypted bids, and prove for themselves that they meet activity rules, and can compute total demand and thus verify price increases without revealing any information about individual demands. In the sealed-bid “proxy phase”, all bids are revealed the auctioneer via time-lapse cryptography and a branch-and-bound algorithm is used to solve the winner-determination problem. Homomorphic encryption is used to prove the correctness of the solution, and establishes the correctness of the solution to any interested party. Still an NP-hard optimization problem, the use of homomorphic encryption imposes additional computational time on winner-determination that is linear in the size of the branch-and-bound search tree, and thus roughly linear in the original (search-based) computational time. The result is a solution that avoids, in the usual case, the exponential complexity of previous cryptographically-secure combinatorial auctions.
Combinatorial reasoning to solve problems
Coenen, Tom; Hof, Frits; Verhoef, Nellie
2016-01-01
This study reports combinatorial reasoning to solve problems. We observed the mathematical thinking of students aged 14-16. We study the variation of the students’ solution strategies in the context of emergent modelling. The results show that the students are tempted to begin the problem solving pr
Algorithms in combinatorial design theory
Colbourn, CJ
1985-01-01
The scope of the volume includes all algorithmic and computational aspects of research on combinatorial designs. Algorithmic aspects include generation, isomorphism and analysis techniques - both heuristic methods used in practice, and the computational complexity of these operations. The scope within design theory includes all aspects of block designs, Latin squares and their variants, pairwise balanced designs and projective planes and related geometries.
The evolution of combinatorial phonology
Zuidema, Willem; de Boer, Bart
2009-01-01
A fundamental, universal property of human language is that its phonology is combinatorial. That is, one can identify a set of basic, distinct units (phonemes, syllables) that can be productively combined in many different ways. In this paper, we develop a methodological framework based on evolution
Combinatorial synthesis of natural products
DEFF Research Database (Denmark)
Nielsen, John
2002-01-01
Combinatorial syntheses allow production of compound libraries in an expeditious and organized manner immediately applicable for high-throughput screening. Natural products possess a pedigree to justify quality and appreciation in drug discovery and development. Currently, we are seeing a rapid...
The Yoccoz Combinatorial Analytic Invariant
DEFF Research Database (Denmark)
Petersen, Carsten Lunde; Roesch, Pascale
2008-01-01
In this paper we develop a combinatorial analytic encoding of the Mandelbrot set M. The encoding is implicit in Yoccoz' proof of local connectivity of M at any Yoccoz parameter, i.e. any at most finitely renormalizable parameter for which all periodic orbits are repelling. Using this encoding we ...
Combinatorial Auctions without Money
2014-05-01
auctions. ICALP, pp. 90-101, 2010. [2] P. Briest, P. Krysta, and B. Vöcking. Approximation techniques for utilitarian mechanism design. STOC, pp. 39-48...Grandoni, P. Krysta, S. Leonardi, and C. Ventre. Utilitarian mechanism design for multi-objective optimization. SODA, pp. 573-584, 2010. [11] J. R
Genetic Algorithm Based Combinatorial Auction Method for Multi-Robot Task Allocation
Institute of Scientific and Technical Information of China (English)
GONG Jian-wei; HUANG Wan-ning; XIONG Guang-ming; MAN Yi-ming
2007-01-01
An improved genetic algorithm is proposed to solve the problem of bad real-time performance or inability to get a global optimal/better solution when applying single-item auction (SIA) method or combinatorial auction method to multi-robot task allocation.The genetic algorithm based combinatorial auction (GACA) method which combines the basic-genetic algorithm with a new concept of ringed chromosome is used to solve the winner determination problem (WDP) of combinatorial auction.The simulation experiments are conducted in OpenSim, a multi-robot simulator.The results show that GACA can get a satisfying solution in a reasonable shot time, and compared with SIA or parthenogenesis algorithm combinatorial auction (PGACA) method, it is the simplest and has higher search efficiency, also, GACA can get a global better/optimal solution and satisfy the high real-time requirement of multi-robot task allocation.
Combinatorial algebra syntax and semantics
Sapir, Mark V
2014-01-01
Combinatorial Algebra: Syntax and Semantics provides a comprehensive account of many areas of combinatorial algebra. It contains self-contained proofs of more than 20 fundamental results, both classical and modern. This includes Golod–Shafarevich and Olshanskii's solutions of Burnside problems, Shirshov's solution of Kurosh's problem for PI rings, Belov's solution of Specht's problem for varieties of rings, Grigorchuk's solution of Milnor's problem, Bass–Guivarc'h theorem about the growth of nilpotent groups, Kleiman's solution of Hanna Neumann's problem for varieties of groups, Adian's solution of von Neumann-Day's problem, Trahtman's solution of the road coloring problem of Adler, Goodwyn and Weiss. The book emphasize several ``universal" tools, such as trees, subshifts, uniformly recurrent words, diagrams and automata. With over 350 exercises at various levels of difficulty and with hints for the more difficult problems, this book can be used as a textbook, and aims to reach a wide and diversified...
Combinatorial Properties of Finite Models
Hubicka, Jan
2010-01-01
We study countable embedding-universal and homomorphism-universal structures and unify results related to both of these notions. We show that many universal and ultrahomogeneous structures allow a concise description (called here a finite presentation). Extending classical work of Rado (for the random graph), we find a finite presentation for each of the following classes: homogeneous undirected graphs, homogeneous tournaments and homogeneous partially ordered sets. We also give a finite presentation of the rational Urysohn metric space and some homogeneous directed graphs. We survey well known structures that are finitely presented. We focus on structures endowed with natural partial orders and prove their universality. These partial orders include partial orders on sets of words, partial orders formed by geometric objects, grammars, polynomials and homomorphism orders for various combinatorial objects. We give a new combinatorial proof of the existence of embedding-universal objects for homomorphism-defined...
Stem cells and combinatorial science.
Fang, Yue Qin; Wong, Wan Qing; Yap, Yan Wen; Orner, Brendan P
2007-09-01
Stem cell-based technologies have the potential to help cure a number of cell degenerative diseases. Combinatorial and high throughput screening techniques could provide tools to control and manipulate the self-renewal and differentiation of stem cells. This review chronicles historic and recent progress in the stem cell field involving both pluripotent and multipotent cells, and it highlights relevant cellular signal transduction pathways. This review further describes screens using libraries of soluble, small-molecule ligands, and arrays of molecules immobilized onto surfaces while proposing future trends in similar studies. It is hoped that by reviewing both the stem cell and the relevant high throughput screening literature, this paper can act as a resource to the combinatorial science community.
Communities of minima in local optima networks of combinatorial spaces
Daolio, Fabio; Tomassini, Marco; Vérel, Sébastien; Ochoa, Gabriela
2011-05-01
In this work, we present a new methodology to study the structure of the configuration spaces of hard combinatorial problems. It consists in building the network that has as nodes the locally optimal configurations and as edges the weighted oriented transitions between their basins of attraction. We apply the approach to the detection of communities in the optima networks produced by two different classes of instances of a hard combinatorial optimization problem: the quadratic assignment problem (QAP). We provide evidence indicating that the two problem instance classes give rise to very different configuration spaces. For the so-called real-like class, the networks possess a clear modular structure, while the optima networks belonging to the class of random uniform instances are less well partitionable into clusters. This is convincingly supported by using several statistical tests. Finally, we briefly discuss the consequences of the findings for heuristically searching the corresponding problem spaces.
Combinatorial Approach of Associative Classification
P. R. Pal; R.C. Jain
2010-01-01
Association rule mining and classification are two important techniques of data mining in knowledge discovery process. Integration of these two has produced class association rule mining or associative classification techniques, which in many cases have shown better classification accuracy than conventional classifiers. Motivated by this study we have explored and applied the combinatorial mathematics in class association rule mining in this paper. Our algorithm is based on producing co...
Combinatorial aspects of covering arrays
Directory of Open Access Journals (Sweden)
Charles J. Colbourn
2004-11-01
Full Text Available Covering arrays generalize orthogonal arrays by requiring that t -tuples be covered, but not requiring that the appearance of t -tuples be balanced.Their uses in screening experiments has found application in software testing, hardware testing, and a variety of fields in which interactions among factors are to be identified. Here a combinatorial view of covering arrays is adopted, encompassing basic bounds, direct constructions, recursive constructions, algorithmic methods, and applications.
Directory of Open Access Journals (Sweden)
Gao Xue
2012-09-01
Full Text Available Abstract Background Microbial polyhydroxyalkanoates (PHA are biopolyesters consisting of diverse monomers. PHA synthase PhaC2Ps cloned from Pseudomonas stutzeri 1317 is able to polymerize short-chain-length (scl 3-hydroxybutyrate (3HB monomers and medium-chain-length (mcl 3-hydroxyalkanoates (3HA with carbon chain lengths ranging from C6 to C12. However, the scl and mcl PHA production in Escherichia coli expressing PhaC2Ps is limited with very low PHA yield. Results To improve the production of PHA with a wide range of monomer compositions in E. coli, a series of optimization strategies were applied on the PHA synthase PhaC2Ps. Codon optimization of the gene and mRNA stabilization with a hairpin structure were conducted and the function of the optimized PHA synthase was tested in E. coli. The transcript was more stable after the hairpin structure was introduced, and western blot analysis showed that both codon optimization and hairpin introduction increased the protein expression level. Compared with the wild type PhaC2Ps, the optimized PhaC2Ps increased poly-3-hydroxybutyrate (PHB production by approximately 16-fold to 30% of the cell dry weight. When grown on dodecanoate, the recombinant E. coli harboring the optimized gene phaC2PsO with a hairpin structure in the 5’ untranslated region was able to synthesize 4-fold more PHA consisting of 3HB and medium-chain-length 3HA compared to the recombinant harboring the wild type phaC2Ps. Conclusions The levels of both PHB and scl-mcl PHA in E. coli were significantly increased by series of optimization strategies applied on PHA synthase PhaC2Ps. These results indicate that strategies including codon optimization and mRNA stabilization are useful for heterologous PHA synthase expression and therefore enhance PHA production.
Microfluidic platform for combinatorial synthesis in picolitre droplets.
Theberge, Ashleigh B; Mayot, Estelle; El Harrak, Abdeslam; Kleinschmidt, Felix; Huck, Wilhelm T S; Griffiths, Andrew D
2012-04-07
This paper presents a droplet-based microfluidic platform for miniaturized combinatorial synthesis. As a proof of concept, a library of small molecules for early stage drug screening was produced. We present an efficient strategy for producing a 7 × 3 library of potential thrombin inhibitors that can be utilized for other combinatorial synthesis applications. Picolitre droplets containing the first type of reagent (reagents A(1), A(2), …, A(m)) were formed individually in identical microfluidic chips and then stored off chip with the aid of stabilizing surfactants. These droplets were then mixed to form a library of droplets containing reagents A(1-m), each individually compartmentalized, which was reinjected into a second microfluidic chip and combinatorially fused with picolitre droplets containing the second reagent (reagents B(1), B(2), …, B(n)) that were formed on chip. The concept was demonstrated with a three-component Ugi-type reaction involving an amine (reagents A(1-3)), an aldehyde (reagents B(1-7)), and an isocyanide (held constant), to synthesize a library of small molecules with potential thrombin inhibitory activity. Our technique produced 10(6) droplets of each reaction at a rate of 2.3 kHz. Each droplet had a reaction volume of 3.1 pL, at least six orders of magnitude lower than conventional techniques. The droplets can then be divided into aliquots for different downstream screening applications. In addition to medicinal chemistry applications, this combinatorial droplet-based approach holds great potential for other applications that involve sampling large areas of chemical parameter space with minimal reagent consumption; such an approach could be beneficial when optimizing reaction conditions or performing combinatorial reactions aimed at producing novel materials.
Dynamic Combinatorial Libraries : From Exploring Molecular Recognition to Systems Chemistry
Li, Jianwei; Nowak, Piotr; Otto, Sijbren
2013-01-01
Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many
Allocation of advertising space by a web service provider using combinatorial auctions
Indian Academy of Sciences (India)
Sandeep Dulluri; N R Srinivasa Raghavan
2005-04-01
Advertising is a critical process for promoting both products and services in global trade. Internet has emerged as a powerful medium for trade and commerce. Online advertising over the internet has increased more than hundredfold since 2001. In the present work, we address problems faced by online advertisement service providers. In this paper, we propose a multi-slot and multi-site combinatorial auction for allocating scarce advertisement slots available on multiple sites. We observe that combinatorial auctions serve as effective mechanisms for allocating advertising slots over the internet. We resort to “ant” systems (ant – social insect/intelligent agent) to solve the above $\\mathcal{NP}$-hard combinatorial optimization problem which involves winner-determination in multi-item and multi-unit combinatorial auctions.
Cubature formulas on combinatorial graphs
Pesenson, Isaac Z
2011-01-01
Many contemporary applications, for example, cataloging of galaxies, document analysis, face recognition, learning theory, image processing, operate with a large amount of data which is often represented as a graph embedded into a high dimensional Euclidean space. The variety of problems arising in contemporary data processing requires development on graphs such topics of the classical harmonic analysis as Shannon sampling, splines, wavelets, cubature formulas. The goal of the paper is to establish cubature formulas on finite combinatorial graphs. The results have direct applications to problems that arise in connection with data filtering, data denoising and data dimension reduction.
Combinatorial algorithms for the seriation problem
Seminaroti, Matteo
2016-01-01
In this thesis we study the seriation problem, a combinatorial problem arising in data analysis, which asks to sequence a set of objects in such a way that similar objects are ordered close to each other. We focus on the combinatorial structure and properties of Robinsonian matrices, a special class
Combinatorial Interpretation of General Eulerian Numbers
Directory of Open Access Journals (Sweden)
Tingyao Xiong
2014-01-01
Full Text Available Since the 1950s, mathematicians have successfully interpreted the traditional Eulerian numbers and q-Eulerian numbers combinatorially. In this paper, the authors give a combinatorial interpretation to the general Eulerian numbers defined on general arithmetic progressions a,a+d,a+2d,….
Combinatorial Solutions to Normal Ordering of Bosons
Blasiak, P; Horzela, A; Penson, K A; Solomon, A I
2005-01-01
We present a combinatorial method of constructing solutions to the normal ordering of boson operators. Generalizations of standard combinatorial notions - the Stirling and Bell numbers, Bell polynomials and Dobinski relations - lead to calculational tools which allow to find explicitly normally ordered forms for a large class of operator functions.
Combinatorial Properties of Finite Models
Hubicka, Jan
2010-09-01
We study countable embedding-universal and homomorphism-universal structures and unify results related to both of these notions. We show that many universal and ultrahomogeneous structures allow a concise description (called here a finite presentation). Extending classical work of Rado (for the random graph), we find a finite presentation for each of the following classes: homogeneous undirected graphs, homogeneous tournaments and homogeneous partially ordered sets. We also give a finite presentation of the rational Urysohn metric space and some homogeneous directed graphs. We survey well known structures that are finitely presented. We focus on structures endowed with natural partial orders and prove their universality. These partial orders include partial orders on sets of words, partial orders formed by geometric objects, grammars, polynomials and homomorphism orders for various combinatorial objects. We give a new combinatorial proof of the existence of embedding-universal objects for homomorphism-defined classes of structures. This relates countable embedding-universal structures to homomorphism dualities (finite homomorphism-universal structures) and Urysohn metric spaces. Our explicit construction also allows us to show several properties of these structures.
Optimization Design of Medium -length Hole Blasting in Opencast Quarry%露天采石场中深孔爆破方案优化设计
Institute of Scientific and Technical Information of China (English)
佟明山
2012-01-01
Medium - length hole blasting was applied in opencast quarry, Shenzhen city. The deficiencies existing in the quality of rock blasting, blasting safety and blasting efficiency in the medium- length hole blasting of the quarry were pointed out by investigation. According to the field conditions of the quarry and theoretical analyses, the optimal design of medium - length hole blasting was made, and field experiment and practical application of the optimized scheme of medium - length hole blasting were carried out, and higher blasting efficiency, good safety of blasting,lower blasting cost and good quality of rock blasting were achieved.%深圳某采石场采用中深孔爆破方案，通过调查分析，指出了该采石场在爆破质量、爆破安全和爆破效率方面存在的不足。根据现场施工实际情况和理论分析，对该石场爆破方案进行了优化设计，并进行了现场试验和生产实践，在爆破效率、爆破安全、爆破成本和爆破质量方面取得了良好的效果。
Combinatorial Chemistry for Optical Sensing Applications
Díaz-García, M. E.; Luis, G. Pina; Rivero-Espejel, I. A.
The recent interest in combinatorial chemistry for the synthesis of selective recognition materials for optical sensing applications is presented. The preparation, screening, and applications of libraries of ligands and chemosensors against molecular species and metal ions are first considered. Included in this chapter are also the developments involving applications of combinatorial approaches to the discovery of sol-gel and acrylic-based imprinted materials for optical sensing of antibiotics and pesticides, as well as libraries of doped sol-gels for high-throughput optical sensing of oxygen. The potential of combinatorial chemistry applied to the discovery of new sensing materials is highlighted.
Muzamil, Akhmad; Haries Firmansyah, Achmad
2017-05-01
The research was done the optimization image of Magnetic Resonance Imaging (MRI) T2 Fast Spin Echo (FSE) with variation Echo Train Length (ETL) on the Rupture Tendon Achilles case. This study aims to find the variations Echo Train Length (ETL) from the results of ankle’s MRI image and find out how the value of Echo Train Length (ETL) works on the MRI ankle to produce optimal image. In this research, the used ETL variations were 12 and 20 with the interval 2 on weighting T2 FSE sagittal. The study obtained the influence of Echo Train Length (ETL) on the quality of ankle MRI image sagittal using T2 FSE weighting and analyzed in 25 images of five patients. The data analysis has done quantitatively with the Region of Interest (ROI) directly on computer MRI image planes which conducted statistical tests Signal to Noise Ratio (SNR) and Contras to Noise Ratio (CNR). The Signal to Noise Ratio (SNR) was the highest finding on fat tissue, while the Contras to Noise Ratio (CNR) on the Tendon-Fat tissue with ETL 12 found in two patients. The statistics test showed the significant SNR value of the 0.007 (pTendon tissue, 0.364 (p>0.05) of the Fat, 0.912 (p>0.05) of the Fibula, and 0.436 (p>0.05) of the Heel Bone. For the contrast to noise ratio (CNR) of the Tendon-FAT tissue was about 0.041 (p>0.05). The results of the study showed that ETL variation with T2 FSE sagittal weighting had difference at Tendon tissue and Tendon-Fat tissue for MRI imaging quality. SNR and CNR were an important aspect on imaging optimization process to give the diagnose information.
Hazra, A; Bhowmik, B; Dutta, K; Chattopadhyay, P P; Bhattacharyya, P
2015-05-13
The present study concerns development of an efficient alcohol sensor by controlling the stoichiometry, length, and wall thickness of electrochemically grown TiO2 nanotube array for its use as the sensing layer. Judicious variation of H2O content (0, 2, 10 and 100% by volume) in the mixed electrolyte comprising ethylene glycol and NH4F resulted into the desired variation of stoichiometry. The sensor study was performed within the temperature range of 27 to 250 °C for detecting the alcohols in the concentration range of 10-1000 ppm. The nanotubes grown with the electrolyte containing 2 vol % H2O offered the maximum response magnitude. For this stoichiometry, variation of corresponding length (1.25-2.4 μm) and wall thickness (19.8-9 nm) of the nanotubes was achieved by varying the anodization time (4-16 h) and temperatures (42-87 °C), respectively. While the variation of length influenced the sensing parameters insignificantly, the best response magnitude was achieved for ∼13 nm wall thickness. The underlying sensing mechanism was correlated with the experimental findings on the basis of structural parameters of the nanotubes.
Combinatorial Game Theory, Well-Tempered Scoring Games, and a Knot Game
Johnson, Will
2011-01-01
We begin by reviewing and proving the basic facts of combinatorial game theory. We then consider scoring games (also known as Milnor games or positional games), focusing on the "fixed-length" games for which all sequences of play terminate after the same number of moves. The theory of fixed-length scoring games is shown to have properties similar to the theory of loopy combinatorial games, with operations similar to onsides and offsides. We give a complete description of the structure of fixed-length scoring games in terms of the class of short partizan games. We also consider fixed-length scoring games taking values in the two-element boolean algebra, and classify these games up to indistinguishability. We then apply these results to analyze some positions in the knotting-unknotting game of Pechenik, Townsend, Henrich, MacNaughton, and Silversmith.
Galtry, Judith; Callister, Paul
2005-01-01
Parental leave is a complex area of public policy. Concerns include health protection for working mothers, equal employment opportunities for women, access to adequate antenatal and birthing care, maternal recovery, optimal nutrition for infants, and gender equality within families. Given this complexity, the design of parental leave schemes,…
Combinatorial Chemical Bath Deposition of CdS Contacts for Chalcogenide Photovoltaics.
Mokurala, Krishnaiah; Baranowski, Lauryn L; de Souza Lucas, Francisco W; Siol, Sebastian; van Hest, Maikel F A M; Mallick, Sudhanshu; Bhargava, Parag; Zakutayev, Andriy
2016-09-12
Contact layers play an important role in thin film solar cells, but new material development and optimization of its thickness is usually a long and tedious process. A high-throughput experimental approach has been used to accelerate the rate of research in photovoltaic (PV) light absorbers and transparent conductive electrodes, however the combinatorial research on contact layers is less common. Here, we report on the chemical bath deposition (CBD) of CdS thin films by combinatorial dip coating technique and apply these contact layers to Cu(In,Ga)Se2 (CIGSe) and Cu2ZnSnSe4 (CZTSe) light absorbers in PV devices. Combinatorial thickness steps of CdS thin films were achieved by removal of the substrate from the chemical bath, at regular intervals of time, and in equal distance increments. The trends in the photoconversion efficiency and in the spectral response of the PV devices as a function of thickness of CdS contacts were explained with the help of optical and morphological characterization of the CdS thin films. The maximum PV efficiency achieved for the combinatorial dip-coating CBD was similar to that for the PV devices processed using conventional CBD. The results of this study lead to the conclusion that combinatorial dip-coating can be used to accelerate the optimization of PV device performance of CdS and other candidate contact layers for a wide range of emerging absorbers.
Combinatorial Chemical Bath Deposition of CdS Contacts for Chalcogenide Photovoltaics
Energy Technology Data Exchange (ETDEWEB)
Mokurala, Krishnaiah; Baranowski, Lauryn L.; de Souza Lucas, Francisco W.; Siol, Sebastian; van Hest, Maikel F. A. M.; Mallick, Sudhanshu; Bhargava, Parag; Zakutayev, Andriy
2016-09-12
Contact layers play an important role in thin film solar cells, but new material development and optimization of its thickness is usually a long and tedious process. A high-throughput experimental approach has been used to accelerate the rate of research in photovoltaic (PV) light absorbers and transparent conductive electrodes, however the combinatorial research on contact layers is less common. Here, we report on the chemical bath deposition (CBD) of CdS thin films by combinatorial dip coating technique and apply these contact layers to Cu(In,Ga)Se2 (CIGSe) and Cu2ZnSnSe4 (CZTSe) light absorbers in PV devices. Combinatorial thickness steps of CdS thin films were achieved by removal of the substrate from the chemical bath, at regular intervals of time, and in equal distance increments. The trends in the photoconversion efficiency and in the spectral response of the PV devices as a function of thickness of CdS contacts were explained with the help of optical and morphological characterization of the CdS thin films. The maximum PV efficiency achieved for the combinatorial dip-coating CBD was similar to that for the PV devices processed using conventional CBD. The results of this study lead to the conclusion that combinatorial dip-coating can be used to accelerate the optimization of PV device performance of CdS and other candidate contact layers for a wide range of emerging absorbers.
Space-efficient parallel algorithms for combinatorial search problems
DEFF Research Database (Denmark)
Pietrcaprina, Andrea; Pucci, Geppino; Silvestri, Francesco;
2015-01-01
We present space-efficient parallel strategies for two fundamental combinatorial search problems, namely, backtrack search and branch-and-bound , both involving the visit of an n-node tree of height h under the assumption that a node can be accessed only through its father or its children. For both...... problems we propose efficient algorithms that run on a p-processor distributed-memory machine. For backtrack search, we give a deterministic algorithm running in O(n/p+hlogp) time, and a Las Vegas algorithm requiring optimal O(n/p+h) time, with high probability. Building on the backtrack search algorithm...
Constructions for Anonymous Secret Sharing Schemes Using Combinatorial Designs
Institute of Scientific and Technical Information of China (English)
Ying-pu Deng; Li-feng Guo; Mu-lan Liu
2007-01-01
In an anonymous secret sharing scheme the secret can be reconstructed without knowledge of which participants hold which shares. In this paper some constructions of anonymous secret sharing schemes with 2 thresholds by using combinatorial designs are given. Let υ(t, ω, q) denote the minimum size of the set of shares of a perfect anonymous (t, ω) threshold secret sharing scheme with q secrets. In this paper we prove that υ(t, ω, q) = Θ(q) if t and ω are fixed and that the lower bound of the size of the set of shares in [4] is not optimal under certain condition.
Conferences on Combinatorial and Additive Number Theory
2014-01-01
This proceedings volume is based on papers presented at the Workshops on Combinatorial and Additive Number Theory (CANT), which were held at the Graduate Center of the City University of New York in 2011 and 2012. The goal of the workshops is to survey recent progress in combinatorial number theory and related parts of mathematics. The workshop attracts researchers and students who discuss the state-of-the-art, open problems, and future challenges in number theory.
A product formula and combinatorial field theory
Horzela, A; Duchamp, G H E; Penson, K A; Solomon, A I
2004-01-01
We treat the problem of normally ordering expressions involving the standard boson operators a, a* where [a,a*]=1. We show that a simple product formula for formal power series - essentially an extension of the Taylor expansion - leads to a double exponential formula which enables a powerful graphical description of the generating functions of the combinatorial sequences associated with such functions - in essence, a combinatorial field theory. We apply these techniques to some examples related to specific physical Hamiltonians.
Cubical version of combinatorial differential forms
DEFF Research Database (Denmark)
Kock, Anders
2010-01-01
The theory of combinatorial differential forms is usually presented in simplicial terms. We present here a cubical version; it depends on the possibility of forming affine combinations of mutual neighbour points in a manifold, in the context of synthetic differential geometry.......The theory of combinatorial differential forms is usually presented in simplicial terms. We present here a cubical version; it depends on the possibility of forming affine combinations of mutual neighbour points in a manifold, in the context of synthetic differential geometry....
LDRD final report : robust analysis of large-scale combinatorial applications.
Energy Technology Data Exchange (ETDEWEB)
Carr, Robert D.; Morrison, Todd (University of Colorado, Denver, CO); Hart, William Eugene; Benavides, Nicolas L. (Santa Clara University, Santa Clara, CA); Greenberg, Harvey J. (University of Colorado, Denver, CO); Watson, Jean-Paul; Phillips, Cynthia Ann
2007-09-01
Discrete models of large, complex systems like national infrastructures and complex logistics frameworks naturally incorporate many modeling uncertainties. Consequently, there is a clear need for optimization techniques that can robustly account for risks associated with modeling uncertainties. This report summarizes the progress of the Late-Start LDRD 'Robust Analysis of Largescale Combinatorial Applications'. This project developed new heuristics for solving robust optimization models, and developed new robust optimization models for describing uncertainty scenarios.
Chan, P; Tsang, H
2005-09-19
Erbium doped fiber amplifier (EDFA) gain transient dynamics are studied in the context of their application in optically reconfigurable networks. We address the question of how to design the EDFA in order to minimize the gain transients present in the output signals of the EDFA when the system is optically reconfigured such that the total average input power levels and wavelengths are changed. Both experimental measurements and theoretical simulations show that the amplitude transients depend on the length of the erbium doped fiber (EDF) and the erbium concentration. We show how it may be possible to reduce the gain transients by appropriate design of the EDFA.
Mapping the Materials Genome through Combinatorial Informatics
Rajan, Krishna
2012-02-01
The recently announced White House Materials Genome Initiative provides an exciting challenge to the materials science community. To meet that challenge one needs to address a critical question, namely what is the materials genome? Some guide on how to the answer this question can be gained by recognizing that a ``gene'' is a carrier of information. In the biological sciences, discovering how to manipulate these genes has generated exciting discoveries in fundamental molecular biology as well as significant advances in biotechnology. Scaling that up to molecular, cellular length scales and beyond, has spawned from genomics, fields such as proteomics, metabolomics and essentially systems biology. The ``omics'' approach requires that one needs to discover and track these ``carriers of information'' and then correlate that information to predict behavior. A similar challenge lies in materials science, where there is a diverse array of modalities of materials ``discovery'' ranging from new materials chemistries and molecular arrangements with novel properties, to the development and design of new micro- and mesoscale structures. Hence to meaningfully adapt the spirit of ``genomics'' style research in materials science, we need to first identify and map the ``genes'' across different materials science applications On the experimental side, combinatorial experiments have opened a new approach to generate data in a high throughput manner, but without a clear way to link that to models, the full value of that data is not realized. Hence along with experimental and computational materials science, we need to add a ``third leg'' to our toolkit to make the ``Materials Genome'' a reality, the science of Materials Informatics. In this presentation we provide an overview of how information science coupled to materials science can in fact achieve the goal of mapping the ``Materials Genome''.
