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At least 271 records · Page 15Linked to original sources

PubMed2004

Distortions induced by radioactive seeds into interstitial brachytherapy dose distributions.

In a previous article, we presented development and verification of an integral transport equation-based deterministic algorithm for computing three-dimensional brachytherapy dose distributions. Recently, we have included fluorescence radiation physics and parallel computation to the standing algorithms so that we can compute dose distributions for a large set of seeds without resorting to the superposition methods. The introduction of parallel computing capability provided a means to compute the dose distribution for multiple seeds in a simultaneous manner. This provided a way to study strong heterogeneity and shadow effects induced by the presence of multiple seeds in an interstitial brachytherapy implant. This article presents the algorithm for computing fluorescence radiation, algorithm for parallel computing, and display results for an 81-seed implant that has a perfect and imperfect lattice. The dosimetry data for a single model 6711 seeds is presented for verification and heterogeneity factor computations using simultaneous and superposition techniques are presented.

Artifacts↗

PubMed1994

High speed pattern matching in genetic data base with reconfigurable hardware.

Homology detection in large data bases is probably the most time consuming operation in molecular genetic computing systems. Moreover, the progresses made all around the world concerning the mapping and sequencing of the genome of Homo Sapiens and other species have increased the size of data bases exponentially. Therefore even the best workstation would not be able to reach the scanning speed required. In order to answer this need we propose an algorithm, A2R2, and its implementation on a massively parallel system. Basically, two kinds of algorithms are used to search in molecular genetic data bases. The first kind is based on dynamic programming and the second on word processing, A2R2 belongs to the second kind. The structure of the motif (pattern) searched by A2R2 can support those from FAST, BLAST and FLASH algorithms. After a short presentation of the reconfigurable hardware concept and technology used in our massively parallel accelerator we present the A2R2 implementation. This parallel implementation outperforms any kind of previously published genetic data base scanning hardware or algorithms. We report up to 25 million nucleotides per scanning seconds as our best results.

Algorithms↗

PubMed2006

Hybrid Monte Carlo simulation of a glass-forming binary mixture.

We propose a different, hybrid Monte Carlo algorithm that combines configurational bias particle swaps with parallel tempering. We use this algorithm to simulate a standard model of a glass-forming binary mixture above and below the so-called mode-coupling temperature T(MCT). We find that an ansatz that was used previously to extrapolate thermodynamic quantities to temperatures below T(MCT) breaks down in the vicinity of the mode-coupling temperature. We also find that the Adam-Gibbs relations D(alpha)exp(-a/TS(c)) and tau(alpha)exp(b/TS(c)), which connect the diffusion coefficient D and the relaxation time tau with the configurational entropy S(c), are valid for all temperatures for which the configurational and vibrational contributions to the free energy decouple.

Journal Article↗

PubMed2001

Where genetic algorithms excel.

We analyze the performance of a genetic algorithm (GA) we call Culling, and a variety of other algorithms, on a problem we refer to as the Additive Search Problem (ASP). We show that the problem of learning the Ising perceptron is reducible to a noisy version of ASP. Noisy ASP is the first problem we are aware of where a genetic-type algorithm bests all known competitors. We generalize ASP to k-ASP to study whether GAs will achieve "implicit parallelism" in a problem with many more schemata. GAs fail to achieve this implicit parallelism, but we describe an algorithm we call Explicitly Parallel Search that succeeds. We also compute the optimal culling point for selective breeding, which turns out to be independent of the fitness function or the population distribution. We also analyze a mean field theoretic algorithm performing similarly to Culling on many problems. These results provide insight into when and how GAs can beat competing methods.

Algorithms↗

PubMed2005

A new analytical method for computing solvent-accessible surface area of macromolecules and its gradients.

In the calculation of thermodynamic properties and three-dimensional structures of macromolecules, such as proteins, it is important to have an efficient algorithm for computing the solvent-accessible surface area of macromolecules. Here, we propose a new analytical method for this purpose. In the proposed algorithm we consider the transformation that maps the spherical circles formed by intersection of the atomic surfaces in three-dimensional space onto the circles on a two-dimensional plane, and the problem of computing the solvent-accessible surface area is reduced to the problem of computing the corresponding curve integrals on the plane. This allows to consider only the integrals along the circular trajectories on the plane. The algorithm is suitable for parallelization. Testings on many proteins as well as the comparison to the other analogous algorithms have shown that our method is accurate and efficient.

