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At least 343 records · Page 19Linked to original sources

PubMed2004

XSophe-Sophe-XeprView. A computer simulation software suite (v. 1.1.3) for the analysis of continuous wave EPR spectra.

The XSophe-Sophe-XeprView computer simulation software suite enables scientists to easily determine spin Hamiltonian parameters from isotropic, randomly oriented and single crystal continuous wave electron paramagnetic resonance (CW EPR) spectra from radicals and isolated paramagnetic metal ion centers or clusters found in metalloproteins, chemical systems and materials science. XSophe provides an X-windows graphical user interface to the Sophe programme and allows: creation of multiple input files, local and remote execution of Sophe, the display of sophelog (output from Sophe) and input parameters/files. Sophe is a sophisticated computer simulation software programme employing a number of innovative technologies including; the Sydney OPera HousE (SOPHE) partition and interpolation schemes, a field segmentation algorithm, the mosaic misorientation linewidth model, parallelization and spectral optimisation. In conjunction with the SOPHE partition scheme and the field segmentation algorithm, the SOPHE interpolation scheme and the mosaic misorientation linewidth model greatly increase the speed of simulations for most spin systems. Employing brute force matrix diagonalization in the simulation of an EPR spectrum from a high spin Cr(III) complex with the spin Hamiltonian parameters g(e) = 2.00, D=0.10 cm(-1), E/D = 0.25, A(x) = 120.0, A(y) = 120.0, A(z) = 240.0 x 10 (-4) cm(-1) requires a SOPHE grid size of N = 400 (to produce a good signal to noise ratio) and takes 229.47 s. In contrast the use of either the SOPHE interpolation scheme or the mosaic misorientation linewidth model requires a SOPHE grid size of only N = 18 and takes 44.08 and 0.79 s, respectively. Results from Sophe are transferred via the Common Object Request Broker Architecture (CORBA) to XSophe and subsequently to XeprView where the simulated CW EPR spectra (1D and 2D) can be compared to the experimental spectra. Energy level diagrams, transition roadmaps and transition surfaces aid the interpretation of complicated randomly oriented CW EPR spectra and can be viewed with a web browser and an OpenInventor scene graph viewer.

Journal Article↗

PubMed2005

Simulated parallel annealing within a neighborhood for optimization of biomechanical systems.

Optimization problems for biomechanical systems have become extremely complex. Simulated annealing (SA) algorithms have performed well in a variety of test problems and biomechanical applications; however, despite advances in computer speed, convergence to optimal solutions for systems of even moderate complexity has remained prohibitive. The objective of this study was to develop a portable parallel version of a SA algorithm for solving optimization problems in biomechanics. The algorithm for simulated parallel annealing within a neighborhood (SPAN) was designed to minimize interprocessor communication time and closely retain the heuristics of the serial SA algorithm. The computational speed of the SPAN algorithm scaled linearly with the number of processors on different computer platforms for a simple quadratic test problem and for a more complex forward dynamic simulation of human pedaling.

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PubMed2001

Action-derived molecular dynamics in the study of rare events.

We present a practical method to generate classical trajectories with fixed initial and final boundary conditions. Our method is based on the minimization of a suitably defined discretized action. The method finds its most natural application in the study of rare events. Its capabilities are illustrated by nontrivial examples. The algorithm lends itself to straightforward parallelization, and when combined with ab initio molecular dynamics it promises to offer a powerful tool for the study of chemical reactions.

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PubMed2004

A meta-algorithm for brain extraction in MRI.

Accurate identification of brain tissue and cerebrospinal fluid (CSF) in a whole-head MRI is a critical first step in many neuroimaging studies. Automating this procedure can eliminate intra- and interrater variance and greatly increase throughput for a labor-intensive step. Many available procedures perform differently across anatomy and under different acquisition protocols. We developed the Brain Extraction Meta-Algorithm (BEMA) to address these concerns. It executes many extraction algorithms and a registration procedure in parallel to combine the results in an intelligent fashion and obtain improved results over any of the individual algorithms. Using an atlas space, BEMA performs a voxelwise analysis of training data to determine the optimal Boolean combination of extraction algorithms to produce the most accurate result for a given voxel. This allows the provided extractors to be used differentially across anatomy, increasing both the accuracy and robustness of the procedure. We tested BEMA using modified forms of BrainSuite's Brain Surface Extractor (BSE), FSL's Brain Extraction Tool (BET), AFNI's 3dIntracranial, and FreeSurfer's MRI Watershed as well as FSL's FLIRT for the registration procedure. Training was performed on T1-weighted scans of 136 subjects from five separate data sets with different acquisition parameters on separate scanners. Testing was performed on 135 separate subjects from the same data sets. BEMA outperformed the individual algorithms, as well as interrater results from a subset of the scans, when compared for the mean Dice coefficient, a rating of the similarity of output masks to the manually defined gold standards.