A new combinatorial approach to the construction of constant composition codes
Institute of Scientific and Technical Information of China (English)
2008-01-01
Constant composition codes(CCCs)are a new generalization of binary constant weight codes and have attracted recent interest due to their numerous applications. In this paper, a new combinatorial approach to the construction of CCCs is proposed, and used to establish new optimal CCCs.
Models of optimum discrete signals on the vector combinatorial configurations
Directory of Open Access Journals (Sweden)
V. V. Riznyk
2016-06-01
code is presented. Proposed vector models of discrete signal optimization provide, essentially, a new approach to generalize them to great class of optimized problems in radio-telecommunications, navigation and information technology. Moreover, the optimization embedded in the underlying combinatorial models. The favourable qualities of the Ideal Ring Vector sequences provide breakthrough opportunities to apply them to numerous branches of science and advanced technology, with direct applications to vector data telecommunications, signal processing, encoded design,and information technology. Structural perfection and harmony exist not only in the abstract models but in real world also.
Energy Technology Data Exchange (ETDEWEB)
Mohammadi, M A [Faculty of Physics, University of Tabriz, Tabriz, Iran (Iran, Islamic Republic of); Verma, R [Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University (Singapore); Sobhanian, S [Faculty of Physics, University of Tabriz, Tabriz, Iran (Iran, Islamic Republic of); Wong, C S [Plasma Research Laboratory, Physics Department, University of Malaya, Kuala Lumpur (Malaysia); Lee, S [Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University (Singapore); Springham, S V [Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University (Singapore); Tan, T L [Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University (Singapore); Lee, P [Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University (Singapore); Rawat, R S [Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University (Singapore)
2007-11-15
The UNU-ICTP plasma focus with a significantly longer than conventional anode can still be a reasonably good neon soft x-ray (SXR) source. The highest average neon SXR yield of 3.3 J was achieved at 3 mbar. The time difference between the two first peaks of the voltage probe signal at the radial collapse phase was found to be inversely related to the SXR yield, i.e. the smaller the time difference, the higher the yield and vice versa. The estimation of average current sheath speeds using the shadowgraphic method coupled with laser and focus peak timing signals showed that the average axial rundown speed is similar to the one obtained for the optimal anode length but the average radial compression speed is decreased significantly. The range of pressure for a good neon SXR yield, however, has become much narrower, making efficient plasma focus operation a very sensitive function of the filling gas pressure for longer than the optimal anode length.
Energy Technology Data Exchange (ETDEWEB)
Martínez-Tossas, L. A. [Department of Mechanical Engineering, Johns Hopkins University, Baltimore 21218 MD USA; Churchfield, M. J. [National Renewable Energy Laboratory, Golden 80401 CO USA; Meneveau, C. [Department of Mechanical Engineering, Johns Hopkins University, Baltimore 21218 MD USA
2017-01-20
The actuator line model (ALM) is a commonly used method to represent lifting surfaces such as wind turbine blades within large-eddy simulations (LES). In the ALM, the lift and drag forces are replaced by an imposed body force that is typically smoothed over several grid points using a Gaussian kernel with some prescribed smoothing width e. To date, the choice of e has most often been based on numerical considerations related to the grid spacing used in LES. However, especially for finely resolved LES with grid spacings on the order of or smaller than the chord length of the blade, the best choice of e is not known. In this work, a theoretical approach is followed to determine the most suitable value of e, based on an analytical solution to the linearized inviscid flow response to a Gaussian force. We find that the optimal smoothing width eopt is on the order of 14%-25% of the chord length of the blade, and the center of force is located at about 13%-26% downstream of the leading edge of the blade for the cases considered. These optimal values do not depend on angle of attack and depend only weakly on the type of lifting surface. It is then shown that an even more realistic velocity field can be induced by a 2-D elliptical Gaussian lift-force kernel. Some results are also provided regarding drag force representation.
Particle swarm optimization with random keys applied to the nuclear reactor reload problem
Energy Technology Data Exchange (ETDEWEB)
Meneses, Anderson Alvarenga de Moura [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Coordenacao dos Programas de Pos-graduacao de Engenharia (COPPE). Programa de Engenharia Nuclear; Fundacao Educacional de Macae (FUNEMAC), RJ (Brazil). Faculdade Professor Miguel Angelo da Silva Santos; Machado, Marcelo Dornellas; Medeiros, Jose Antonio Carlos Canedo; Schirru, Roberto [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Coordenacao dos Programas de Pos-graduacao de Engenharia (COPPE). Programa de Engenharia Nuclear]. E-mails: ameneses@con.ufrj.br; marcelo@lmp.ufrj.br; canedo@lmp.ufrj.br; schirru@lmp.ufrj.br
2007-07-01
In 1995, Kennedy and Eberhart presented the Particle Swarm Optimization (PSO), an Artificial Intelligence metaheuristic technique to optimize non-linear continuous functions. The concept of Swarm Intelligence is based on the socials aspects of intelligence, it means, the ability of individuals to learn with their own experience in a group as well as to take advantage of the performance of other individuals. Some PSO models for discrete search spaces have been developed for combinatorial optimization, although none of them presented satisfactory results to optimize a combinatorial problem as the nuclear reactor fuel reloading problem (NRFRP). In this sense, we developed the Particle Swarm Optimization with Random Keys (PSORK) in previous research to solve Combinatorial Problems. Experiences demonstrated that PSORK performed comparable to or better than other techniques. Thus, PSORK metaheuristic is being applied in optimization studies of the NRFRP for Angra 1 Nuclear Power Plant. Results will be compared with Genetic Algorithms and the manual method provided by a specialist. In this experience, the problem is being modeled for an eight-core symmetry and three-dimensional geometry, aiming at the minimization of the Nuclear Enthalpy Power Peaking Factor as well as the maximization of the cycle length. (author)
Combinatorial stresses kill pathogenic Candida species.
Kaloriti, Despoina; Tillmann, Anna; Cook, Emily; Jacobsen, Mette; You, Tao; Lenardon, Megan; Ames, Lauren; Barahona, Mauricio; Chandrasekaran, Komelapriya; Coghill, George; Goodman, Daniel; Gow, Neil A R; Grebogi, Celso; Ho, Hsueh-Lui; Ingram, Piers; McDonagh, Andrew; de Moura, Alessandro P S; Pang, Wei; Puttnam, Melanie; Radmaneshfar, Elahe; Romano, Maria Carmen; Silk, Daniel; Stark, Jaroslav; Stumpf, Michael; Thiel, Marco; Thorne, Thomas; Usher, Jane; Yin, Zhikang; Haynes, Ken; Brown, Alistair J P
2012-10-01
Pathogenic microbes exist in dynamic niches and have evolved robust adaptive responses to promote survival in their hosts. The major fungal pathogens of humans, Candida albicans and Candida glabrata, are exposed to a range of environmental stresses in their hosts including osmotic, oxidative and nitrosative stresses. Significant efforts have been devoted to the characterization of the adaptive responses to each of these stresses. In the wild, cells are frequently exposed simultaneously to combinations of these stresses and yet the effects of such combinatorial stresses have not been explored. We have developed a common experimental platform to facilitate the comparison of combinatorial stress responses in C. glabrata and C. albicans. This platform is based on the growth of cells in buffered rich medium at 30°C, and was used to define relatively low, medium and high doses of osmotic (NaCl), oxidative (H(2)O(2)) and nitrosative stresses (e.g., dipropylenetriamine (DPTA)-NONOate). The effects of combinatorial stresses were compared with the corresponding individual stresses under these growth conditions. We show for the first time that certain combinations of combinatorial stress are especially potent in terms of their ability to kill C. albicans and C. glabrata and/or inhibit their growth. This was the case for combinations of osmotic plus oxidative stress and for oxidative plus nitrosative stress. We predict that combinatorial stresses may be highly significant in host defences against these pathogenic yeasts.
Mastellone, Daniela; Fedi, Maurizio; Ialongo, Simone; Paoletti, Valeria
2014-12-01
Many methods have been used to upward continue potential field data. Most techniques employ the Fast Fourier transform, which is an accurate, quick way to compute level-to-level upward continuation or spatially varying scale filters for level-to-draped surfaces. We here propose a new continuation approach based on the minimum-length solution of the inverse potential field problem, which we call Volume Continuation (VOCO). For real data the VOCO is obtained as the regularized solution to the Tikhonov problem. We tested our method on several synthetic examples involving all types of upward continuation and downward continuation (level-to-level, level-to-draped, draped-to-level, draped-to-draped). We also employed the technique to upward continue to a constant height (2500 m a.s.l.), the high-resolution draped aeromagnetic data of the Ischia Island in Southern Italy. We found that, on the average, they are consistent with the aeromagnetic regional data measured at the same altitude. The main feature of our method is that it does not only provide continued data over a specified surface, but it yields a volume of upward continuation. For example, the continued data refers to a volume and thus, any surface may be easily picked up within the volume to get upward continuation to different surfaces. This approach, based on inversion of the measured data, tends to be especially advantageous over the classical techniques when dealing with draped-to-level upward continuation. It is also useful to obtain a more stable downward continuation and to continue noisy data. The inversion procedure involved in the method implies moderate computational costs, which are well compensated by getting a 3D set of upward continued data to achieve high quality results.
Partition functions and graphs: A combinatorial approach
Solomon, A I; Duchamp, G; Horzela, A; Penson, K A; Solomon, Allan I.; Blasiak, Pawel; Duchamp, Gerard; Horzela, Andrzej; Penson, Karol A.
2004-01-01
Although symmetry methods and analysis are a necessary ingredient in every physicist's toolkit, rather less use has been made of combinatorial methods. One exception is in the realm of Statistical Physics, where the calculation of the partition function, for example, is essentially a combinatorial problem. In this talk we shall show that one approach is via the normal ordering of the second quantized operators appearing in the partition function. This in turn leads to a combinatorial graphical description, giving essentially Feynman-type graphs associated with the theory. We illustrate this methodology by the explicit calculation of two model examples, the free boson gas and a superfluid boson model. We show how the calculation of partition functions can be facilitated by knowledge of the combinatorics of the boson normal ordering problem; this naturally gives rise to the Bell numbers of combinatorics. The associated graphical representation of these numbers gives a perturbation expansion in terms of a sequen...
Combinatorial study of colored Hurwitz polyz\\^etas
Enjalbert, Jean-Yves; Minh, Hoang Ngoc
2012-01-01
A combinatorial study discloses two surjective morphisms between generalized shuffle algebras and algebras generated by the colored Hurwitz polyz\\^etas. The combinatorial aspects of the products and co-products involved in these algebras will be examined.
Combinatorial set theory partition relations for cardinals
Erdös, P; Hajnal, A; Rado, P
2011-01-01
This work presents the most important combinatorial ideas in partition calculus and discusses ordinary partition relations for cardinals without the assumption of the generalized continuum hypothesis. A separate section of the book describes the main partition symbols scattered in the literature. A chapter on the applications of the combinatorial methods in partition calculus includes a section on topology with Arhangel''skii''s famous result that a first countable compact Hausdorff space has cardinality, at most continuum. Several sections on set mappings are included as well as an account of
Toward Chemical Implementation of Encoded Combinatorial Libraries
DEFF Research Database (Denmark)
Nielsen, John; Janda, Kim D.
1994-01-01
by existing methodologies. Here we detail the synthesis of several matrices and the necessary chemistry to implement the conceptual scheme. In addition, we disclose how this novel technology permits a controlled ′dendritic" display of the chemical libraries. © 1994 Academic Press. All rights reserved.......The recent application of "combinatorial libraries" to supplement existing drug screening processes might simplify and accelerate the search for new lead compounds or drugs. Recently, a scheme for encoded combinatorial chemistry was put forward to surmount a number of the limitations possessed...
Combinatorial designs a tribute to Haim Hanani
Hartman, A
1989-01-01
Haim Hanani pioneered the techniques for constructing designs and the theory of pairwise balanced designs, leading directly to Wilson''s Existence Theorem. He also led the way in the study of resolvable designs, covering and packing problems, latin squares, 3-designs and other combinatorial configurations.The Hanani volume is a collection of research and survey papers at the forefront of research in combinatorial design theory, including Professor Hanani''s own latest work on Balanced Incomplete Block Designs. Other areas covered include Steiner systems, finite geometries, quasigroups, and t-designs.
Topics in combinatorial pattern matching
DEFF Research Database (Denmark)
Vildhøj, Hjalte Wedel
Problem. Given m documents of total length n, we consider the problem of finding a longest string common to at least d ≥ 2 of the documents. This problem is known as the longest common substring (LCS) problem and has a classic O(n) space and O(n) time solution (Weiner [FOCS’73], Hui [CPM’92]). However...
Tilli, Tatiana M; Carels, Nicolas; Tuszynski, Jack A; Pasdar, Manijeh
2016-09-27
Network-based strategies provided by systems biology are attractive tools for cancer therapy. Modulation of cancer networks by anticancer drugs may alter the response of malignant cells and/or drive network re-organization into the inhibition of cancer progression. Previously, using systems biology approach and cancer signaling networks, we identified top-5 highly expressed and connected proteins (HSP90AB1, CSNK2B, TK1, YWHAB and VIM) in the invasive MDA-MB-231 breast cancer cell line. Here, we have knocked down the expression of these proteins, individually or together using siRNAs. The transfected cell lines were assessed for in vitro cell growth, colony formation, migration and invasion relative to control transfected MDA-MB-231, the non-invasive MCF-7 breast carcinoma cell line and the non-tumoral mammary epithelial cell line MCF-10A. The knockdown of the top-5 upregulated connectivity hubs successfully inhibited the in vitro proliferation, colony formation, anchorage independence, migration and invasion in MDA-MB-231 cells; with minimal effects in the control transfected MDA-MB-231 cells or MCF-7 and MCF-10A cells. The in vitro validation of bioinformatics predictions regarding optimized multi-target selection for therapy suggests that protein expression levels together with protein-protein interaction network analysis may provide an optimized combinatorial target selection for a highly effective anti-metastatic precision therapy in triple-negative breast cancer. This approach increases the ability to identify not only druggable hubs as essential targets for cancer survival, but also interactions most susceptible to synergistic drug action. The data provided in this report constitute a preliminary step toward the personalized clinical application of our strategy to optimize the therapeutic use of anti-cancer drugs.
A New Approach for Proving or Generating Combinatorial Identities
Gonzalez, Luis
2010-01-01
A new method for proving, in an immediate way, many combinatorial identities is presented. The method is based on a simple recursive combinatorial formula involving n + 1 arbitrary real parameters. Moreover, this formula enables one not only to prove, but also generate many different combinatorial identities (not being required to know them "a…
Combinatorial metabolic engineering of Saccharomyces cerevisiae for terminal alkene production.
Chen, Binbin; Lee, Dong-Yup; Chang, Matthew Wook
2015-09-01
Biological production of terminal alkenes has garnered a significant interest due to their industrial applications such as lubricants, detergents and fuels. Here, we engineered the yeast Saccharomyces cerevisiae to produce terminal alkenes via a one-step fatty acid decarboxylation pathway and improved the alkene production using combinatorial engineering strategies. In brief, we first characterized eight fatty acid decarboxylases to enable and enhance alkene production. We then increased the production titer 7-fold by improving the availability of the precursor fatty acids. We additionally increased the titer about 5-fold through genetic cofactor engineering and gene expression tuning in rich medium. Lastly, we further improved the titer 1.8-fold to 3.7 mg/L by optimizing the culturing conditions in bioreactors. This study represents the first report of terminal alkene biosynthesis in S. cerevisiae, and the abovementioned combinatorial engineering approaches collectively increased the titer 67.4-fold. We envision that these approaches could provide insights into devising engineering strategies to improve the production of fatty acid-derived biochemicals in S. cerevisiae.
Spreading lengths of Hermite polynomials
Sánchez-Moreno, P; Manzano, D; Yáñez, R; 10.1016/j.cam.2009.09.043
2009-01-01
The Renyi, Shannon and Fisher spreading lengths of the classical or hypergeometric orthogonal polynomials, which are quantifiers of their distribution all over the orthogonality interval, are defined and investigated. These information-theoretic measures of the associated Rakhmanov probability density, which are direct measures of the polynomial spreading in the sense of having the same units as the variable, share interesting properties: invariance under translations and reflections, linear scaling and vanishing in the limit that the variable tends towards a given definite value. The expressions of the Renyi and Fisher lengths for the Hermite polynomials are computed in terms of the polynomial degree. The combinatorial multivariable Bell polynomials, which are shown to characterize the finite power of an arbitrary polynomial, play a relevant role for the computation of these information-theoretic lengths. Indeed these polynomials allow us to design an error-free computing approach for the entropic moments (w...
Combinatorial biosynthesis of medicinal plant secondary metabolites
Julsing, Mattijs K.; Koulman, Albert; Woerdenbag, Herman J.; Quax, Wim J.; Kayser, Oliver
2006-01-01
Combinatorial biosynthesis is a new tool in the generation of novel natural products and for the production of rare and expensive natural products. The basic concept is combining metabolic pathways in different organisms on a genetic level. As a consequence heterologous organisms provide precursors
Grobner Basis Approach to Some Combinatorial Problems
Directory of Open Access Journals (Sweden)
Victor Ufnarovski
2012-10-01
Full Text Available We consider several simple combinatorial problems and discuss different ways to express them using polynomial equations and try to describe the \\GB of the corresponding ideals. The main instruments are complete symmetric polynomials that help to express different conditions in rather compact way.
Grobner Basis Approach to Some Combinatorial Problems
2012-01-01
We consider several simple combinatorial problems and discuss different ways to express them using polynomial equations and try to describe the \\GB of the corresponding ideals. The main instruments are complete symmetric polynomials that help to express different conditions in rather compact way.
Infinitary Combinatory Reduction Systems: Normalising Reduction Strategies
Ketema, Jeroen; Simonsen, Jakob Grue
2010-01-01
We study normalising reduction strategies for infinitary Combinatory Reduction Systems (iCRSs). We prove that all fair, outermost-fair, and needed-fair strategies are normalising for orthogonal, fully-extended iCRSs. These facts properly generalise a number of results on normalising strategies in fi
Erratum to Ordered Partial Combinatory Algebras
Hofstra, P.; Oosten, J. van
2003-01-01
To our regret the paper Ordered Partial Combinatory Algebras contains a mistake which we correct here The flaw concerns the definition of compu tational density definition 3.5 which appeared in section 3.3 page 451 This definition is too rigid and as a consequence Lemma 3.6 on page 452
A Model of Students' Combinatorial Thinking
Lockwood, Elise
2013-01-01
Combinatorial topics have become increasingly prevalent in K-12 and undergraduate curricula, yet research on combinatorics education indicates that students face difficulties when solving counting problems. The research community has not yet addressed students' ways of thinking at a level that facilitates deeper understanding of how students…
A Model of Students' Combinatorial Thinking
Lockwood, Elise
2013-01-01
Combinatorial topics have become increasingly prevalent in K-12 and undergraduate curricula, yet research on combinatorics education indicates that students face difficulties when solving counting problems. The research community has not yet addressed students' ways of thinking at a level that facilitates deeper understanding of how students…
Recent developments in dynamic combinatorial chemistry
Otto, Sijbren; Furlan, Ricardo L.E.; Sanders, Jeremy K.M.
2002-01-01
Generating combinatorial libraries under equilibrium conditions has the important advantage that the libraries are adaptive (i.e. they can respond to exterior influences in the form of molecular recognition events). Thus, a ligand will direct and amplify the formation of its ideal receptor and vice
Boltzmann Samplers for Colored Combinatorial Objects
Bodini, Olivier
2009-01-01
In this paper, we give a general framework for the Boltzmann generation of colored objects belonging to combinatorial constructible classes. We propose an intuitive notion called profiled objects which allows the sampling of size-colored objects (and also of k-colored objects) although the corresponding class cannot be described by an analytic ordinary generating function.
Combinatorial biosynthesis of medicinal plant secondary metabolites
Julsing, Mattijs K.; Koulman, Albert; Woerdenbag, Herman J.; Quax, Wim J.; Kayser, Oliver
2006-01-01
Combinatorial biosynthesis is a new tool in the generation of novel natural products and for the production of rare and expensive natural products. The basic concept is combining metabolic pathways in different organisms on a genetic level. As a consequence heterologous organisms provide precursors
PIPERIDINE OLIGOMERS AND COMBINATORIAL LIBRARIES THEREOF
DEFF Research Database (Denmark)
1999-01-01
The present invention relates to piperidine oligomers, methods for the preparation of piperidine oligomers and compound libraries thereof, and the use of piperidine oligomers as drug substances. The present invention also relates to the use of combinatorial libraries of piperidine oligomers...... in libraries (arrays) of compounds especially suitable for screening purposes....
Some combinatorial models for reduced expressions in Coxeter groups
Denoncourt, Hugh
2011-01-01
Stanley's formula for the number of reduced expressions of a permutation regarded as a Coxeter group element raises the question of how to enumerate the reduced expressions of an arbitrary Coxeter group element. We provide a framework for answering this question by constructing combinatorial objects that represent the inversion set and the reduced expressions for an arbitrary Coxeter group element. The framework also provides a formula for the length of an element formed by deleting a generator from a Coxeter group element. Fan and Hagiwara, et al$.$ showed that for certain Coxeter groups, the short-braid avoiding elements characterize those elements that give reduced expressions when any generator is deleted from a reduced expression. We provide a characterization that holds in all Coxeter groups. Lastly, we give applications to the freely braided elements introduced by Green and Losonczy, generalizing some of their results that hold in simply-laced Coxeter groups to the arbitrary Coxeter group setting.
You, Hongmin; Chen, Jin; Zhou, Jingjing; Huang, Hua; Pan, Junxi; Wang, Ziye; Lv, Lin; Zhang, Lujun; Li, Juan; Qin, Bin; Yang, Yongtao; Xie, Peng
2015-11-01
Major depressive disorder (MDD) is a prevalent, debilitating mood disorder that has been associated with several genetic polymorphisms. One such polymorphism, namely that of apolipoprotein E (APOE), has three allelic forms (ε2, ε3 and ε4) that encode for six unique isoforms of the APOE protein. A growing number of techniques have been developed for APOE genotyping; however, not all polymerase chain reaction (PCR)‑based genotyping techniques are equally accurate or cost‑effective. In order to find a more accurate and cost‑effective APOE genotyping method for MDD screening in large populations, the present study comparatively evaluated two genotyping methods, amplification refractory mutation system PCR (ARMS‑PCR) and optimized PCR restriction‑fragment length polymorphism (PCR‑RFLP), in blood samples taken from a population of 708 MDD patients. Although either of the two methods were able to detect all six unique APOE genotypes, comparisons of the two methods with Sanger sequencing demonstrated that ARMS‑PCR (94%) was significantly more accurate than optimized PCR‑RFLP (82%). ARMS‑PCR should prove useful in quickly verifying ambiguous results obtained by other APOE genotyping methods and can be cost-effectively performed in the setting of a small laboratory or a population-based screening program.
Combinatorial structures to modeling simple games and applications
Molinero, Xavier
2017-09-01
We connect three different topics: combinatorial structures, game theory and chemistry. In particular, we establish the bases to represent some simple games, defined as influence games, and molecules, defined from atoms, by using combinatorial structures. First, we characterize simple games as influence games using influence graphs. It let us to modeling simple games as combinatorial structures (from the viewpoint of structures or graphs). Second, we formally define molecules as combinations of atoms. It let us to modeling molecules as combinatorial structures (from the viewpoint of combinations). It is open to generate such combinatorial structures using some specific techniques as genetic algorithms, (meta-)heuristics algorithms and parallel programming, among others.
Piva, Simone; Dora, Giancarlo; Minelli, Cosetta; Michelini, Mariachiara; Turla, Fabio; Mazza, Stefania; D'Ottavi, Patrizia; Moreno-Duarte, Ingrid; Sottini, Caterina; Eikermann, Matthias; Latronico, Nicola
2015-12-01
We validated the Italian version of Surgical Optimal Mobility Score (SOMS) and evaluated its ability to predict intensive care unit (ICU) and hospital length of stay (LOS), and hospital mortality in a mixed population of ICU patients. We applied the Italian version of SOMS in a consecutive series of prospectively enrolled, adult ICU patients. Surgical Optimal Mobility Score level was assessed twice a day by ICU nurses and twice a week by an expert mobility team. Zero-truncated Poisson regression was used to identify predictors for ICU and hospital LOS, and logistic regression for hospital mortality. All models were adjusted for potential confounders. Of 98 patients recruited, 19 (19.4%) died in hospital, of whom 17 without and 2 with improved mobility level achieved during the ICU stay. SOMS improvement was independently associated with lower hospital mortality (odds ratio, 0.07; 95% confidence interval [CI], 0.01-0.42) but increased hospital LOS (odds ratio, 1.21; 95% CI: 1.10-1.33). A higher first-morning SOMS on ICU admission, indicating better mobility, was associated with lower ICU and hospital LOS (rate ratios, 0.89 [95% CI, 0.80-0.99] and 0.84 [95% CI, 0.79-0.89], respectively). The first-morning SOMS on ICU admission predicted ICU and hospital LOS in a mixed population of ICU patients. SOMS improvement was associated with reduced hospital mortality but increased hospital LOS, suggesting the need of optimizing hospital trajectories after ICU discharge. Copyright © 2015 Elsevier Inc. All rights reserved.
Green, Martin L.; Takeuchi, Ichiro; Hattrick-Simpers, Jason R.
2013-06-01
High throughput (combinatorial) materials science methodology is a relatively new research paradigm that offers the promise of rapid and efficient materials screening, optimization, and discovery. The paradigm started in the pharmaceutical industry but was rapidly adopted to accelerate materials research in a wide variety of areas. High throughput experiments are characterized by synthesis of a "library" sample that contains the materials variation of interest (typically composition), and rapid and localized measurement schemes that result in massive data sets. Because the data are collected at the same time on the same "library" sample, they can be highly uniform with respect to fixed processing parameters. This article critically reviews the literature pertaining to applications of combinatorial materials science for electronic, magnetic, optical, and energy-related materials. It is expected that high throughput methodologies will facilitate commercialization of novel materials for these critically important applications. Despite the overwhelming evidence presented in this paper that high throughput studies can effectively inform commercial practice, in our perception, it remains an underutilized research and development tool. Part of this perception may be due to the inaccessibility of proprietary industrial research and development practices, but clearly the initial cost and availability of high throughput laboratory equipment plays a role. Combinatorial materials science has traditionally been focused on materials discovery, screening, and optimization to combat the extremely high cost and long development times for new materials and their introduction into commerce. Going forward, combinatorial materials science will also be driven by other needs such as materials substitution and experimental verification of materials properties predicted by modeling and simulation, which have recently received much attention with the advent of the Materials Genome
ProSAR: a new methodology for combinatorial library design.
Chen, Hongming; Börjesson, Ulf; Engkvist, Ola; Kogej, Thierry; Svensson, Mats A; Blomberg, Niklas; Weigelt, Dirk; Burrows, Jeremy N; Lange, Tim
2009-03-01
A method is introduced for performing reagent selection for chemical library design based on topological (2D) pharmacophore fingerprints. Optimal reagent selection is achieved by optimizing the Shannon entropy of the 2D pharmacophore distribution for the reagent set. The method, termed ProSAR, is therefore expected to enumerate compounds that could serve as a good starting point for deriving a structure activity relationship (SAR) in combinatorial library design. This methodology is exemplified by library design examples where the active compounds were already known. The results show that most of the pharmacophores on the substituents for the active compounds are covered by the designed library. This strategy is further expanded to include product property profiles for aqueous solubility, hERG risk assessment, etc. in the optimization process so that the reagent pharmacophore diversity and the product property profile are optimized simultaneously via a genetic algorithm. This strategy is applied to a two-dimensional library design example and compared with libraries designed by a diversity based strategy which minimizes the average ensemble Tanimoto similarity. Our results show that by using the PSAR methodology, libraries can be designed with simultaneously good pharmacophore coverage and product property profile.
Three Syntactic Theories for Combinatory Graph Reduction
DEFF Research Database (Denmark)
Danvy, Olivier; Zerny, Ian
2011-01-01
We present a purely syntactic theory of graph reduction for the canonical combinators S, K, and I, where graph vertices are represented with evaluation contexts and let expressions. We express this syntactic theory as a reduction semantics, which we refocus into the first storeless abstract machine...... for combinatory graph reduction, which we refunctionalize into the first storeless natural semantics for combinatory graph reduction.We then factor out the introduction of let expressions to denote as many graph vertices as possible upfront instead of on demand, resulting in a second syntactic theory, this one...... of term graphs in the sense of Barendregt et al. The corresponding storeless abstract machine and natural semantics follow mutatis mutandis. We then interpret let expressions as operations over a global store (thus shifting, in Strachey's words, from denotable entities to storable entities), resulting...
Three Syntactic Theories for Combinatory Graph Reduction
DEFF Research Database (Denmark)
Danvy, Olivier; Zerny, Ian
2013-01-01
We present a purely syntactic theory of graph reduction for the canonical combinators S, K, and I, where graph vertices are represented with evaluation contexts and let expressions. We express this rst syntactic theory as a storeless reduction semantics of combinatory terms. We then factor out...... the introduction of let expressions to denote as many graph vertices as possible upfront instead of on demand . The factored terms can be interpreted as term graphs in the sense of Barendregt et al. We express this second syntactic theory, which we prove equivalent to the rst, as a storeless reduction semantics...... of combinatory term graphs. We then recast let bindings as bindings in a global store, thus shifting, in Strachey's words, from denotable entities to storable entities. The store-based terms can still be interpreted as term graphs. We express this third syntactic theory, which we prove equivalent to the second...