Algorithms↗

PubMed1991

Evaluation of a parallel implementation of the learning portion of the backward error propagation neural network: experiments in artifact identification.

Various methods have been proposed in an attempt to solve problems in artifact and/or alarm identification including expert systems, statistical signal processing techniques, and artificial neural networks (ANN). ANNs consist of a large number of simple processing units connected by weighted links. To develop truly robust ANNs, investigators are required to train their networks on huge training data sets, requiring enormous computing power. We implemented a parallel version of the backward error propagation neural network training algorithm in the widely portable parallel programming language C-Linda. A maximum speedup of 4.06 was obtained with six processors. This speedup represents a reduction in total run-time from approximately 6.4 hours to 1.5 hours. We conclude that use of the master-worker model of parallel computation is an excellent method for obtaining speedups in the backward error propagation neural network training algorithm.

Algorithms↗

PubMed2005

Ab initio crystal structure prediction-I. Rigid molecules.

A new methodology for the prediction of molecular crystal structures using only the atomic connectivity of the molecule under consideration is presented. The approach is based on the global minimization of the lattice enthalpy of the crystal. The modeling of the electrostatic interactions is accomplished through a set of distributed charges that are optimally and automatically selected and positioned based on results of quantum mechanical calculations. A four-step global optimization algorithm is used for the identification of the local minima of the lattice enthalpy surface. A parallelized implementation of the algorithm permits a much more extensive search of the solution space than has hitherto been possible, allowing the identification of crystal structures in less frequently occurring space groups and with more than one molecule in the asymmetric unit. The algorithm has been applied successfully to the prediction of the crystal structures of 3-aza-bicyclo(3.3.1)nonane-2,4-dione (P2(1)/a, Z' = 1), allopurinol (P2(1)/c, Z' = 1), 1,3,4,6,7,9-hexa-azacycl(3.3.3)azine (Pbca, Z' = 2), and triethylenediamine (P6(3)/m, Z' = 1). In all cases, the experimentally known structure is among the most stable predicted structures, but not necessarily the global minimum.

Journal Article↗

PubMed1983

A geometric approach to the filtered backpropagation algorithm.

We show how the filtered backpropagation algorithm [1] for parallel-beam diffraction tomography can be implemented geometrically by weighted straight-line projections. The resulting algorithm is formally equivalent to the original approach using Fourier transforms [2], but reorganizes the calculations to separately backpropagate each plane-wave component of the filtered data. In principle, at least, the projection method also suggests the design of an ultrasound scanner that records the wavefield with line detectors.

Fourier Analysis↗

PubMed2001

A cone beam filtered backprojection (CB-FBP) reconstruction algorithm for a circle-plus-two-arc orbit.

The circle-plus-arc orbit possesses advantages over other "circle-plus" orbits for the application of x-ray cone beam (CB) volume CT in image-guided interventional procedures requiring intraoperative imaging, in which movement of the patient table is to be avoided. A CB circle-plus-two-arc orbit satisfying the data sufficiency condition and a filtered backprojection (FBP) algorithm to reconstruct longitudinally unbounded objects is presented here. In the circle suborbit, the algorithm employs Feldkamp's formula and another FBP implementation. In the arc suborbits, an FBP solution is obtained originating from Grangeat's formula, and the reconstruction computation is significantly reduced using a window function to exclude redundancy in Radon domain. The performance of the algorithm has been thoroughly evaluated through computer-simulated phantoms and preliminarily evaluated through experimental data, revealing that the algorithm can regionally reconstruct longitudinally unbounded objects exactly and efficiently, is insensitive to the variation of the angle sampling interval along the arc suborbits, and is robust over practical x-ray quantum noise. The algorithm's merits include: only 1D filtering is implemented even in a 3D reconstruction, only separable 2D interpolation is required to accomplish the CB backprojection, and the algorithm structure is appropriate for parallel computation.

Algorithms↗

PubMedDate not supplied

Simulation of CT reconstruction artifacts associated with multiple-rotation fan-beam data collection.

Artifacts in reconstructed image caused by the errors in projection data depend on the source of the error itself, on the data collection mode and on the reconstruction algorithm. The effect of the multiple-rotation fan-beam data collection modes and corresponding reordered parallel convolution-backprojection algorithms on reconstruction artifacts of this type is analysed.

