Exploring Dimensionality, Systematic Mutations and Number of Contacts in Simple HP ab-initio Protein Folding Using a Blackboard-based Agent Platform

A computational platform is presented in this contribution. It has been designed as a virtual laboratory to be used for exploring optimization algorithms in biological problems. This platform is built on a blackboard-based agent architecture. As a test case, the version of the platform presented here is devoted to the study of protein folding, initially with a bead-like description of the chain and with the widely used model of hydrophobic and polar residues (HP model). Some details of the platform design are presented along with its capabilities and also are revised some explorations of the protein folding problems with different types of discrete space. It is also shown the capability of the platform to incorporate specific tools for the structural analysis of the runs in order to understand and improve the optimization process. Accordingly, the results obtained demonstrate that the ensemble of computational tools into a single platform is worthwhile by itself, since experiments developed on it can be designed to fulfill different levels of information in a self-consistent fashion. By now, it is being explored how an experiment design can be useful to create a computational agent to be included within the platform. These inclusions of designed agents –or software pieces– are useful for the better accomplishment of the tasks to be developed by the platform. Clearly, while the number of agents increases the new version of the virtual laboratory thus enhances in robustness and functionality.

New Approach for Manipulation of Stratified Programs

Negation is useful in the majority of the real world applications. However, its introduction leads to semantic and canonical problems. We propose in this paper an approach based on stratification to deal with negation problems. This approach is based on an extension of predicates nets. It is characterized with two main contributions. The first concerns the management of the whole class of stratified programs. The second contribution is related to usual operations optimizations on stratified programs (maximal stratification, incremental updates ...).

Optimization of Growth of Rhodobacter Sphaeroides Using Mixed Volatile Fatty Acidsby Response Surface Methodology

A combination of photosynthetic bacteria along with anaerobic acidogenic bacteria is an ideal option for efficient hydrogen production. In the present study, the optimum concentration of substrates for the growth of Rhodobacter sphaeroides was found by response surface methodology. The optimum combination of three individual fatty acids was determined by Box Behnken design. Increase of volatile fatty acid concentration decreased the growth. Combination of sodium acetate and sodium propionate was most significant for the growth of the organism. The results showed that a maximum biomass concentration of 0.916 g/l was obtained when the concentrations of acetate, propionate and butyrate were 0.73g/l,0.99g/l and 0.799g/l, respectively. The growth was studied under an optimum concentration of volatile fatty acids and at a light intensity of 3000 lux, initial pH of 7 and a temperature of 35°C.The maximum biomass concentration of 0.92g/l was obtained which verified the practicability of this optimization.

Optimization for Reducing Handoff Latency and Utilization of Bandwidth in ATM Networks

To support mobility in ATM networks, a number of technical challenges need to be resolved. The impact of handoff schemes in terms of service disruption, handoff latency, cost implications and excess resources required during handoffs needs to be addressed. In this paper, a one phase handoff and route optimization solution using reserved PVCs between adjacent ATM switches to reroute connections during inter-switch handoff is studied. In the second phase, a distributed optimization process is initiated to optimally reroute handoff connections. The main objective is to find the optimal operating point at which to perform optimization subject to cost constraint with the purpose of reducing blocking probability of inter-switch handoff calls for delay tolerant traffic. We examine the relation between the required bandwidth resources and optimization rate. Also we calculate and study the handoff blocking probability due to lack of bandwidth for resources reserved to facilitate the rapid rerouting.

Optimization of Three-dimensional Electrical Performance in a Solid Oxide Fuel Cell Stack by a Neural Network

By the application of an improved back-propagation neural network (BPNN), a model of current densities for a solid oxide fuel cell (SOFC) with 10 layers is established in this study. To build the learning data of BPNN, Taguchi orthogonal array is applied to arrange the conditions of operating parameters, which totally 7 factors act as the inputs of BPNN. Also, the average current densities achieved by numerical method acts as the outputs of BPNN. Comparing with the direct solution, the learning errors for all learning data are smaller than 0.117%, and the predicting errors for 27 forecasting cases are less than 0.231%. The results show that the presented model effectively builds a mathematical algorithm to predict performance of a SOFC stack immediately in real time. Also, the calculating algorithms are applied to proceed with the optimization of the average current density for a SOFC stack. The operating performance window of a SOFC stack is found to be between 41137.11 and 53907.89. Furthermore, an inverse predicting model of operating parameters of a SOFC stack is developed here by the calculating algorithms of the improved BPNN, which is proved to effectively predict operating parameters to achieve a desired performance output of a SOFC stack.

