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PubMed1990

The development of a high-order Taylor expansion solution to the chemical rate equation for the simulation of complex biochemical systems.

A numerical method for evaluating chemical rate equations is presented. This method was developed by expressing the system of coupled, first-degree, ordinary differential chemical rate equations as a single tensor equation. The tensorial rate equation is invariant in form for all reversible and irreversible reaction schemes that can be expressed as first- and second-order reaction steps, and can accommodate any number of reactive components. The tensor rate equation was manipulated to obtain a simple formula (in terms of rate constants and initial concentrations) for the power coefficients of the Taylor expansion of the chemical rate equation. The Taylor expansion formula was used to develop a FORTRAN algorithm for analysing the time development of chemical systems. A computational experiment was performed with a Michaelis-Menten scheme in which step size and expansion order (to the 100th term) were varied; the inclusion of high-order terms of the Taylor expansion was shown to reduce truncation and round-off errors associated with Runge-Kutta methods and lead to increased computational efficiency.

Algorithms↗
PubMed1990

POLCA, a library running in a modern environment, implements a protocol for averaging randomly oriented images.

The library POLCA implements the averaging of biological structures whose images are recorded in digital form from electron micrographs. The averaging protocol is based upon a method developed about ten years ago, which allows one to operate on a sequence of objects oriented and displaced at random within their frame; the relative rotations and the displacements of the structures are detected with the use of correlation algorithms and modified to make all objects appear the same, apart from their noisy components. The average image is then obtained by a simple addition and the signal-to-noise ratio is improved by a factor equal to the square root of the number of objects used to calculate the average. With respect to the original implementation of the method, two novel features characterize the library: the first one deals with the functions that are cross-correlated to determine the relative rotations of the structures; the functions used here are the inverse transforms of the amplitude spectra (IAS functions), which give rise to sharp maxima when they are cross-correlated. The second peculiarity is the systematic adoption, in the transformations of coordinates and in other circumstances, of an interpolation technique based upon the Fourier series kernel. POLCA is written in C and runs on a VME machine under the UNIX V/68 operating system. A programming style has been adopted to exploit fully the machine resources.

Algorithms↗
PubMed1991

Building structural models of peptides: a semi-automatic software.

We present a software package that allows the construction and display of structural models of proteins starting from the amino acid sequence written in the one-letter code of standard data bank format. The software includes a very fast and efficient algorithm aimed at finding the global energy minimum of the potential function describing the molecular interactions. The whole package is conceived to have maximum flexibility. Completely automatic procedures are envisaged for standard problems. For non-standard problems, the construction procedure can be interactively adopted to meet with different options.

Algorithms↗
PubMed1991

Parallel computation and FASTA: confronting the problem of parallel database search for a fast sequence comparison algorithm.

We have parallelized the FASTA algorithm for biological sequence comparison using Linda, a machine-independent parallel programming language. The resulting parallel program runs on a variety of different parallel machines. A straight-forward parallelization strategy works well if the amount of computation to be done is relatively large. When the amount of computation is reduced, however, disk I/O becomes a bottleneck which may prevent additional speed-up as the number of processors is increased. The paper describes the parallelization of FASTA, and uses FASTA to illustrate the I/O bottleneck problem that may arise when performing parallel database search with a fast sequence comparison algorithm. The paper also describes several program design strategies that can help with this problem. The paper discusses how this bottleneck is an example of a general problem that may occur when parallelizing, or otherwise speeding up, a time-consuming computation.

Algorithms↗
PubMed2000

Unsupervised learning of binary vectors: a Gaussian scenario.

We study a model of unsupervised learning where the real-valued data vectors are isotropically distributed, except for a single symmetry-breaking binary direction Bin¿-1,+1¿(N), onto which the projections have a Gaussian distribution. We show that a candidate vector J undergoing Gibbs learning in this discrete space, approaches the perfect match J=B exponentially. In addition to the second-order "retarded learning" phase transition for unbiased distributions, we show that first-order transitions can also occur. Extending the known result that the center of mass of the Gibbs ensemble has Bayes-optimal performance, we show that taking the sign of the components of this vector (clipping) leads to the vector with optimal performance in the binary space. These upper bounds are shown generally not to be saturated with the technique of transforming the components of a special continuous vector, except in asymptotic limits and in a special linear case. Simulations are presented which are in excellent agreement with the theoretical results.