Dynamic combinatorial self-replicating systems.
Moulin, Emilie; Giuseppone, Nicolas
2012-01-01
Thanks to their intrinsic network topologies, dynamic combinatorial libraries (DCLs) represent new tools for investigating fundamental aspects related to self-organization and adaptation processes. Very recently the first examples integrating self-replication features within DCLs have pushed even further the idea of implementing dynamic combinatorial chemistry (DCC) towards minimal systems capable of self-construction and/or evolution. Indeed, feedback loop processes - in particular in the form of autocatalytic reactions - are keystones to build dynamic supersystems which could possibly approach the roots of "Darwinian" evolvability at mesoscale. This topic of current interest also shows significant potentialities beyond its fundamental character, because truly smart and autonomous materials for the future will have to respond to changes of their environment by selecting and by exponentially amplifying their fittest constituents.
Assessment of structural diversity in combinatorial synthesis.
Fergus, Suzanne; Bender, Andreas; Spring, David R
2005-06-01
This article covers the combinatorial synthesis of small molecules with maximal structural diversity to generate a collection of pure compounds that are attractive for lead generation in a phenotypic, high-throughput screening approach. Nature synthesises diverse small molecules, but there are disadvantages with using natural product sources. The efficient chemical synthesis of structural diversity (and complexity) is the aim of diversity-oriented synthesis, and recent progress is reviewed. Specific highlights include a discussion of strategies to obtain structural diversity and an analysis of molecular descriptors used to classify compounds. The assessment of how successful one synthesis is versus another is subjective, therefore we test-drive software to assess structural diversity in combinatorial synthesis, which is freely available via a web interface.
DNA-Encoded Dynamic Combinatorial Chemical Libraries.
Reddavide, Francesco V; Lin, Weilin; Lehnert, Sarah; Zhang, Yixin
2015-06-26
Dynamic combinatorial chemistry (DCC) explores the thermodynamic equilibrium of reversible reactions. Its application in the discovery of protein binders is largely limited by difficulties in the analysis of complex reaction mixtures. DNA-encoded chemical library (DECL) technology allows the selection of binders from a mixture of up to billions of different compounds; however, experimental results often show low a signal-to-noise ratio and poor correlation between enrichment factor and binding affinity. Herein we describe the design and application of DNA-encoded dynamic combinatorial chemical libraries (EDCCLs). Our experiments have shown that the EDCCL approach can be used not only to convert monovalent binders into high-affinity bivalent binders, but also to cause remarkably enhanced enrichment of potent bivalent binders by driving their in situ synthesis. We also demonstrate the application of EDCCLs in DNA-templated chemical reactions.
High throughput combinatorial screening of semiconductor materials
Mao, Samuel S.
2011-11-01
This article provides an overview of an advanced combinatorial material discovery platform developed recently for screening semiconductor materials with properties that may have applications ranging from radiation detectors to solar cells. Semiconductor thin-film libraries, each consisting of 256 materials of different composition arranged into a 16×16 matrix, were fabricated using laser-assisted evaporation process along with a combinatorial mechanism to achieve variations. The composition and microstructure of individual materials on each thin-film library were characterized with an integrated scanning micro-beam x-ray fluorescence and diffraction system, while the band gaps were determined by scanning optical reflection and transmission of the libraries. An ultrafast ultraviolet photon-induced charge probe was devised to measure the mobility and lifetime of individual thin-film materials on semiconductor libraries. Selected results on the discovery of semiconductors with desired band gaps and transport properties are illustrated.
COMBINATORIAL DESIGN APPROACHES FOR TEST GENERATION
Institute of Scientific and Technical Information of China (English)
Shi Liang; Xu Baowen; Nie Changhai
2005-01-01
The n-way combination testing is a specification-based testing criterion, which requires that for a system consisted of a few parameters, every combination of valid values of arbitrary n(n ≥ 2) parameters be covered by at least one test. This letter proposed two different test generation algorithms based on combinatorial design for the n-way coverage criterion. The automatic test generators are implemented and some valuable empirical results are obtained.
Switched Systems and Motion Coordination: Combinatorial Challenges
Sadovsky, Alexander V.
2016-01-01
Problems of routing commercial air traffic in a terminal airspace encounter different constraints: separation assurance, aircraft performance limitations, regulations. The general setting of these problems is that of a switched control system. Such a system combines the differentiable motion of the aircraft with the combinatorial choices of choosing precedence when traffic routes merge and choosing branches when the routes diverge. This presentation gives an overview of the problem, the ATM context, related literature, and directions for future research.
One-parameter groups and combinatorial physics
Duchamp, G; Solomon, A I; Horzela, A; Blasiak, P; Duchamp, Gerard; Penson, Karol A.; Solomon, Allan I.; Horzela, Andrej; Blasiak, Pawel
2004-01-01
In this communication, we consider the normal ordering of sums of elements of the form (a*^r a a*^s), where a* and a are boson creation and annihilation operators. We discuss the integration of the associated one-parameter groups and their combinatorial by-products. In particular, we show how these groups can be realized as groups of substitutions with prefunctions.
Combinatorial Cis-regulation in Saccharomyces Species
Directory of Open Access Journals (Sweden)
Aaron T. Spivak
2016-03-01
Full Text Available Transcriptional control of gene expression requires interactions between the cis-regulatory elements (CREs controlling gene promoters. We developed a sensitive computational method to identify CRE combinations with conserved spacing that does not require genome alignments. When applied to seven sensu stricto and sensu lato Saccharomyces species, 80% of the predicted interactions displayed some evidence of combinatorial transcriptional behavior in several existing datasets including: (1 chromatin immunoprecipitation data for colocalization of transcription factors, (2 gene expression data for coexpression of predicted regulatory targets, and (3 gene ontology databases for common pathway membership of predicted regulatory targets. We tested several predicted CRE interactions with chromatin immunoprecipitation experiments in a wild-type strain and strains in which a predicted cofactor was deleted. Our experiments confirmed that transcription factor (TF occupancy at the promoters of the CRE combination target genes depends on the predicted cofactor while occupancy of other promoters is independent of the predicted cofactor. Our method has the additional advantage of identifying regulatory differences between species. By analyzing the S. cerevisiae and S. bayanus genomes, we identified differences in combinatorial cis-regulation between the species and showed that the predicted changes in gene regulation explain several of the species-specific differences seen in gene expression datasets. In some instances, the same CRE combinations appear to regulate genes involved in distinct biological processes in the two different species. The results of this research demonstrate that (1 combinatorial cis-regulation can be inferred by multi-genome analysis and (2 combinatorial cis-regulation can explain differences in gene expression between species.
Methods for combinatorial and parallel library design.
Schnur, Dora M; Beno, Brett R; Tebben, Andrew J; Cavallaro, Cullen
2011-01-01
Diversity has historically played a critical role in design of combinatorial libraries, screening sets and corporate collections for lead discovery. Large library design dominated the field in the 1990s with methods ranging anywhere from purely arbitrary through property based reagent selection to product based approaches. In recent years, however, there has been a downward trend in library size. This was due to increased information about the desirable targets gleaned from the genomics revolution and to the ever growing availability of target protein structures from crystallography and homology modeling. Creation of libraries directed toward families of receptors such as GPCRs, kinases, nuclear hormone receptors, proteases, etc., replaced the generation of libraries based primarily on diversity while single target focused library design has remained an important objective. Concurrently, computing grids and cpu clusters have facilitated the development of structure based tools that screen hundreds of thousands of molecules. Smaller "smarter" combinatorial and focused parallel libraries replaced those early un-focused large libraries in the twenty-first century drug design paradigm. While diversity still plays a role in lead discovery, the focus of current library design methods has shifted to receptor based methods, scaffold hopping/bio-isostere searching, and a much needed emphasis on synthetic feasibility. Methods such as "privileged substructures based design" and pharmacophore based design still are important methods for parallel and small combinatorial library design. This chapter discusses some of the possible design methods and presents examples where they are available.
Theoretical principles of in vitro selection using combinatorial nucleic acid libraries.
Vant-Hull, B; Gold, L; Zichi, D A
2000-02-01
A new paradigm for drug discovery and biological research has developed from technologies that integrate combinatorial chemistry with rounds of selection and amplification, a technique called in vitro selection or systematic evolution of ligands by exponential enrichment (SELEX). This overview unit discusses nucleic acid libraries that can be used, affinity probability distributions, an equilibrium model for SELEX, and optimal conditions including concentrations and signal-to-noise ratios.
Generalized topological spaces in evolutionary theory and combinatorial chemistry.
Stadler, Bärbel M R; Stadler, Peter F
2002-01-01
The search spaces in combinatorial chemistry as well as the sequence spaces underlying (molecular) evolution are conventionally thought of as graphs. Recombination, however, implies a nongraphical structure of the combinatorial search spaces. These structures, and their implications for search process itself, are heretofore not well understood in general. In this contribution we review a very general formalism from point set topology and discuss its application to combinatorial search spaces, fitness landscapes, evolutionary trajectories, and artificial chemistries.
Earth Data Analysis Center, University of New Mexico — Flame length was modeled using FlamMap, an interagency fire behavior mapping and analysis program that computes potential fire behavior characteristics. The tool...
Advanced Aqueous Phase Catalyst Development using Combinatorial Methods Project
National Aeronautics and Space Administration — Combinatorial methods are proposed to develop advanced Aqueous Oxidation Catalysts (AOCs) with the capability to mineralize organic contaminants present in effluents...
Effects of Suboptimal Bidding in Combinatorial Auctions
Schneider, Stefan; Shabalin, Pasha; Bichler, Martin
Though the VCG auction assumes a central place in the mechanism design literature, there are a number of reasons for favoring iterative combinatorial auction designs. Several promising ascending auction formats have been developed throughout the past few years based on primal-dual and subgradient algorithms and linear programming theory. Prices are interpreted as a feasible dual solution and the provisional allocation is interpreted as a feasible primal solution. iBundle( 3) (Parkes and Ungar 2000), dVSV (de Vries et al. 2007) and the Ascending Proxy auction (Ausubel and Milgrom 2002) result in VCG payoffs when the coalitional value function satisfies the buyer submodularity condition and bidders bid straightforward, which is an expost Nash equilibrium in that case. iBEA and CreditDebit auctions (Mishra and Parkes 2007) do not even require the buyer submodularity condition and achieve the same properties for general valuations. In many situations, however, one cannot assume bidders to bid straightforward and it is not clear from the theory how these non-linear personalized price auctions (NLPPAs) perform in this case. Robustness of auctions with respect to different bidding behavior is therefore a critical issue for any application. We have conducted a large number of computational experiments to analyze the performance of NLPPA designs with respect to different bidding strategies and different valuation models. We compare the results of NLPPAs to those of the VCG auction and those of iterative combinatorial auctions with approximate linear prices, such as ALPS (Bichler et al. 2009) and the Combinatorial Clock auction (Porter et al. 2003).
Algebraic and combinatorial Brill-Noether theory
Caporaso, Lucia
2011-01-01
The interplay between algebro-geometric and combinatorial Brill-Noether theory is studied. The Brill-Noether variety of a graph shown to be non-empty if the Brill-Noether number is non-negative, as a consequence of the analogous fact for smooth projective curves. Similarly, the existence of a graph for which the Brill-Noether variety is empty implies the emptiness of the corresponding Brill-Noether variety for a general curve. The main tool is a refinement of Baker's Specialization Lemma.
Method and apparatus for combinatorial chemistry
Foote, Robert S.
2007-02-20
A method and apparatus are provided for performing light-directed reactions in spatially addressable channels within a plurality of channels. One aspect of the invention employs photoactivatable reagents in solutions disposed into spatially addressable flow streams to control the parallel synthesis of molecules immobilized within the channels. The reagents may be photoactivated within a subset of channels at the site of immobilized substrate molecules or at a light-addressable site upstream from the substrate molecules. The method and apparatus of the invention find particularly utility in the synthesis of biopolymer arrays, e.g., oligonucleotides, peptides and carbohydrates, and in the combinatorial synthesis of small molecule arrays for drug discovery.
Apparatus for combinatorial screening of electrochemical materials
A high throughput combinatorial screening method and apparatus for the evaluation of electrochemical materials using a single voltage source is disclosed wherein temperature changes arising from the application of an electrical load to a cell array are used to evaluate the relative electrochemical efficiency of the materials comprising the array. The apparatus may include an array of electrochemical cells that are connected to each other in parallel or in series, an electronic load for applying a voltage or current to the electrochemical cells , and a device , external to the cells, for monitoring the relative temperature of each cell when the load is applied.
2009-12-15
A high throughput combinatorial screening method and apparatus for the evaluation of electrochemical materials using a single voltage source (2) is disclosed wherein temperature changes arising from the application of an electrical load to a cell array (1) are used to evaluate the relative electrochemical efficiency of the materials comprising the array. The apparatus may include an array of electrochemical cells (1) that are connected to each other in parallel or in series, an electronic load (2) for applying a voltage or current to the electrochemical cells (1), and a device (3), external to the cells, for monitoring the relative temperature of each cell when the load is applied.
Combinatorial level densities for practical applications
Directory of Open Access Journals (Sweden)
Sin M.
2010-03-01
Full Text Available We review our calculated energy-, spin- and parity-dependent nuclear level densities based on the microscopic combinatorial model described in ref. [1]. We show that this model predicts the experimental sand p-wave neutron resonance spacings with a degree of accuracy comparable to that of the best global models available and also provides reasonable description of low energies cumulative number of levels as well as of the experimental data obtained by the Oslo group [2]. We also provide a renormalization recipe which enables to play with the tabulated results for practical applications. Finally, we study the impact of temperature dependent calculation on s-wave neutron resonance spacings.
Combinatorial nuclear level-density model
Energy Technology Data Exchange (ETDEWEB)
Moller, Peter [Los Alamos National Laboratory; Aberg, Sven [LUND SWEDEN; Uhrenhoit, Henrik [LUND SWEDEN; Ickhikawa, Takatoshi [RIKEN
2008-01-01
A microscopic nuclear level-density model is presented. The model is a completely combinatorial (micro-canonical) model based on the folded-Yukawa single-particle potential and includes explicit treatment of pairing, rotational and vibrational states. The microscopic character of all states enables extraction of level distribution functions with respect to pairing gaps, parity and angular momentum. The results of the model are compared to available experimental data: neutron separation energy level spacings, data on total level-density functions from the Oslo method and data on parity ratios.
On Definitions and Existence of Combinatorial Entropy of 2d Fields
DEFF Research Database (Denmark)
Forchhammer, Søren Otto; Shtarkov, Yuri; Justesen, Jørn
1998-01-01
Different definitions of combinatorial entropy is presented and conditions for their existence examined.......Different definitions of combinatorial entropy is presented and conditions for their existence examined....
Analysis of selection methodologies for combinatorial library design.
Pascual, Rosalia; Borrell, José I; Teixidó, Jordi
2003-01-01
We have implemented and adapted in Pralins (Program for Rational Analysis of Libraries in silico), the most popular sparse (cherry picking) and full array (sublibrary) selection algorithms: hierarchical clustering, k-means clustering, Optimum Binning, Jarvis Patrick, Pral-SE (partitioning techniques) and MaxSum, MaxMin, MaxMin averaged, DN2, CTD (distance-based methods). We have validated the program with an already synthesized three-component combinatorial library of FXR partial agonists characterized by standard computational chemistry descriptors as case study. This has let us analyze the goodness of both the partitioning techniques for space division and all the selection methodologies with respect to representativity in terms of population and space coverage for different selection sizes. Within the chemical space analyzed, both hierarchical clustering and Optimum Binning division strategies are found to be the most advantageous reference space divisions to be used in the subsequent population and space coverage studies. Complete hierarchical clustering appears also to be the preferred selection methodology for both sparse and full array problems. The full array restriction fulfillment can easily be overcome by convenient optimization algorithms that allow optimal reagent selection preserving > 90% of the population coverage.
Baer, Michael B
2008-01-01
Huffman coding finds an optimal prefix code for a given probability mass function. Consider situations in which one wishes to find an optimal code with the restriction that all codewords have lengths that lie in a user-specified set of lengths (or, equivalently, no codewords have lengths that lie in a complementary set). This paper introduces a polynomial-time dynamic programming algorithm that finds optimal codes for this reserved-length prefix coding problem. This has applications to quickly encoding and decoding lossless codes. In addition, one modification of the approach solves any quasiarithmetic prefix coding problem, while another finds optimal codes restricted to the set of codes with g codeword lengths for user-specified g (e.g., g=2).
Self-encoding resin beads of combinatorial library screening
Lei, Du; Zhao, Yuandi; Cheng, Tongsheng; Zeng, Shaoqun; Luo, Qingming
2003-07-01
The latest self-encoding resin bead is a novel technology for solid phase synthesis combinatorial library screening. A new encode-positional deconvolution strategy which was based on that technology been illustrated compared with positional scanning and iterative strategies. The self-encoding resin beads technology provides an efficient method for improving the high-throughput screening of combinatorial library.
A combinatorial morphospace for angiosperm pollen
Mander, Luke
2016-04-01
The morphology of angiosperm (flowering plant) pollen is extraordinarily diverse. This diversity results from variations in the morphology of discrete anatomical components. These components include the overall shape of a pollen grain, the stratification of the exine, the number and form of any apertures, the type of dispersal unit, and the nature of any surface ornamentation. Different angiosperm pollen morphotypes reflect different combinations of these discrete components. In this talk, I ask the following question: given the anatomical components of angiosperm pollen that are known to exist in the plant kingdom, how many unique biologically plausible combinations of these components are there? I explore this question from the perspective of enumerative combinatorics using an algorithm I have written in the Python programming language. This algorithm (1) calculates the number of combinations of these components; (2) enumerates those combinations; and (3) graphically displays those combinations. The result is a combinatorial morphospace that reflects an underlying notion that the process of morphogenesis in angiosperm pollen can be thought of as an n choose k counting problem. I compare the morphology of extant and fossil angiosperm pollen grains to this morphospace, and suggest that from a combinatorial point of view angiosperm pollen is not as diverse as it could be, which may be a result of developmental constraints.
Combinatorial design of textured mechanical metamaterials.
Coulais, Corentin; Teomy, Eial; de Reus, Koen; Shokef, Yair; van Hecke, Martin
2016-07-28
The structural complexity of metamaterials is limitless, but, in practice, most designs comprise periodic architectures that lead to materials with spatially homogeneous features. More advanced applications in soft robotics, prosthetics and wearable technology involve spatially textured mechanical functionality, which requires aperiodic architectures. However, a naive implementation of such structural complexity invariably leads to geometrical frustration (whereby local constraints cannot be satisfied everywhere), which prevents coherent operation and impedes functionality. Here we introduce a combinatorial strategy for the design of aperiodic, yet frustration-free, mechanical metamaterials that exhibit spatially textured functionalities. We implement this strategy using cubic building blocks-voxels-that deform anisotropically, a local stacking rule that allows cooperative shape changes by guaranteeing that deformed building blocks fit together as in a three-dimensional jigsaw puzzle, and three-dimensional printing. These aperiodic metamaterials exhibit long-range holographic order, whereby the two-dimensional pixelated surface texture dictates the three-dimensional interior voxel arrangement. They also act as programmable shape-shifters, morphing into spatially complex, but predictable and designable, shapes when uniaxially compressed. Finally, their mechanical response to compression by a textured surface reveals their ability to perform sensing and pattern analysis. Combinatorial design thus opens up a new avenue towards mechanical metamaterials with unusual order and machine-like functionalities.
Combinatorial design of textured mechanical metamaterials
Coulais, Corentin; Teomy, Eial; de Reus, Koen; Shokef, Yair; van Hecke, Martin
2016-07-01
The structural complexity of metamaterials is limitless, but, in practice, most designs comprise periodic architectures that lead to materials with spatially homogeneous features. More advanced applications in soft robotics, prosthetics and wearable technology involve spatially textured mechanical functionality, which requires aperiodic architectures. However, a naive implementation of such structural complexity invariably leads to geometrical frustration (whereby local constraints cannot be satisfied everywhere), which prevents coherent operation and impedes functionality. Here we introduce a combinatorial strategy for the design of aperiodic, yet frustration-free, mechanical metamaterials that exhibit spatially textured functionalities. We implement this strategy using cubic building blocks—voxels—that deform anisotropically, a local stacking rule that allows cooperative shape changes by guaranteeing that deformed building blocks fit together as in a three-dimensional jigsaw puzzle, and three-dimensional printing. These aperiodic metamaterials exhibit long-range holographic order, whereby the two-dimensional pixelated surface texture dictates the three-dimensional interior voxel arrangement. They also act as programmable shape-shifters, morphing into spatially complex, but predictable and designable, shapes when uniaxially compressed. Finally, their mechanical response to compression by a textured surface reveals their ability to perform sensing and pattern analysis. Combinatorial design thus opens up a new avenue towards mechanical metamaterials with unusual order and machine-like functionalities.
Locating Minimal Fault Interaction in Combinatorial Testing
Directory of Open Access Journals (Sweden)
Wei Zheng
2016-01-01
Full Text Available Combinatorial testing (CT technique could significantly reduce testing cost and increase software system quality. By using the test suite generated by CT as input to conduct black-box testing towards a system, we are able to detect interactions that trigger the system’s faults. Given a test case, there may be only part of all its parameters relevant to the defects in system and the interaction constructed by those partial parameters is key factor of triggering fault. If we can locate those parameters accurately, this will facilitate the software diagnosing and testing process. This paper proposes a novel algorithm named complete Fault Interaction Location (comFIL to locate those interactions that cause system’s failures and meanwhile obtains the minimal set of target interactions in test suite produced by CT. By applying this method, testers can analyze and locate the factors relevant to defects of system more precisely, thus making the process of software testing and debugging easier and more efficient. The results of our empirical study indicate that comFIL performs better compared with known fault location techniques in combinatorial testing because of its improved effectiveness and precision.
Data-Driven Online and Real-Time Combinatorial Optimization
2013-10-30
Problem , the online Traveling Salesman Problem , and variations of the online Quota Hamil- tonian Path Problem and the online Traveling ...has the lowest competitive ratio among all algorithms of this kind. Second, we consider the Online Traveling Salesman Problem , and consider randomized...matroid secretary problem on a partition matroid. 6. Jaillet, P. and X. Lu. “Online Traveling Salesman Problems with Rejection Options”, submitted
Probabilistic Analysis of Combinatorial Optimization Problems on Hypergraph Matchings
2012-02-01
PfBng; (16) where Bn is the event that there are no empty boxes, for which it holds (see, e.g., Feller , 1968): PfBng D nX iD0 .1/i n i ! 1 i n...Combinatorics, Academic Press, New York. Feller , W. (1968) An Introduction to Probability Theory and Its Applications, volume I, John Wiley & Sons, New York, 3rd
On the Border Length Minimization Problem (BLMP) on a Square Array
Kundeti, Vamsi; Dinh, Hieu
2010-01-01
Protein/Peptide microarrays are rapidly gaining momentum in the diagnosis of cancer. High-density and highthroughput peptide arrays are being extensively used to detect tumor biomarkers, examine kinase activity, identify antibodies having low serum titers and locate antibody signatures. Improving the yield of microarray fabrication involves solving a hard combinatorial optimization problem called the Border Length Minimization Problem (BLMP). An important question that remained open for the past seven years is if the BLMP is tractable or not. We settle this open problem by proving that the BLMP is NP-hard. We also present a hierarchical refinement algorithm which can refine any heuristic solution for the BLMP problem. We also prove that the TSP+1-threading heuristic is an O(N)- approximation. The hierarchical refinement solver is available as an opensource code at http://launchpad.net/blm-solve.
Directory of Open Access Journals (Sweden)
Huidan Zhang
Full Text Available Constitutively active KRAS mutations have been found to be involved in various processes of cancer development, and render tumor cells resistant to EGFR-targeted therapies. Mutation detection methods with higher sensitivity will increase the possibility of choosing the correct individual therapy. Here, we established a highly sensitive and efficient microfluidic capillary electrophoresis-based restriction fragment length polymorphism (µCE-based RFLP platform for low-abundance KRAS genotyping with the combination of µCE and RFLP techniques. By using our self-built sensitive laser induced fluorescence (LIF detector and a new DNA intercalating dye YOYO-1, the separation conditions of µCE for ΦX174 HaeIII DNA marker were first optimized. Then, a Mav I digested 107-bp KRAS gene fragment was directly introduced into the microfluidic device and analyzed by µCE, in which field amplified sample stacking (FASS technique was employed to obtain the enrichment of the RFLP digestion products and extremely improved the sensitivity. The accurate analysis of KRAS statuses in HT29, LS174T, CCL187, SW480, Clone A, and CX-1 colorectal cancer (CRC cell lines by µCE-based RFLP were achieved in 5 min with picoliter-scale sample consumption, and as low as 0.01% of mutant KRAS could be identified from a large excess of wild-type genomic DNA (gDNA. In 98 paraffin-embedded CRC tissues, KRAS codon 12 mutations were discovered in 28 (28.6%, significantly higher than that obtained by direct sequencing (13, 13.3%. Clone sequencing confirmed these results and showed this system could detect at least 0.4% of the mutant KRAS in CRC tissue slides. Compared with direct sequencing, the new finding of the µCE-based RFLP platform was that KRAS mutations in codon 12 were correlated with the patient's age. In conclusion, we established a sensitive, fast, and cost-effective screening method for KRAS mutations, and successfully detected low-abundance KRAS mutations in clinical
Carver, Charles S.; Scheier, Michael F.; Segerstrom, Suzanne C.
2010-01-01
Optimism is an individual difference variable that reflects the extent to which people hold generalized favorable expectancies for their future. Higher levels of optimism have been related prospectively to better subjective well-being in times of adversity or difficulty (i.e., controlling for previous well-being). Consistent with such findings, optimism has been linked to higher levels of engagement coping and lower levels of avoidance, or disengagement, coping. There is evidence that optimism is associated with taking proactive steps to protect one's health, whereas pessimism is associated with health-damaging behaviors. Consistent with such findings, optimism is also related to indicators of better physical health. The energetic, task-focused approach that optimists take to goals also relates to benefits in the socioeconomic world. Some evidence suggests that optimism relates to more persistence in educational efforts and to higher later income. Optimists also appear to fare better than pessimists in relationships. Although there are instances in which optimism fails to convey an advantage, and instances in which it may convey a disadvantage, those instances are relatively rare. In sum, the behavioral patterns of optimists appear to provide models of living for others to learn from. PMID:20170998
Ant colony optimization and constraint programming
Solnon, Christine
2013-01-01
Ant colony optimization is a metaheuristic which has been successfully applied to a wide range of combinatorial optimization problems. The author describes this metaheuristic and studies its efficiency for solving some hard combinatorial problems, with a specific focus on constraint programming. The text is organized into three parts. The first part introduces constraint programming, which provides high level features to declaratively model problems by means of constraints. It describes the main existing approaches for solving constraint satisfaction problems, including complete tree search
Pearce, Charles
2009-01-01
Focuses on mathematical structure, and on real-world applications. This book includes developments in several optimization-related topics such as decision theory, linear programming, turnpike theory, duality theory, convex analysis, and queuing theory.
Combinatorial Approximation Algorithms for MaxCut using Random Walks
Kale, Satyen
2010-01-01
We give the first combinatorial approximation algorithm for Maxcut that beats the trivial 0.5 factor by a constant. The main partitioning procedure is very intuitive, natural, and easily described. It essentially performs a number of random walks and aggregates the information to provide the partition. We can control the running time to get an approximation factor-running time tradeoff. We show that for any constant b > 1.5, there is an O(n^{b}) algorithm that outputs a (0.5+delta)-approximation for Maxcut, where delta = delta(b) is some positive constant. One of the components of our algorithm is a weak local graph partitioning procedure that may be of independent interest. Given a starting vertex $i$ and a conductance parameter phi, unless a random walk of length ell = O(log n) starting from i mixes rapidly (in terms of phi and ell), we can find a cut of conductance at most phi close to the vertex. The work done per vertex found in the cut is sublinear in n.
Identification and Interrogation of Combinatorial Histone Modifications
Directory of Open Access Journals (Sweden)
Kelly R Karch
2013-12-01
Full Text Available Histone proteins are dynamically modified to mediate a variety of cellular processes including gene transcription, DNA damage repair, and apoptosis. Regulation of these processes occurs through the recruitment of non-histone proteins to chromatin by specific combinations of histone post-translational modifications (PTMs. Mass spectrometry has emerged as an essential tool to discover and quantify histone PTMs both within and between samples in an unbiased manner. Developments in mass spectrometry that allow for characterization of large histone peptides or intact protein has made it possible to determine which modifications occur simultaneously on a single histone polypeptide. A variety of techniques from biochemistry, biophysics, and chemical biology have been employed to determine the biological relevance of discovered combinatorial codes. This review first describes advancements in the field of mass spectrometry that have facilitated histone PTM analysis and then covers notable approaches to probe the biological relevance of these modifications in their nucleosomal context.
