Search results for: Multi-objective sequencing problem

Authors: Fereshteh Shacheraghi, Mohammad Reza Shakibaie, Hanieh Noveiri

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Fourty one strains of ESBL producing P.aeruginosa which were previously isolated from burn patients in Kerman University general hospital, Iran were subjected to PCR, RFLP and sequencing in order to determine the type of extended spectrum β- lactamases (ESBL), the restriction digestion pattern and possibility of mutation among detected genes. DNA extraction was carried out by phenol chloroform method. PCR for detection of bla genes was performed using specific primer for each gene. Restriction Fragment Length Polymorphism (RFLP) for ESBL genes was carried out using EcoRI, NheI, PVUII, EcoRV, DdeI, and PstI restriction enzymes. The PCR products were subjected to direct sequencing of both the strands for identification of the ESBL genes.The blaCTX-M, blaVEB-1, blaPER-1, blaGES-1, blaOXA-1, blaOXA-4 and blaOXA-10 genes were detected in the (n=1) 2.43%, (n=41)100%, (n=28) 68.3%, (n=10) 24.4%, (n=29) 70.7%, (n=7)17.1% and (n=38) 92.7% of the ESBL producing isolates respectively. The RFLP analysis showed that each ESBL gene has identical pattern of digestion among the isolated strains. Sequencing of the ESBL genes confirmed the genuinety of PCR products and revealed no mutation in the restriction sites of the above genes. From results of the present investigation it can be concluded that blaVEB-1 and blaCTX-M were the most and the least frequently isolated ESBL genes among the P.aeruginosa strains isolated from burn patients. The RFLP and sequencing analysis revealed that same clone of the bla genes were indeed existed among the antibiotic resistant strains.

Keywords: ESBL genes, PCR, RFLP, Sequencing, P.aeruginosa

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Authors: Camelia Petrescu, Lavinia Ferariu

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The paper presents an optimization study based on genetic algorithms (GA-s) for a radio-frequency applicator used in heating dielectric band products. The weakly coupled electro-thermal problem is analyzed using 2D-FEM. The design variables in the optimization process are: the voltage of a supplementary “guard" electrode and six geometric parameters of the applicator. Two objective functions are used: temperature uniformity and total active power absorbed by the dielectric. Both mono-objective and multiobjective formulations are implemented in GA optimization.

Keywords: Dielectric heating, genetic algorithms, optimization, RF applicators.

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Authors: M. Sadeghi, H. Pezeshk, R. Tusserkani, A. Sharifi Zarchi, A. Malekpour, M. Foroughmand, S. Goliaei, M. Totonchi, N. Ansari–Pour

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The role and relative importance of intrinsic and extrinsic factors in the development of complex diseases such as cancer still remains a controversial issue. Determining the amount of variation explained by these factors needs experimental data and statistical models. These models are nevertheless based on the occurrence and accumulation of random mutational events during stem cell division, thus rendering cancer development a stochastic outcome. We demonstrate that not only individual genome sequencing is uninformative in determining cancer risk, but also assigning a unique genome sequence to any given individual (healthy or affected) is not meaningful. Current whole-genome sequencing approaches are therefore unlikely to realize the promise of personalized medicine. In conclusion, since genome sequence differs from cell to cell and changes over time, it seems that determining the risk factor of complex diseases based on genome sequence is somewhat unrealistic, and therefore, the resulting data are likely to be inherently uninformative.

Keywords: Cancer risk, extrinsic factors, genome sequencing, intrinsic factors.

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Authors: C. Ardil

Abstract:

In this research, a multidimensional  compromise optimization method is proposed for multidimensional decision making analysis in the development ranking of the Gulf Cooperation Council Countries and Turkey. The proposed approach presents ranking solutions resulting from different multicriteria decision analyses, which yield different ranking orders for the same ranking problem, consisting of a set of alternatives in terms of numerous competing criteria when they are applied with the same numerical data. The multiobjective optimization decision making problem is considered in three sequential steps. In the first step, five different criteria related to the development ranking are gathered from the research field. In the second step, identified evaluation criteria are, objectively, weighted using standard deviation procedure. In the third step, a country selection problem is illustrated with a numerical example as an application of the proposed multidimensional  compromise optimization model. Finally, multidimensional  compromise optimization approach is applied to rank the Gulf Cooperation Council Countries and Turkey. 