Bayes Theorem↗
PubMed2000

Navier-Stokes simulation with constraint forces: finite-difference method for particle-laden flows and complex geometries.

Building on an idea of Fogelson and Peskin [J. Comput. Phys. 79, 50 (1988)] we describe the implementation and verification of a simulation technique for systems of non-Brownian particles in fluids at Reynolds numbers up to about 20 on the particle scale. This direct simulation technique fills a gap between simulations in the viscous regime and high-Reynolds-number modeling. It also combines sufficient computational accuracy with numerical efficiency and allows studies of several thousand, in principle arbitrarily shaped, extended and hydrodynamically interacting particles on regular work stations. We verify the algorithm in two and three dimensions for (i) single falling particles and (ii) a fluid flowing through a bed of fixed spheres. In the context of sedimentation we compute the volume fraction dependence of the mean sedimentation velocity. The results are compared with experimental and other numerical results both in the viscous and inertial regime and we find very satisfactory agreement.

Algorithms↗
PubMed2000

Efficient dynamic importance sampling of rare events in one dimension.

Exploiting stochastic path-integral theory, we obtain by simulation substantial gains in efficiency for the computation of reaction rates in one-dimensional, bistable, overdamped stochastic systems. Using a well-defined measure of efficiency, we compare implementations of "dynamic importance sampling" (DIMS) methods to unbiased simulation. The best DIMS algorithms are shown to increase efficiency by factors of approximately 20 for a 5k(B)T barrier height and 300 for 9k(B)T, compared to unbiased simulation. The gains result from close emulation of natural (unbiased), instantonlike crossing events with artificially decreased waiting times between events that are corrected for in rate calculations. The artificial crossing events are generated using the closed-form solution to the most probable crossing event described by the Onsager-Machlup action. While the best biasing methods require the second derivative of the potential (resulting from the "Jacobian" term in the action, which is discussed at length), algorithms employing solely the first derivative do nearly as well. We discuss the importance of one-dimensional models to larger systems, and suggest extensions to higher-dimensional systems.

Algorithms↗
PubMed1989

Local convolution in ectomography.

In tomographic imaging, using limited angular sampling, details outside the imaged section are displaced along circles of blur. In ectomography, these are eliminated by a spatial convolution process. It is shown that the convolution function has to be as long as the projected dimension of the imaged object perpendicular to the section and twice the dimension parallel to the section.

Image Processing, Computer-Assisted↗
PubMed1990

Approximation of surfaces in quantitative 3-D reconstructions.

In serial section reconstructions a series of planar profiles are taken representing curves on the surface of the structure to be reconstructed. For a number of quantitative serial section methods, approximation of a surface is done by the formation of tiles between points of adjacent profiles. As generally proposed, finding this approximation has been difficult due to the inordinately large number of possible solutions resulting from different combinations of tiles between points. Current algorithms have either applied heuristic criteria to force the formation of only one solution or have searched all acceptable combinations for one that minimizes some cost function. The algorithm presented has been developed to choose the tiling which minimizes the estimated error when the tile approximation of the surface is used in subsequent quantitative algorithm such as the calculation of surface area.

Algorithms↗
PubMed2001

Computational modeling of three-dimensional microwave tomography of breast cancer.

Microwave tomographic approach is proposed to detect and image breast cancers. Taking into account the big difference in dielectrical properties between normal and malignant tissues, we have proposed using the microwave tomographic method to image a human breast. Because of the anatomical features of the objects, this case has to be referred to the tomography with a limited angle of observation. As a result of computer experiments we have established that multiview cylindrical configurations are able to provide microwave tomograms of the breast with a small size tumor inside. Using the gradient method, we have developed a computer code to create images of the three-dimensional objects in dielectrical properties on microwave frequencies.