Adult↗

PubMed2004

Weighted FBP--a simple approximate 3D FBP algorithm for multislice spiral CT with good dose usage for arbitrary pitch.

A new 3D reconstruction scheme, weighted filtered backprojection (WFBP) for multirow spiral CT based on an extension of the two-dimensional SMPR algorithm is described and results are presented. In contrast to other 3D algorithms available, the algorithm makes use of all available data for all pitch values. The algorithm is a FBP algorithm: linear convolution of the parallel data along the row direction followed by a 3D backprojection. Data usage for arbitrary pitch values is maintained through a weighting scheme which takes into account redundant data. If proper row weighting is applied, the image quality is superior to the image quality of the SMPR algorithm.

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PubMed2006

Free-energy calculations with multiple Gaussian modified ensembles.

We present a Monte Carlo algorithm, which samples free energies of complex systems. Less probable configurations are populated with the help of a multitude of additional Gaussian weights and parallel tempering is used for efficient Monte Carlo moves within phase space. The algorithm is easily parallelized and can be applied to a wide class of problems. We discuss algorithmic performance for the case of low-temperature phase separation in two-dimensional and three-dimensional Ising models, where we determine the magnetic interface tension. Multiple Gaussian modified ensemble simulations, unlike multicanonical ensemble simulations do not require a priori knowledge of the free energy and are of similar efficiency as multicanonical ensemble and Wang-Landau simulations.

Journal Article↗

PubMed1991

Molecular dynamics simulation on a network of workstations using a machine-independent parallel programming language.

Molecular dynamics simulations investigate local and global motion in molecules. Several parallel computing approaches have been taken to attack the most computationally expensive phase of molecular simulations, the evaluation of long range interactions. This paper develops a straightforward but effective algorithm for molecular dynamics simulations using the machine-independent parallel programming language, Linda. The algorithm was run both on a shared memory parallel computer and on a network of high performance Unix workstations. Performance benchmarks were performed on both systems using two proteins. This algorithm offers a portable cost-effective alternative for molecular dynamics simulations. In view of the increasing numbers of networked workstations, this approach could help make molecular dynamics simulations more easily accessible to the research community.

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PubMed2005

An FDK-like cone-beam SPECT reconstruction algorithm for non-uniform attenuated projections acquired using a circular trajectory.

In this paper, Novikov's inversion formula of the attenuated two-dimensional (2D) Radon transform is applied to the reconstruction of attenuated fan-beam projections acquired with equal detector spacing and of attenuated cone-beam projections acquired with a flat planar detector and circular trajectory. The derivation of the fan-beam algorithm is obtained by transformation from parallel-beam coordinates to fan-beam coordinates. The cone-beam reconstruction algorithm is an extension of the fan-beam reconstruction algorithm using Feldkamp-Davis-Kress's (FDK) method. Computer simulations indicate that the algorithm is efficient and is accurate in reconstructing slices close to the central slice of the cone-beam orbit plane. When the attenuation map is set to zero the implementation is equivalent to the FDK method. Reconstructed images are also shown for noise corrupted projections.

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PubMed2001

Parallel computation of a maximum-likelihood estimator of a physical map.

Reconstructing a physical map of a chromosome from a genomic library presents a central computational problem in genetics. Physical map reconstruction in the presence of errors is a problem of high computational complexity that provides the motivation for parallel computing. Parallelization strategies for a maximum-likelihood estimation-based approach to physical map reconstruction are presented. The estimation procedure entails a gradient descent search for determining the optimal spacings between probes for a given probe ordering. The optimal probe ordering is determined using a stochastic optimization algorithm such as simulated annealing or microcanonical annealing. A two-level parallelization strategy is proposed wherein the gradient descent search is parallelized at the lower level and the stochastic optimization algorithm is simultaneously parallelized at the higher level. Implementation and experimental results on a distributed-memory multiprocessor cluster running the parallel virtual machine (PVM) environment are presented using simulated and real hybridization data.

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PubMed1988

Multiple DNA and protein sequence alignment on a workstation and a supercomputer.