Keywords: Standard deviation, performance evaluation, multicriteria decision making, multidimensional compromise optimization, vector normalization, multicriteria decision making, multicriteria analysis, multidimensional decision analysis.

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Authors: Amin Mojiri, Akiyoshi Ohashi, Tomonori Kindaichi

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Synthetic domestic wastewater was treated via combining treatment methods, including electrochemical oxidation, adsorption, and sequencing batch reactor (SBR). In the upper part of the reactor, an anode and a cathode (Ti/RuO₂-IrO₂) were organized in parallel for the electrochemical oxidation procedure. Sodium sulfate (Na₂SO₄) with a concentration of 2.5 g/L was applied as the electrolyte. The voltage and current were fixed on 7.50 V and 0.40 A, respectively. Then, 15% working value of the reactor was filled by activated sludge, and 85% working value of the reactor was added with synthetic wastewater. Powdered cockleshell, 1.5 g/L, was added in the reactor to do ion-exchange. Response surface methodology was employed for statistical analysis. Reaction time (h) and pH were considered as independent factors. A total of 97.0% biochemical oxygen demand, 99.9% phosphorous and 88.6% cadmium were eliminated at the optimum reaction time (80.0 min) and pH (6.4).

Keywords: Adsorption, electrochemical oxidation, metals, sequencing batch reactor.

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Authors: Badr M. Alshammari, T. Guesmi

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In recent years, the combined economic and emission power dispatch is one of the main problems of electrical power system. It aims to schedule the power generation of generators in order to minimize cost production and emission of harmful gases caused by fossil-fueled thermal units such as CO, CO₂, NO_x, and SO₂. To solve this complicated multi-objective problem, an improved version of the particle swarm optimization technique that includes non-dominated sorting concept has been proposed. Valve point loading effects and system losses have been considered. The three-unit and ten-unit benchmark systems have been used to show the effectiveness of the suggested optimization technique for solving this kind of nonconvex problem. The simulation results have been compared with those obtained using genetic algorithm based method. Comparison results show that the proposed approach can provide a higher quality solution with better performance.

Keywords: Power dispatch, valve point loading effects, multiobjective optimization, Pareto solutions.

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Authors: Hany Osman, M. F. Baki

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We address the balancing problem of transfer lines in this paper to find the optimal line balancing that minimizes the nonproductive time. We focus on the tool change time and face orientation change time both of which influence the makespane. We consider machine capacity limitations and technological constraints associated with the manufacturing process of auto cylinder heads. The problem is represented by a mixed integer programming model that aims at distributing the design features to workstations and sequencing the machining processes at a minimum non-productive time. The proposed model is solved by an algorithm established using linearization schemes and Benders- decomposition approach. The experiments show the efficiency of the algorithm in reaching the exact solution of small and medium problem instances at reasonable time.

Keywords: Transfer line balancing, Benders' decomposition, Linearization.

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Authors: Wandili S. Awuor, Onyango D. Miruka, Waindi N. Eliud

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Foodborne Salmonella infections have become a major problem world wide. Salmonellosis transmitted from fish are quite common. Established quality control measures exist for export oriented fish, none exists for fish consumed locally. This study aimed at characterization of Salmonella isolated from Nile tilapia . The study was carried out in selected beaches along L. Victoria in Western Kenya between March and June 2007. One hundred and twenty fish specimens were collected. Salmonella isolates were confirmed using serotyping, biochemical testing in addition to malic acid dehydrogenase (mdh) and fliC gene sequencing. Twenty Salmonella isolates were confirmed by mdh gene sequencing. Nine (9) were S. enterica serotype typhimurium, four (4) were S. enterica Serotype, enteritidis and seven (7) were S. enterica serotype typhi. Nile tilapia have a role in transmission of Salmonellosis in the study area, poor sanitation was a major cause of pollution at the beach inshore waters.

