A Deterministic Optimization Approach to Protein Sequence Design Using Continuous Models

Determining the sequence of amino acid residues in a heteropolymer chain of a protein with a given conformation is a discrete combinatorial problem that is not generally amenable for gradient-based continuous optimization algorithms. In this paper we present a new approach to this problem using continuous models. In this modeling, continuous "state functions" are proposed to designate the type of each residue in the chain. Such a continuous model helps define a continuous sequence space in which a chosen criterion is optimized to find the most appropriate sequence. Searching a continuous sequence space using a deterministic optimization algorithm makes it possible to find the optimal sequences with much less computation than many other approaches. The computational efficiency of this method is further improved by combining it with a graph spectral method, which explicitly takes into account the topology of the desired conformation and also helps make the combined method more robust. The continuous modeling used here appears to have additional advantages in mimicking the folding pathways and in creating the energy landscapes that help find sequences with high stability and kinetic accessibility. To illustrate the new approach, a widely used simplifying assumption is made by considering only two types of residues: hydrophobic (H) and polar (P). Self-avoiding compact lattice models are used to validate the method with known results in the literature and data that can be practically obtained by exhaustive enumeration on a desktop computer. We also present examples of sequence design for the HP models of some real proteins, which are solved in less than five minutes on a single-processor desktop computer Some open issues and future extensions are noted.

Compiler-assisted power optimization for clustered VLIW architectures

Clustered VLIW architectures solve the scalability problem associated with flat VLIW architectures by partitioning the register file and connecting only a subset of the functional units to a register file. However, inter-cluster communication in clustered architectures leads to increased leakage in functional components and a high number of register accesses. In this paper, we propose compiler scheduling algorithms targeting two previously ignored power-hungry components in clustered VLIW architectures, viz., instruction decoder and register file. We consider a split decoder design and propose a new energy-aware instruction scheduling algorithm that provides 14.5% and 17.3% benefit in the decoder power consumption on an average over a purely hardware based scheme in the context of 2-clustered and 4-clustered VLIW machines. In the case of register files, we propose two new scheduling algorithms that exploit limited register snooping capability to reduce extra register file accesses. The proposed algorithms reduce register file power consumption on an average by 6.85% and 11.90% (10.39% and 17.78%), respectively, along with performance improvement of 4.81% and 5.34% (9.39% and 11.16%) over a traditional greedy algorithm for 2-clustered (4-clustered) VLIW machine. (C) 2010 Elsevier B.V. All rights reserved.

Stochastic Approximation Algorithms for Constrained Optimization via Simulation

We develop four algorithms for simulation-based optimization under multiple inequality constraints. Both the cost and the constraint functions are considered to be long-run averages of certain state-dependent single-stage functions. We pose the problem in the simulation optimization framework by using the Lagrange multiplier method. Two of our algorithms estimate only the gradient of the Lagrangian, while the other two estimate both the gradient and the Hessian of it. In the process, we also develop various new estimators for the gradient and Hessian. All our algorithms use two simulations each. Two of these algorithms are based on the smoothed functional (SF) technique, while the other two are based on the simultaneous perturbation stochastic approximation (SPSA) method. We prove the convergence of our algorithms and show numerical experiments on a setting involving an open Jackson network. The Newton-based SF algorithm is seen to show the best overall performance.

Adaptive optimization of continuous bioreactor using neural network model

An adaptive optimization algorithm using backpropogation neural network model for dynamic identification is developed. The algorithm is applied to maximize the cellular productivity of a continuous culture of baker's yeast. The robustness of the algorithm is demonstrated in determining and maintaining the optimal dilution rate of the continuous bioreactor in presence of disturbances in environmental conditions and microbial culture characteristics. The simulation results show that a significant reduction in time required to reach optimal operating levels can be achieved using neural network model compared with the traditional dynamic linear input-output model. The extension of the algorithm for multivariable adaptive optimization of continuous bioreactor is briefly discussed.