Combinatorial Pharmacophore-Based 3D-QSAR Analysis and Virtual Screening of FGFR1 Inhibitors
Directory of Open Access Journals (Sweden)
Nannan Zhou
2015-06-01
Full Text Available The fibroblast growth factor/fibroblast growth factor receptor (FGF/FGFR signaling pathway plays crucial roles in cell proliferation, angiogenesis, migration, and survival. Aberration in FGFRs correlates with several malignancies and disorders. FGFRs have proved to be attractive targets for therapeutic intervention in cancer, and it is of high interest to find FGFR inhibitors with novel scaffolds. In this study, a combinatorial three-dimensional quantitative structure-activity relationship (3D-QSAR model was developed based on previously reported FGFR1 inhibitors with diverse structural skeletons. This model was evaluated for its prediction performance on a diverse test set containing 232 FGFR inhibitors, and it yielded a SD value of 0.75 pIC50 units from measured inhibition affinities and a Pearson’s correlation coefficient R2 of 0.53. This result suggests that the combinatorial 3D-QSAR model could be used to search for new FGFR1 hit structures and predict their potential activity. To further evaluate the performance of the model, a decoy set validation was used to measure the efficiency of the model by calculating EF (enrichment factor. Based on the combinatorial pharmacophore model, a virtual screening against SPECS database was performed. Nineteen novel active compounds were successfully identified, which provide new chemical starting points for further structural optimization of FGFR1 inhibitors.
Institute of Scientific and Technical Information of China (English)
Reza Mirnejad; Reza Hosseini Doust; Reza Kachuei; Seied Mojtaba Mortazavi; Mehdi Khoobdel; Ali Ahamadi
2012-01-01
Objective:To evaluate simultaneous detection and differentiates of Brucella abortus(B. abortus) and Brucella melitensis (B. melitensis) through the combinatorial PCR method. Methods:This study was designed using three primers that could simultaneously identify and differentiate two major species of pathogenic Brucella in humans and animals. Identification and differentiation of each species using the size of the PCR product were determined. To determine the specificity of the method, bacteria close to the genus Brucella were used. Finally, to confirm PCR products, In addition to the products sequence, RFLP was performed on PCR products using restriction enzymes. Results:The method of optimized combinatorial PCR in this study could simultaneously detect and differentiate B. abortus and B. melitensis with high specificity and sensitivity in clinical samples. Differentiation of species is based on the resulting bands;therefore, the band 494 bp for B. abortus and 733 bp for B. melitensis were obtained. RFLP and sequencing results confirmed PCR results. Conclusions:The results of this study shows that without routine diagnostic methods such as culture and serology tests, using the molecular method of combinatorial PCR, important species of Brucella can be simultaneously identified and differentiated in clinical samples.
Combinatorial approaches for the identification of brain drug delivery targets.
Stutz, Charles C; Zhang, Xiaobin; Shusta, Eric V
2014-01-01
The blood-brain barrier (BBB) represents a large obstacle for the treatment of central nervous system diseases. Targeting endogenous nutrient transporters that transcytose the BBB is one promising approach to selectively and noninvasively deliver a drug payload to the brain. The main limitations of the currently employed transcytosing receptors are their ubiquitous expression in the peripheral vasculature and the inherent low levels of transcytosis mediated by such systems. In this review, approaches designed to increase the repertoire of transcytosing receptors which can be targeted for the purpose of drug delivery are discussed. In particular, combinatorial protein libraries can be screened on BBB cells in vitro or in vivo to isolate targeting peptides or antibodies that can trigger transcytosis. Once these targeting reagents are discovered, the cognate BBB transcytosis system can be identified using techniques such as expression cloning or immunoprecipitation coupled with mass spectrometry. Continued technological advances in BBB genomics and proteomics, membrane protein manipulation, and in vitro BBB technology promise to further advance the capability to identify and optimize peptides and antibodies capable of mediating drug transport across the BBB.
An improved combinatorial geometry model for arbitrary geometry in DSMC
Kargaran, H.; Minuchehr, A.; Zolfaghari, A.
2017-03-01
This paper focuses on a new direct simulation Monte Carlo (DSMC) code based on combinatorial geometry (CG) for simulation of any rarefied gas flow. The developed code, called DgSMC-A, has been supplied with an improved CG modeling able to significantly optimize the particle-tracking process, resulting in a highly reduced runtime compared to the conventional codes. The improved algorithm inserts a grid over the geometry and saves those grid elements containing some part of the geometry border. Since only a small part of a grid is engaged with the geometry border, significant time can be saved using the proposed algorithm. Embedding the modified algorithm in the DgSMC-A resulted in a fast, robust and self-governing code needless to any mesh generator. The code completely handles complex geometries created with first-and second-order surfaces. In addition, we developed a new surface area calculator in the CG methodology for complex geometries based on the Monte Carlo method with acceptable accuracy. Several well-known test cases are examined to indicate the code ability to deal with a wide range of realistic problems. Results are also found to be in good agreement with references and experimental data.
Petersen, Latrisha K; Chavez-Santoscoy, Ana V; Narasimhan, Balaji
2012-09-06
Polyanhydrides are a class of biomaterials with excellent biocompatibility and drug delivery capabilities. While they have been studied extensively with conventional one-sample-at-a-time synthesis techniques, a more recent high-throughput approach has been developed enabling the synthesis and testing of large libraries of polyanhydrides(1). This will facilitate more efficient optimization and design process of these biomaterials for drug and vaccine delivery applications. The method in this work describes the combinatorial synthesis of biodegradable polyanhydride film and nanoparticle libraries and the high-throughput detection of protein release from these libraries. In this robotically operated method (Figure 1), linear actuators and syringe pumps are controlled by LabVIEW, which enables a hands-free automated protocol, eliminating user error. Furthermore, this method enables the rapid fabrication of micro-scale polymer libraries, reducing the batch size while resulting in the creation of multivariant polymer systems. This combinatorial approach to polymer synthesis facilitates the synthesis of up to 15 different polymers in an equivalent amount of time it would take to synthesize one polymer conventionally. In addition, the combinatorial polymer library can be fabricated into blank or protein-loaded geometries including films or nanoparticles upon dissolution of the polymer library in a solvent and precipitation into a non-solvent (for nanoparticles) or by vacuum drying (for films). Upon loading a fluorochrome-conjugated protein into the polymer libraries, protein release kinetics can be assessed at high-throughput using a fluorescence-based detection method (Figures 2 and 3) as described previously(1). This combinatorial platform has been validated with conventional methods(2) and the polyanhydride film and nanoparticle libraries have been characterized with (1)H NMR and FTIR. The libraries have been screened for protein release kinetics, stability and
Implementation of a combinatorial cleavage and deprotection scheme
DEFF Research Database (Denmark)
Nielsen, John; Rasmussen, Palle H.
1996-01-01
Phthalhydrazide libraries are synthesized in solution from substituted hydrazines and phthalimides in several different library formats including single compounds, indexed sub-libraries and a full library. When carried out during solid-phase synthesis, this combinatorial cleavage and deprotection...
Combinatorial polynomials as moments, Hankel transforms and exponential Riordan arrays
Barry, Paul
2011-01-01
In the case of two combinatorial polynomials, we show that they can exhibited as moments of paramaterized families of orthogonal polynomials, and hence derive their Hankel transforms. Exponential Riordan arrays are the main vehicles used for this.
Advanced Aqueous Phase Catalyst Development using Combinatorial Methods Project
National Aeronautics and Space Administration — The use of combinatorial methods is proposed to rapidly screen catalyst formulations for the advanced development of aqueous phase oxidation catalysts with greater...
New opioid peptides, peptidomimetics, and heterocyclic compounds from combinatorial libraries.
Dooley, C T; Houghten, R A
1999-01-01
Here we review the use of combinatorial libraries in opioid receptor assays. Following a brief description of the history of the combinatorial field, methods for the generation of synthetic libraries and the deconvolution of mixture-based libraries are presented. Case studies involving opioid assays used to demonstrate the viability of combinatorial libraries are described. The identification of new opioid peptides from combinatorial libraries is reviewed. The peptides found are composed of L-amino acids, D-amino acids, or L-, D-, and unnatural amino acids, and range from tetrapeptides to decapeptides. Likewise, new opioid compounds identified from peptidomimetic libraries, such as peptoids and alkylated dipeptides, and those identified from acyclic (e.g., polyamine, urea) and heterocyclic (e.g., bicyclic guanidine) libraries, are reviewed.
Combinatorial Hopf Algebras in (Noncommutative) Quantum Field Theory
Tanasa, Adrian
2010-01-01
We briefly review the r\\^ole played by algebraic structures like combinatorial Hopf algebras in the renormalizability of (noncommutative) quantum field theory. After sketching the commutative case, we analyze the noncommutative Grosse-Wulkenhaar model.
Reinvigorating natural product combinatorial biosynthesis with synthetic biology.
Kim, Eunji; Moore, Bradley S; Yoon, Yeo Joon
2015-09-01
Natural products continue to play a pivotal role in drug-discovery efforts and in the understanding if human health. The ability to extend nature's chemistry through combinatorial biosynthesis--altering functional groups, regiochemistry and scaffold backbones through the manipulation of biosynthetic enzymes--offers unique opportunities to create natural product analogs. Incorporating emerging synthetic biology techniques has the potential to further accelerate the refinement of combinatorial biosynthesis as a robust platform for the diversification of natural chemical drug leads. Two decades after the field originated, we discuss the current limitations, the realities and the state of the art of combinatorial biosynthesis, including the engineering of substrate specificity of biosynthetic enzymes and the development of heterologous expression systems for biosynthetic pathways. We also propose a new perspective for the combinatorial biosynthesis of natural products that could reinvigorate drug discovery by using synthetic biology in combination with synthetic chemistry.
Dynamic Combinatorial Libraries of Disulfide Cages in Water
West, Kevin R.; Bake, Kyle D.; Otto, Sijbren
2005-01-01
Dynamic combinatorial libraries (DCLs) containing water-soluble disulfide-linked cages (alongside macrocyclic structures) have been generated and characterized. Unlike most other strategies for generating molecular cages, the structures are held together by covalent bonds, which are formed under
Capacity Allocation and Revenue Sharing in Airline Alliances: A Combinatorial Auction-Based Modeling
Directory of Open Access Journals (Sweden)
Ying-jing Gu
2017-01-01
Full Text Available This paper attempts to establish a framework to help airline alliances effectively allocate their seat capacity with the purpose of maximizing alliances’ revenue. By assuming the airline alliance as the auctioneer and seat capacity in an itinerary as lots, the combinatorial auction model is constructed to optimize the allocation of the seat, and the revenue sharing method is established to share revenue between partners by Vickrey-Clarke-Groves (VCG mechanism. The result of the numerical study shows that the seat capacity allocation is effective even without information exchanging completely and the twofold revenue shares method shows more excitation for the airlines.
Variational Splines and Paley--Wiener Spaces on Combinatorial Graphs
Pesenson, Isaac
2011-01-01
Notions of interpolating variational splines and Paley-Wiener spaces are introduced on a combinatorial graph G. Both of these definitions explore existence of a combinatorial Laplace operator onG. The existence and uniqueness of interpolating variational splines on a graph is shown. As an application of variational splines, the paper presents a reconstruction algorithm of Paley-Wiener functions on graphs from their uniqueness sets.
Variational Splines and Paley--Wiener Spaces on Combinatorial Graphs
Pesenson, Isaac
2011-01-01
Notions of interpolating variational splines and Paley-Wiener spaces are introduced on a combinatorial graph G. Both of these definitions explore existence of a combinatorial Laplace operator onG. The existence and uniqueness of interpolating variational splines on a graph is shown. As an application of variational splines, the paper presents a reconstruction algorithm of Paley-Wiener functions on graphs from their uniqueness sets.
Sampling, Filtering and Sparse Approximations on Combinatorial Graphs
Pesenson, Isaac Z
2011-01-01
In this paper we address sampling and approximation of functions on combinatorial graphs. We develop filtering on graphs by using Schr\\"odinger's group of operators generated by combinatorial Laplace operator. Then we construct a sampling theory by proving Poincare and Plancherel-Polya-type inequalities for functions on graphs. These results lead to a theory of sparse approximations on graphs and have potential applications to filtering, denoising, data dimension reduction, image processing, image compression, computer graphics, visualization and learning theory.
Combinatorial Dyson-Schwinger equations and inductive data types
Kock, Joachim
2016-06-01
The goal of this contribution is to explain the analogy between combinatorial Dyson-Schwinger equations and inductive data types to a readership of mathematical physicists. The connection relies on an interpretation of combinatorial Dyson-Schwinger equations as fixpoint equations for polynomial functors (established elsewhere by the author, and summarised here), combined with the now-classical fact that polynomial functors provide semantics for inductive types. The paper is expository, and comprises also a brief introduction to type theory.
Combinatorial Dyson-Schwinger equations and inductive data types
Kock, Joachim
2015-01-01
The goal of this contribution is to explain the analogy between combinatorial Dyson-Schwinger equations and inductive data types to a readership of mathematical physicists. The connection relies on an interpretation of combinatorial Dyson-Schwinger equations as fixpoint equations for polynomial functors (established elsewhere by the author, and summarised here), combined with the now-classical fact that polynomial functors provide semantics for inductive types. The paper is expository, and co...
Geometric and Combinatorial Structure of Hypersurface Coamoebas
Nisse, Mounir
2009-01-01
Let $V$ be a complex algebraic hypersurface defined by a polynomial $f$ with Newton polytope $\\Delta$. It is well known that the spine of its amoeba has a structure of a tropical hypersurface. We prove in this paper that there exists a complex tropical hypersurface $V_{\\infty, f}$ such that its coamoeba is homeomorphic to the closure in the real torus of the coamoeba of $V$. Moreover, the coamoeba of $V_{\\infty, f}$ contains an arrangement of $(n-1)$-torus depending only on the geometry of $\\Delta$ and the coefficients of $f$. In addition, we can consider this arrangement, as a weighted codual hyperplanes arrangement in the universal covering of the real torus, and the balancing condition (the analogous to that of tropical hypersurfaces) is satisfied. This codual hyperplanes arrangement is called the {\\em shell} of the complex coamoeba (the cousin of the spine of the complex amoeba). %(or the {\\em average contour} of the complex coamoeba). Using this combinatorial coamoebas structure, we show that the amoebas...
Similarity searching in large combinatorial chemistry spaces
Rarey, Matthias; Stahl, Martin
2001-06-01
We present a novel algorithm, called Ftrees-FS, for similarity searching in large chemistry spaces based on dynamic programming. Given a query compound, the algorithm generates sets of compounds from a given chemistry space that are similar to the query. The similarity search is based on the feature tree similarity measure representing molecules by tree structures. This descriptor allows handling combinatorial chemistry spaces as a whole instead of looking at subsets of enumerated compounds. Within few minutes of computing time, the algorithm is able to find the most similar compound in very large spaces as well as sets of compounds at an arbitrary similarity level. In addition, the diversity among the generated compounds can be controlled. A set of 17 000 fragments of known drugs, generated by the RECAP procedure from the World Drug Index, was used as the search chemistry space. These fragments can be combined to more than 1018 compounds of reasonable size. For validation, known antagonists/inhibitors of several targets including dopamine D4, histamine H1, and COX2 are used as queries. Comparison of the compounds created by Ftrees-FS to other known actives demonstrates the ability of the method to jump between structurally unrelated molecule classes.
Scalable Combinatorial Tools for Health Disparities Research
Directory of Open Access Journals (Sweden)
Michael A. Langston
2014-10-01
Full Text Available Despite staggering investments made in unraveling the human genome, current estimates suggest that as much as 90% of the variance in cancer and chronic diseases can be attributed to factors outside an individual’s genetic endowment, particularly to environmental exposures experienced across his or her life course. New analytical approaches are clearly required as investigators turn to complicated systems theory and ecological, place-based and life-history perspectives in order to understand more clearly the relationships between social determinants, environmental exposures and health disparities. While traditional data analysis techniques remain foundational to health disparities research, they are easily overwhelmed by the ever-increasing size and heterogeneity of available data needed to illuminate latent gene x environment interactions. This has prompted the adaptation and application of scalable combinatorial methods, many from genome science research, to the study of population health. Most of these powerful tools are algorithmically sophisticated, highly automated and mathematically abstract. Their utility motivates the main theme of this paper, which is to describe real applications of innovative transdisciplinary models and analyses in an effort to help move the research community closer toward identifying the causal mechanisms and associated environmental contexts underlying health disparities. The public health exposome is used as a contemporary focus for addressing the complex nature of this subject.
Dynamic combinatorial libraries of artificial repeat proteins.
Eisenberg, Margarita; Shumacher, Inbal; Cohen-Luria, Rivka; Ashkenasy, Gonen
2013-06-15
Repeat proteins are found in almost all cellular systems, where they are involved in diverse molecular recognition processes. Recent studies have suggested that de novo designed repeat proteins may serve as universal binders, and might potentially be used as practical alternative to antibodies. We describe here a novel chemical methodology for producing small libraries of repeat proteins, and screening in parallel the ligand binding of library members. The first stage of this research involved the total synthesis of a consensus-based three-repeat tetratricopeptide (TPR) protein (~14 kDa), via sequential attachment of the respective peptides. Despite the effectiveness of the synthesis and ligation steps, this method was found to be too demanding for the production of proteins containing variable number of repeats. Additionally, the analysis of binding of the individual proteins was time consuming. Therefore, we designed and prepared novel dynamic combinatorial libraries (DCLs), and show that their equilibration can facilitate the formation of TPR proteins containing up to eight repeating units. Interestingly, equilibration of the library building blocks in the presence of the biologically relevant ligands, Hsp90 and Hsp70, induced their oligomerization into forming more of the proteins with large recognition surfaces. We suggest that this work presents a novel simple and rapid tool for the simultaneous screening of protein mixtures with variable binding surfaces, and for identifying new binders for ligands of interest.
The Combinatorial Multi-Mode Resource Constrained Multi-Project Scheduling Problem
Directory of Open Access Journals (Sweden)
Denis Pinha
2016-11-01
Full Text Available This paper presents the formulation and solution of the Combinatorial Multi-Mode Resource Constrained Multi-Project Scheduling Problem. The focus of the proposed method is not on finding a single optimal solution, instead on presenting multiple feasible solutions, with cost and duration information to the project manager. The motivation for developing such an approach is due in part to practical situations where the definition of optimal changes on a regular basis. The proposed approach empowers the project manager to determine what is optimal, on a given day, under the current constraints, such as, change of priorities, lack of skilled worker. The proposed method utilizes a simulation approach to determine feasible solutions, under the current constraints. Resources can be non-consumable, consumable, or doubly constrained. The paper also presents a real-life case study dealing with scheduling of ship repair activities.
Neural blackboard architectures of combinatorial structures in cognition.
van der Velde, Frank; de Kamps, Marc
2006-02-01
Human cognition is unique in the way in which it relies on combinatorial (or compositional) structures. Language provides ample evidence for the existence of combinatorial structures, but they can also be found in visual cognition. To understand the neural basis of human cognition, it is therefore essential to understand how combinatorial structures can be instantiated in neural terms. In his recent book on the foundations of language, Jackendoff described four fundamental problems for a neural instantiation of combinatorial structures: the massiveness of the binding problem, the problem of 2, the problem of variables, and the transformation of combinatorial structures from working memory to long-term memory. This paper aims to show that these problems can be solved by means of neural "blackboard" architectures. For this purpose, a neural blackboard architecture for sentence structure is presented. In this architecture, neural structures that encode for words are temporarily bound in a manner that preserves the structure of the sentence. It is shown that the architecture solves the four problems presented by Jackendoff. The ability of the architecture to instantiate sentence structures is illustrated with examples of sentence complexity observed in human language performance. Similarities exist between the architecture for sentence structure and blackboard architectures for combinatorial structures in visual cognition, derived from the structure of the visual cortex. These architectures are briefly discussed, together with an example of a combinatorial structure in which the blackboard architectures for language and vision are combined. In this way, the architecture for language is grounded in perception. Perspectives and potential developments of the architectures are discussed.
Submodular functions and optimization
Fujishige, Satoru
2005-01-01
It has widely been recognized that submodular functions play essential roles in efficiently solvable combinatorial optimization problems. Since the publication of the 1st edition of this book fifteen years ago, submodular functions have been showing further increasing importance in optimization, combinatorics, discrete mathematics, algorithmic computer science, and algorithmic economics, and there have been made remarkable developments of theory and algorithms in submodular functions. The 2nd edition of the book supplements the 1st edition with a lot of remarks and with new two chapters: "Submodular Function Minimization" and "Discrete Convex Analysis." The present 2nd edition is still a unique book on submodular functions, which is essential to students and researchers interested in combinatorial optimization, discrete mathematics, and discrete algorithms in the fields of mathematics, operations research, computer science, and economics. Key features: - Self-contained exposition of the theory of submodular ...
Chen, Lei; Chu, Cheng-I; Chen, Kuo-Ju; Chen, Po-Yuan; Hu, Shu-Fen; Liu, Ru-Shi
2011-01-01
A significant advance made in combinatorial approach research was that the emphasis shifted from simple mixing to intelligent screening, so as to improve the efficiency and accuracy of discovering new materials from a larger number of diverse compositions. In this study, the long-lasting luminescence of SrAl(2)O(4), which is co-doped with Eu(2+), Ce(3+), Dy(3+), Li(+) and H(3)BO(3), was investigated based on a combinatorial approach in conjunction with the Taguchi method. The minimal number of 16 samples to be tested (five dopants and four levels of concentration) were designed using the Taguchi method. The samples to be screened were synthesized using a parallel combinatorial strategy based on ink-jetting of precursors into an array of micro-reactor wells. The relative brightness of luminescence of the different phosphors over a particular period was assessed. Ce(3+) was identified as the constituent that detrimentally affected long-lasting luminescence. Its concentration was optimized to zero. Li(+) had a minor effect on long-lasting luminescence but the main factors that contributed to the objective property (long-lasting luminescence) were Eu(2+), Dy(3+) and H(3)BO(3), and the concentrations of these dopants were optimized to 0.020, 0.030 and 0.300, respectively, for co-doping into SrAl(2)O(4). This study demonstrates that the utility of the combinatorial approach for evaluating the effect of components on an objective property (e.g. phosphorescence) and estimating the expected performance under the optimal conditions can be improved by the Taguchi method.
Solid-Phase Synthesis of Small Molecule Libraries using Double Combinatorial Chemistry
DEFF Research Database (Denmark)
Nielsen, John; Jensen, Flemming R.
1997-01-01
The first synthesis of a combinatorial library using double combinatorial chemistry is presented. Coupling of unprotected Fmoc-tyrosine to the solid support was followed by Mitsunobu O-alkylation. Introduction of a diacid linker yields a system in which the double combinatorial step can be demons......The first synthesis of a combinatorial library using double combinatorial chemistry is presented. Coupling of unprotected Fmoc-tyrosine to the solid support was followed by Mitsunobu O-alkylation. Introduction of a diacid linker yields a system in which the double combinatorial step can...... be demonstrated. The resulting library of model compounds was verified by LC-MS analysis. (C) 1997 Elsevier Science Ltd....
Combinatorial effects on clumped isotopes and their significance in biogeochemistry
Yeung, Laurence Y.
2016-01-01
The arrangement of isotopes within a collection of molecules records their physical and chemical histories. Clumped-isotope analysis interrogates these arrangements, i.e., how often rare isotopes are bound together, which in many cases can be explained by equilibrium and/or kinetic isotope fractionation. However, purely combinatorial effects, rooted in the statistics of pairing atoms in a closed system, are also relevant, and not well understood. Here, I show that combinatorial isotope effects are most important when two identical atoms are neighbors on the same molecule (e.g., O2, N2, and D-D clumping in CH4). When the two halves of an atom pair are either assembled with different isotopic preferences or drawn from different reservoirs, combinatorial effects cause depletions in clumped-isotope abundance that are most likely between zero and -1‰, although they could potentially be -10‰ or larger for D-D pairs. These depletions are of similar magnitude, but of opposite sign, to low-temperature equilibrium clumped-isotope effects for many small molecules. Enzymatic isotope-pairing reactions, which can have site-specific isotopic fractionation factors and atom reservoirs, should express this class of combinatorial isotope effect, although it is not limited to biological reactions. Chemical-kinetic isotope effects, which are related to a bond-forming transition state, arise independently and express second-order combinatorial effects related to the abundance of the rare isotope. Heteronuclear moeties (e.g., Csbnd O and Csbnd H), are insensitive to direct combinatorial influences, but secondary combinatorial influences are evident. In general, both combinatorial and chemical-kinetic factors are important for calculating and interpreting clumped-isotope signatures of kinetically controlled reactions. I apply this analytical framework to isotope-pairing reactions relevant to geochemical oxygen, carbon, and nitrogen cycling that may be influenced by combinatorial
The priming of basic combinatory responses in MEG.
Blanco-Elorrieta, Esti; Ferreira, Victor S; Del Prato, Paul; Pylkkänen, Liina
2017-09-21
Priming has been a powerful tool for the study of human memory and especially the memory representations relevant for language. However, although it is well established that lexical access can be primed, we do not know exactly what types of computations can be primed above the word level. This work took a neurobiological approach and assessed the ways in which the complex representation of a minimal combinatory phrase, such as red boat, can be primed, as evidenced by the spatiotemporal profiles of magnetoencephalography (MEG) signals. Specifically, we built upon recent progress on the neural signatures of phrasal composition and tested whether the brain activities implicated for the basic combination of two words could be primed. In two experiments, MEG was recorded during a picture naming task where the prime trials were designed to replicate previously reported combinatory effects and the target trials to test whether those combinatory effects could be primed. The manipulation of the primes was successful in eliciting larger activity for adjective-noun combinations than single nouns in left anterior temporal and ventromedial prefrontal cortices, replicating prior MEG studies on parallel contrasts. Priming of similarly timed activity was observed during target trials in anterior temporal cortex, but only when the prime and target shared an adjective. No priming in temporal cortex was observed for single word repetition and two control tasks showed that the priming effect was not elicited if the prime pictures were simply viewed but not named. In sum, this work provides evidence that very basic combinatory operations can be primed, with the necessity for some lexical overlap between prime and target suggesting combinatory conceptual, as opposed to syntactic processing. Both our combinatory and priming effects were early, onsetting between 100 and 150ms after picture onset and thus are likely to reflect the very earliest planning stages of a combinatory message
Deterministic Global Optimization
Scholz, Daniel
2012-01-01
This monograph deals with a general class of solution approaches in deterministic global optimization, namely the geometric branch-and-bound methods which are popular algorithms, for instance, in Lipschitzian optimization, d.c. programming, and interval analysis.It also introduces a new concept for the rate of convergence and analyzes several bounding operations reported in the literature, from the theoretical as well as from the empirical point of view. Furthermore, extensions of the prototype algorithm for multicriteria global optimization problems as well as mixed combinatorial optimization
Invention as a combinatorial process: evidence from US patents.
Youn, Hyejin; Strumsky, Deborah; Bettencourt, Luis M A; Lobo, José
2015-05-06
Invention has been commonly conceptualized as a search over a space of combinatorial possibilities. Despite the existence of a rich literature, spanning a variety of disciplines, elaborating on the recombinant nature of invention, we lack a formal and quantitative characterization of the combinatorial process underpinning inventive activity. Here, we use US patent records dating from 1790 to 2010 to formally characterize invention as a combinatorial process. To do this, we treat patented inventions as carriers of technologies and avail ourselves of the elaborate system of technology codes used by the United States Patent and Trademark Office to classify the technologies responsible for an invention's novelty. We find that the combinatorial inventive process exhibits an invariant rate of 'exploitation' (refinements of existing combinations of technologies) and 'exploration' (the development of new technological combinations). This combinatorial dynamic contrasts sharply with the creation of new technological capabilities-the building blocks to be combined-that has significantly slowed down. We also find that, notwithstanding the very reduced rate at which new technologies are introduced, the generation of novel technological combinations engenders a practically infinite space of technological configurations.
Pizzolorusso, Gianfranco; Cerritelli, Francesco; Accorsi, Alessandro; Lucci, Chiara; Tubaldi, Lucia; Lancellotti, Jenny; Barlafante, Gina; Renzetti, Cinzia; D'Incecco, Carmine; Perri, Francesco Paolo
2014-01-01
Introduction. Little research has been conducted looking at the effects of osteopathic manipulative treatment (OMT) on preterm infants. Aim of the Study. This study hypothesized that osteopathic care is effective in reducing length of hospital stay and that early OMT produces the most pronounced benefit, compared to moderately early and late OMT. A secondary outcome was to estimate hospital cost savings by the use of OMT. Methods. 110 newborns ranging from 32- to 37-week gestation were randomized to receive either OMT or usual pediatric care. Early, moderately early, and late OMT were defined as <4, <9, and <14 days from birth, respectively. Result. Hospital stay was shorter in infants receiving late OMT (−2.03; 95% CI −3.15, −0.91; P < 0.01) than controls. Subgroup analysis of infants receiving early and moderately early OMT resulted in shorter LOS (early OMT: −4.16; −6.05, −2.27; P < 0.001; moderately early OMT: −3.12; −4.36, −1.89; P < 0.001). Costs analysis showed that OMT significantly produced a net saving of €740 (−1309.54, −170.33; P = 0.01) per newborn per LOS. Conclusions. This study shows evidence that the sooner OMT is provided, the shorter their hospital stay is. There is also a positive association of OMT with overall reduction in cost of care. PMID:25506381
Institute of Scientific and Technical Information of China (English)
许东京; 叶明; 周成锋
2012-01-01
利用ANSYS软件建立了悬臂梁结构的模型,采用了工程中常用的模型,即非等长复合压电振子模型.设计了一种呈阵列分布的多圆孔基板材料压电振子,通过仿真分析,该结构的压电振子在尺寸与外加载荷一定的情况下,输出电压较优化前提高了14.1％,同时其固有频率与自身质量均较优化前有所降低.最后仿真结果也说明了这种多圆孔压电振子对于提高能量转换效率的可行性和有效性.%Using ANSYS software to establish the model of piezoelectric cantilever beam which the length and the width between piezoelectric and base plate is not equal. There are many multi - hole arrays in the piezoelectric vibrator's base plate, through the simulation shows that the output voltage increase 14.1% than before when the dimension and extra force are not changed, besides, thenatural frequency and its quality decrease. Simulation result also shows that the model can improve energy conversion efficiency for the feasibility and effectiveness.