Keywords: fliC, mdh, Salmonellosis, Serotype

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Authors: Anis Gharbi

Abstract:

This paper considers the problem of scheduling maintenance actions for identical aircraft gas turbine engines. Each one of the turbines consists of parts which frequently require replacement. A finite inventory of spare parts is available and all parts are ready for replacement at any time. The inventory consists of both new and refurbished parts. Hence, these parts have different field lives. The goal is to find a replacement part sequencing that maximizes the time that the aircraft will keep functioning before the inventory is replenished. The problem is formulated as an identical parallel machine scheduling problem where the minimum completion time has to be maximized. Two models have been developed. The first one is an optimization model which is based on a 0-1 linear programming formulation, while the second one is an approximate procedure which consists in decomposing the problem into several two-machine subproblems. Each subproblem is optimally solved using the first model. Both models have been implemented using Lingo and have been tested on two sets of randomly generated data with up to 150 parts and 10 turbines. Experimental results show that the optimization model is able to solve only instances with no more than 4 turbines, while the decomposition procedure often provides near-optimal solutions within a maximum CPU time of 3 seconds.

Keywords: Aircraft turbines, Scheduling, Identical parallel machines, 0-1 linear programming, Heuristic.

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Authors: John R. Rose, James P. Cleveland, Alvin Fox

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Tandem mass spectrometry (MS/MS) is the engine driving high-throughput protein identification. Protein mixtures possibly representing thousands of proteins from multiple species are treated with proteolytic enzymes, cutting the proteins into smaller peptides that are then analyzed generating MS/MS spectra. The task of determining the identity of the peptide from its spectrum is currently the weak point in the process. Current approaches to de novo sequencing are able to compute candidate peptides efficiently. The problem lies in the limitations of current scoring functions. In this paper we introduce the concept of proteome signature. By examining proteins and compiling proteome signatures (amino acid usage) it is possible to characterize likely combinations of amino acids and better distinguish between candidate peptides. Our results strongly support the hypothesis that a scoring function that considers amino acid usage patterns is better able to distinguish between candidate peptides. This in turn leads to higher accuracy in peptide prediction.

Keywords: Tandem mass spectrometry, proteomics, scoring, peptide, de novo, mutual information

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Authors: H. Kazemi Karegar, S. Jalilzadeh, V. Nabaei, A. Shabani

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In this paper, the problem of finding the optimal topological configuration of a deregulated distribution network is considered. The new features of this paper are proposing a multiobjective function and its application on deregulated distribution networks for finding the optimal configuration. The multi-objective function will be defined for minimizing total Energy Supply Costs (ESC) and energy losses subject to load flow constraints. The optimal configuration will be obtained by using Binary Genetic Algorithm (BGA).The proposed method has been tested to analyze a sample and a practical distribution networks.

Keywords: Binary Genetic Algorithm, Deregulated Distribution Network, Minimizing Cost, Reconfiguration.

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Authors: Chien-Ju Li, Chun-Hui Yu, Chi-Chuan Hwang, Tsunglin Liu , Darby Tien-Hao Chang

Abstract:

De novo genome assembly is always fragmented. Assembly fragmentation is more serious using the popular next generation sequencing (NGS) data because NGS sequences are shorter than the traditional Sanger sequences. As the data throughput of NGS is high, the fragmentations in assemblies are usually not the result of missing data. On the contrary, the assembled sequences, called contigs, are often connected to more than one other contigs in a complicated manner, leading to the fragmentations. False connections in such complicated connections between contigs, named a contig graph, are inevitable because of repeats and sequencing/assembly errors. Simplifying a contig graph by removing false connections directly improves genome assembly. In this work, we have developed a tool, SIMGraph, to resolve ambiguous connections between contigs using NGS data. Applying SIMGraph to the assembly of a fungus and a fish genome, we resolved 27.6% and 60.3% ambiguous contig connections, respectively. These results can reduce the experimental efforts in resolving contig connections.