Constrained optimization of heat exchangers

Optimizing a shell and tube heat exchanger for a given duty is an important and relatively difficult task. There is a need for a simple, general and reliable method for realizing this task. The authors present here one such method for optimizing single phase shell-and-tube heat exchangers with given geometric and thermohydraulic constraints. They discuss the problem in detail. Then they introduce a basic algorithm for optimizing the exchanger. This algorithm is based on data from an earlier study of a large collection of feasible designs generated for different process specifications. The algorithm ensures a near-optimal design satisfying the given heat duty and geometric constraints. The authors also provide several sub-algorithms to satisfy imposed velocity limitations. They illustrate how useful these sub-algorithms are with several examples where the exchanger weight is minimized.

Optimization of Helicopter Rotor Using Polynomial and Neural Network Metamodels

This study aims to determine optimal locations of dual trailing-edge flaps and blade stiffness to achieve minimum hub vibration levels in a helicopter, with low penalty in terms of required trailing-edge flap control power. An aeroelastic analysis based on finite elements in space and time is used in conjunction with an optimal control algorithm to determine the flap time history for vibration minimization. Using the aeroelastic analysis, it is found that the objective functions are highly nonlinear and polynomial response surface approximations cannot describe the objectives adequately. A neural network is then used for approximating the objective functions for optimization. Pareto-optimal points minimizing both helicopter vibration and flap power ale obtained using the response surface and neural network metamodels. The two metamodels give useful improved designs resulting in about 27% reduction in hub vibration and about 45% reduction in flap power. However, the design obtained using response surface is less sensitive to small perturbations in the design variables.

Multiscale stochastic approximation for parametric optimization of hidden Markov models

A two-time scale stochastic approximation algorithm is proposed for simulation-based parametric optimization of hidden Markov models, as an alternative to the traditional approaches to ''infinitesimal perturbation analysis.'' Its convergence is analyzed, and a queueing example is presented.

The actor-critic algorithm as multi-time-scale stochastic approximation

The actor-critic algorithm of Barto and others for simulation-based optimization of Markov decision processes is cast as a two time Scale stochastic approximation. Convergence analysis, approximation issues and an example are studied.

Shape optimization of RC flexural members

A natural velocity field method for shape optimization of reinforced concrete (RC) flexural members has been demonstrated. The possibility of shape optimization by modifying the shape of an initially rectangular section, in addition to variation of breadth and depth along the length, has been explored. Necessary shape changes have been computed using the sequential quadratic programming (SQP) technique. Genetic algorithm (Goldberg and Samtani 1986) has been used to optimize the diameter and number of main reinforcement bars. A limit-state design approach has been adopted for the nonprismatic RC sections. Such relevant issues as formulation of optimization problem, finite-element modeling, and solution procedure have been described. Three design examples-a simply supported beam, a cantilever beam, and a two-span continuous beam, all under uniformly distributed loads-have been optimized. The results show a significant savings (40-56%) in material and cost and also result in aesthetically pleasing structures. This procedure will lead to considerable cost saving, particularly in cases of mass-produced precast members and a heavy cast-in-place member such as a bridge girder.

Neural network based optimal routing algorithm for communication networks

This paper presents the capability of the neural networks as a computational tool for solving constrained optimization problem, arising in routing algorithms for the present day communication networks. The application of neural networks in the optimum routing problem, in case of packet switched computer networks, where the goal is to minimize the average delays in the communication have been addressed. The effectiveness of neural network is shown by the results of simulation of a neural design to solve the shortest path problem. Simulation model of neural network is shown to be utilized in an optimum routing algorithm known as flow deviation algorithm. It is also shown that the model will enable the routing algorithm to be implemented in real time and also to be adaptive to changes in link costs and network topology. (C) 2002 Elsevier Science Ltd. All rights reserved.