Algorithms↗
PubMed2003

The physical basis of microtubule structure and stability.

Microtubules are cylindrical polymers found in every eukaryotic cell. They have a unique helical structure that has implications at both the cellular level, in terms of the functions they perform, and at the multicellular level, such as determining the left-right symmetry in plants. Through the combination of an atomically detailed model for a microtubule and large-scale computational techniques for computing electrostatic interactions, we are able to explain the observed microtubule structure. On the basis of the lateral interactions between protofilaments, we have determined that B lattice is the most favorable configuration. Further, we find that these lateral bonds are significantly weaker than the longitudinal bonds along protofilaments. This explains observations of microtubule disassembly and may serve as another step toward understanding the basis for dynamic instability.

Computational Biology↗
PubMed1994

Semi-automated measurement of true chord length distributions and moments by video microscopy and image analysis.

The distribution of the lengths of airspace chords in pulmonary parenchyma characterizes many architectural features of the alveoli and alveolar ducts. Laborious to obtain manually, the distributions and density functions may be acquired semi-automatically by video microscopy, digitization and image processing. The accuracy of the estimation is influenced by the microscopical methods and also by the techniques used (i) to convert the digitized greyscale picture to a two-valued image, (ii) to collect the chord lengths and (iii) to compensate for finite field widths. The last problem arises because some chords are completely visible within a field while others are only partially seen, since one of the two air-tissue boundaries lies outside the field of view. This error systematically biases the observed distribution. This paper contains solutions to hardware, software and analytic problems encountered while developing the capability to measure airspace chord length density functions semi-automatically. Formulas for estimating the true chord length density function from samples of observed chord lengths are presented. Also given are formulas for the estimation of the first and second moments of the true chord length distribution from the means of observed chord lengths. These techniques of image preparation and analysis should be suitable for characterizing particle, grain or cell size distributions, especially where many profiles fall partially outside the field of view.

Animals↗
PubMed1995

Image quality in digital chromosome analysis systems.

This paper reports on an investigation into the differences in image quality of different components used in a digital image processing system for chromosome analysis. As chromosome aberrations are important tools in the cloning of genes, it is important to know if the introduction of computerized analysis systems increases the risk of missing small aberrations. In this investigation the number of visible bands on a number of chromosomes has been used as a measure of quality. The images compared are microscope ocular images, photographs from a microscope built-in camera, digital images from a high and from a standard resolution camera, presented both on screen and print-out on paper. The main conclusions are that: (1) the view in the microscope ocular gives the best resolution, (2) there are risks of losing vital information using the digital image processing system for chromosome analysis, and (3) this risk is significantly reduced when using a high resolution camera.

Chromosome Banding↗
PubMed2002

Spatial coherence analysis applied to aberration correction using a two-dimensional array system.

Complex degree of coherence functions are computed using synthetic and measured ultrasound data to demonstrate noteworthy aspects of coherence analysis in the context of aberration correction. Coherence functions calculated from synthetic data illustrate the importance of proper normalization of the constituent cross-correlation integrals when weak elements and receiver directivity are significant factors. The synthetic data also show that a spike can occur at the zero-lag position of the coherence function when the signal-to-noise ratio is reduced by element directivity near the edges of a large aperture. The latter observation is confirmed by experimental data acquired through tissue-mimicking distributed aberration phantoms using a low f-number two-dimensional array system. The coherence of data acquired at neighboring elements is not changed by time-shift compensation of transmit and receive focusing, but time-shift compensation does improve the coherence of echoes measured over larger separations. The resulting increase in coherence widths evaluated at levels between 0.2 and 0.5 is correlated with narrower -10 dB and -20 dB effective widths in focuses visualized using single-transmit images. Iterative focus compensation methods may benefit from aberration estimation algorithms that take advantage of these longer-range correlations in random-scattering waveforms.

Artifacts↗