Topology Optimization of Aircraft Fuselage Structure

Topology Optimization is a defined as the method of determining optimal distribution of material for the assumed design space with functionality, loads and boundary conditions [1]. Topology optimization can be used to optimize shape for the purposes of weight reduction, minimizing material requirements or selecting cost effective materials [2]. Topology optimization has been implemented through the use of finite element methods for the analysis, and optimization techniques based on the method of moving asymptotes, genetic algorithms, optimality criteria method, level sets and topological derivatives. Case study of Typical “Fuselage design" is considered for this paper to explain the benefits of Topology Optimization in the design cycle. A cylindrical shell is assumed as the design space and aerospace standard pay loads were applied on the fuselage with wing attachments as constraints. Then topological optimization is done using Finite Element (FE) based software. This optimization results in the structural concept design which satisfies all the design constraints using minimum material.

Reliability Optimization for 3G Cellular Access Networks

This paper address the network reliability optimization problem in the optical access network design for the 3G cellular systems. We presents a novel 0-1 integer programming model for designing optical access network topologies comprised of multi-rings with common-edge in order to guarantee always-on services. The results show that the proposed model yields access network topologies with the optimal reliablity and satisfies both network cost limitations and traffic demand requirements.

Exergy Analysis of Combined Cycle of Air Separation and Natural Gas Liquefaction

This paper presented a novel combined cycle of air separation and natural gas liquefaction. The idea is that natural gas can be liquefied, meanwhile gaseous or liquid nitrogen and oxygen are produced in one combined cryogenic system. Cycle simulation and exergy analysis were performed to evaluate the process and thereby reveal the influence of the crucial parameter, i.e., flow rate ratio through two stages expanders β on heat transfer temperature difference, its distribution and consequent exergy loss. Composite curves for the combined hot streams (feeding natural gas and recycled nitrogen) and the cold stream showed the degree of optimization available in this process if appropriate β was designed. The results indicated that increasing β reduces temperature difference and exergy loss in heat exchange process. However, the maximum limit value of β should be confined in terms of minimum temperature difference proposed in heat exchanger design standard and heat exchanger size. The optimal βopt under different operation conditions corresponding to the required minimum temperature differences was investigated.

Optimization of Breast Tumor Cells Isolation Efficiency and Purity by Membrane Filtration

Size based filtration is one of the common methods employed to isolate circulating tumor cells (CTCs) from whole blood. It is well known that this method suffers from isolation efficiency to purity tradeoff. However, this tradeoff is poorly understood. In this paper, we present the design and manufacturing of a special rectangular slit filter. The filter was designed to retain maximal amounts of nucleated cells, while minimizing the pressure on cells, thereby preserving their morphology. The key parameter, namely, input pressure, was optimized to retain the maximal number of tumor cells, whilst maximizing the depletion of normal blood cells (red and white blood cells and platelets). Our results indicate that for a slit geometry of 5 × 40 μm on a 13 mm circular membrane with a fill factor of 21%, a pressure of 6.9 mBar yields the optimum for maximizing isolation of MCF-7 and depletion of normal blood cells.

A Hybrid Heuristic for the Team Orienteering Problem

In this work, we propose a hybrid heuristic in order to solve the Team Orienteering Problem (TOP). Given a set of points (or customers), each with associated score (profit or benefit), and a team that has a fixed number of members, the problem to solve is to visit a subset of points in order to maximize the total collected score. Each member performs a tour starting at the start point, visiting distinct customers and the tour terminates at the arrival point. In addition, each point is visited at most once, and the total time in each tour cannot be greater than a given value. The proposed heuristic combines beam search and a local optimization strategy. The algorithm was tested on several sets of instances and encouraging results were obtained.