Keywords: Contig graph, NGS, de novo assembly, scaffold.

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Authors: Farhad Kolahan, Vahid Kayvanfar

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In this paper we address a multi-objective scheduling problem for unrelated parallel machines. In unrelated parallel systems, the processing cost/time of a given job on different machines may vary. The objective of scheduling is to simultaneously determine the job-machine assignment and job sequencing on each machine. In such a way the total cost of the schedule is minimized. The cost function consists of three components, namely; machining cost, earliness/tardiness penalties and makespan related cost. Such scheduling problem is combinatorial in nature. Therefore, a Simulated Annealing approach is employed to provide good solutions within reasonable computational times. Computational results show that the proposed approach can efficiently solve such complicated problems.

Keywords: Makespan, Parallel machines, Scheduling, Simulated Annealing

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Authors: Minghui Wang, Shanrui Hu

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An inverse problem of doubly center matrices is discussed. By translating the constrained problem into unconstrained problem, two iterative methods are proposed. A numerical example illustrate our algorithms.

Keywords: doubly center matrix, electric network theory, iterative methods, least-square problem.

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Authors: Abdulrahim Shamayleh

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In this work, the surgical theater of a local hospital in KSA was analyzed using simulation. The focus was on attempting to answer questions related to how many Operating Rooms (ORs) to open and to analyze the performance of the surgical theater in general and mainly the Post Anesthesia Care Unit (PACU) to assist making decisions regarding PACU staffing. The surgical theater consists of ten operating rooms and the PACU unit which has a maximum capacity of fifteen beds. Different sequencing rules to sequence the surgical cases were tested and the Longest Case First (LCF) were superior to others. The results of the different alternatives developed and tested can be used by the manager as a tool to plan and manage the OR and PACU

Keywords: Operating room, post anesthesia care unit, PACUstaffing, sequencing, healthcare

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Authors: H. Alkhatib, J. Duveau

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Genetic algorithms (GAs) have been widely used for global optimization problems. The GA performance depends highly on the choice of the search space for each parameter to be optimized. Often, this choice is a problem-based experience. The search space being a set of potential solutions may contain the global optimum and/or other local optimums. A bad choice of this search space results in poor solutions. In this paper, our approach consists in extending the search space boundaries during the GA optimization, only when it is required. This leads to more diversification of GA population by new solutions that were not available with fixed search space boundaries. So, these dynamic search spaces can improve the GA optimization performances. The proposed approach is applied to power system stabilizer optimization for multimachine power system (16-generator and 68-bus). The obtained results are evaluated and compared with those obtained by ordinary GAs. Eigenvalue analysis and nonlinear system simulation results show the effectiveness of the proposed approach to damp out the electromechanical oscillation and enhance the global system stability.

Keywords: Genetic Algorithms, Multiobjective Optimization, Power System Stabilizer, Small Signal Stability.

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Authors: Darwin Gouwanda, S. G. Ponnambalam

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Set covering problem is a classical problem in computer science and complexity theory. It has many applications, such as airline crew scheduling problem, facilities location problem, vehicle routing, assignment problem, etc. In this paper, three different techniques are applied to solve set covering problem. Firstly, a mathematical model of set covering problem is introduced and solved by using optimization solver, LINGO. Secondly, the Genetic Algorithm Toolbox available in MATLAB is used to solve set covering problem. And lastly, an ant colony optimization method is programmed in MATLAB programming language. Results obtained from these methods are presented in tables. In order to assess the performance of the techniques used in this project, the benchmark problems available in open literature are used.

Keywords: Set covering problem, genetic algorithm, ant colony optimization, LINGO.

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Authors: Chao Wang, Ting-Zhu Huang Chen Jia

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In this paper, we propose a new linear complementarity problem named as bi-linear complementarity problem (BLCP) and the method for solving BLCP. In addition, the algorithm for error estimation of BLCP is also given. Numerical experiments show that the algorithm is efficient.

