Analysis of grid file algorithms

Grid file algorithms were suggested in [12] to provide multi-key access to records in a dynamically growing file. We specify here two algorithms and derive the average sizes of the corresponding directories. We provide an asymptotic analysis. The growth of the indexes appears to be non-linear for uniform distributions:O(v ^c ) orO(v ), wherec=1+b^–1, =1+(s-1)/(sb+1),s is the number of attributes being used,v the file size, andb the page capacity of the system. Finally we give corresponding results for biased distributions and compare transient phases.     

Lattice models of peptide aggregation: evaluation of conformational search algorithms

We present a series of conformational search calculations on the aggregation of short peptide fragments that form fibrils similar to those seen in many protein mis-folding diseases. The proteins were represented by a face-centered cubic lattice model with the conformational energies calculated using the Miyazawa-Jernigan potential. The searches were performed using algorithms based on the Metropolis Monte Carlo method, including simulated annealing and replica exchange. We also present the results of searches using the tabu search method, an algorithm that has been used for many optimization problems, but has rarely been used in protein conformational searches. The replica exchange algorithm consistently found more stable structures then the other algorithms, and was particularly effective for the octamers and larger systems.     

MM3 parametrization of four‐ and five‐coordinated rhenium complexes by a genetic algorithm—Which factors influence the optimization performance?

Genetic algorithms (GA) were used to solve one of the multidimensional problems in computational chemistry, the optimization of force field parameters. The correlation between the composition of the GA, its parameters (p(c), p(m)) and the quality of the results were investigated. The composition was studied for all combinations of a Simple GA/Steady State GA with a Roulette Wheel/Tournament Selector using different values each for crossover (0.5, 0.7, 0.9) and mutation rates (0.01, 0.02, 0.05, 0.10, 0.20). The results show that the performance is strongly dependent on the GA scheme, where the Simple GA/Tournament Selector yields the best results. Two new MM3 parameters were introduced for rhenium compounds with coordination number four (204) and coordination number five (205), the formal oxidation states of rhenium ranging from +V to +VII. A manifold of parameters (Re-C, N, O, S) was obtained by using a diverse set of CSD structures. The advantage of the GA vs. UFF calculations is shown by comparison of several examples. The GA optimized parameters were able to reproduce the geometrical data of the X-ray structures.     

Selecting variables for k-means cluster analysis by using a genetic algorithm that optimises the silhouettes

The goal of present work is to analyse the effect of having non-informative variables (NIV) in a data set when applying cluster analysis and to propose a method computationally capable of detecting and removing these variables. The method proposed is based on the use of a genetic algorithm to select those variables important to make the presence of groups in data clear. The procedure has been implemented to be used with k-means and using the cluster silhouettes as fitness function for the genetic algorithm.The main problem that can appear when applying the method to real data is the fact that, in general, we do not know a priori what the real cluster structure is (number and composition of the groups).The work explores the evolution of the silhouette values computed from the clusters built by using k-means when non-informative variables are added to the original data set in both a literature data set as well as some simulated data in higher dimension. The procedure has also been applied to real data sets.     

Complete graph conjecture for inner-core electrons: homogeneous index case

The complete graph conjecture that encodes the inner-core electrons of atoms with principal quantum number n >or= 2 with complete graphs, and especially with odd complete graphs, is discussed. This conjecture is used to derive new values for the molecular connectivity and pseudoconnectivity basis indices of hydrogen-suppressed chemical pseudographs. For atoms with n = 2 the new values derived with this conjecture are coincident with the old ones. The modeling ability of the new homogeneous basis indices, and of the higher-order terms, is tested and compared with previous modeling studies, which are centered on basis indices that are either based on quantum concepts or partially based on this new conjecture for the inner-core electrons. Two similar algorithms have been proposed with this conjecture, and they parallel the two "quantum" algorithms put forward by molecular connectivity for atoms with n > 2. Nine properties of five classes of compounds have been tested: the molecular polarizabilities of a class of organic compounds, the dipole moment, molar refraction, boiling points, ionization energies, and parachor of a series of halomethanes, the lattice enthalpy of metal halides, the rates of hydrogen abstraction of chlorofluorocarbons, and the pED(50) of phenylalkylamines. The two tested algorithms based on the odd complete graph conjecture give rise to a highly interesting model of the nine properties, and three of them can even be modeled by the same set of basis indices. Interesting is the role of some basis indices all along the model.     