Humans↗

PubMed1985

Computer-assisted analysis of two-dimensional electrophoresis images using an array processor.

The CLIP4 machine has been used to analyze two-dimensional electrophoresis gel images. The architecture of the CLIP4 machine allows high-speed processing of gel images unavailable on conventional machines. The paper gives a brief review of the CLIP system followed by a detailed description of the segmentation and comparison algorithms. The segmentation algorithm makes full use of methods already designed for other gel analysis systems, but optimized for use on the highly parallel CLIP4 machine. The comparison algorithm is a totally new method using, to the full, the parallel efficiency of the CLIP4 computer. The algorithm attempts to match each spot on one gel with a corresponding spot on a second gel, operating simultaneously on all pairs of spots.

Biometry↗

PubMed2006

Multimillion atom simulations of dynamics of oxidation of an aluminum nanoparticle and nanoindentation on ceramics.

We have developed a first-principles-based hierarchical simulation framework, which seamlessly integrates (1) a quantum mechanical description based on the density functional theory (DFT), (2) multilevel molecular dynamics (MD) simulations based on a reactive force field (ReaxFF) that describes chemical reactions and polarization, a nonreactive force field that employs dynamic atomic charges, and an effective force field (EFF), and (3) an atomistically informed continuum model to reach macroscopic length scales. For scalable hierarchical simulations, we have developed parallel linear-scaling algorithms for (1) DFT calculation based on a divide-and-conquer algorithm on adaptive multigrids, (2) chemically reactive MD based on a fast ReaxFF (F-ReaxFF) algorithm, and (3) EFF-MD based on a space-time multiresolution MD (MRMD) algorithm. On 1920 Intel Itanium2 processors, we have demonstrated 1.4 million atom (0.12 trillion grid points) DFT, 0.56 billion atom F-ReaxFF, and 18.9 billion atom MRMD calculations, with parallel efficiency as high as 0.953. Through the use of these algorithms, multimillion atom MD simulations have been performed to study the oxidation of an aluminum nanoparticle. Structural and dynamic correlations in the oxide region are calculated as well as the evolution of charges, surface oxide thickness, diffusivities of atoms, and local stresses. In the microcanonical ensemble, the oxidizing reaction becomes explosive in both molecular and atomic oxygen environments, due to the enormous energy release associated with Al-O bonding. In the canonical ensemble, an amorphous oxide layer of a thickness of approximately 40 angstroms is formed after 466 ps, in good agreement with experiments. Simulations have been performed to study nanoindentation on crystalline, amorphous, and nanocrystalline silicon nitride and silicon carbide. Simulation on nanocrystalline silicon carbide reveals unusual deformation mechanisms in brittle nanophase materials, due to coexistence of brittle grains and soft amorphous-like grain boundary phases. Simulations predict a crossover from intergranular continuous deformation to intragrain discrete deformation at a critical indentation depth.

Journal Article↗

PubMed2004

BAPS 2: enhanced possibilities for the analysis of genetic population structure.

UNLABELLED: Bayesian statistical methods based on simulation techniques have recently been shown to provide powerful tools for the analysis of genetic population structure. We have previously developed a Markov chain Monte Carlo (MCMC) algorithm for characterizing genetically divergent groups based on molecular markers and geographical sampling design of the dataset. However, for large-scale datasets such algorithms may get stuck to local maxima in the parameter space. Therefore, we have modified our earlier algorithm to support multiple parallel MCMC chains, with enhanced features that enable considerably faster and more reliable estimation compared to the earlier version of the algorithm. We consider also a hierarchical tree representation, from which a Bayesian model-averaged structure estimate can be extracted. The algorithm is implemented in a computer program that features a user-friendly interface and built-in graphics. The enhanced features are illustrated by analyses of simulated data and an extensive human molecular dataset. AVAILABILITY: Freely available at http://www.rni.helsinki.fi/~jic/bapspage.html.

Algorithms↗

PubMed2001

Sequence analysis with the Kestrel SIMD parallel processor.