Directory of Open Access Journals (Sweden)
Gianfranco Pizzolorusso
2014-01-01
Full Text Available Introduction. Little research has been conducted looking at the effects of osteopathic manipulative treatment (OMT on preterm infants. Aim of the Study. This study hypothesized that osteopathic care is effective in reducing length of hospital stay and that early OMT produces the most pronounced benefit, compared to moderately early and late OMT. A secondary outcome was to estimate hospital cost savings by the use of OMT. Methods. 110 newborns ranging from 32- to 37-week gestation were randomized to receive either OMT or usual pediatric care. Early, moderately early, and late OMT were defined as <4, <9, and <14 days from birth, respectively. Result. Hospital stay was shorter in infants receiving late OMT (−2.03; 95% CI −3.15, −0.91; P<0.01 than controls. Subgroup analysis of infants receiving early and moderately early OMT resulted in shorter LOS (early OMT: −4.16; −6.05, −2.27; P<0.001; moderately early OMT: −3.12; −4.36, −1.89; P<0.001. Costs analysis showed that OMT significantly produced a net saving of €740 (−1309.54, −170.33; P=0.01 per newborn per LOS. Conclusions. This study shows evidence that the sooner OMT is provided, the shorter their hospital stay is. There is also a positive association of OMT with overall reduction in cost of care.
Pizzolorusso, Gianfranco; Cerritelli, Francesco; Accorsi, Alessandro; Lucci, Chiara; Tubaldi, Lucia; Lancellotti, Jenny; Barlafante, Gina; Renzetti, Cinzia; D'Incecco, Carmine; Perri, Francesco Paolo
2014-01-01
Introduction. Little research has been conducted looking at the effects of osteopathic manipulative treatment (OMT) on preterm infants. Aim of the Study. This study hypothesized that osteopathic care is effective in reducing length of hospital stay and that early OMT produces the most pronounced benefit, compared to moderately early and late OMT. A secondary outcome was to estimate hospital cost savings by the use of OMT. Methods. 110 newborns ranging from 32- to 37-week gestation were randomized to receive either OMT or usual pediatric care. Early, moderately early, and late OMT were defined as OMT (-2.03; 95% CI -3.15, -0.91; P OMT resulted in shorter LOS (early OMT: -4.16; -6.05, -2.27; P OMT: -3.12; -4.36, -1.89; P OMT significantly produced a net saving of €740 (-1309.54, -170.33; P = 0.01) per newborn per LOS. Conclusions. This study shows evidence that the sooner OMT is provided, the shorter their hospital stay is. There is also a positive association of OMT with overall reduction in cost of care.
Combinatorics of locally optimal RNA secondary structures.
Fusy, Eric; Clote, Peter
2014-01-01
It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is 1.104366∙n-3/2∙2.618034n. Motivated by the kinetics of RNA secondary structure formation, we are interested in determining the asymptotic number of secondary structures that are locally optimal, with respect to a particular energy model. In the Nussinov energy model, where each base pair contributes -1 towards the energy of the structure, locally optimal structures are exactly the saturated structures, for which we have previously shown that asymptotically, there are 1.07427∙n-3/2∙2.35467n many saturated structures for a sequence of length n. In this paper, we consider the base stacking energy model, a mild variant of the Nussinov model, where each stacked base pair contributes -1 toward the energy of the structure. Locally optimal structures with respect to the base stacking energy model are exactly those secondary structures, whose stems cannot be extended. Such structures were first considered by Evers and Giegerich, who described a dynamic programming algorithm to enumerate all locally optimal structures. In this paper, we apply methods from enumerative combinatorics to compute the asymptotic number of such structures. Additionally, we consider analogous combinatorial problems for secondary structures with annotated single-stranded, stacking nucleotides (dangles).
Combinatorial vector fields and the valley structure of fitness landscapes.
Stadler, Bärbel M R; Stadler, Peter F
2010-12-01
Adaptive (downhill) walks are a computationally convenient way of analyzing the geometric structure of fitness landscapes. Their inherently stochastic nature has limited their mathematical analysis, however. Here we develop a framework that interprets adaptive walks as deterministic trajectories in combinatorial vector fields and in return associate these combinatorial vector fields with weights that measure their steepness across the landscape. We show that the combinatorial vector fields and their weights have a product structure that is governed by the neutrality of the landscape. This product structure makes practical computations feasible. The framework presented here also provides an alternative, and mathematically more convenient, way of defining notions of valleys, saddle points, and barriers in landscape. As an application, we propose a refined approximation for transition rates between macrostates that are associated with the valleys of the landscape.
Dynamic Combinatorial Chemistry with Diselenides, Disulfides, Imines and Metal Coordination
DEFF Research Database (Denmark)
Sørensen, Anne
The design and preparation of strong and selective artificial receptors, especially biomi-metic receptors that function in aqueous solution, has proved truly challenging. In this thesis it will be described how the strengths of dynamic combinatorial chemistry can be used to great advantage...... in this field. The aim of this project has therefore been to develop new ways of using dynamic combinatorial libraries for molecular recognition in aqueous media. The focus has been on using what has been learned from the well-established di-sulfide exchange chemistry to incorporate a new reaction into dynamic...... combinatorial chemistry, namely the reversible diselenide exchange reaction. The first part of the thesis describes the development of a thermally induced OAr → SeAr migration reaction. Here, it was proven possible to rearrange a variety of substituted O-aryl selenocarbamates into the corresponding Se...
Combinatorial Constructions for Sifting Primes and Enumerating the Rationals
Gnang, Edinah K
2012-01-01
We describe a combinatorial approach for investigating properties of rational numbers. The overall approach rests on structural bijections between rational numbers and familiar combinatorial objects, namely rooted trees. We emphasize that such mappings achieve much more than enumeration of rooted trees. We discuss two related structural bijections. The first corresponds to a bijective map between integers and rooted trees. The first bijection also suggests a new algorithm for sifting primes. The second bijection extends the first one in order to map rational numbers to a family of rooted trees. The second bijection suggests a new combinatorial construction for generating reduced rational numbers, thereby producing refinements of the output of the Wilf-Calkin[1] Algorithm.
Combinatorial Selection and Least Absolute Shrinkage via the CLASH Algorithm
Kyrillidis, Anastasios
2012-01-01
The least absolute shrinkage and selection operator (LASSO) for linear regression exploits the geometric interplay of the $\\ell_2$-data error objective and the $\\ell_1$-norm constraint to arbitrarily select sparse models. Guiding this uninformed selection process with sparsity models has been precisely the center of attention over the last decade in order to improve learning performance. To this end, we alter the selection process of LASSO to explicitly leverage combinatorial sparsity models (CSMs) via the combinatorial selection and least absolute shrinkage (CLASH) operator. We provide concrete guidelines how to leverage combinatorial constraints within CLASH, and characterize CLASH's guarantees as a function of the set restricted isometry constants of the sensing matrix. Finally, our experimental results show that CLASH can outperform both LASSO and model-based compressive sensing in sparse estimation.
Key Updating Methods for Combinatorial Design Based Key Management Schemes
Directory of Open Access Journals (Sweden)
Chonghuan Xu
2014-01-01
Full Text Available Wireless sensor network (WSN has become one of the most promising network technologies for many useful applications. However, for the lack of resources, it is different but important to ensure the security of the WSNs. Key management is a corner stone on which to build secure WSNs for it has a fundamental role in confidentiality, authentication, and so on. Combinatorial design theory has been used to generate good-designed key rings for each sensor node in WSNs. A large number of combinatorial design based key management schemes have been proposed but none of them have taken key updating into consideration. In this paper, we point out the essence of key updating for the unital design based key management scheme and propose two key updating methods; then, we conduct performance analysis on the two methods from three aspects; at last, we generalize the two methods to other combinatorial design based key management schemes and enhance the second method.
Combinatorial realizations of crystals via torus actions on quiver varieties
Sam, Steven V
2012-01-01
Consider Kashiwara's crystal associated to a highest weight representation of a symmetric Kac--Moody algebra. There is a geometric realization of this object using Nakajima's quiver varieties. In many particular cases it can also be realized by elementary combinatorial methods. Here we propose a framework for extracting combinatorial realizations from the geometric picture: we construct certain torus actions on the quiver varieties and use Morse theory to index the irreducible components by connected components of the subvariety of torus fixed points. We then discuss the case of affine sl(n). There the fixed point components are just points, and are naturally indexed by multi-partitions. There is some choice in our construction, leading to a family of combinatorial realizations for each highest weight crystal. In the case of the crystal of the fundamental representation we recover a family of realizations which was recently constructed by Fayers. This gives a more conceptual proof of Fayers' result as well as...
Directory of Open Access Journals (Sweden)
Yong Zhang
2015-12-01
Full Text Available In Long Term Evolution-Advanced (LTE-A networks, Device-to-device (D2D communications can be utilized to enhance the performance of multicast services by leveraging D2D relays to serve nodes with worse channel conditions within a cluster. For traditional D2D relay schemes, D2D links with poor channel condition may be the bottleneck of system sum data rate. In this paper, to optimize the throughput of D2D communications, we introduce an iterative combinatorial auction algorithm for efficient D2D relay selection. In combinatorial auctions, the User Equipments (UEs that fails to correctly receive multicast data from eNodeB (eNB are viewed as bidders that compete for D2D relays, while the eNB is treated as the auctioneer. We also give properties of convergency and low-complexity and present numerical simulations to verify the efficiency of the proposed algorithm.
Recent advances in combinatorial biosynthesis for drug discovery
Directory of Open Access Journals (Sweden)
Sun H
2015-02-01
Full Text Available Huihua Sun,1,* Zihe Liu,1,* Huimin Zhao,1,2 Ee Lui Ang1 1Metabolic Engineering Research Laboratory, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, Singapore; 2Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA *These authors contributed equally to this work Abstract: Because of extraordinary structural diversity and broad biological activities, natural products have played a significant role in drug discovery. These therapeutically important secondary metabolites are assembled and modified by dedicated biosynthetic pathways in their host living organisms. Traditionally, chemists have attempted to synthesize natural product analogs that are important sources of new drugs. However, the extraordinary structural complexity of natural products sometimes makes it challenging for traditional chemical synthesis, which usually involves multiple steps, harsh conditions, toxic organic solvents, and byproduct wastes. In contrast, combinatorial biosynthesis exploits substrate promiscuity and employs engineered enzymes and pathways to produce novel “unnatural” natural products, substantially expanding the structural diversity of natural products with potential pharmaceutical value. Thus, combinatorial biosynthesis provides an environmentally friendly way to produce natural product analogs. Efficient expression of the combinatorial biosynthetic pathway in genetically tractable heterologous hosts can increase the titer of the compound, eventually resulting in less expensive drugs. In this review, we will discuss three major strategies for combinatorial biosynthesis: 1 precursor-directed biosynthesis; 2 enzyme-level modification, which includes swapping of the entire domains, modules and subunits, site-specific mutagenesis, and directed evolution; 3 pathway-level recombination. Recent examples of combinatorial biosynthesis employing these
Energy Technology Data Exchange (ETDEWEB)
Weber, Stephen G. [University of Pittsburgh, Pittsburgh, Pennsylvania
1998-08-22
The power of combinatorial chemistry and related high throughput synthetic strategies is currently being pursued as a fruitful way to develop molecules and materials with new properties. The strategy is motivated, for example in the pharmaceutical industry, by the difficulty of designing molecules to bind to specific sites on target biomolecules. By synthesizing a variety of similar structures, and then finding the one that has the most potent activity, new so-called lead structures will be found rapidly. Existing lead structures can be optimized. This relatively new approach has many implications for separation science. The most obvious is the call for more separations power: higher resolution, lower concentrations, higher speed. This pressure butresses the traditional directions of research into the development of more useful separations. The advent of chip-based, electroosmotically pumped systems1 will certainly accelerate progress in this traditional direction. The progress in combinatorial chemistry and related synthetic strategies gives rise to two other, broadly significant possibilities for large changes in separation science. One possibility results from the unique requirements of the synthesis of a huge number of products simultaneously. Can syntheses and separations be designed to work together to create strategies that lead to mixtures containing only desired products but without side products? The other possibility results from the need for molecular selectivity in separations. Can combinatorial syntheses and related strategies be used in the development of better separations media? A workshop in two parts was held. In one half-day session, pedagogical presentations educated across the barriers of discipline and scale. In the second half-day session, the participants broke into small groups to flesh out new ideas. A panel summarized the breakout discussions.
A COMBINATORIAL PROPERTY OF PALLET-CONSTRAINED TWO MACHINE FLOW SHOP PROBLEM IN MINIMIZING MAKESPAN
Institute of Scientific and Technical Information of China (English)
HOU Sixiang; Han Hoogeveen; Petra Schuurman
2002-01-01
We consider the problem of scheduling n jobs in a pallet-constrained flowshop so as to minimize the makespan. In such a flow shop environment, each job needs apallet the entire time, from the start of its first operation until the completion of the lastoperation, and the number of pallets in the shop at any given time is limited by a positiveinteger K ≤ n. Generally speaking, the optimal schedules may be passing schedules. In thispaper, we present a combinatorial property which shows that for two machines, K(K ≥ 3)pallets, there exists a no-passing schedule which is an optimal schedule for n ≤ 2K - 1 and2K - 1 is tight.
Wernérus, H; Lehtiö, J; Teeri, T; Nygren, P A; Ståhl, S
2001-10-01
Ni(2+)-binding staphylococci were generated through surface display of combinatorially engineered variants of a fungal cellulose-binding domain (CBD) from Trichoderma reesei cellulase Cel7A. Novel CBD variants were generated by combinatorial protein engineering through the randomization of 11 amino acid positions, and eight potentially Ni(2+)-binding CBDs were selected by phage display technology. These new variants were subsequently genetically introduced into chimeric surface proteins for surface display on Staphylococcus carnosus cells. The expressed chimeric proteins were shown to be properly targeted to the cell wall of S. carnosus cells, since full-length proteins could be extracted and affinity purified. Surface accessibility for the chimeric proteins was demonstrated, and furthermore, the engineered CBDs, now devoid of cellulose-binding capacity, were shown to be functional with regard to metal binding, since the recombinant staphylococci had gained Ni(2+)-binding capacity. Potential environmental applications for such tailor-made metal-binding bacteria as bioadsorbents in biofilters or biosensors are discussed.
Improving Combinatorial Ambiguities of ttbar Events Using Neural Networks
Shim, Ji Hyun
2014-01-01
We present a method for resolving the combinatorial issues in the \\ttbar lepton+jets events occurring at the Tevatron collider. By incorporating multiple information into an artificial neural network, we introduce a novel event reconstruction method for such events. We find that this method significantly reduces the number of combinatorial ambiguities. Compared to the classical reconstruction method, our method provides significantly higher purity with same efficiency. We illustrate the reconstructed observables for the realistic top-quark mass and the forward-backward asymmetry measurements. A Monte Carlo study shows that our method provides meaningful improvements in the top-quark measurements using same amount of data as other methods.
Revisiting Combinatorial Ambiguities at Hadron Colliders with MT2
Baringer, Philip; McCaskey, Mathew; Noonan, Daniel
2011-01-01
We present a method to resolve combinatorial issues in multi-particle final states at hadron colliders. The use of kinematic variables such as MT2 and invariant mass significantly reduces combinatorial ambiguities in the signal, but at a cost of losing statistics. We illustrate this idea with gluino pair production leading to 4 jets $+\\met$ in the final state as well as $t\\bar{t}$ production in the dilepton channel. Compared to results in recent studies, our method provides greater efficiency with similar purity
Combinatorial theory of Macdonald polynomials I: Proof of Haglund's formula
Haglund, J.; Haiman, M.; Loehr, N
2005-01-01
Haglund recently proposed a combinatorial interpretation of the modified Macdonald polynomials H̃μ. We give a combinatorial proof of this conjecture, which establishes the existence and integrality of H̃μ. As corollaries, we obtain the cocharge formula of Lascoux and Schützenberger for Hall–Littlewood polynomials, a formula of Sahi and Knop for Jack's symmetric functions, a generalization of this result to the integral Macdonald polynomials Jμ, a formula for H̃μ in terms of Lascoux–Leclerc–Th...
Combinatorial reasoning an introduction to the art of counting
DeTemple, Duane
2014-01-01
Written by well-known scholars in the field, this book introduces combinatorics alongside modern techniques, showcases the interdisciplinary aspects of the topic, and illustrates how to problem solve with a multitude of exercises throughout. The authors' approach is very reader-friendly and avoids the ""scholarly tone"" found in many books on this topic. Combinatorial Reasoning: An Introduction to the Art of Counting: Focuses on enumeration and combinatorial thinking as a way to develop a variety of effective approaches to solving counting problemsIncludes brief summaries of basic concepts f
Fast Combinatorial Algorithm for the Solution of Linearly Constrained Least Squares Problems
Van Benthem, Mark H.; Keenan, Michael R.
2008-11-11
A fast combinatorial algorithm can significantly reduce the computational burden when solving general equality and inequality constrained least squares problems with large numbers of observation vectors. The combinatorial algorithm provides a mathematically rigorous solution and operates at great speed by reorganizing the calculations to take advantage of the combinatorial nature of the problems to be solved. The combinatorial algorithm exploits the structure that exists in large-scale problems in order to minimize the number of arithmetic operations required to obtain a solution.
Acevedo-Rocha, Carlos G; Reetz, Manfred T
2014-01-01
The method dubbed Assembly of Designed Oligonucleotides (ADO) is a powerful tool in synthetic biology to create combinatorial DNA libraries for gene, protein, metabolic, and genome engineering. In directed evolution of proteins, ADO benefits from using reduced amino acid alphabets for saturation mutagenesis and/or DNA shuffling, but all 20 canonical amino acids can be also used as building blocks. ADO is performed in a two-step reaction. The first involves a primer-free, polymerase cycling assembly or overlap extension PCR step using carefully designed overlapping oligonucleotides. The second step is a PCR amplification using the outer primers, resulting in a high-quality and bias-free double-stranded DNA library that can be assembled with other gene fragments and/or cloned into a suitable plasmid subsequently. The protocol can be performed in a few hours. In theory, neither the length of the DNA library nor the number of DNA changes has any limits. Furthermore, with the costs of synthetic DNA dropping every year, after an initial investment is made in the oligonucleotides, these can be exchanged for alternative ones with different sequences at any point in the process, fully exploiting the potential of creating highly diverse combinatorial libraries. In the example chosen here, we show the construction of a high-quality combinatorial ADO library targeting sixteen different codons simultaneously with nonredundant degenerate codons encoding various reduced alphabets of four amino acids along the heme region of the monooxygenase P450-BM3.
Solid-Phase Synthesis of Small Molecule Libraries using Double Combinatorial Chemistry
DEFF Research Database (Denmark)
Nielsen, John; Jensen, Flemming R.
1997-01-01
The first synthesis of a combinatorial library using double combinatorial chemistry is presented. Coupling of unprotected Fmoc-tyrosine to the solid support was followed by Mitsunobu O-alkylation. Introduction of a diacid linker yields a system in which the double combinatorial step can...
Combinatorial analysis of interacting RNA molecules
Li, Thomas J X
2010-01-01
Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with two backbones drawn horizontally on top of each other such that (1) intramolecular and intermolecular bonds are noncrossing and (2) there is no "zig-zag" configuration. This paper studies joint structures with arc-length at least four in which both, interior and exterior stack-lengths are at least two (no isolated arcs). The key idea in this paper is to consider a new type of shape, based on which joint structures can be derived via symbolic enumeration. Our results imply simple asymptotic formulas for the number of joint structures with surprisingly small exponential growth rates. They are of interest in the context of designing prediction algorithms for RNA-RNA interactions.
Exploiting cost distributions for query optimization
Waas, F.; Pellenkoft, A.J.
1998-01-01
Large-scale query optimization is, besides its practical relevance, a hard test case for optimization techniques. Since exact methods cannot be applied due to the combinatorial explosion of the search space, heuristics and probabilistic strategies have been deployed for more than a decade. However,
Skorupska, Katarzyna; Maggard, Paul A; Eichberger, Rainer; Schwarzburg, Klaus; Shahbazi, Paria; Zoellner, Brandon; Parkinson, Bruce A
2015-12-14
High-throughput combinatorial methods have been useful in identifying new oxide semiconductors with the potential to be applied to solar water splitting. Most of these techniques have been limited to producing and screening oxide phases formed at temperatures below approximately 550 °C. We report the development of a combinatorial approach to discover and optimize high temperature phases for photoelectrochemical water splitting. As a demonstration material, we chose to produce thin films of high temperature CuNb oxide phases by inkjet printing on two different substrates: fluorine-doped tin oxide and crystalline Si, which required different sample pyrolysis procedures. The selection of pyrolysis parameters, such as temperature/time programs, and the use of oxidizing, nonreactive or reducing atmospheres determines the composition of the thin film materials and their photoelectrochemical performance. XPS, XRD, and SEM analyses were used to determine the composition and oxidation states within the copper niobium oxide phases and to then guide the production of target Cu(1+)Nb(5+)-oxide phases. The charge carrier dynamics of the thin films produced by the inkjet printing are compared with pure CuNbO3 microcrystalline material obtained from inorganic bulk synthesis.
Directory of Open Access Journals (Sweden)
Yoichiro Ito
Full Text Available Combinatorial screening used together with a broad library of gene expression cassettes is expected to produce a powerful tool for the optimization of the simultaneous expression of multiple enzymes. Recently, we proposed a highly tunable protein expression system that utilized multiple genome-integrated target genes to fine-tune enzyme expression in yeast cells. This tunable system included a library of expression cassettes each composed of three gene-expression control elements that in different combinations produced a wide range of protein expression levels. In this study, four gene expression cassettes with graded protein expression levels were applied to the expression of three cellulases: cellobiohydrolase 1, cellobiohydrolase 2, and endoglucanase 2. After combinatorial screening for transgenic yeasts simultaneously secreting these three cellulases, we obtained strains with higher cellulase expressions than a strain harboring three cellulase-expression constructs within one high-performance gene expression cassette. These results show that our method will be of broad use throughout the field of metabolic engineering.
Directory of Open Access Journals (Sweden)
Khalid K Alam
2015-01-01
Full Text Available High-throughput sequence (HTS analysis of combinatorial selection populations accelerates lead discovery and optimization and offers dynamic insight into selection processes. An underlying principle is that selection enriches high-fitness sequences as a fraction of the population, whereas low-fitness sequences are depleted. HTS analysis readily provides the requisite numerical information by tracking the evolutionary trajectory of individual sequences in response to selection pressures. Unlike genomic data, for which a number of software solutions exist, user-friendly tools are not readily available for the combinatorial selections field, leading many users to create custom software. FASTAptamer was designed to address the sequence-level analysis needs of the field. The open source FASTAptamer toolkit counts, normalizes and ranks read counts in a FASTQ file, compares populations for sequence distribution, generates clusters of sequence families, calculates fold-enrichment of sequences throughout the course of a selection and searches for degenerate sequence motifs. While originally designed for aptamer selections, FASTAptamer can be applied to any selection strategy that can utilize next-generation DNA sequencing, such as ribozyme or deoxyribozyme selections, in vivo mutagenesis and various surface display technologies (peptide, antibody fragment, mRNA, etc.. FASTAptamer software, sample data and a user's guide are available for download at http://burkelab.missouri.edu/fastaptamer.html.
Institute of Scientific and Technical Information of China (English)
无
2003-01-01
A novel combinatorial photoelectrochemical (CPE) technology with combination of ultraviolet (UV)- photolysis and direct current (DC) electrolysis is studied and discussed for drinking water purification. In the self-made compositive photo-electrolysis incorporate reactor, removal rate of the 2-chlorophenol as model environmental pollutants has been investigated experimentally in terms of applied voltage, pH value, flow velocity, temperature, and aeration conditions. A primary analysis of the combinatorial photoelectric synergic effect on the degradation of organic pollutants has been carried out. It is found that the best performance of CPE oxidation is achieved by the following conditions: DC voltage of 5.0 V combined with UV-254-raidation, near neutral of pH 8 with aeration of pure oxygen. The influences of circular velocity, temperature, and initial concentration of the pollutant are minor. Under the optimal conditions, removal ratio of 2-CP is higher than 50% in 30 min, and 100% removal ratio of 2-CP (5 × 10-6) can be reached and TOC removal ratio reached above 90% in 2.5 h. Complete mineralization is achieved eventually. It shows in our investigation that under the studied conditions the synergic effect of UV photolysis and DC electrolysis on the degradation of the model pollutant is remarkable and validated, which may be derived from the coexistence of mutual complementary mechanisms of photoelectrochemical action, and the radicals chain reactions resulted from photo activation and electrolysis excitation in the process of CPE oxidation.
Leading log expansion of combinatorial Dyson Schwinger equations
Delage, Lucas
2016-01-01
We study combinatorial Dyson Schwinger equations, expressed in the Hopf algebra of words with a quasi shuffle product. We map them into an algebra of polynomials in one indeterminate L and show that the leading log expansion one obtains with such a mapping are simple power law like expression
Dynamic Combinatorial Libraries of Disulfide Cages in Water
West, Kevin R.; Bake, Kyle D.; Otto, Sijbren
2005-01-01
Dynamic combinatorial libraries (DCLs) containing water-soluble disulfide-linked cages (alongside macrocyclic structures) have been generated and characterized. Unlike most other strategies for generating molecular cages, the structures are held together by covalent bonds, which are formed under the
A Synthetic Receptor for Nicotine from a Dynamic Combinatorial Library
Hamieh, Saleh; Ludlow, R. Frederick; Perraud, Olivier; West, Kevin R.; Mattia, Elio; Otto, Sijbren
2012-01-01
Designing synthetic receptors that bind biologically relevant guests in an aqueous solution remains a considerable challenge. We now report a new synthetic receptor for nicotine, selected from a dynamic combinatorial library, that binds this guest in water at neutral pH through a combination of hydr
Isocyanide based multi component reactions in combinatorial chemistry.
Dömling, A.
1998-01-01
Although usually regarded as a recent development, the combinatorial approach to the synthesis of libraries of new drug candidates was first described as early as 1961 using the isocyanide-based one-pot multicomponent Ugi reaction. Isocyanide-based multi component reactions (MCR's) markedly differ f
Identities for Generalized Fibonacci Numbers: A Combinatorial Approach
Plaza, A.; Falcon, S.
2008-01-01
This note shows a combinatorial approach to some identities for generalized Fibonacci numbers. While it is a straightforward task to prove these identities with induction, and also by arithmetical manipulations such as rearrangements, the approach used here is quite simple to follow and eventually reduces the proof to a counting problem. (Contains…
Combinatorial structures and processing in neural blackboard architectures
van der Velde, Frank; van der Velde, Frank; de Kamps, Marc; Besold, Tarek R.; d'Avila Garcez, Artur; Marcus, Gary F.; Miikkulainen, Risto
2015-01-01
We discuss and illustrate Neural Blackboard Architectures (NBAs) as the basis for variable binding and combinatorial processing the brain. We focus on the NBA for sentence structure. NBAs are based on the notion that conceptual representations are in situ, hence cannot be copied or transported.
A graphical formalism for mixed multi-unit combinatorial auctions
Gionvannucci, A.; Cerquides, J.; Endriss, U.; Rodríguez-Aguilar, J.A.
2010-01-01
Mixed multi-unit combinatorial auctions are auctions that allow participants to bid for bundles of goods to buy, for bundles of goods to sell, and for transformations of goods. The intuitive meaning of a bid for a transformation is that the bidder is offering to produce a set of output goods after h
Solids: a combinatorial auction for a housing corporation
Goossens, D.R.; Onderstal, S.; Spieksma, F.C.R.; Coles, P.; Das, S.; Lahaie, S.; Szymanski, B.
2012-01-01
On May 7, 2011, over one hundred bidders took part in a combinatorial auction for housing space in a newly erected building in Amsterdam (the Netherlands). This paper describes the development of this auction. We sketch our collaboration with the housing corporation that resulted in design choices
Dithioacetal Exchange: A New Reversible Reaction for Dynamic Combinatorial Chemistry.
Orrillo, A Gastón; Escalante, Andrea M; Furlan, Ricardo L E
2016-05-10
Reversibility of dithioacetal bond formation is reported under acidic mild conditions. Its utility for dynamic combinatorial chemistry was explored by combining it with orthogonal disulfide exchange. In such a setup, thiols are positioned at the intersection of both chemistries, constituting a connecting node between temporally separated networks.
Automated Combinatorial Chemistry in the Organic Chemistry Majors Laboratory
Nichols, Christopher J.; Hanne, Larry F.