Keywords: Bi-linear complementarity problem, Linear complementarity problem, Extended linear complementarity problem, Error estimation, P-matrix, M-matrix.

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Authors: Sukhveer Singh, Sandeep Singh

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A bi-objective fuzzy transportation problem with the objectives to minimize the total fuzzy cost and fuzzy time of transportation without according priorities to them is considered. To the best of our knowledge, there is no method in the literature to find efficient solutions of the bi-objective transportation problem under uncertainty. In this paper, a bi-objective transportation problem in an uncertain environment has been formulated. An algorithm has been proposed to find efficient solutions of the bi-objective transportation problem under uncertainty. The proposed algorithm avoids the degeneracy and gives the optimal solution faster than other existing algorithms for the given uncertain transportation problem.

Keywords: Transportation problem, efficient solution, ranking function, fuzzy transportation problem.

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Authors: Didier Casner, Jean Renaud, Remy Houssin, Dominique Knittel

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In this paper, a novel approach for the multidisciplinary design optimization (MDO) of complex mechatronic systems. This approach, which is a part of a global project aiming to include the MDO aspect inside an innovative design process. As a first step, the paper considers the MDO as a redesign approach which is limited to the parametric optimization. After defining and introducing the different keywords, the proposed method which is based on the V-Model which is commonly used in mechatronics.

Keywords: mechatronics, Multidisciplinary Design Optimization (MDO), multiobjective optimization, engineering design.

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Authors: Kenza Aida Amara, Bachir Djebbar

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We treat the two-dimensional bin packing problem which involves packing a given set of rectangles into a minimum number of larger identical rectangles called bins. This combinatorial problem is NP-hard. We propose a pretreatment for the oriented version of the problem that allows the valorization of the lost areas in the bins and the reduction of the size problem. A heuristic method based on the strategy first-fit adapted to this problem is presented. We present an approach of resolution by bee colony optimization. Computational results express a comparison of the number of bins used with and without pretreatment.

Keywords: Bee colony optimization, bin packing, heuristic algorithm, pretreatment.

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Authors: Elsheikh Asser

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Time and cost are the main goals of the construction project management. The first schedule developed may not be a suitable schedule for beginning or completing the project to achieve the target completion time at a minimum total cost. In general, there are trade-offs between time and cost (TCT) to complete the activities of a project. This research presents genetic algorithms (GAs) multiobjective model for project scheduling considering different scenarios such as least cost, least time, and target time.

Keywords: Genetic algorithms, Time-cost trade-off.

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Authors: Tsuyoshi Okita, Tatsuya Niwa

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For a given specific problem an efficient algorithm has been the matter of study. However, an alternative approach orthogonal to this approach comes out, which is called a reduction. In general for a given specific problem this reduction approach studies how to convert an original problem into subproblems. This paper proposes a formal modeling language to support this reduction approach. We show three examples from the wide area of learning problems. The benefit is a fast prototyping of algorithms for a given new problem.

Keywords: Formal language, statistical inference problem, reduction.

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Authors: M. Ahmad, M. Gourgand, C. Caux

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The Resource-Constrained Project Scheduling Problem (RCPSP) is concerned with single-item or small batch production where limited resources have to be allocated to dependent activities over time. Over the past few decades, a lot of work has been made with the use of optimal solution procedures for this basic problem type and its extensions. Brucker and Knust[1] discuss, how timetabling problems can be modeled as a RCPSP. Authors discuss high school timetabling and university course timetabling problem as an example. We have formulated two mathematical formulations of course timetabling problem in a new way which are the prototype of single-mode RCPSP. Our focus is to show, how course timetabling problem can be transformed into RCPSP. We solve this transformation model with genetic algorithm.