On affine scaling algorithms for nonconvex quadratic programming

We investigate the use of interior algorithms, especially the affine-scaling algorithm, to solve nonconvex — indefinite or negative definite — quadratic programming (QP) problems. Although the nonconvex QP with a polytope constraint is a hard problem, we show that the problem with an ellipsoidal constraint is easy. When the hard QP is solved by successively solving the easy QP, the sequence of points monotonically converge to a feasible point satisfying both the first and the second order optimality conditions.Research supported in part by NSF Grant DDM-8922636 and the College Summer Grant, College of Business Administration, The University of Iowa.     

Numerical solution of minimax problems of optimal control,part 1

This paper contains general transformation techniques useful to convert minimax problems of optimal control into the Mayer-Bolza problem of the calculus of variations [Problem (P)]. We consider two types of minimax problems: minimax problems of Type (Q), in which the minimax function depends on the state and does not depend on the control; and minimax problems of Type (R), in which the minimax function depends on both the state and the control. Both Problem (Q) and Problem (R) can be reduced to Problem (P).For Problem (Q), we exploit the analogy with a bounded-state problem in combination with a transformation of the Jacobson type. This requires the proper augmentation of the state vectorx(t), the control vectoru(t), and the parameter vector , as well as the proper augmentation of the constraining relations. As a result of the transformation, the unknown minimax value of the performance index becomes a component of the parameter vector being optimized.For Problem (R), we exploit the analogy with a bounded-control problem in combination with a transformation of the Valentine type. This requires the proper augmentation of the control vectoru(t) and the parameter vector , as well as the proper augmentation of the constraining relations. As a result of the transformation, the unknown minimax value of the performance index becomes a component of the parameter vector being optimized.In a subsequent paper (Part 2), the transformation techniques presented here are employed in conjunction with the sequential gradient-restoration algorithm for solving optimal control problems on a digital computer; both the single-subarc approach and the multiple-subarc approach are discussed.This research was supported by the National Science Foundation, Grant No. ENG-79-18667, and by Wright-Patterson Air Force Base, Contract No. F33615-80-C3000. This paper is a condensation of the investigations reported in Refs. 1–7. The authors are indebted to E. M. Coker and E. M. Sims for analytical and computational assistance.     

Discontinuous Galerkin methods on graphics processing units for nonlinear hyperbolic conservation laws

We present a novel implementation of the modal DG method for hyperbolic conservation laws in two dimensions on graphics processing units (GPUs) using NVIDIA's Compute Unified Device Architecture. Both flexible and highly accurate, DG methods accommodate parallel architectures well as their discontinuous nature produces element‐local approximations. High‐performance scientific computing suits GPUs well, as these powerful, massively parallel, cost‐effective devices have recently included support for double‐precision floating‐point numbers. Computed examples for Euler equations over unstructured triangle meshes demonstrate the effectiveness of our implementation on an NVIDIA GTX 580 device. Profiling of our method reveals performance comparable with an existing nodal DG‐GPU implementation for linear problems. Copyright © 2014 John Wiley & Sons, Ltd.     

Imperialist competitive algorithm combined with chaos for global optimization

A novel chaotic improved imperialist competitive algorithm (CICA) is presented for global optimization. The ICA is a new meta-heuristic optimization developed based on a socio-politically motivated strategy and contains two main steps: the movement of the colonies and the imperialistic competition. Here different chaotic maps are utilized to improve the movement step of the algorithm. Seven different chaotic maps are investigated and the Logistic and Sinusoidal maps are found as the best choices. Comparing the new algorithm with the other ICA-based methods demonstrates the superiority of the CICA for the benchmark functions.