2010-01-01
A multidisciplinary experiment has been developed in which students each synthesize a combinatorial library of 48 hydrazones with the aid of a liquid-handling robot. Each product is then subjected to a Kirby-Bauer disk diffusion assay to assess its antibacterial activity. Students gain experience working with automation and at the…
Synthetic receptors for ammonium ions using dynamic combinatorial chemistry
Hamieh, Saleh
2015-01-01
The general topic of this dissertation is the development of synthetic receptors for organic ammonium ions in near physiological conditions using disulfide dynamic combinatorial chemistry (DCC). Chapter 1 explains the importance of this development and the associated difficulties when using the conv
Isocyanide based multi component reactions in combinatorial chemistry.
Dömling, A.
1998-01-01
Although usually regarded as a recent development, the combinatorial approach to the synthesis of libraries of new drug candidates was first described as early as 1961 using the isocyanide-based one-pot multicomponent Ugi reaction. Isocyanide-based multi component reactions (MCR's) markedly differ
Dynamic combinatorial chemistry at the phospholipid bilayer interface
Mansfeld, Friederike M.; Au-Yeung, Ho Yu; Sanders, Jeremy K.M.; Otto, Sijbren
2010-01-01
Background: Molecular recognition at the environment provided by the phospholipid bilayer interface plays an important role in biology and is subject of intense investigation. Dynamic combinatorial chemistry is a powerful approach for exploring molecular recognition, but has thus far not been
Proceedings of the 8th Nordic Combinatorial Conference
DEFF Research Database (Denmark)
Geil, Olav; Andersen, Lars Døvling
The Nordic Combinatorial Conferences were initiated in 1981 by mathematicians from Stavanger. Held approximately every three years since then, the conferences have been able to sustain the interest from combinatorialists all over the Nordic countries. In 2004 the 8th conference is held in Aalborg...
Analysis of Berth Length Optimization of Indonesia Power Plant Terminal Project%印尼某电站码头工程泊位长度优化分析
Institute of Scientific and Technical Information of China (English)
刘奇虎
2014-01-01
Based on one power plant terminal project in Indonesia,the length of coal unloading berth in the bidding document is compared with the optimized length that is approved in the detailed design,which shows otherwise that the execution of overseas projects,especially EPC projects,require not only the promotion of China standards and codes to the world,but also the thorough investigation and exact grasp of local market,China standards must combine with local conditions to reduce the project risk and gain higher economic benefit.%本文通过介绍印度尼西亚某电站码头工程卸煤码头泊位长度投标长度和施工图批准的泊位长度的优化对比，从侧面来说明在国外实施项目，尤其是EPC项目，不仅要将中国的规范和标准推向世界，更需要彻底调查和准确掌握当地市场情况，将中国规范结合当地实际情况来降低实施项目的风险并获得较好的经济效益。
Institute of Scientific and Technical Information of China (English)
赵春来; 马心坦; 郭志军
2011-01-01
在声屏障声学设计和测量规范的基础上,分析公路交通线声源对受声点声级的影响,提出线声源有效长度的概念.综合考虑位置,高度,长度等因素对声屏障降噪性及经济性的影响,建立以经济性为目标函数,降噪要求为约束条件的数学模型,运用MATLAB软件进行优化设计.根据公路交通噪声1/3倍频程谱分析插入损失,使结果更精确.通过算例对比,验证考虑线声源有效长度的优化方案在经济性和降噪性方面的优越性.%Based on the specifications of survey and design of noise barriers, the effects of the linear acoustic source of highway traffic on the noise level at the barrier are analyzed.The concept of effective length of linear sound source is proposed.Considering the impact of its position, height and length on the cost and noise reduction effect of the sound barrier, a mathematical model is set up with the cost of the noise barrier as an objective function and noise reduction as acoustic constrains.The MATLAB software is used for optimal design.The third-octave band of a representative spectrum is used to calculate the insertion loss, which makes the result more accurate.This method of design, considering the effective length of linear sound source, is proved to be superior in the aspects of economy and noise reduction.
A COMBINATORIAL APPROACH TO THE OXIDATION RESISTANCE OF(Ti,Al)N AND Ti-Al-Si-N HARD COATINGS
Institute of Scientific and Technical Information of China (English)
R.Cremer; D.Neuschütz
2002-01-01
The increasing complexity of modern functional materials leads to the demand of acost efficient tool for the development of new products. One possible approach to thisquestion is the adaptation of combinatorial methods to the specific requirements of ma-terials industry. These methods, originally developed for the pharmaceutical industry,have recently been applied to the screening of superconductive, magnetoresistant andphotoluminescent materials. The principle of these combinatorial approaches is thedeposition of large materials libraries in one process combined with fast methods forthe determination of the resulting properties. In this paper, the deposition and charac-terization of laterally graded materials libraries (composition spread) is presented. Thefilms have been deposited by reactive magnetron sputtering, using two or three metallictargets at a low angle to the substrate surface as well as a system of apertures. Toillustrate the advantages of combinatorial approaches for the development of advancedmaterials, the multicomponent metastable hardcoatings (Ti, Al)N and Ti-Al-Si-N arediscussed with special emphasis on the relations between structure and composition onthe one hand and the oxidation resistance of these coatings on the other. The resultsillustrate that the composition spread approach is a powerful and cost efficient tool forthe development and optimization of new multicomponent functional materials.
Optimal Decision of Quality and Warranty Length and Its Supply Chain Performance%质量和包修期限的优化决策及其供应链绩效
Institute of Scientific and Technical Information of China (English)
张汉江; 雷慧娟; 赖明勇
2015-01-01
The paper, from the perspective of the interaction of upstream and downstream of the supply chain, ap⁃plies the game theory to analyze the impact of warranty length commitment and quality improvement effort in house⁃hold electrical appliance industry on the overall performance of the supply chain and its optimal equilibrium out⁃come. Based on the qualitative and quantitative analyses of the impact of quality improvement effort and warranty length on market demand and enterprise cost,the paper builds three related Stackelberg game models respectively, which are supply chain strategic models, and calculates the corresponding optimal level of quality, commitment to warranty length,the price strategy of wholesalers as well as the best pricing strategy of retailers. By comparing the changes of corporate profits in the above three different contexts,the paper gains some suggestions which may con⁃tribute to corporate management decisions.%文章从上下游互动的角度采用博弈论的理论方法分析研究了家电行业中包修期限承诺和质量提升努力对供应链整体绩效的影响及其最优的均衡结果。在质量提升努力和包修期限长短对市场需求和企业成本变化影响的定性定量分析的基础上分别建立了三个彼此相关的供应链策略互动的斯坦克伯格博弈模型，分别求出了制造商决策的最优质量水平、承诺包修期限和批发价格策略，以及零售商的最优价格策略，通过比较上述三种不同情形下企业利润的变化得到了一些可能有助于企业经营管理决策的建议。
Simultaneous Disulfide and Boronic Acid Ester Exchange in Dynamic Combinatorial Libraries
DEFF Research Database (Denmark)
Diemer, Sanna L.; Kristensen, Morten; Rasmussen, Brian
2015-01-01
Dynamic combinatorial chemistry has emerged as a promising tool for the discovery of complex receptors in supramolecular chemistry. At the heart of dynamic combinatorial chemistry are the reversible reactions that enable the exchange of building blocks between library members in dynamic combinato......Dynamic combinatorial chemistry has emerged as a promising tool for the discovery of complex receptors in supramolecular chemistry. At the heart of dynamic combinatorial chemistry are the reversible reactions that enable the exchange of building blocks between library members in dynamic...... combinatorial libraries (DCLs) ensuring thermodynamic control over the system. If more than one reversible reaction operates in a single dynamic combinatorial library, the complexity of the system increases dramatically, and so does its possible applications. One can imagine two reversible reactions...... that operate simultaneously or two reversible reactions that operate independently. Both these scenarios have advantages and disadvantages. In this contribution, we show how disulfide exchange and boronic ester transesterification can function simultaneous in dynamic combinatorial libraries under appropriate...
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
The genome length is a fundamental feature of a species. This note outlined the general concept and estimation method of the physical and genetic length. Some formulae for estimating the genetic length were derived in detail. As examples, the genome genetic length of Pinus pinaster Ait. and the genetic length of chromosome Ⅵ of Oryza sativa L. were estimated from partial linkage data.
EDITORIAL: Combinatorial and High-Throughput Materials Research
Potyrailo, Radislav A.; Takeuchi, Ichiro
2005-01-01
The success of combinatorial and high-throughput methodologies relies greatly on the availability of various characterization tools with new and improved capabilities [1]. Indeed, how useful can a combinatorial library of 250, 400, 25 000 or 2 000 000 compounds be [2-5] if one is unable to characterize its properties of interest fairly quickly? How useful can a set of thousands of spectra or chromatograms be if one is unable to analyse them in a timely manner? For these reasons, the development of new approaches for materials characterization is one of the most active areas in combinatorial materials science. The importance of this aspect of research in the field has been discussed in numerous conferences including the Pittsburgh Conferences, the American Chemical Society Meetings, the American Physical Society Meetings, the Materials Research Society Symposia and various Gordon Research Conferences. Naturally, the development of new measurement instrumentation attracts the attention not only of practitioners of combinatorial materials science but also of those who design new software for data manipulation and mining. Experimental designs of combinatorial libraries are pursued with available and realistic synthetic and characterization capabilities in mind. It is becoming increasingly critical to link the design of new equipment for high-throughput parallel materials synthesis with integrated measurement tools in order to enhance the efficacy of the overall experimental strategy. We have received an overwhelming response to our proposal and call for papers for this Special Issue on Combinatorial Materials Science. The papers in this issue of Measurement Science and Technology are a very timely collection that captures the state of modern combinatorial materials science. They demonstrate the significant advances that are taking place in the field. In some cases, characterization tools are now being operated in the factory mode. At the same time, major challenges
Directory of Open Access Journals (Sweden)
Dikant F.
2016-12-01
Full Text Available Combinatorial library of novel benzenesulfonamides was docked (Schrodinger Glide into mycobacterial carbonic anhydrase (mtCA II and human (hCA II isoforms with an aim to find drug candidates with selective activity on mtCA II. The predicted selectivity was calculated based on optimized MM-GBSA free energies for ligand enzyme interactions. Selectivity, LogP (o/w and interaction energy were used to calculate the selection index which determined the subset of best scoring molecules selected for further evaluation. Structure-activity relationship was found for fragment subsets, showing us the possible way regarding how to influence lipophilicity without affecting ligand-enzyme binding properties.
Kirousis, Lefteris; Ortiz-Gracia, Luis; Serna, Maria
2017-01-01
This book is divided into two parts, the first of which seeks to connect the phase transitions of various disciplines, including game theory, and to explore the synergies between statistical physics and combinatorics. Phase Transitions has been an active multidisciplinary field of research, bringing together physicists, computer scientists and mathematicians. The main research theme explores how atomic agents that act locally and microscopically lead to discontinuous macroscopic changes. Adopting this perspective has proven to be especially useful in studying the evolution of random and usually complex or large combinatorial objects (like networks or logic formulas) with respect to discontinuous changes in global parameters like connectivity, satisfiability etc. There is, of course, an obvious strategic element in the formation of a transition: the atomic agents “selfishly” seek to optimize a local parameter. However, up to now this game-theoretic aspect of abrupt, locally triggered changes had not been e...
A multi-objective stochastic approach to combinatorial technology space exploration
Patel, Chirag B.
Historically, aerospace development programs have frequently been marked by performance shortfalls, cost growth, and schedule slippage. New technologies included in systems are considered to be one of the major sources of this programmatic risk. Decisions regarding the choice of technologies to include in a design are therefore crucial for a successful development program. This problem of technology selection is a challenging exercise in multi-objective decision making. The complexity of this selection problem is compounded by the geometric growth of the combinatorial space with the number of technologies being considered and the uncertainties inherent in the knowledge of the technological attributes. These problems are not typically addressed in the selection methods employed in common practice. Consequently, a method is desired to aid the selection of technologies for complex systems design with consideration of the combinatorial complexity, multi-dimensionality, and the presence of uncertainties. Several categories of techniques are explored to address the shortcomings of current approaches and to realize the goal of an efficient and effective combinatorial technology space exploration method. For the multi-objective decision making, a posteriori preference articulation is implemented. To realize this, a stochastic algorithm for Pareto optimization is formulated based on the concepts of SPEA2. Techniques to address the uncertain nature of technology impact on the system are also examined. Monte Carlo simulations using the surrogate models are used for uncertainty quantification. The concepts of graph theory are used for modeling and analyzing compatibility constraints among technologies and assessing their impact on the technology combinatorial space. The overall decision making approach is enabled by the application of an uncertainty quantification technique under the framework of an efficient probabilistic Pareto optimization algorithm. As a result, multiple
Multi-line split DNA synthesis: a novel combinatorial method to make high quality peptide libraries
Directory of Open Access Journals (Sweden)
Ueno Shingo
2004-09-01
Full Text Available Abstract Background We developed a method to make a various high quality random peptide libraries for evolutionary protein engineering based on a combinatorial DNA synthesis. Results A split synthesis in codon units was performed with mixtures of bases optimally designed by using a Genetic Algorithm program. It required only standard DNA synthetic reagents and standard DNA synthesizers in three lines. This multi-line split DNA synthesis (MLSDS is simply realized by adding a mix-and-split process to normal DNA synthesis protocol. Superiority of MLSDS method over other methods was shown. We demonstrated the synthesis of oligonucleotide libraries with 1016 diversity, and the construction of a library with random sequence coding 120 amino acids containing few stop codons. Conclusions Owing to the flexibility of the MLSDS method, it will be able to design various "rational" libraries by using bioinformatics databases.
Directory of Open Access Journals (Sweden)
Tobias Buer
2010-10-01
Full Text Available The procurement of transportation services via large-scale combinatorial auctions involves a couple of complex decisions whose outcome highly influences the performance of the tender process. This paper examines the shipper's task of selecting a subset of the submitted bids which efficiently trades off total procurement cost against expected carrier performance. To solve this bi-objective winner determination problem, we propose a Pareto-based greedy randomized adaptive search procedure (GRASP. As a post-optimizer we use a path relinking procedure which is hybridized with branch-and-bound. Several variants of this algorithm are evaluated by means of artificial test instances which comply with important real-world characteristics. The two best variants prove superior to a previously published Pareto-based evolutionary algorithm.
Bicker, Kevin L.; Sun, Jing; Lavigne, John J.; Thompson, Paul R.
2011-01-01
Aberrant glycosylation of cell membrane and secreted glycoproteins is a hallmark of various disease states, including cancer. The natural lectins currently used in the recognition of these glycoproteins are costly, difficult to produce, and unstable towards rigorous use. Herein we describe the design and synthesis of several boronic acid functionalized peptide-based synthetic lectin (SL) libraries, as well as the optimized methodology for obtaining peptide sequences of these SLs. SL libraries were subsequently used to identify SLs with as high as 5-fold selectivity for various glycoproteins. SLs will inevitably find a role in cancer diagnositics, given that they do not suffer from the drawbacks of natural lectins and that the combinatorial nature of these libraries allows for the identification of an SL for nearly any glycosylated biomolecule. PMID:21405093
Institute of Scientific and Technical Information of China (English)
YUAN; Yiran(袁益让)
2002-01-01
For combinatorial system of multilayer dynamics of fluids in porous media, the second order and first order upwind finite difference fractional steps schemes applicable to parallel arithmetic are put forward and two-dimensional and three-dimensional schemes are used to form a complete set. Some techniques,such as implicit-explicit difference scheme, calculus of variations, multiplicative commutation rule of difference operators, decomposition of high order difference operators and prior estimates, are adopted. Optimal order estimates in L2 norm are derived to determine the error in the second order approximate solution. This method has already been applied to the numerical simulation of migration-accumulation of oil resources.
Parsing Combinatory Categorial Grammar with Answer Set Programming: Preliminary Report
Lierler, Yuliya
2011-01-01
Combinatory categorial grammar (CCG) is a grammar formalism used for natural language parsing. CCG assigns structured lexical categories to words and uses a small set of combinatory rules to combine these categories to parse a sentence. In this work we propose and implement a new approach to CCG parsing that relies on a prominent knowledge representation formalism, answer set programming (ASP) - a declarative programming paradigm. We formulate the task of CCG parsing as a planning problem and use an ASP computational tool to compute solutions that correspond to valid parses. Compared to other approaches, there is no need to implement a specific parsing algorithm using such a declarative method. Our approach aims at producing all semantically distinct parse trees for a given sentence. From this goal, normalization and efficiency issues arise, and we deal with them by combining and extending existing strategies. We have implemented a CCG parsing tool kit - AspCcgTk - that uses ASP as its main computational mean...
Laguerre-type derivatives: Dobinski relations and combinatorial identities
Penson, K A; Horzela, A; Solomon, A I; Duchamp, G H E
2009-01-01
We consider properties of the operators D(r,M)=a^r(a^\\dag a)^M (which we call generalized Laguerre-type derivatives), with r=1,2,..., M=0,1,..., where a and a^\\dag are boson annihilation and creation operators respectively, satisfying [a,a^\\dag]=1. We obtain explicit formulas for the normally ordered form of arbitrary Taylor-expandable functions of D(r,M) with the help of an operator relation which generalizes the Dobinski formula. Coherent state expectation values of certain operator functions of D(r,M) turn out to be generating functions of combinatorial numbers. In many cases the corresponding combinatorial structures can be explicitly identified.
Combinatorial Gene Regulation through Kinetic Control of the Transcription Cycle.
Scholes, Clarissa; DePace, Angela H; Sánchez, Álvaro
2017-01-25
Cells decide when, where, and to what level to express their genes by "computing" information from transcription factors (TFs) binding to regulatory DNA. How is the information contained in multiple TF-binding sites integrated to dictate the rate of transcription? The dominant conceptual and quantitative model is that TFs combinatorially recruit one another and RNA polymerase to the promoter by direct physical interactions. Here, we develop a quantitative framework to explore kinetic control, an alternative model in which combinatorial gene regulation can result from TFs working on different kinetic steps of the transcription cycle. Kinetic control can generate a wide range of analog and Boolean computations without requiring the input TFs to be simultaneously bound to regulatory DNA. We propose experiments that will illuminate the role of kinetic control in transcription and discuss implications for deciphering the cis-regulatory "code."
Quasi-combinatorial energy landscapes for nanoalloy structure optimisation.
Schebarchov, D; Wales, D J
2015-11-14
We formulate nanoalloy structure prediction as a mixed-variable optimisation problem, where the homotops can be associated with an effective, quasi-combinatorial energy landscape in permutation space. We survey this effective landscape for a representative set of binary systems modelled by the Gupta potential. In segregating systems with small lattice mismatch, we find that homotops have a relatively straightforward landscape with few local optima - a scenario well-suited for local (combinatorial) optimisation techniques that scale quadratically with system size. Combining these techniques with multiple local-neighbourhood structures yields a search for multiminima, and we demonstrate that generalised basin-hopping with a metropolis acceptance criterion in the space of multiminima can then be effective for global optimisation of binary and ternary nanoalloys.
An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man
Ravasi, Timothy
2010-03-01
Combinatorial interactions among transcription factors are critical to directing tissue-specific gene expression. To build a global atlas of these combinations, we have screened for physical interactions among the majority of human and mouse DNA-binding transcription factors (TFs). The complete networks contain 762 human and 877 mouse interactions. Analysis of the networks reveals that highly connected TFs are broadly expressed across tissues, and that roughly half of the measured interactions are conserved between mouse and human. The data highlight the importance of TF combinations for determining cell fate, and they lead to the identification of a SMAD3/FLI1 complex expressed during development of immunity. The availability of large TF combinatorial networks in both human and mouse will provide many opportunities to study gene regulation, tissue differentiation, and mammalian evolution.
Institute of Scientific and Technical Information of China (English)
陈星明; 肖正学; 谭诚; 尹轶东
2012-01-01
Achieve higher efficiency is a aim of mining enterprises on the basis of safety produce, choice of the blasting method is an important restraining factor about mining costs. The deficiencies of medium-length hole blasting in small-scale and opencast quarry of Mianyang area were analyzed and pointed out by detailed survey. The suitable method of medium-length hole blasting in small-scale and opencast quarry of Mianyang area were designed according to deposit condition of mine and production status. It achieved good results on safe production and economic efficiency by carrying out the design. The optimization design can promote and improve small Small-scale and opencast quarry safety in production and economy efficiency.%钻孔爆破方式的选择是采矿成本高低的一个重要制约因素:通过调研绵阳地区部分小型露天采石场使用的中深孔爆破的方案,分析并指出其在爆破质量、生产安全性能和效率方面存在的不足之处,根据矿体赋存条件和实际生产状况对该中深孔爆破方案进行了重新设计,并进行了矿山现场实践,在安全生产和经济效果方面取得了良好的效果.研究成果可用于小型采石场.
Combinatorial Solid-Phase Synthesis of Balanol Analogues
DEFF Research Database (Denmark)
Nielsen, John; Lyngsø, Lars Ole
1996-01-01
The natural product balanol has served as a template for the design and synthesis of a combinatorial library using solid-phase chemistry. Using a retrosynthetic analysis, the structural analogues have been assembled from three relatively accessible building blocks. The solid-phase chemistry inclu...... including MSNT-mediated esterification of both support-bound alcohols and carboxylic acids has been implemented successfully. Copyright (C) 1996 Elsevier Science Ltd....
Combinatorial Solid-Phase Synthesis of Balanol Analogues
DEFF Research Database (Denmark)
Nielsen, John; Lyngsø, Lars Ole
1996-01-01
The natural product balanol has served as a template for the design and synthesis of a combinatorial library using solid-phase chemistry. Using a retrosynthetic analysis, the structural analogues have been assembled from three relatively accessible building blocks. The solid-phase chemistry inclu...... including MSNT-mediated esterification of both support-bound alcohols and carboxylic acids has been implemented successfully. Copyright (C) 1996 Elsevier Science Ltd....
Immobilized OBOC combinatorial bead array to facilitate multiplicative screening
Xiao, Wenwu; Bononi, Fernanda C.; Townsend, Jared; Li, Yuanpei; Liu, Ruiwu; Lam, Kit S.
2013-01-01
One-bead-one-compound (OBOC) combinatorial library screening has been broadly utilized for the last two decades to identify small molecules, peptides or peptidomimetics targeting variable screening probes such as cell surface receptors, bacteria, protein kinases, phosphatases, proteases etc. In previous screening methods, library beads were suspended in solution and screened against one single probe. Only the positive beads were tracked and isolated for additional screens and finally selected...
The evolution of combinatorial gene regulation in fungi.
Tuch, Brian B.; Galgoczy, David J.; Hernday, Aaron D.; Hao Li; Johnson, Alexander D.
2008-01-01
It is widely suspected that gene regulatory networks are highly plastic. The rapid turnover of transcription factor binding sites has been predicted on theoretical grounds and has been experimentally demonstrated in closely related species. We combined experimental approaches with comparative genomics to focus on the role of combinatorial control in the evolution of a large transcriptional circuit in the fungal lineage. Our study centers on Mcm1, a transcriptional regulator that, in combinati...
A Combinatorial interpretation of Hofstadter's G-sequence
Rahman, Mustazee
2011-01-01
We give a combinatorial interpretation of a classical meta-Fibonacci sequence defined by G(n) = n - G(G(n-1)) with the initial condition G(1) = 1, which appears in Hofstadter's 'Godel, Escher, Bach: An Eternal Golden Braid'. The interpretation is in terms of an infinite labelled tree. We then show a few corollaries about the behaviour of the sequence G(n) directly from the interpretation.
Institute of Scientific and Technical Information of China (English)
曾晓晶; 同登科
2011-01-01
针对油藏中分支水平井的稳态渗流问题,基于渗流力学理论,采用全三维方法,导出了油藏稳态渗流与分支水平井井筒流的耦合模型.用改进的Su方法以及一种新方法计算了裸眼完井分支水平井井筒内的压降,分析和比较了井筒内压力和采油指的分布情况；同时,给出了考虑经济因素的分支水平井水平段最优长度的计算方法.结果表明,分支水平井的单个分支内的流动况和水平井近似；由于摩擦因素的影响,分支水平井的水平分支不是越长越好,而是有一个最优值.这些结论可用于实际油藏中支水平井的设计和产能预测.%In terms of the time-invariant seepage of multi-lateral horizontal wells in oil reservoirs, a coupled model of the time-invariant seepage in reservoirs and the wellbore flow in multi-lateral horizontal wells was deduced with the full 3D analytical method based on the filtration mechanic theory. The pressure drop in barefoot completion multi-lateral horizontal wellbores was calculated using the improved Su method and a new approach, and distributions of pressure and productive indices in wellbores were analyzed and compared. At the same time, a computing method with the consideration of economic factors was proposed to optimize the length of the horizontal section for multi-lateral horizontal wells. The results derived from calculations and analyses of some real cases indicated that the flowing status within an individual branch of multi-lateral horizontal wells was similar to that in horizontal wells, the length of lateral branches of multi-lateral horizontal wells is not the longer, the better, but instead, it has an optimal value due to the friction effect. These conclusions are available for designing multi-lateral horizontal wells and forecasting the productivity of this kind of wells.
Combinatorial study of ceramic tape-casting slurries.
Liu, Zhifu; Wang, Yiling; Li, Yongxiang
2012-03-12
Ceramic tape-casting slurries are complex systems composed of ceramic powder, solvent, and a number of organic components. Conventionally, the development of ceramic tape-casting slurries is time-consuming and of low efficiency. In this work, combinatorial approaches were applied to screen the ethanol and ethyl-acetate binary solvent based slurry for ceramic green tape-casting. The combinatorial libraries were designed considering the variation of the amount of PVB (Poly vinyl-butyral) binder, polyethylene-400, and butyl-benzyl-phthalate plasticizers, and glyceryl triacetate dispersant. A parallel magnetic stirring process was used to make the combinatorial slurry library. The properties mapping of the slurry library was obtained by investigating the sedimentation and rheological characteristics of the slurries. The slurry composition was refined by scaling up the experiments and comparing the microstructure, mechanical property, and sintering behavior of green tapes made from the selected slurries. Finally, a kind of ethanol-ethyl acetate binary solvent based slurry system suitable for making X7R dielectric ceramic green tapes was achieved.
Controlling Combinatorial Complexity in Software and Malware Behavior Computation
Energy Technology Data Exchange (ETDEWEB)
Pleszkoch, Mark G [ORNL; Linger, Richard C [ORNL
2015-01-01
Virtually all software is out of intellectual control in that no one knows its full behavior. Software Behavior Computation (SBC) is a new technology for understanding everything software does. SBC applies the mathematics of denotational semantics implemented by function composition in Functional Trace Tables (FTTs) to compute the behavior of programs, expressed as disjoint cases of conditional concurrent assignments. In some circumstances, combinatorial explosions in the number of cases can occur when calculating the behavior of sequences of multiple branching structures. This paper describes computational methods that avoid combinatorial explosions. The predicates that control branching structures such as ifthenelses can be organized into three categories: 1) Independent, resulting in no behavior case explosion, 2) Coordinated, resulting in two behavior cases, or 3) Goaloriented, with potential exponential growth in the number of cases. Traditional FTT-based behavior computation can be augmented by two additional computational methods, namely, Single-Value Function Abstractions (SVFAs) and, introduced in this paper, Relational Trace Tables (RTTs). These methods can be applied to the three predicate categories to avoid combinatorial growth in behavior cases while maintaining mathematical correctness.
Hybrid Genetic Algorithm with PSO Effect for Combinatorial Optimisation Problems
Directory of Open Access Journals (Sweden)
M. H. Mehta
2012-12-01
Full Text Available In engineering field, many problems are hard to solve in some definite interval of time. These problems known as “combinatorial optimisation problems” are of the category NP. These problems are easy to solve in some polynomial time when input size is small but as input size grows problems become toughest to solve in some definite interval of time. Long known conventional methods are not able to solve the problems and thus proper heuristics is necessary. Evolutionary algorithms based on behaviours of different animals and species have been invented and studied for this purpose. Genetic Algorithm is considered a powerful algorithm for solving combinatorial optimisation problems. Genetic algorithms work on these problems mimicking the human genetics. It follows principle of “survival of the fittest” kind of strategy. Particle swarm optimisation is a new evolutionary approach that copies behaviour of swarm in nature. However, neither traditional genetic algorithms nor particle swarm optimisation alone has been completely successful for solving combinatorial optimisation problems. Here a hybrid algorithm is proposed in which strengths of both algorithms are merged and performance of proposed algorithm is compared with simple genetic algorithm. Results show that proposed algorithm works definitely better than the simple genetic algorithm.
Popova, Blagovesta; Schubert, Steffen; Bulla, Ingo; Buchwald, Daniela; Kramer, Wilfried
2015-01-01
A major challenge in gene library generation is to guarantee a large functional size and diversity that significantly increases the chances of selecting different functional protein variants. The use of trinucleotides mixtures for controlled randomization results in superior library diversity and offers the ability to specify the type and distribution of the amino acids at each position. Here we describe the generation of a high diversity gene library using tHisF of the hyperthermophile Thermotoga maritima as a scaffold. Combining various rational criteria with contingency, we targeted 26 selected codons of the thisF gene sequence for randomization at a controlled level. We have developed a novel method of creating full-length gene libraries by combinatorial assembly of smaller sub-libraries. Full-length libraries of high diversity can easily be assembled on demand from smaller and much less diverse sub-libraries, which circumvent the notoriously troublesome long-term archivation and repeated proliferation of high diversity ensembles of phages or plasmids. We developed a generally applicable software tool for sequence analysis of mutated gene sequences that provides efficient assistance for analysis of library diversity. Finally, practical utility of the library was demonstrated in principle by assessment of the conformational stability of library members and isolating protein variants with HisF activity from it. Our approach integrates a number of features of nucleic acids synthetic chemistry, biochemistry and molecular genetics to a coherent, flexible and robust method of combinatorial gene synthesis.