Keywords: Course Timetabling, Integer programming, Combinatorial optimizations

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Authors: Nicolas Zufferey

Abstract:

The vehicle routing problem (VRP) is a famous combinatorial optimization problem. Because of its well-known difficulty, metaheuristics are the most appropriate methods to tackle large and realistic instances. The goal of this paper is to highlight the key ideas for designing VRP metaheuristics according to the following criteria: efficiency, speed, robustness, and ability to take advantage of the problem structure. Such elements can obviously be used to build solution methods for other combinatorial optimization problems, at least in the deterministic field.

Keywords: Vehicle routing problem, Metaheuristics, Combinatorial optimization.

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Authors: Patcharee Intanoo, Jittipan Chavadej, Sumaeth Chavadej

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The objective of this study was to investigate hydrogen production from alcohol wastewater by anaerobic sequencing batch reactor (ASBR) under thermophillic operation. The ASBR unit used in this study had a liquid holding volume of 4 L and was operated at 6 cycles per day. The seed sludge taken from an upflow anaerobic sludge blanket unit treating the same wastewater was boiled at 95 °C for 15 min before being fed to the ASBR unit. The ASBR system was operated at different COD loading rates at a thermophillic temperature (55 °C), and controlled pH of 5.5. When the system was operated under optimum conditions (providing maximum hydrogen production performance) at a feed COD of 60 000 mg/l, and a COD loading rate of 68 kg/m3 d, the produced gas contained 43 % H2 content in the produced gas. Moreover, the hydrogen yield and the specific hydrogen production rate (SHPR) were 130 ml H2/g COD removed and 2100 ml H2/l d, respectively.

Keywords: Biohydrogen, Alcohol wastewater, Anaerobic sequencing batch reactor (ASBR), Thermophillic operation

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Authors: Mohammed Salem Alzahrani

Abstract:

In this paper the optimality of the solution of an existing real word assignment problem known as the seat assignment problem using Seat Assignment Method (SAM) is discussed. SAM is the newly driven method from three existing methods, Hungarian Method, Northwest Corner Method and Least Cost Method in a special way that produces the easiness & fairness among all methods that solve the seat assignment problem.

Keywords: Assignment Problem, Hungarian Method, Least Cost Method, Northwest Corner Method, Seat Assignment Method (SAM), A Real Word Assignment Problem.

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Authors: Mhand Hifi, Hedi Mhalla, Mustapha Michaphy

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In this paper, we study the multi-scenario knapsack problem, a variant of the well-known NP-Hard single knapsack problem. We investigate the use of an adaptive algorithm for solving heuristically the problem. The used method combines two complementary phases: a size reduction phase and a dynamic 2- opt procedure one. First, the reduction phase applies a polynomial reduction strategy; that is used for reducing the size problem. Second, the adaptive search procedure is applied in order to attain a feasible solution Finally, the performances of two versions of the proposed algorithm are evaluated on a set of randomly generated instances.

Keywords: combinatorial optimization, max-min optimization, knapsack, heuristics, problem reduction

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Authors: Zohreh O. Akbari

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In this paper a deterministic polynomial-time algorithm is presented for the Clique problem. The case is considered as the problem of omitting the minimum number of vertices from the input graph so that none of the zeroes on the graph-s adjacency matrix (except the main diagonal entries) would remain on the adjacency matrix of the resulting subgraph. The existence of a deterministic polynomial-time algorithm for the Clique problem, as an NP-complete problem will prove the equality of P and NP complexity classes.

Keywords: Clique problem, Deterministic Polynomial-time Algorithm, Equality of P and NP Complexity Classes.

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Authors: Ben Mohamed Ahemed Mohamed, Yassine Adnan

Abstract:

The problem of bin-packing in two dimensions (2BP) consists in placing a given set of rectangular items in a minimum number of rectangular and identical containers, called bins. This article treats the case of objects with a free orientation of 90Ôùª. We propose an approach of resolution combining optimization by colony of ants (ACO) and the heuristic method IMA to resolve this NP-Hard problem.

Keywords: Ant colony algorithm, bin-packing problem, heuristics methods.

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