Unified Vdd Vth Optimization Based DVFM Controller for a Logic Block

In this paper analytical expressions for optimal Vdd and Vth to minimize energy for a given speed constraint are derived. These expressions are based on the EKV model for transistors and are valid in both strong inversion and sub threshold regions. The effect of gate leakage on the optimal Vdd and Vth is analyzed. A new gradient based algorithm for controlling Vdd and Vth based on delay and power monitoring results is proposed. A Vdd-Vth controller which uses the algorithm to dynamically control the supply and threshold voltage of a representative logic block (sum of absolute difference computation of an MPEG decoder) is designed. Simulation results using 65 nm predictive technology models are given.

A Nash Bargaining Approach to Retention Enhancing Bid Optimization in Sponsored Search Auctions with Discrete Bids

Bid optimization is now becoming quite popular in sponsored search auctions on the Web. Given a keyword and the maximum willingness to pay of each advertiser interested in the keyword, the bid optimizer generates a profile of bids for the advertisers with the objective of maximizing customer retention without compromising the revenue of the search engine. In this paper, we present a bid optimization algorithm that is based on a Nash bargaining model where the first player is the search engine and the second player is a virtual agent representing all the bidders. We make the realistic assumption that each bidder specifies a maximum willingness to pay values and a discrete, finite set of bid values. We show that the Nash bargaining solution for this problem always lies on a certain edge of the convex hull such that one end point of the edge is the vector of maximum willingness to pay of all the bidders. We show that the other endpoint of this edge can be computed as a solution of a linear programming problem. We also show how the solution can be transformed to a bid profile of the advertisers.

Accurate Parameter Estimation of Contaminant Transport Inverse Problem using Paartaicle Swarm Optimization

Swarm Intelligence techniques such as particle swarm optimization (PSO) are shown to be incompetent for an accurate estimation of global solutions in several engineering applications. This problem is more severe in case of inverse optimization problems where fitness calculations are computationally expensive. In this work, a novel strategy is introduced to alleviate this problem. The proposed inverse model based on modified particle swarm optimization algorithm is applied for a contaminant transport inverse model. The inverse models based on standard-PSO and proposed-PSO are validated to estimate the accuracy of the models. The proposed model is shown to be out performing the standard one in terms of accuracy in parameter estimation. The preliminary results obtained using the proposed model is presented in this work.

A Comparative Study of the Formulations for Topology Optimization of Compliant Mechanisms

The topology optimization problem for the synthesis of compliant mechanisms has been formulated in many different ways in the last 15 years, but there is not yet a definitive formulation that is universally accepted. Furthermore, there are two unresolved issues in this problem. In this paper, we present a comparative study of five distinctly different formulations that are reported in the literature. Three benchmark examples are solved with these formulations using the same input and output specifications and the same numerical optimization algorithm. A total of 35 different synthesis examples are implemented. The examples are limited to desired instantaneous output direction for prescribed input force direction. Hence, this study is limited to linear elastic modeling with small deformations. Two design parameterizations, namely, the frame element based ground structure and the density approach using continuum elements, are used. The obtained designs are evaluated with all other objective functions and are compared with each other. The checkerboard patterns, point flexures, the ability to converge from an unbiased uniform initial guess, and the computation time are analyzed. Some observations are noted based on the extensive implementation done in this study. Complete details of the benchmark problems and the results are included. The computer codes related to this study are made available on the internet for ready access.

Exploring isospectral spring-mass systems with firefly algorithm

This paper investigates in-line spring-mass systems (An), fixed at one end and free at the other, with n-degrees of freedom (d.f.). The objective is to find feasible in-line systems (B(n)) that are isospectral to a given system. The spring-mass systems, A(n) and B(n), are represented by Jacobi matrices. An error function is developed with the help of the Jacobi matrices A(n) and B(n). The problem of finding the isospectral systems is posed as an optimization problem with the aim of minimizing the error function. The approach for creating isospectral systems uses the fact that the trace of two isospectral Jacobi matrices A(n) and B(n) should be identical. A modification is made to the diagonal elements of the given Jacobi matrix (A(n)), to create the isospectral systems. The optimization problem is solved using the firefly algorithm augmented by a local search procedure. Numerical results are obtained and resulting isospectral systems are shown for 4 d.f. and 10 d.f. systems.