Directory of Open Access Journals (Sweden)
Blagovesta Popova
Full Text Available A major challenge in gene library generation is to guarantee a large functional size and diversity that significantly increases the chances of selecting different functional protein variants. The use of trinucleotides mixtures for controlled randomization results in superior library diversity and offers the ability to specify the type and distribution of the amino acids at each position. Here we describe the generation of a high diversity gene library using tHisF of the hyperthermophile Thermotoga maritima as a scaffold. Combining various rational criteria with contingency, we targeted 26 selected codons of the thisF gene sequence for randomization at a controlled level. We have developed a novel method of creating full-length gene libraries by combinatorial assembly of smaller sub-libraries. Full-length libraries of high diversity can easily be assembled on demand from smaller and much less diverse sub-libraries, which circumvent the notoriously troublesome long-term archivation and repeated proliferation of high diversity ensembles of phages or plasmids. We developed a generally applicable software tool for sequence analysis of mutated gene sequences that provides efficient assistance for analysis of library diversity. Finally, practical utility of the library was demonstrated in principle by assessment of the conformational stability of library members and isolating protein variants with HisF activity from it. Our approach integrates a number of features of nucleic acids synthetic chemistry, biochemistry and molecular genetics to a coherent, flexible and robust method of combinatorial gene synthesis.
Combinatorial Gene Regulation Using Auto-Regulation
Hermsen, Rutger; Ursem, Bas; ten Wolde, Pieter Rein
2010-01-01
As many as 59% of the transcription factors in Escherichia coli regulate the transcription rate of their own genes. This suggests that auto-regulation has one or more important functions. Here, one possible function is studied. Often the transcription rate of an auto-regulator is also controlled by additional transcription factors. In these cases, the way the expression of the auto-regulator responds to changes in the concentrations of the “input” regulators (the response function) is obviously affected by the auto-regulation. We suggest that, conversely, auto-regulation may be used to optimize this response function. To test this hypothesis, we use an evolutionary algorithm and a chemical–physical model of transcription regulation to design model cis-regulatory constructs with predefined response functions. In these simulations, auto-regulation can evolve if this provides a functional benefit. When selecting for a series of elementary response functions—Boolean logic gates and linear responses—the cis-regulatory regions resulting from the simulations indeed often exploit auto-regulation. Surprisingly, the resulting constructs use auto-activation rather than auto-repression. Several design principles show up repeatedly in the simulation results. They demonstrate how auto-activation can be used to generate sharp, switch-like activation and repression circuits and how linearly decreasing response functions can be obtained. Auto-repression, on the other hand, resulted only when a high response speed or a suppression of intrinsic noise was also selected for. The results suggest that, while auto-repression may primarily be valuable to improve the dynamical properties of regulatory circuits, auto-activation is likely to evolve even when selection acts on the shape of response function only. PMID:20548950
Hybrid constraint programming and metaheuristic methods for large scale optimization problems
2011-01-01
This work presents hybrid Constraint Programming (CP) and metaheuristic methods for the solution of Large Scale Optimization Problems; it aims at integrating concepts and mechanisms from the metaheuristic methods to a CP-based tree search environment in order to exploit the advantages of both approaches. The modeling and solution of large scale combinatorial optimization problem is a topic which has arisen the interest of many researcherers in the Operations Research field; combinatori...
Optimization by GRASP greedy randomized adaptive search procedures
Resende, Mauricio G C
2016-01-01
This is the first book to cover GRASP (Greedy Randomized Adaptive Search Procedures), a metaheuristic that has enjoyed wide success in practice with a broad range of applications to real-world combinatorial optimization problems. The state-of-the-art coverage and carefully crafted pedagogical style lends this book highly accessible as an introductory text not only to GRASP, but also to combinatorial optimization, greedy algorithms, local search, and path-relinking, as well as to heuristics and metaheuristics, in general. The focus is on algorithmic and computational aspects of applied optimization with GRASP with emphasis given to the end-user, providing sufficient information on the broad spectrum of advances in applied optimization with GRASP. For the more advanced reader, chapters on hybridization with path-relinking and parallel and continuous GRASP present these topics in a clear and concise fashion. Additionally, the book offers a very complete annotated bibliography of GRASP and combinatorial optimizat...
Swain, Basudev; Hong, Myung Hwan; Kang, Lee-Seung; Lee, Chan Gi
2016-11-01
With the use of a microfluidic-assisted combinatorial reactor, the synthesis of CdSe quantum dots was optimized by varying one parameter at a time, and the isothermal growth kinetics of CdSe quantum dots using various models was analyzed. To understand precisely the nucleation and growth characteristics of CdSe quantum dots (QDs), we synthesized the CdSe QDs using various experimental conditions. Different model equations, like acceleratory growth-time curves, sigmoidal growth-time curves or Johnson-Mehl-Avrami-Kolmogorov (JMAK), acceleratory growthtime curves based on diffusion, geometric model growth-time curves, and nth order growth-time curves were fitted. Among all growth models, the JMAK model with α = 1 - {e^{ - {{(kt)}^n}}}, and n = 1 was the best fitting model with the MATLAB interactive curve-fitting procedure were used. Errors associated with the best-fitting model and statistics for the goodness of fit were analyzed. Most of the models were not as good as the other than the proposed model. The errors associated with the proposed model were minimal, and the growth kinetics and other associated statistical factors are very similar, for all the variables investigated. The minimal error associated with the reproducibility and the similar data for growth kinetics for all studied parameters indicated that microfluidic-assisted combinatorial synthesis can be used in the industrial production of QDs. By using the proposed model to obtain an understanding of growth of QDs, their size and properties can be managed and simulated.
Nag, S; Banerjee, R; Fraser, H L
2007-05-01
The new generation of metallic biomaterials for prosthesis implantation (orthopedic and dental) typically have a Ti base with fully biocompatible alloying additions such as Nb, Ta, Zr, Mo, Fe and Sn. While the binary Ti-Ta and the ternary Ti-Nb-Ta systems are promising, the large composition space afforded by these systems offers tremendous scope in terms of alloy design via optimization of alloy composition and thermomechanical treatment. In the present paper a novel combinatorial approach has been developed for rapidly exploring the microstructural evolution and microstructure-microhardness (or elastic modulus) relationships in these systems. Using directed laser deposition, compositionally graded alloy samples have been fabricated and subsequently heat-treated to affect different microstructures in terms of the volume fraction and distribution of the alpha phase in the beta matrix as a function of composition. Subsequently, composition-specific indentation-based hardness and modulus information has been obtained from these graded samples, and the resulting data have been used to develop relationships between the composition, microstructure and mechanical properties. Such rapid combinatorial assessments can be very useful in optimizing not only the alloy composition but also the desired microstructure for achieving the best combination of properties for specific orthopedic or dental applications.
Ant Colony Optimization and Hypergraph Covering Problems
Pat, Ankit
2011-01-01
Ant Colony Optimization (ACO) is a very popular metaheuristic for solving computationally hard combinatorial optimization problems. Runtime analysis of ACO with respect to various pseudo-boolean functions and different graph based combinatorial optimization problems has been taken up in recent years. In this paper, we investigate the runtime behavior of an MMAS*(Max-Min Ant System) ACO algorithm on some well known hypergraph covering problems that are NP-Hard. In particular, we have addressed the Minimum Edge Cover problem, the Minimum Vertex Cover problem and the Maximum Weak- Independent Set problem. The influence of pheromone values and heuristic information on the running time is analysed. The results indicate that the heuristic information has greater impact towards improving the expected optimization time as compared to pheromone values. For certain instances of hypergraphs, we show that the MMAS* algorithm gives a constant order expected optimization time when the dominance of heuristic information is ...
Estimating meme fitness in adaptive memetic algorithms for combinatorial problems.
Smith, J E
2012-01-01
Among the most promising and active research areas in heuristic optimisation is the field of adaptive memetic algorithms (AMAs). These gain much of their reported robustness by adapting the probability with which each of a set of local improvement operators is applied, according to an estimate of their current value to the search process. This paper addresses the issue of how the current value should be estimated. Assuming the estimate occurs over several applications of a meme, we consider whether the extreme or mean improvements should be used, and whether this aggregation should be global, or local to some part of the solution space. To investigate these issues, we use the well-established COMA framework that coevolves the specification of a population of memes (representing different local search algorithms) alongside a population of candidate solutions to the problem at hand. Two very different memetic algorithms are considered: the first using adaptive operator pursuit to adjust the probabilities of applying a fixed set of memes, and a second which applies genetic operators to dynamically adapt and create memes and their functional definitions. For the latter, especially on combinatorial problems, credit assignment mechanisms based on historical records, or on notions of landscape locality, will have limited application, and it is necessary to estimate the value of a meme via some form of sampling. The results on a set of binary encoded combinatorial problems show that both methods are very effective, and that for some problems it is necessary to use thousands of variables in order to tease apart the differences between different reward schemes. However, for both memetic algorithms, a significant pattern emerges that reward based on mean improvement is better than that based on extreme improvement. This contradicts recent findings from adapting the parameters of operators involved in global evolutionary search. The results also show that local reward schemes
Combinatorial Hopf Algebras in Quantum Field Theory I
Figueroa, Héctor; Gracia-Bondía, José M.
This paper stands at the interface between combinatorial Hopf algebra theory and renormalization theory. Its plan is as follows: Sec. 1.1 is the introduction, and contains an elementary invitation to the subject as well. The rest of Sec. 1 is devoted to the basics of Hopf algebra theory and examples in ascending level of complexity. Section 2 turns around the all-important Faà di Bruno Hopf algebra. Section 2.1 contains a first, direct approach to it. Section 2.2 gives applications of the Faà di Bruno algebra to quantum field theory and Lagrange reversion. Section 2.3 rederives the related Connes-Moscovici algebras. In Sec. 3, we turn to the Connes-Kreimer Hopf algebras of Feynman graphs and, more generally, to incidence bialgebras. In Sec. 3.1, we describe the first. Then in Sec. 3.2, we give a simple derivation of (the properly combinatorial part of) Zimmermann's cancellation-free method, in its original diagrammatic form. In Sec. 3.3, general incidence algebras are introduced, and the Faà di Bruno bialgebras are described as incidence bialgebras. In Sec. 3.4, deeper lore on Rota's incidence algebras allows us to reinterpret Connes-Kreimer algebras in terms of distributive lattices. Next, the general algebraic-combinatorial proof of the cancellation-free formula for antipodes is ascertained. The structure results for commutative Hopf algebras are found in Sec. 4. An outlook section very briefly reviews the coalgebraic aspects of quantization and the Rota-Baxter map in renormalization.
Combinatorial antibody libraries: new advances, new immunological insights.
Lerner, Richard A
2016-08-01
Immunochemists have become quite proficient in engineering existing antibody molecules to control their pharmacological properties. However, in terms of generating new antibodies, the combinatorial antibody library has become a central feature of modern immunochemistry. These libraries are essentially an immune system in a test tube and enable the selection of antibodies without the constraints of whole animal or cell-based systems. This Review provides an overview of how antibody libraries are constructed and discusses what can be learnt from these synthetic systems. In particular, the Review focuses on new biological insights from antibody libraries - such as the concept of 'SOS antibodies' - and the growing use of intracellular antibodies to perturb cellular functions.
Combinatorial Yang-Baxter maps arising from the tetrahedron equation
Kuniba, A.
2016-10-01
We survey the matrix product solutions of the Yang-Baxter equation recently obtained from the tetrahedron equation. They form a family of quantum R-matrices of generalized quantum groups interpolating the symmetric tensor representations of U q ( A n-1 (1)) and the antisymmetric tensor representations of {U_{ - {q^{ - 1}}}}( {A_{n - 1}^{( 1 )}} ) . We show that at q = 0, they all reduce to the Yang-Baxter maps called combinatorial R-matrices and describe the latter by an explicit algorithm.
Proceedings of the 8th Nordic Combinatorial Conference
DEFF Research Database (Denmark)
Geil, Olav; Andersen, Lars Døvling
The Nordic Combinatorial Conferences were initiated in 1981 by mathematicians from Stavanger. Held approximately every three years since then, the conferences have been able to sustain the interest from combinatorialists all over the Nordic countries. In 2004 the 8th conference is held in Aalborg......, Denmark. We are pleased that so many people have chosen to attend, and that lectures were offered from more participants than we had originally reserved time for. We asked two mathematicians to give special lectures and are happy that both accepted immediately. Andries Brouwer from the Technical...
Learning Combinatorial Map Information from Permutations of Landmarks
2010-10-04
Learning Combinatorial Map Information from Permutations of Landmarks Benjamı́n Tovar ∗, Luigi Freda†, and Steven M. LaValle‡ Abstract This paper...is B. Tovar . This work was founded by NSF grant 0904501 (IIS robotics), DARPA SToMP grant HR0011-05-1-0008, and MURI/ONR grant N00014-09-1-1052. ∗B... Tovar is with the Dept. of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 602081, USA. email: b- tovar
Multifunctional combinatorial-designed nanoparticles for nucleic acid therapy
Amiji, Mansoor M.
2016-05-01
Recent advances in biomedical sciences, especially in the field of human genetics, is increasingly considered to facilitate a new frontier in development of novel disease-modifying therapeutics. One of major challenges in the development of nucleic acid therapeutics is efficient and specific delivery of the molecules to the target tissue and cell upon systemic administration. In this report, I discuss our strategy to develop combinatorial-designed multifunctional nanoparticle assemblies based on natural biocompatible and biodegradable polymers for nucleic acid delivery in: (1) overcoming tumor drug resistance and (2) genetic modulation of macrophage functional phenotype from M1 to M2 in treatment of inflammatory diseases.
Combinatorial polarization, code loops, and codes of high level
Directory of Open Access Journals (Sweden)
Petr Vojtěchovský
2004-07-01
Full Text Available We first find the combinatorial degree of any map f:VÃ¢Â†Â’F, where F is a finite field and V is a finite-dimensional vector space over F. We then simplify and generalize a certain construction, due to Chein and Goodaire, that was used in characterizing code loops as finite Moufang loops that possess at most two squares. The construction yields binary codes of high divisibility level with prescribed Hamming weights of intersections of codewords.
Applications of combinatorial matrix theory to Laplacian matrices of graphs
Molitierno, Jason J
2012-01-01
On the surface, matrix theory and graph theory seem like very different branches of mathematics. However, adjacency, Laplacian, and incidence matrices are commonly used to represent graphs, and many properties of matrices can give us useful information about the structure of graphs. Applications of Combinatorial Matrix Theory to Laplacian Matrices of Graphs is a compilation of many of the exciting results concerning Laplacian matrices developed since the mid 1970s by well-known mathematicians such as Fallat, Fiedler, Grone, Kirkland, Merris, Mohar, Neumann, Shader, Sunder, and more. The text i
Pricing in combinatorial double auction-based grid allocation model
Institute of Scientific and Technical Information of China (English)
LI Li; LIU Yuan-an; LIU Kai-ming; MA Xiao-lei; YANG Ming
2009-01-01
This article proposes a novel grid resource allocation model, in which the users and the grid service providers participate in the combinatorial double auction for the resource allocation. To obtain the detailed resource allocation status and the price information, a novel pricing algorithm is designed for the allocation model. Simulation results demonstrate that the proposed algorithm completes the resource allocation and pricing efficiently, and exhibits incentive compatible characteristic. Moreover,users with the higher average price and providers with the lower average price get compensation during the pricing process.
Yeast surface display for screening combinatorial polypeptide libraries.
Boder, E T; Wittrup, K D
1997-06-01
Display on the yeast cell wall is well suited for engineering mammalian cell-surface and secreted proteins (e.g., antibodies, receptors, cytokines) that require endoplasmic reticulum-specific post-translational processing for efficient folding and activity. C-terminal fusion to the Aga2p mating adhesion receptor of Saccharomyces cerevisiae has been used for the selection of scFv antibody fragments with threefold decreased antigen dissociation rate from a randomly mutated library. A eukaryotic host should alleviate expression biases present in bacterially propagated combinatorial libraries. Quantitative flow cytometric analysis enables fine discrimination of kinetic parameters for protein binding to soluble ligands.
Optimal evacuation routes on cruise ship in fire based on equivalent length%基于当量长度的游船火灾人员最优疏散路径
Institute of Scientific and Technical Information of China (English)
刘红; 罗旋
2012-01-01
In order to select a reasonable evacuation route to avoid or reduce injuries and deaths when the fire breaks out on cruise ship, the equivalent length is introduced to establish the cruise ship emergency evacuation model in case of fire. Dijkstra algorithm is adopted to get multiple shortest evacuation routes between the disaster area and the emergency exits, and the solutions are obtained by MATLAB. Cruise ship "Ocean Oasis" is selected to do the empirical research. In the case that fire in passenger cabin is known, the influences of path occupation and the expanding of fire on the optimal evacuation routes are discussed. The result shows that the evacuation model is of reliability.%为能够在游船发生火灾时选择合理的疏散路径,避免和减少人员伤亡,引入当量长度,建立火灾时游船应急疏散模型,选用最短路径算法得到火灾区域至各逃生出口的多条最优疏散路径,并利用MATLAB编程实现.选取“海洋绿洲”号游船进行实证研究,在客舱着火点位置确定的情况下分别考虑游船通道阻塞和火灾扩散对最优疏散路径的影响.研究结果表明,所建立的疏散模型是可靠的.
Measuring Thermodynamic Length
Energy Technology Data Exchange (ETDEWEB)
Crooks, Gavin E
2007-09-07
Thermodynamic length is a metric distance between equilibrium thermodynamic states. Among other interesting properties, this metric asymptotically bounds the dissipation induced by a finite time transformation of a thermodynamic system. It is also connected to the Jensen-Shannon divergence, Fisher information, and Rao's entropy differential metric. Therefore, thermodynamic length is of central interestin understanding matter out of equilibrium. In this Letter, we will consider how to denethermodynamic length for a small system described by equilibrium statistical mechanics and how to measure thermodynamic length within a computer simulation. Surprisingly, Bennett's classic acceptance ratio method for measuring free energy differences also measures thermodynamic length.
Ant Colony Optimization and the Minimum Cut Problem
DEFF Research Database (Denmark)
Kötzing, Timo; Lehre, Per Kristian; Neumann, Frank
2010-01-01
Ant Colony Optimization (ACO) is a powerful metaheuristic for solving combinatorial optimization problems. With this paper we contribute to the theoretical understanding of this kind of algorithm by investigating the classical minimum cut problem. An ACO algorithm similar to the one that was prov...
Optimization Techniques for Analysis of Biological and Social Networks
2012-03-28
systematic fashion under a unifying theoretical and algorithmic framework . Optimization, Complex Networks, Social Network Analysis, Computational...analyzing a new metaheuristic technique, variable objective search. 3. Experimentation and application: Implement the proposed algorithms, test and fine...exact solutions are presented. In [3], we introduce the variable objective search framework for combinatorial optimization. The method utilizes
Combinatorial development of antibacterial Zr-Cu-Al-Ag thin film metallic glasses
Liu, Yanhui; Padmanabhan, Jagannath; Cheung, Bettina; Liu, Jingbei; Chen, Zheng; Scanley, B. Ellen; Wesolowski, Donna; Pressley, Mariyah; Broadbridge, Christine C.; Altman, Sidney; Schwarz, Udo D.; Kyriakides, Themis R.; Schroers, Jan
2016-05-01
Metallic alloys are normally composed of multiple constituent elements in order to achieve integration of a plurality of properties required in technological applications. However, conventional alloy development paradigm, by sequential trial-and-error approach, requires completely unrelated strategies to optimize compositions out of a vast phase space, making alloy development time consuming and labor intensive. Here, we challenge the conventional paradigm by proposing a combinatorial strategy that enables parallel screening of a multitude of alloys. Utilizing a typical metallic glass forming alloy system Zr-Cu-Al-Ag as an example, we demonstrate how glass formation and antibacterial activity, two unrelated properties, can be simultaneously characterized and the optimal composition can be efficiently identified. We found that in the Zr-Cu-Al-Ag alloy system fully glassy phase can be obtained in a wide compositional range by co-sputtering, and antibacterial activity is strongly dependent on alloy compositions. Our results indicate that antibacterial activity is sensitive to Cu and Ag while essentially remains unchanged within a wide range of Zr and Al. The proposed strategy not only facilitates development of high-performing alloys, but also provides a tool to unveil the composition dependence of properties in a highly parallel fashion, which helps the development of new materials by design.
Kawashima, Kazuhiro; Okamoto, Yuji; Annayev, Orazmuhammet; Toyokura, Nobuo; Takahashi, Ryota; Lippmaa, Mikk; Itaka, Kenji; Suzuki, Yoshikazu; Matsuki, Nobuyuki; Koinuma, Hideomi
2017-01-01
As an extension of combinatorial molecular layer epitaxy via ablation of perovskite oxides by a pulsed excimer laser, we have developed a laser molecular beam epitaxy (MBE) system for parallel integration of nano-scaled thin films of organic-inorganic hybrid materials. A pulsed infrared (IR) semiconductor laser was adopted for thermal evaporation of organic halide (A-site: CH3NH3I) and inorganic halide (B-site: PbI2) powder targets to deposit repeated A/B bilayer films where the thickness of each layer was controlled on molecular layer scale by programming the evaporation IR laser pulse number, length, or power. The layer thickness was monitored with an in situ quartz crystal microbalance and calibrated against ex situ stylus profilometer measurements. A computer-controlled movable mask system enabled the deposition of combinatorial thin film libraries, where each library contains a vertically homogeneous film with spatially programmable A- and B-layer thicknesses. On the composition gradient film, a hole transport Spiro-OMeTAD layer was spin-coated and dried followed by the vacuum evaporation of Ag electrodes to form the solar cell. The preliminary cell performance was evaluated by measuring I-V characteristics at seven different positions on the 12.5 mm × 12.5 mm combinatorial library sample with seven 2 mm × 4 mm slits under a solar simulator irradiation. The combinatorial solar cell library clearly demonstrated that the energy conversion efficiency sharply changes from nearly zero to 10.2% as a function of the illumination area in the library. The exploration of deposition parameters for obtaining optimum performance could thus be greatly accelerated. Since the thickness ratio of PbI2 and CH3NH3I can be freely chosen along the shadow mask movement, these experiments show the potential of this system for high-throughput screening of optimum chemical composition in the binary film library and application to halide perovskite solar cell.
A Barcode-Free Combinatorial Screening Platform for Matrix Metalloproteinase Screening
Rane, Tushar D.; Zec, Helena C.; Wang, Tza-Huei
2014-01-01
Application of droplet microfluidics to combinatorial screening applications remains elusive because of the need for composition-identifying unique barcodes. Here we propose a barcode-free continuous flow droplet microfluidic platform to suit the requirements of combinatorial screening applications. We demonstrate robust and repeatable functioning of this platform with matrix metalloproteinase activity screening as a sample application.
Parallel detection of antigen-specific T cell responses by combinatorial encoding of MHC multimers
DEFF Research Database (Denmark)
Andersen, Rikke Sick; Kvistborg, Pia; Frøsig, Thomas Mørch;
2012-01-01
-dimensional combinatorial matrix, these eight fluorochromes are combined to generate 28 unique two-color codes. By the use of combinatorial encoding, a large number of different T cell populations can be detected in a single sample. The method can be used for T cell epitope mapping, and also for the monitoring of CD8...
A barcode-free combinatorial screening platform for matrix metalloproteinase screening.
Rane, Tushar D; Zec, Helena C; Wang, Tza-Huei
2015-02-03
Application of droplet microfluidics to combinatorial screening applications remains elusive because of the need for composition-identifying unique barcodes. Here we propose a barcode-free continuous flow droplet microfluidic platform to suit the requirements of combinatorial screening applications. We demonstrate robust and repeatable functioning of this platform with matrix metalloproteinase activity screening as a sample application.
Enumeration of Combinatorial Classes of Single Variable Complex Polynomial Vector Fields
DEFF Research Database (Denmark)
Dias, Kealey
A vector field in the space of degree d monic, centered single variable complex polynomial vector fields has a combinatorial structure which can be fully described by a combinatorial data set consisting of an equivalence relation and a marked subset on the integers mod 2d-2, satisfying certain...
Comparing winner determination algorithms for mixed multi-unit combinatorial auctions
Ottens, B.; Endriss, U.; Padgham, L.; Parkes, D.; Müller, J.; Parsons, S.
2008-01-01
Mixed multi-unit combinatorial auctions are combinatorial auctions in which the auctioneer and the bidders negotiate over transformations rather than over simple goods. By proposing a transformation a bidder is offering to produce a certain set of output goods after having received the specified inp
Combinatorial arrays and parallel screening for positive electrode discovery
Spong, A. D.; Vitins, G.; Guerin, S.; Hayden, B. E.; Russell, A. E.; Owen, John R.
Combinatorial techniques have been applied to the preparation and screening of positive electrode candidates for lithium batteries. This work describes the automated parallel synthesis of 64-electrode arrays using a Packard Multiprobe II liquid handling system. A cell was constructed with a single lithium reference-counter electrode and 64, three-millimeter-diameter working electrodes containing Li xMn 2O 4 active material, PVdF-HFP binder and carbon black as a conducting additive. Eight duplicate electrodes, each of eight respective compositions, were deposited on the array and the mass fraction of carbon was varied in steps from 1 to 25%. The results showed a rapid increase in capacity at the percolation limit of 3% for most cells. Some groups of nominally identical cells showed random variations in capacity, especially at low carbon loadings. The overall result is a demonstration of advantages of the combinatorial concept, which were time-saving and an improved statistical significance of the results compared with on-off experiments.
Combinatorial Hopf algebras in quantum field theory I
Figueroa, H; Figueroa, Hector; Gracia-Bondia, Jose M.
2004-01-01
This manuscript collects and expands for the most part a series of lectures on the interface between combinatorial Hopf algebra theory (CHAT) and renormalization theory, delivered by the second-named author in the framework of the joint mathematical physics seminar of the Universites d'Artois and Lille 1, from late January till mid-February 2003. The plan is as follows: Section 1 is the introduction, and Section 2 contains an elementary invitation to the subject. Sections 3-7 are devoted to the basics of Hopf algebra theory and examples, in ascending level of complexity. Section 8 contains a first, direct approach to the Faa di Bruno Hopf algebra. Section 9 gives applications of that to quantum field theory and Lagrange reversion. Section 10 rederives the Connes-Moscovici algebras. In Section 11 we turn to Hopf algebras of Feynman graphs. Then in Section 12 we give an extremely simple derivation of (the properly combinatorial part of) Zimmermann's method, in its original diagrammatic form. In Section 13 gener...
Device for preparing combinatorial libraries in powder metallurgy.
Yang, Shoufeng; Evans, Julian R G
2004-01-01
This paper describes a powder-metering, -mixing, and -dispensing mechanism that can be used as a method for producing large numbers of samples for metallurgical evaluation or electrical or mechanical testing from multicomponent metal and cermet powder systems. It is designed to make use of the same commercial powders that are used in powder metallurgy and, therefore, to produce samples that are faithful to the microstructure of finished products. The particle assemblies produced by the device could be consolidated by die pressing, isostatic pressing, laser sintering, or direct melting. The powder metering valve provides both on/off and flow rate control of dry powders in open capillaries using acoustic vibration. The valve is simple and involves no relative movement, avoiding seizure with fine powders. An orchestra of such valves can be arranged on a building platform to prepare multicomponent combinatorial libraries. As with many combinatorial devices, identification and evaluation of sources of mixing error as a function of sample size is mandatory. Such an analysis is presented.
On Range Searching in the Group Model and Combinatorial Discrepancy
DEFF Research Database (Denmark)
Larsen, Kasper Green
2011-01-01
In this paper we establish an intimate connection between dynamic range searching in the group model and combinatorial discrepancy. Our result states that, for a broad class of range searching data structures (including all known upper bounds), it must hold that $t_ut_q = Omega(disc^2/lg n)$ where...... $t_u$ is the worst case update time, $t_q$ the worst case query time and $disc$ is the combinatorial discrepancy of the range searching problem in question. This relation immediately implies a whole range of exceptionally high and near-tight lower bounds for all of the basic range searching problems....... We list a few of them in the following:begin{itemize}item For half space range searching in $d$-dimensional space, we get a lower bound of $t_u t_q = Omega(n^{1-1/d}/lg n)$. This comes within a $lg n lg lg n$ factor of the best known upper bound. item For orthogonal range searching in $d...
ON range searching in the group model and combinatorial discrepancy
DEFF Research Database (Denmark)
Larsen, Kasper Green
2014-01-01
In this paper we establish an intimate connection between dynamic range searching in the group model and combinatorial discrepancy. Our result states that, for a broad class of range searching data structures (including all known upper bounds), it must hold that $t_u t_q=\\Omega(\\mbox{disc}^2......)$, where $t_u$ is the worst case update time, $t_q$ is the worst case query time, and disc is the combinatorial discrepancy of the range searching problem in question. This relation immediately implies a whole range of exceptionally high and near-tight lower bounds for all of the basic range searching...... problems. We list a few of them in the following: (1) For $d$-dimensional halfspace range searching, we get a lower bound of $t_u t_q=\\Omega(n^{1-1/d})$. This comes within an lg lg $n$ factor of the best known upper bound. (2) For orthogonal range searching, we get a lower bound of $t_u t...