Finding an Optimized Discriminate Function for Internet Application Recognition

Everyday the usages of the Internet increase and simply a world of the data become accessible. Network providers do not want to let the provided services to be used in harmful or terrorist affairs, so they used a variety of methods to protect the special regions from the harmful data. One of the most important methods is supposed to be the firewall. Firewall stops the transfer of such packets through several ways, but in some cases they do not use firewall because of its blind packet stopping, high process power needed and expensive prices. Here we have proposed a method to find a discriminate function to distinguish between usual packets and harmful ones by the statistical processing on the network router logs. So an administrator can alarm to the user. This method is very fast and can be used simply in adjacent with the Internet routers.

Experimental and Statistical Study of Nonlinear Effect of Carbon Nanotube on Mechanical Properties of Polypropylene Composites

In this study concept of experimental design is successfully applied for the determination of optimum condition to produce PP/SWCNT (Polypropylene/Single wall carbon nanotube) nanocomposite. Central composite design as one of experimental design techniques is employed for the optimization and statistical determination of the significant factors influencing on the tensile modulus and yield stress as mechanical properties of this nanocomposite. The significant factors are SWCNT weight fraction and acid treatment time for functionalizing the nanoparticles. Optimum conditions are in 0.7 % of SWCNT weight fraction and 210 min as acid treatment time for 1112.75 ± 28 MPa as maximum tensile modulus and in 216 min and 0.65 % as acid treatment time and SWCNT weight fraction respectively for 40.26 ± 0.3 MPa as maximum yield stress. Also after setting new experiments for test these optimum conditions, found excelent agreement with predicted values.

Optimization of Lakes Aeration Process

The aeration process via injectors is used to combat the lack of oxygen in lakes due to eutrophication. A 3D numerical simulation of the resulting flow using a simplified model is presented. In order to generate the best dynamic in the fluid with respect to the aeration purpose, the optimization of the injectors location is considered. We propose to adapt to this problem the topological sensitivity analysis method which gives the variation of a criterion with respect to the creation of a small hole in the domain. The main idea is to derive the topological sensitivity analysis of the physical model with respect to the insertion of an injector in the fluid flow domain. We propose in this work a topological optimization algorithm based on the studied asymptotic expansion. Finally we present some numerical results, showing the efficiency of our approach

Generational PipeLined Genetic Algorithm (PLGA)using Stochastic Selection

In this paper, a pipelined version of genetic algorithm, called PLGA, and a corresponding hardware platform are described. The basic operations of conventional GA (CGA) are made pipelined using an appropriate selection scheme. The selection operator, used here, is stochastic in nature and is called SA-selection. This helps maintaining the basic generational nature of the proposed pipelined GA (PLGA). A number of benchmark problems are used to compare the performances of conventional roulette-wheel selection and the SA-selection. These include unimodal and multimodal functions with dimensionality varying from very small to very large. It is seen that the SA-selection scheme is giving comparable performances with respect to the classical roulette-wheel selection scheme, for all the instances, when quality of solutions and rate of convergence are considered. The speedups obtained by PLGA for different benchmarks are found to be significant. It is shown that a complete hardware pipeline can be developed using the proposed scheme, if parallel evaluation of the fitness expression is possible. In this connection a low-cost but very fast hardware evaluation unit is described. Results of simulation experiments show that in a pipelined hardware environment, PLGA will be much faster than CGA. In terms of efficiency, PLGA is found to outperform parallel GA (PGA) also.

Neural Network Controller for Mobile Robot Motion Control

In this paper the neural network-based controller is designed for motion control of a mobile robot. This paper treats the problems of trajectory following and posture stabilization of the mobile robot with nonholonomic constraints. For this purpose the recurrent neural network with one hidden layer is used. It learns relationship between linear velocities and error positions of the mobile robot. This neural network is trained on-line using the backpropagation optimization algorithm with an adaptive learning rate. The optimization algorithm is performed at each sample time to compute the optimal control inputs. The performance of the proposed system is investigated using a kinematic model of the mobile robot.

A Joint Routing-Scheduling Approach for Throughput Optimization in WMNs

Wireless Mesh Networking is a promising proposal for broadband data transmission in a large area with low cost and acceptable QoS. These features- trade offs in WMNs is a hot research field nowadays. In this paper a mathematical optimization framework has been developed to maximize throughput according to upper bound delay constraints. IEEE 802.11 based infrastructure backhauling mode of WMNs has been considered to formulate the MINLP optimization problem. Proposed method gives the full routing and scheduling procedure in WMN in order to obtain mentioned goals.