This paper describes a multiple alignment method using a workstation and supercomputer. The method is based on the alignment of a set of aligned sequences with the new sequence, and uses a recursive procedure of such alignment. The alignment is executed in a reasonable computation time on diverse levels from a workstation to a supercomputer, from the viewpoint of alignment results and computational speed by parallel processing. The application of the algorithm is illustrated by several examples of multiple alignment of 12 amino acid and DNA sequences of HIV (human immunodeficiency virus) env genes. Colour graphic programs on a workstation and parallel processing on a supercomputer are discussed.

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PubMed2000

Multislice helical CT: image temporal resolution.

A multislice helical computed tomography (CT) halfscan (HS) reconstruction algorithm is proposed for cardiac applications. The imaging performances (in terms of the temporal resolution, z-axis resolution, image noise, and image artifacts) of the HS algorithm are compared to the existing algorithms using theoretical models and clinical data. A theoretical model of the temporal resolution performance (in terms of the temporal sensitivity profile) is established for helical CT, in general, i.e., for any number of detector rows and any reconstruction algorithm used. It is concluded that the HS reconstruction results in improved image temporal resolution than the corresponding 180 degrees LI (linear interpolation) reconstruction and is more immune to the inconsistent data problem induced by cardiac motions. The temporal resolution of multislice helical CT with the HS algorithm is comparable to that of single-slice helical CT with the HS algorithm. In practice, the 180 degrees LI and HS-LI algorithms can be used in parallel to generate two image sets from the same scan acquisition, one (180 degrees LI) for improved z-resolution and noises, and the other (HS-LI) for improved image temporal resolution.

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PubMed2005

Atmospheric wavefront phase recovery by use of specialized hardware: graphical processing units and field-programmable gate arrays.

To achieve the wavefront phase-recovery stage of an adaptive-optics loop computed in real time for 32 x 32 or a greater number of subpupils in a Shack-Hartmann sensor, we present here, for what is to our knowledge the first time, preliminary results that we obtained by using innovative techniques: graphical processing units (GPUs) and field-programmable gate arrays (FPGAs). We describe the stream-computing paradigm of the GPU and adapt a zonal algorithm to take advantage of the parallel computational power of the GPU. We also present preliminary results we obtained by use of FPGAs on the same algorithm. GPUs have proved to be a promising technique, but FPGAs are already a feasible solution to adaptive-optics real-time requirements, even for a large number of subpupils.

Journal Article↗

PubMed2003

Nonrigid image registration in shared-memory multiprocessor environments with application to brains, breasts, and bees.

One major problem with nonrigid image registration techniques is their high computational cost. Because of this, these methods have found limited application to clinical situations where fast execution is required, e.g., intraoperative imaging. This paper presents a parallel implementation of a nonrigid image registration algorithm. It takes advantage of shared-memory multiprocessor computer architectures using multithreaded programming by partitioning of data and partitioning of tasks, depending on the computational subproblem. For three different biomedical applications (intraoperative brain deformation, contrast-enhanced MR mammography, intersubject brain registration), the scaling behavior of the algorithm is quantitatively analyzed. The method is demonstrated to perform the computation of intra-operative brain deformation in less than a minute using 64 CPUs on a 128-CPU shared-memory supercomputer (SGI Origin 3800). It is shown that its serial component is no more than 2% of the total computation time, allowing a speedup of at least a factor of 50. In most cases, the theoretical limit of the speedup is substantially higher (up to 132-fold in the application examples presented in this paper). The parallel implementation of our algorithm is, therefore, capable of solving nonrigid registration problems with short execution time requirements and may be considered an important step in the application of such techniques to clinically important problems such as the computation of brain deformation during cranial image-guided surgery.

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PubMedDate not supplied

Projection domain compensation of missing angles for fan-beam CT reconstruction.

An improved method is proposed for fan-beam computed tomographic (CT) reconstruction from data with limited views. Compensation for the missing projections for fan-beam CT can be partially accomplished by using the coincident ray or by an interpolation technique using circular sample theory. In this article, the authors propose a more accurate compensation method for the missing projections whether the coincident ray pairs exist or not. The fan-beam reprojection algorithm, which is the inverse operator of the convolution filter, was extended from the projection space iteration reconstruction-reprojection (PSIRR) in parallel beam geometry. In addition, this algorithm was validated by applying the Shepp-Logan phantom for a computer simulation in the equi-angular fan-beam CT geometry.

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PubMed2000

An iterative approach to the beam hardening correction in cone beam CT.