Computer aided sequence analysis is a critical aspect of current biological research. Sequence information from the genome sequencing projects fills databases so quickly that humans cannot examine it all. Hence there is a heavy reliance on computer algorithms to point out the few important nuggets for human examination. Sequence search algorithms range from simple to complex, as does the representation of the biological data. Typically though, simple algorithms are used on the simplest of data representations because of the large computational demands of anything more complex. This leads to missed hits because the simple search techniques are often not sufficiently sensitive. Here we describe the implementation of several sensitive sequence analysis algorithms on the Kestrel parallel processor, a single-instruction multiple-data (SIMD) processor developed and built at UCSC. Performance of the Smith-Waterman and Hidden Markov Model algorithms, with both Viterbi and Expectation Maximization methods ranges from 6 to 20 times faster than standard computers.

Algorithms↗

PubMed2006

Superlinear scaling in master-slave quantum chemical calculations using in-core storage of two-electron integrals.

We describe the implementation of a parallel, in-core, integral-direct Hartree-Fock and density functional theory code for the efficient calculation of Hartree-Fock wave functions and density functional theory. The algorithm is based on a parallel master-slave algorithm, and the two-electron integrals calculated by a slave are stored in available local memory. To ensure the greatest computational savings, the master node keeps track of all integral batches stored on the different slaves. The code can reuse undifferentiated two-electron integrals both in the wave function optimization and in the evaluation of second-, third-, and fourth-order molecular properties. Superlinear scaling is achieved in a series of test examples, with speedups of up to 55 achieved for calculations run on medium-sized molecules on 16 processors with respect to the time used on a single processor.

Journal Article↗

PubMed1995

A structure-from-motion scheme that looks for parallels, and its implications for apparent reversals in rotating trapezia.

Apparent reversals in rotating trapezia have been regarded as evidence that human vision favours methods which are heuristic or form dependent. However, the argument is based on the assumption that general algorithmic methods would avoid the illusion, and that has never been clear. A general algorithm for interpreting moving parallels has been developed to address the issue. It handles a considerable range of stimuli successfully, but finds multiple interpretations in situations which correspond closely to those where apparent reversals occur. This strengthens the hypothesis that apparent reversals may occur when general algorithmic methods fail and heuristics are invoked as a stopgap.

Form Perception↗

PubMed2003

An algorithm for three-way data analysis that alternatively minimizes coupled vector (COV) resolution error and PARAFAC error.

A novel algorithm, alternatively minimizing coupled vector (COV) resolution error and PARAFAC error algorithm, is proposed in this paper. This algorithm can overcome the problem of slow convergence and is insensitive to the estimation of component number, such problems are unavoidable while using the traditional parallel factors analysis (PARAFAC) algorithm. In other words, this algorithm is capable of improving the computing speed and providing accurate resolutions provided that the number of factors used in the computation is no less than that of the actual underlying ones. The characteristic performances were demonstrated with a novel fluorescence data array.

Journal Article↗

PubMed2002

[Simultaneous determination of isomers of dihydroxybenzene using alternating trilinear decomposition algorithm combined with reversed-phase high performance liquid chromatography/diode array detection].

Alternating trilinear decomposition (ATLD) algorithm is a promising method for second-order calibration, which is based on an alternating least-squares principle to overcome some shortcomings of the traditional parallel factor analysis (PARAFAC) algorithms, such as the sensitivity to the estimated component numbers and slow convergence. It utilizes an iterative procedure involving Moore-Penrose generalized inverse computations based on singular value decomposition and can be applied to the simultaneous determination of several organic components even in the presence of unknown interfering components. The overlapped chromatogram and spectra system of dihydroxybenzenes were resolved by ATLD combined with reversed-phase high performance liquid chromatography (RP-HPLC)/ diode array detection (DAD). The elution time was set from 1.086 min to 1.399 min with an interval of 1/150 min and the ultraviolet wavelength from 268 nm to 298 nm with an interval of 1 nm. The resolved results were in agreement with the actual results excellently. Catechol (CAT), resorcinol (RES) and hydroquinone (HYD) in aqueous solution were determined simultaneously, whose recoveries were (100.1 +/- 1.0)%, (99.4 +/- 1.4)% and (100.5 +/- 1.7)%, respectively. The results showed this experiment can be easily performed without resorting to time-consuming and complicated procedures and quantified accurately. It successfully solved the resolving problem caused by chromatogram and spectra overlapping in the presence of interfering components. It also revealed the ATLD algorithm can be efficiently applied to solve the second-order calibration problem in HPLC-DAD.

English Abstract↗