Transmission Lines Loading Enhancement Using ADPSO Approach

Discrete particle swarm optimization (DPSO) is a powerful stochastic evolutionary algorithm that is used to solve the large-scale, discrete and nonlinear optimization problems. However, it has been observed that standard DPSO algorithm has premature convergence when solving a complex optimization problem like transmission expansion planning (TEP). To resolve this problem an advanced discrete particle swarm optimization (ADPSO) is proposed in this paper. The simulation result shows that optimization of lines loading in transmission expansion planning with ADPSO is better than DPSO from precision view point.

Optimization of Some Process Parameters to Produce Raisin Concentrate in Khorasan Region of Iran

Raisin Concentrate (RC) are the most important products obtained in the raisin processing industries. These RC products are now used to make the syrups, drinks and confectionery productions and introduced as natural substitute for sugar in food applications. Iran is a one of the biggest raisin exporter in the world but unfortunately despite a good raw material, no serious effort to extract the RC has been taken in Iran. Therefore, in this paper, we determined and analyzed affected parameters on extracting RC process and then optimizing these parameters for design the extracting RC process in two types of raisin (round and long) produced in Khorasan region. Two levels of solvent (1:1 and 2:1), three levels of extraction temperature (60°C, 70°C and 80°C), and three levels of concentration temperature (50°C, 60°C and 70°C) were the treatments. Finally physicochemical characteristics of the obtained concentrate such as color, viscosity, percentage of reduction sugar, acidity and the microbial tests (mould and yeast) were counted. The analysis was performed on the basis of factorial in the form of completely randomized design (CRD) and Duncan's multiple range test (DMRT) was used for the comparison of the means. Statistical analysis of results showed that optimal conditions for production of concentrate is round raisins when the solvent ratio was 2:1 with extraction temperature of 60°C and then concentration temperature of 50°C. Round raisin is cheaper than the long one, and it is more economical to concentrate production. Furthermore, round raisin has more aromas and the less color degree with increasing the temperature of concentration and extraction. Finally, according to mentioned factors the concentrate of round raisin is recommended.

A Green Design for Assembly Model for Integrated Design Evaluation and Assembly and Disassembly Sequence Planning

A green design for assembly model is presented to integrate design evaluation and assembly and disassembly sequence planning by evaluating the three activities in one integrated model. For an assembled product, an assembly sequence planning model is required for assembling the product at the start of the product life cycle. A disassembly sequence planning model is needed for disassembling the product at the end. In a green product life cycle, it is important to plan how a product can be disassembled, reused, or recycled, before the product is actually assembled and produced. Given a product requirement, there may be several design alternative cases to design the same product. In the different design cases, the assembly and disassembly sequences for producing the product can be different. In this research, a new model is presented to concurrently evaluate the design and plan the assembly and disassembly sequences. First, the components are represented by using graph based models. Next, a particle swarm optimization (PSO) method with a new encoding scheme is developed. In the new PSO encoding scheme, a particle is represented by a position matrix defining an assembly sequence and a disassembly sequence. The assembly and disassembly sequences can be simultaneously planned with an objective of minimizing the total of assembly costs and disassembly costs. The test results show that the presented method is feasible and efficient for solving the integrated design evaluation and assembly and disassembly sequence planning problem. An example product is implemented and illustrated in this paper.

Optimal Preventive Maintenance of the Reserve Source in the Industrial Electric Network

The great majority of the electric installations belong to the first and second category. In order to ensure a high level of reliability of their electric system feeder, two power supply sources are envisaged, one principal, the other of reserve, generally a cold reserve (electric diesel group). The principal source being under operation, its control can be ideal and sure, however for the reserve source being in stop, a preventive maintenance-s which proceeds on time intervals (periodicity) and for well defined lengths of time are envisaged, so that this source will always available in case of the principal source failure. The choice of the periodicity of preventive maintenance of the source of reserve influences directly the reliability of the electric feeder system. On the basis of the semi-markovians processes, the influence of the periodicity of the preventive maintenance of the source of reserve is studied and is given the optimal periodicity.