Single-Parameter Combinatorial Auctions with Partially Public Valuations
Goel, Gagan; Karande, Chinmay; Wang, Lei
We consider the problem of designing truthful auctions, when the bidders' valuations have a public and a private component. In particular, we consider combinatorial auctions where the valuation of an agent i for a set S of items can be expressed as v i f(S), where v i is a private single parameter of the agent, and the function f is publicly known. Our motivation behind studying this problem is two-fold: (a) Such valuation functions arise naturally in the case of ad-slots in broadcast media such as Television and Radio. For an ad shown in a set S of ad-slots, f(S) is, say, the number of unique viewers reached by the ad, and v i is the valuation per-unique-viewer. (b) From a theoretical point of view, this factorization of the valuation function simplifies the bidding language, and renders the combinatorial auction more amenable to better approximation factors. We present a general technique, based on maximal-in-range mechanisms, that converts any α-approximation non-truthful algorithm (α ≤ 1) for this problem into Ω(α/log{n}) and Ω(α)-approximate truthful mechanisms which run in polynomial time and quasi-polynomial time, respectively.
NIST Combinatorial Methods Center: Model for Industrial Outreach
Amis, Eric J.; Karim, Alamgir
2002-03-01
The measurements, standards, and test methods developed by NIST, in partnership with other organizations, often help unlock the potential of new discoveries and budding technologies. Combinatorial methods are a textbook example. These emerging tools can speed innovation in many fields - pharmaceuticals, chemistry, and, most recently, materials. In the diverse realm of materials, combinatorial methods hold promise for all classes, including metals, polymers, ceramics, and biomaterials. NIST has established the NCMC as a model for collaboration, in order to share expertise, facilities, resources, and information thereby reducing obstacles to participating in this fast-moving and instrument-intensive area. Although collaborations with multiple partners can be difficult, the goal is to foster cross-fertilization of ideas and research strategies, and to spur progress on many fronts by crossing boundaries of organizations, disciplines, and interests. Members have access to technical workshops, short courses, data libraries, and electronic bulletin boards; they can participate in non-proprietary focused projects; and they can enter into specific cooperative research and development agreements with controlled intellectual property.
Algebraic and combinatorial aspects of sandpile monoids on directed graphs
Chapman, Scott; Garcia, Rebecca; Malandro, Martin E; Smith, Ken W
2011-01-01
We study the abelian sandpile model on a finite directed graph. We begin by reviewing the necessary background material starting with the identification, by Babai and Toumpakari, of the sandpile group on a directed graph as the minimal ideal of its sandpile monoid, and continuing through some of their recent results concerning the connections between the idempotent structure of a sandpile monoid and the cycle structure of its graph. We then build on these results to give our first main result, which is a combinatorial classification of the maximal subgroups of a sandpile monoid on a directed graph X in terms of the sandpile groups of certain easily-identifiable subgraphs of X. We then return to undirected graphs and give our second main result, which is a combinatorial classification of the sandpile group identity of every undirected distance regular graph. Along the way we give several new algebraic results for sandpiles based on directed graphs, and we point out parallels to previously known results for und...
Institute of Scientific and Technical Information of China (English)
Lu Haibo; Liu Weiqiang
2013-01-01
This paper focuses on the usage of the forward-facing cavity and opposing jet combinatorial configuration as the thermal protection system (TPS) for hypersonic vehicles.A hemispherecone nose-tip with the combinatorial configuration is investigated numerically in hypersonic free stream.Some numerical results are validated by experiments.The flow field parameters,aerodynamic force and surface heat flux distribution are obtained.The influence of the opposing jet stagnation pressure on cooling efficiency of the combinatorial TPS is discussed.The detailed numerical results show that the aerodynamic heating is reduced remarkably by the combinatorial system.The recirculation region plays a pivotal role for the reduction of heat flux.The larger the stagnation pressure of opposing jet is,the more the heating reduction is.This kind of combinatorial system is suitable to be the TPS for the high-speed vehicles which need long-range and long time flight.
Simultaneous Disulfide and Boronic Acid Ester Exchange in Dynamic Combinatorial Libraries
Diemer, Sanna L.; Kristensen, Morten; Rasmussen, Brian; Beeren, Sophie R.; Pittelkow, Michael
2015-01-01
Dynamic combinatorial chemistry has emerged as a promising tool for the discovery of complex receptors in supramolecular chemistry. At the heart of dynamic combinatorial chemistry are the reversible reactions that enable the exchange of building blocks between library members in dynamic combinatorial libraries (DCLs) ensuring thermodynamic control over the system. If more than one reversible reaction operates in a single dynamic combinatorial library, the complexity of the system increases dramatically, and so does its possible applications. One can imagine two reversible reactions that operate simultaneously or two reversible reactions that operate independently. Both these scenarios have advantages and disadvantages. In this contribution, we show how disulfide exchange and boronic ester transesterification can function simultaneous in dynamic combinatorial libraries under appropriate conditions. We describe the detailed studies necessary to establish suitable reaction conditions and highlight the analytical techniques appropriate to study this type of system. PMID:26378519
Simultaneous Disulfide and Boronic Acid Ester Exchange in Dynamic Combinatorial Libraries
Directory of Open Access Journals (Sweden)
Sanna L. Diemer
2015-09-01
Full Text Available Dynamic combinatorial chemistry has emerged as a promising tool for the discovery of complex receptors in supramolecular chemistry. At the heart of dynamic combinatorial chemistry are the reversible reactions that enable the exchange of building blocks between library members in dynamic combinatorial libraries (DCLs ensuring thermodynamic control over the system. If more than one reversible reaction operates in a single dynamic combinatorial library, the complexity of the system increases dramatically, and so does its possible applications. One can imagine two reversible reactions that operate simultaneously or two reversible reactions that operate independently. Both these scenarios have advantages and disadvantages. In this contribution, we show how disulfide exchange and boronic ester transesterification can function simultaneous in dynamic combinatorial libraries under appropriate conditions. We describe the detailed studies necessary to establish suitable reaction conditions and highlight the analytical techniques appropriate to study this type of system.
Directory of Open Access Journals (Sweden)
J. Vierinen
2011-06-01
Full Text Available We present a novel approach for modulating radar transmissions in order to improve target range and Doppler estimation accuracy. This is achieved by using non-uniform baud lengths. With this method it is possible to increase sub-baud range-resolution of phase coded radar measurements while maintaining a narrow transmission bandwidth. We first derive target backscatter amplitude estimation error covariance matrix for arbitrary targets when estimating backscatter in amplitude domain. We define target optimality and discuss different search strategies that can be used to find well performing transmission envelopes. We give several simulated examples of the method showing that fractional baud-length coding results in smaller estimation errors than conventional uniform baud length transmission codes when estimating the target backscatter amplitude at sub-baud range resolution. We also demonstrate the method in practice by analyzing the range resolved power of a low-altitude meteor trail echo that was measured using a fractional baud-length experiment with the EISCAT UHF system.
Directory of Open Access Journals (Sweden)
K. Lenin
2013-03-01
Full Text Available Reactive Power Optimization is a complex combinatorial optimization problem involving non-linear function having multiple local minima, non-linear and discontinuous constrains. This paper presents Attractive and repulsive Particle Swarm Optimization (ARPSO and Random Virus Algorithm (RVA in trying to overcome the Problem of premature convergence. RVA and ARPSO is applied to Reactive Power Optimization problem and is evaluated on standard IEEE 30Bus System. The results show that RVA prevents premature convergence to high degree but still keeps a rapid convergence. It gives best solution when compared to Attractive and repulsive Particle Swarm Optimization (ARPSO and Particle Swarm Optimization (PSO.
Brosius, Stephanie N; Turk, Amy N; Byer, Stephanie J; Longo, Jody Fromm; Kappes, John C; Roth, Kevin A; Carroll, Steven L
2014-11-01
Chemotherapeutic agents effective against malignant peripheral nerve sheath tumors (MPNSTs) are urgently needed. We recently found that tamoxifen potently impedes xenograft growth. In vitro, tamoxifen inhibits MPNST proliferation and survival in an estrogen receptor-independent manner; these effects are phenocopied by the calmodulin inhibitor trifluoperazine. The present study was performed to establish the mechanism of action of tamoxifen in vivo and optimize its therapeutic effectiveness. To determine if tamoxifen has estrogen receptor-dependent effects in vivo, we grafted MPNST cells in castrated and ovariectomized mice; xenograft growth was unaffected by reductions in sex hormones. To establish whether tamoxifen and trifluoperazine additively or synergistically impede MPNST growth, mice xenografted with neurofibromatosis type 1-associated or sporadic MPNST cells were treated with tamoxifen, trifluoperazine, or both drugs for 30 days. Both monotherapies inhibited graft growth by 50%, whereas combinatorial treatment maximally reduced graft mass by 90% and enhanced decreases in proliferation and survival. Kinomic analyses showed that tamoxifen and trifluoperazine have both shared and distinct targets in MPNSTs. In addition, trifluoperazine prevented tamoxifen-induced increases in serum/glucocorticoid regulated kinase 1, a protein linked to tamoxifen resistance. These findings suggest that combinatorial therapy with tamoxifen and trifluoperazine is effective against MPNSTs because these agents target complementary pathways that are essential for MPNST pathogenesis.
Rubio-Godoy, Verena; Ayyoub, Maha; Dutoit, Valerie; Servis, Catherine; Schink, Amy; Rimoldi, Donata; Romero, Pedro; Cerottini, Jean-Charles; Simon, Richard; Zhao, Yindong; Houghten, Richard A; Pinilla, Clemencia; Valmori, Danila
2002-08-01
A novel approach for the identification of tumor antigen-derived sequences recognized by CD8(+) cytolytic T lymphocytes (CTL) consists in using synthetic combinatorial peptide libraries. Here we have screened a library composed of 3.1 x 10(11) nonapeptides arranged in a positional scanning format, in a cytotoxicity assay, to search the antigen recognized by melanoma-reactive CTL of unknown specificity. The results of this analysis enabled the identification of several optimal peptide ligands, as most of the individual nonapeptides deduced from the primary screening were efficiently recognized by the CTL. The results of the library screening were also analyzed with a mathematical approach based on a model of independent and additive contribution of individual amino acids to antigen recognition. This biometrical data analysis enabled the retrieval, in public databases, of the native antigenic peptide SSX-2(41-49), whose sequence is highly homologous to the ones deduced from the library screening, among the ones with the highest stimulatory score. These results underline the high predictive value of positional scanning synthetic combinatorial peptide library analysis and encourage its use for the identification of CTL ligands.
Pinilla, C; Rubio-Godoy, V; Dutoit, V; Guillaume, P; Simon, R; Zhao, Y; Houghten, R A; Cerottini, J C; Romero, P; Valmori, D
2001-07-01
The recent identification of molecularly defined human tumor antigens recognized by autologous CTLs has opened new opportunities for the development of antigen-specific cancer vaccines. Despite extensive work, however, the number of CTL-defined tumor antigens that are suitable targets for generic vaccination of cancer patients is still limited, mostly because of the painstaking and lengthy nature of the procedures currently used for their identification. A novel approach is based on the combined use of combinatorial peptide libraries in positional scanning format (positional scanning synthetic combinatorial peptide libraries, PS-SCLs) and tumor-reactive CTL clones. To validate this approach, we herein analyzed in detail the recognition of PS-SCLs by Melan-A-specific CTL clones. Our results indicate that, at least for some clones, most of the amino acids composing the native antigenic peptide can be identified through the use of PS-SCLs. Interestingly, this analysis also allowed the identification of peptide analogues with increased antigenic activity as well as agonist peptides containing multiple amino-acid substitutions. In addition, biometrical analysis of the data generated by PS-SCL screening allowed the identification of the native ligand in a public database. Overall, these data demonstrate the successful use of PS-SCLs for the identification and optimization of tumor-associated CTL epitopes.
Estimation of the length of interactions in arena game semantics
Clairambault, Pierre
2011-01-01
We estimate the maximal length of interactions between strategies in HO/N game semantics, in the spirit of the work by Schwichtenberg and Beckmann for the length of reduction in simply typed lambdacalculus. Because of the operational content of game semantics, the bounds presented here also apply to head linear reduction on lambda-terms and to the execution of programs by abstract machines (PAM/KAM), including in presence of computational effects such as non-determinism or ground type references. The proof proceeds by extracting from the games model a combinatorial rewriting rule on trees of natural numbers, which can then be analyzed independently of game semantics or lambda-calculus.
Strong Combination of Ant Colony Optimization with Constraint Programming Optimization
Khichane, Madjid; Albert, Patrick; Solnon, Christine
We introduce an approach which combines ACO (Ant Colony Optimization) and IBM ILOG CP Optimizer for solving COPs (Combinatorial Optimization Problems). The problem is modeled using the CP Optimizer modeling API. Then, it is solved in a generic way by a two-phase algorithm. The first phase aims at creating a hot start for the second: it samples the solution space and applies reinforcement learning techniques as implemented in ACO to create pheromone trails. During the second phase, CP Optimizer performs a complete tree search guided by the pheromone trails previously accumulated. The first experimental results on knapsack, quadratic assignment and maximum independent set problems show that this new algorithm enhances the performance of CP Optimizer alone.
Combinatorial method for overexpression of membrane proteins in Escherichia coli.
Leviatan, Shani; Sawada, Keisuke; Moriyama, Yoshinori; Nelson, Nathan
2010-07-30
Membrane proteins constitute 20-30% of all proteins encoded by the genome of various organisms. Large amounts of purified proteins are required for activity and crystallization attempts. Thus, there is an unmet need for a heterologous membrane protein overexpression system for purification, crystallization, and activity determination. We developed a combinatorial method for overexpressing and purifying membrane proteins using Escherichia coli. This method utilizes short hydrophilic bacterial proteins, YaiN and YbeL, fused to the ends of the membrane proteins to serve as facilitating factors for expression and purification. Fourteen prokaryotic and mammalian membrane proteins were expressed using this system. Moderate to high expression was obtained for most proteins, and detergent solubilization combined with a short purification process produced stable, monodispersed membrane proteins. Five of the mammalian membrane proteins, overexpressed using our system, were reconstituted into liposomes and exhibited transport activity comparable with the native transporters.
Combinatorial Method for Overexpression of Membrane Proteins in Escherichia coli*
Leviatan, Shani; Sawada, Keisuke; Moriyama, Yoshinori; Nelson, Nathan
2010-01-01
Membrane proteins constitute 20–30% of all proteins encoded by the genome of various organisms. Large amounts of purified proteins are required for activity and crystallization attempts. Thus, there is an unmet need for a heterologous membrane protein overexpression system for purification, crystallization, and activity determination. We developed a combinatorial method for overexpressing and purifying membrane proteins using Escherichia coli. This method utilizes short hydrophilic bacterial proteins, YaiN and YbeL, fused to the ends of the membrane proteins to serve as facilitating factors for expression and purification. Fourteen prokaryotic and mammalian membrane proteins were expressed using this system. Moderate to high expression was obtained for most proteins, and detergent solubilization combined with a short purification process produced stable, monodispersed membrane proteins. Five of the mammalian membrane proteins, overexpressed using our system, were reconstituted into liposomes and exhibited transport activity comparable with the native transporters. PMID:20525689
Rapid thermal conductivity measurements for combinatorial thin films.
McDowell, Matthew G; Hill, Ian G
2013-05-01
A simple and inexpensive automated method for determining the thermal conductivity of a combinatorial library of thin films is demonstrated by measuring the thermal conductivity of a sputtered silicon dioxide film of varying thickness deposited on single crystal silicon. Using 3ω measurements, two methods for calculating the substrate thermal conductivity and two methods for determining the film thermal conductivity are demonstrated and compared. The substrate thermal conductivity was found to be 139 ± 3 W/m·K. Using the measured variation in film thickness, the film thermal conductivity was found to be 1.11 ± 0.05 W/m·K, in excellent agreement with published values for sputtered SiO2, demonstrating the accuracy of the method.
Non-orthodox combinatorial models based on discordant structures
Romanov, V F
2010-01-01
This paper introduces a novel method for compact representation of sets of n-dimensional binary sequences in a form of compact triplets structures (CTS), supposing both logic and arithmetic interpretations of data. Suitable illustration of CTS application is the unique graph-combinatorial model for the classic intractable 3-Satisfiability problem and a polynomial algorithm for the model synthesis. The method used for Boolean formulas analysis and classification by means of the model is defined as a bijective mapping principle for sets of components of discordant structures to a basic set. The statistic computer-aided experiment showed efficiency of the algorithm in a large scale of problem dimension parameters, including those that make enumeration procedures of no use. The formulated principle expands resources of constructive approach to investigation of intractable problems.
High resolution MAS-NMR in combinatorial chemistry.
Shapiro, M J; Gounarides, J S
High-resolution magic angle spinning (hr-MAS) NMR is a powerful tool for characterizing organic reactions on solid support. Because magic angle spinning reduces the line-broadening due to dipolar coupling and variations in bulk magnetic susceptibility, line widths approaching those obtained in solution-phase NMR can be obtained. The magic angle spinning method is amenable for use in conjunction with a variety of NMR-pulse sequences, making it possible to perform full-structure determinations and conformational analysis on compounds attached to a polymer support. Diffusion-weighted MAS-NMR methods such as SPEEDY (Spin-Echo-Enhanced Diffusion-Filtered Spectroscopy) can be used to remove unwanted signals from the solvent, residual reactants, and the polymer support from the MAS-NMR spectrum, leaving only those signals arising from the resin-bound product. This review will present the applications of high-resolution magic angle spinning NMR for use in combinatorial chemistry research.
Combinatorial Analysis of a Subtraction Game on Graphs
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Richard Adams
2016-01-01
Full Text Available We define a two-player combinatorial game in which players take alternate turns; each turn consists of deleting a vertex of a graph, together with all the edges containing such vertex. If any vertex became isolated by a player’s move then it would also be deleted. A player wins the game when the other player has no moves available. We study this game under various viewpoints: by finding specific strategies for certain families of graphs, through using properties of a graph’s automorphism group, by writing a program to look at Sprague-Grundy numbers, and by studying the game when played on random graphs. When analyzing Grim played on paths, using the Sprague-Grundy function, we find a connection to a standing open question about Octal games.
Combinatorial Algebra for second-quantized Quantum Theory
Blasiak, P; Solomon, A I; Horzela, A; Penson, K A
2010-01-01
We describe an algebra G of diagrams which faithfully gives a diagrammatic representation of the structures of both the Heisenberg-Weyl algebra H - the associative algebra of the creation and annihilation operators of quantum mechanics - and U(L_H), the enveloping algebra of the Heisenberg Lie algebra L_H. We show explicitly how G may be endowed with the structure of a Hopf algebra, which is also mirrored in the structure of U(L_H). While both H and U(L_H) are images of G, the algebra G has a richer structure and therefore embodies a finer combinatorial realization of the creation-annihilation system, of which it provides a concrete model.
Yeast mating for combinatorial Fab library generation and surface display
Energy Technology Data Exchange (ETDEWEB)
Feldhaus, Jane M.; Lou, Jianlong; Coleman, James R.; Siegel, Robert W.; Marks, James D.; Feldhaus, Michael
2004-04-23
Yeast display of antibody fragments has proven to be an efficient and productive means for directed evolution of single chain Fv (scFv) antibodies for increased affinity and thermal stability, and more recently for the display and screening of a non-immune library. In this paper, we describe an elegant and simple method for constructing large combinatorial Fab libraries for display on the surface of Saccharomyces cerevisiae, from modestly sized, and easily constructed, heavy and light chain libraries. To this end, we have constructed a set of yeast strains and a two vector system for heavy chain and light chain surface display of Fab fragments with free native amino termini. Through yeast mating of the haploid libraries, a very large heterodimeric immune Fab library was displayed on the diploids and high affinity antigen specific Fabs were isolated from the library.
Combinatorial Methodology for Screening Selectivity in Polymeric Pervaporation Membranes.
Godbole, Rutvik V; Ma, Lan; Doerfert, Michael D; Williams, Porsche; Hedden, Ronald C
2015-11-01
Combinatorial methodology is described for rapid screening of selectivity in polymeric pervaporation membrane materials for alcohol-water separations. The screening technique is demonstrated for ethanol-water separation using a model polyacrylate system. The materials studied are cross-linked random copolymers of a hydrophobic comonomer (n-butyl acrylate, B) and a hydrophilic comonomer (2-hydroxyethyl acrylate, H). A matrix of materials is prepared that has orthogonal variations in two key variables, H:B ratio and cross-linker concentration. For mixtures of ethanol and water, equilibrium selectivities and distribution coefficients are obtained by combining swelling measurements with high-throughput HPLC analysis. Based on the screening results, two copolymers are selected for further study as pervaporation membranes to quantify permeability selectivity and the flux of ethanol. The screening methodology described has good potential to accelerate the search for new membrane materials, as it is adaptable to a broad range of polymer chemistries.
Spreadsheet modelling for solving combinatorial problems: The vendor selection problem
Ipsilandis, Pandelis G
2008-01-01
Spreadsheets have grown up and became very powerful and easy to use tools in applying analytical techniques for solving business problems. Operations managers, production managers, planners and schedulers can work with them in developing solid and practical Do-It-Yourself Decision Support Systems. Small and Medium size organizations, can apply OR methodologies without the presence of specialized software and trained personnel, which in many cases cannot afford anyway. This paper examines an efficient approach in solving combinatorial programming problems with the use of spreadsheets. A practical application, which demonstrates the approach, concerns the development of a spreadsheet-based DSS for the Multi Item Procurement Problem with Fixed Vendor Cost. The DSS has been build using exclusively standard spreadsheet feature and can solve real problems of substantial size. The benefits and limitations of the approach are also discussed.
Histone code or not? Combinatorial pattern analyses of histone modifications
Zang, Chongzhi; Peng, Weiqun; Wang, Zhibin; Schones, Dustin E.; Barski, Artem; Cuddapah, Suresh; Cui, Kairong; Roh, Tae-Young; Zhao, Keji; Rosenfeld, Jeffrey; Zhang, Michael
2008-03-01
Eukaryotic genomes are organized into chromatin, the structure of which plays critical role in the program of gene expression. Chromatin structure and function is regulated by a myriad of posttranslational modifications on histone tails of the nucleosomes, the fundamental unit of chromatin. It remains unclear how different modifications interact. Based on high- resolution genomic maps of close to 40 histone methylations and acetylations in human T-cells obtained experimentally by ChIP- Seq technique, we investigated the combinatorial patterns of histone modifications at gene promoter regions. We found that a very limited number of patterns dominate. Modifications within a pattern are strongly correlated and each pattern is associated with a distinct gene expression distribution. Our results suggest that it is the patterns rather than the individual modifications that affect the downstream readout.
A Combinatorial Auction Based Algorithm for Flexible Seat Reservation Systems
Otomura, Kazutoshi; Tomii, Norio
We present algorithms for flexible seat distribution problems, which is defined as a problem to give an appropriate travel plan to each passenger after receiving their requests concerning their travel demands. Seat distribution problems occur when a flexible seat reservation system is implemented in which passengers are allowed to reserve seats by submitting their demands instead of specifying trains. To solve the seat distribution problem, we have formalized it as a winner determination problem of the combinatorial auction mechanism. It should be noted that difficulty of the seat distribution problem varies depending on instances of the problem, because the number of demands often varies and users' requests sometimes converge on particular trains. This suggests that in order to get solutions with high quality, algorithms that appropriately control the search space are indispensable. In this paper, we present three kinds of such algorithms for the seat distribution problem together with the results of several experiments.
Combinatorial strategies for the induction of immunogenic cell death
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Lorenzo eGalluzzi
2015-04-01
Full Text Available The term immunogenic cell death (ICD is commonly employed to indicate a peculiar instance of regulated cell death (RCD that engages the adaptive arm of the immune system. The inoculation of cancer cells undergoing ICD into immunocompetent animals elicits a specific immune response associated with the establishment of immunological memory. Only a few agents are intrinsically endowed with the ability to trigger ICD. These include a few chemotherapeutics that are routinely employed in the clinic, like doxorubicin, mitoxantrone, oxaliplatin and cyclophosphamide, as well as some agents that have not yet been approved for use in humans. Accumulating clinical data indicate that the activation of adaptive immune responses against dying cancer cells is associated with improved disease outcome in patients affected by various neoplasms. Thus, novel therapeutic regimens that trigger ICD are urgently awaited. Here, we discuss current combinatorial approaches to convert otherwise non-immunogenic instances of RCD into bona fide ICD.
Consistency and axiomatization of a natural extensional combinatory logic
Institute of Scientific and Technical Information of China (English)
蒋颖
1996-01-01
In the light of a question of J. L. Krivine about the consistency of an extensional λ-theory,an extensional combinatory logic ECL+U(G)+RU_∞+ is established, with its consistency model provedtheoretically and it is shown the it is not equivalent to any system of universal axioms. It is expressed bythe theory in first order logic that, for every given group G of order n, there simultaneously exist infinitelymany universal retractions and a surjective n-tuple notion, such that each element of G acts as a permutationof the components of the n-tuple, and as an Ap-automorphism of the model; further each of the universalretractions is invarian under the action of the Ap-automorphisms induced by G The difference between thetheory and that of Krivine is the G need not be a symmetric group.
Combinatorial Clustering and the Beta Negative Binomial Process.
Broderick, Tamara; Mackey, Lester; Paisley, John; Jordan, Michael I
2015-02-01
We develop a Bayesian nonparametric approach to a general family of latent class problems in which individuals can belong simultaneously to multiple classes and where each class can be exhibited multiple times by an individual. We introduce a combinatorial stochastic process known as the negative binomial process ( NBP ) as an infinite-dimensional prior appropriate for such problems. We show that the NBP is conjugate to the beta process, and we characterize the posterior distribution under the beta-negative binomial process ( BNBP) and hierarchical models based on the BNBP (the HBNBP). We study the asymptotic properties of the BNBP and develop a three-parameter extension of the BNBP that exhibits power-law behavior. We derive MCMC algorithms for posterior inference under the HBNBP , and we present experiments using these algorithms in the domains of image segmentation, object recognition, and document analysis.
Combinatorial microfluidic droplet engineering for biomimetic material synthesis
Bawazer, Lukmaan A.; McNally, Ciara S.; Empson, Christopher J.; Marchant, William J.; Comyn, Tim P.; Niu, Xize; Cho, Soongwon; McPherson, Michael J.; Binks, Bernard P.; deMello, Andrew; Meldrum, Fiona C.
2016-01-01
Although droplet-based systems are used in a wide range of technologies, opportunities for systematically customizing their interface chemistries remain relatively unexplored. This article describes a new microfluidic strategy for rapidly tailoring emulsion droplet compositions and properties. The approach uses a simple platform for screening arrays of droplet-based microfluidic devices and couples this with combinatorial selection of the droplet compositions. Through the application of genetic algorithms over multiple screening rounds, droplets with target properties can be rapidly generated. The potential of this method is demonstrated by creating droplets with enhanced stability, where this is achieved by selecting carrier fluid chemistries that promote titanium dioxide formation at the droplet interfaces. The interface is a mixture of amorphous and crystalline phases, and the resulting composite droplets are biocompatible, supporting in vitro protein expression in their interiors. This general strategy will find widespread application in advancing emulsion properties for use in chemistry, biology, materials, and medicine.
Length and coverage of inhibitory decision rules
Alsolami, Fawaz
2012-01-01
Authors present algorithms for optimization of inhibitory rules relative to the length and coverage. Inhibitory rules have a relation "attribute ≠ value" on the right-hand side. The considered algorithms are based on extensions of dynamic programming. Paper contains also comparison of length and coverage of inhibitory rules constructed by a greedy algorithm and by the dynamic programming algorithm. © 2012 Springer-Verlag.
Quantitative control of organ shape by combinatorial gene activity.
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Min-Long Cui
Full Text Available The development of organs with particular shapes, like wings or flowers, depends on regional activity of transcription factors and signalling molecules. However, the mechanisms that link these molecular activities to the morphogenetic events underlying shape are poorly understood. Here we describe a combination of experimental and computational approaches that address this problem, applying them to a group of genes controlling flower shape in the Snapdragon (Antirrhinum. Four transcription factors are known to play a key role in the control of floral shape and asymmetry in Snapdragon. We use quantitative shape analysis of mutants for these factors to define principal components underlying flower shape variation. We show that each transcription factor has a specific effect on the shape and size of regions within the flower, shifting the position of the flower in shape space. These shifts are further analysed by generating double mutants and lines that express some of the genes ectopically. By integrating these observations with known gene expression patterns and interactions, we arrive at a combinatorial scheme for how regional effects on shape are genetically controlled. We evaluate our scheme by incorporating the proposed interactions into a generative model, where the developing flower is treated as a material sheet that grows according to how genes modify local polarities and growth rates. The petal shapes generated by the model show a good quantitative match with those observed experimentally for each petal in numerous genotypes, thus validating the hypothesised scheme. This article therefore shows how complex shapes can be accounted for by combinatorial effects of transcription factors on regional growth properties. This finding has implications not only for how shapes develop but also for how they may have evolved through tinkering with transcription factors and their targets.