In computed tomography (CT), the beam hardening effect has been known to be one of the major sources of deterministic error that leads to inaccuracy and artifact in the reconstructed images. Because of the polychromatic nature of the x-ray source used in CT and the energy-dependent attenuation of most materials, Beer's law no longer holds. As a result, errors are present in the acquired line integrals or measurements of the attenuation coefficients of the scanned object. In the past, many studies have been conducted to combat image artifacts induced by beam hardening. In this paper, we present an iterative beam hardening correction approach for cone beam CT. An algorithm that utilizes a tilted parallel beam geometry is developed and subsequently employed to estimate the projection error and obtain an error estimation image, which is then subtracted from the initial reconstruction. A theoretical analysis is performed to investigate the accuracy of our methods. Phantom and animal experiments are conducted to demonstrate the effectiveness of our approach.

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PubMed2001

A computational algorithm for computing nonlinear auditory frequency selectivity.

Computational algorithms that mimic the response of the basilar membrane must be capable of reproducing a range of complex features that are characteristic of the animal observations. These include complex input output functions that are nonlinear near the site's best frequency, but linear elsewhere. This nonlinearity is critical when using the output of the algorithm as the input to models of inner hair cell function and subsequent auditory-nerve models of low- and high-spontaneous rate fibers. We present an algorithm that uses two processing units operating in parallel: one linear and the other compressively nonlinear. The output from the algorithm is the sum of the outputs of the linear and nonlinear processing units. Input to the algorithm is stapes motion and output represents basilar membrane motion. The algorithm is evaluated against published chinchilla and guinea pig observations of basilar membrane and Reissner's membrane motion made using laser velocimetry. The algorithm simulates both quantitatively and qualitatively, differences in input/output functions among three different sites along the cochlear partition. It also simulates quantitatively and qualitatively a range of phenomena including isovelocity functions, phase response, two-tone suppression, impulse response, and distortion products. The algorithm is potentially suitable for development as a bank of filters, for use in more comprehensive models of the peripheral auditory system.

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PubMed2004

Automatic recognition of small cell carcinoma based on the self-organizing neural network.

In this paper the recognition of Small Cell Carcinoma (SCC) is studied. For each type we select 128 samples for training, and randomly measure 200 cells in each sample. We introduce multi-scale morphology based on centroid coordinates to extract the boundaries of nuclei and obtain feature images of nuclei. The features of lung cancer cells are described by morphological and colorimetrical parameters, which is valuable to recognize SCC. Then the architecture of self-organizing feature mapping (SOFM) neural network is studied for recognition of SCC. The weights of the network are adjusted by self-organizing competition, and finally inputted patterns are classified. This algorithm has the advantage of parallelism and fast-convergence, and may simplify the analysis of SCC. Clinical experiment results show that the correctness ratio of this system may reach 95.3% while recognizing lung cancer cell types. Our work is significant to the pathological researches of lung cancer, assistant clinic diagnosis, and assessment of therapeutic effects. Meanwhile a software system named as SCC. LUNG is established for automatic analysis.

Adult↗

PubMed2004

Extended parallel backprojection for standard three-dimensional and phase-correlated four-dimensional axial and spiral cone-beam CT with arbitrary pitch, arbitrary cone-angle, and 100% dose usage.

We have developed a new approximate Feldkamp-type algorithm that we call the extended parallel backprojection (EPBP). Its main features are a phase-weighted backprojection and a voxel-by-voxel 180 degrees normalization. The first feature ensures three-dimensional (3-D) and 4-D capabilities with one and the same algorithm; the second ensures 100% detector usage (each ray is accounted for). The algorithm was evaluated using simulated data of a thorax phantom and a cardiac motion phantom for scanners with up to 256 slices. Axial (circle and sequence) and spiral scan trajectories were investigated. The standard reconstructions (EPBPStd) are of high quality, even for as many as 256 slices. The cardiac reconstructions (EPBPCI) are of high quality as well and show no significant deterioration of objects even far off the center of rotation. Since EPBPCI uses the cardio interpolation (CI) phase weighting the temporal resolution is equivalent to that of the well-established single-slice and multislice cardiac approaches 180 degrees CI, 180 degrees MCI, and ASSRCI, respectively, and lies in the order of 50 to 100 ms for rotation times between 0.4 and 0.5 s. EPBP appears to fulfill all required demands. Especially the phase-correlated EPBP reconstruction of cardiac multiple circle scan data is of high interest, e.g., for dynamic perfusion studies of the heart.

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