Simulated-annealing-based genetic algorithm for modeling the optical constants of solids

We propose a simulated-annealing-based genetic algorithm for solving model parameter estimation problems. The algorithm incorporates advantages of both genetic algorithms and simulated annealing. Tests on computer-generated synthetic data that closely resemble optical constants of a metal were performed to compare the efficiency of plain genetic algorithms against the simulated-annealing-based genetic algorithms. These tests assess the ability of the algorithms to and the global minimum and the accuracy of values obtained for model parameters. Finally, the algorithm with the best performance is used to fit the model dielectric function to data for platinum and aluminum. (C) 1997 Optical Society of America.

Generation of eigenstates using the phase-estimation algorithm

The phase estimation algorithm is so named because it allows an estimation of the eigenvalues associated with an operator. However, it has been proposed that the algorithm can also be used to generate eigenstates. Here we extend this proposal for small quantum systems, identifying the conditions under which the phase-estimation algorithm can successfully generate eigenstates. We then propose an implementation scheme based on an ion trap quantum computer. This scheme allows us to illustrate two simple examples, one in which the algorithm effectively generates eigenstates, and one in which it does not.

Complex natural resonances of conducting planar objects buried in a dielectric half-space

A scheme is presented to incorporate a mixed potential integral equation (MPIE) using Michalski's formulation C with the method of moments (MoM) for analyzing the scattering of a plane wave from conducting planar objects buried in a dielectric half-space. The robust complex image method with a two-level approximation is used for the calculation of the Green's functions for the half-space. To further speed up the computation, an interpolation technique for filling the matrix is employed. While the induced current distributions on the object's surface are obtained in the frequency domain, the corresponding time domain responses are calculated via the inverse fast Fourier transform (FFT), The complex natural resonances of targets are then extracted from the late time response using the generalized pencil-of-function (GPOF) method. We investigate the pole trajectories as we vary the distance between strips and the depth and orientation of single, buried strips, The variation from the pole position of a single strip in a homogeneous dielectric medium was only a few percent for most of these parameter variations.

An algorithm to predict 3 ' intron splice sites in Plasmodium falciparum genomic sequences

A new algorithm, PfAGSS, for predicting 3' splice sites in Plasmodium falciparum genomic sequences is described. Application of this program to the published P. falciparum chromosome 2 and 3 data suggests that existing programs result in a high error rate in assigning 3' intron boundaries. (C) 2001 Elsevier Science B.V. All rights reserved.

A flexible method for rapid force computation in elliptical magnets

The design of open-access elliptical cross-section magnet systems has recently come under consideration. Obtaining values for the forces generated within these unusual magnets is important to progress the designs towards feasible instruments. This paper presents a novel and flexible method for the rapid computation of forces within elliptical magnets. The method is demonstrated by the analysis of a clinical magnetic resonance imaging magnet of elliptical cross-section and open design. The analysis reveals the non-symmetric nature of the generated Maxwell forces, which are an important consideration, particularly in the design of superconducting systems.

A simulated annealing algorithm for finding consensus sequences

Motivation: A consensus sequence for a family of related sequences is, as the name suggests, a sequence that captures the features common to most members of the family. Consensus sequences are important in various DNA sequencing applications and are a convenient way to characterize a family of molecules. Results: This paper describes a new algorithm for finding a consensus sequence, using the popular optimization method known as simulated annealing. Unlike the conventional approach of finding a consensus sequence by first forming a multiple sequence alignment, this algorithm searches for a sequence that minimises the sum of pairwise distances to each of the input sequences. The resulting consensus sequence can then be used to induce a multiple sequence alignment. The time required by the algorithm scales linearly with the number of input sequences and quadratically with the length of the consensus sequence. We present results demonstrating the high quality of the consensus sequences and alignments produced by the new algorithm. For comparison, we also present similar results obtained using ClustalW. The new algorithm outperforms ClustalW in many cases.

Computation of the linear elastic properties of random porous materials with a wide variety of microstructure

A finite-element method is used to study the elastic properties of random three-dimensional porous materials with highly interconnected pores. We show that Young's modulus, E, is practically independent of Poisson's ratio of the solid phase, nu(s), over the entire solid fraction range, and Poisson's ratio, nu, becomes independent of nu(s) as the percolation threshold is approached. We represent this behaviour of nu in a flow diagram. This interesting but approximate behaviour is very similar to the exactly known behaviour in two-dimensional porous materials. In addition, the behaviour of nu versus nu(s) appears to imply that information in the dilute porosity limit can affect behaviour in the percolation threshold limit. We summarize the finite-element results in terms of simple structure-property relations, instead of tables of data, to make it easier to apply the computational results. Without using accurate numerical computations, one is limited to various effective medium theories and rigorous approximations like bounds and expansions. The accuracy of these equations is unknown for general porous media. To verify a particular theory it is important to check that it predicts both isotropic elastic moduli, i.e. prediction of Young's modulus alone is necessary but not sufficient. The subtleties of Poisson's ratio behaviour actually provide a very effective method for showing differences between the theories and demonstrating their ranges of validity. We find that for moderate- to high-porosity materials, none of the analytical theories is accurate and, at present, numerical techniques must be relied upon.

Universal simulation of Hamiltonian dynamics for quantum systems with finite-dimensional state spaces

What interactions are sufficient to simulate arbitrary quantum dynamics in a composite quantum system? Dodd [Phys. Rev. A 65, 040301(R) (2002)] provided a partial solution to this problem in the form of an efficient algorithm to simulate any desired two-body Hamiltonian evolution using any fixed two-body entangling N-qubit Hamiltonian, and local unitaries. We extend this result to the case where the component systems are qudits, that is, have D dimensions. As a consequence we explain how universal quantum computation can be performed with any fixed two-body entangling N-qudit Hamiltonian, and local unitaries.