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At least 289 records · Page 16Linked to original sources
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↗
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↗
PubMed1998

Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution.

An implementation of classical molecular dynamics on parallel computers of increased efficiency has enabled a simulation of protein folding with explicit representation of water for 1 microsecond, about two orders of magnitude longer than the longest simulation of a protein in water reported to date. Starting with an unfolded state of villin headpiece subdomain, hydrophobic collapse and helix formation occur in an initial phase, followed by conformational readjustments. A marginally stable state, which has a lifetime of about 150 nanoseconds, a favorable solvation free energy, and shows significant resemblance to the native structure, is observed; two pathways to this state have been found.

Carrier Proteins↗
PubMed1995

Real time binocular detection of horizontal vertical and torsional eye movements by an infra red video-eye tracker.

So far it has only been possible to detect horizontal and vertical eye movements during real time; torsional eye movements have to be calculated from video-tape that have been processed several times, and each investigation takes considerable time. We developed a real time binocular infra red video eye tracker for routine clinical examination which allows real time graphical visualization of horizontal, vertical and torsional eye movements with a bandwidth of 12 Hz (25 Hz refresh frequency). Eye movements in three dimensions can now be obtained as easy as has been done before with electronystagmography for the horizontal component. In contrast to previous systems described, we analyze only those parts of the video-frame that are essential for detection of all three eye movements. This results in a huge data-reduction accompanied by a speed-up of analysis. The black pupil centre is detected by an iterative process of analyzing several horizontal and vertical lines of the even video field. The algorithm searches for regions of minimal intensity. Horizontal and vertical eye rotation is then calculated and transformed into Fick's coordinates. Based upon the centre of the pupil four concentric segments are defined in the iris to detect torsion and to enable correction for false rotation. Torsion is detected by cross-correlation of each segment and estimated from the outcome of the correlation coefficients. All transformations are established by predefined stored transformation matrices thus making real time calculations for transformation unnecessary. After corrections for eccentricity and assuming that fixation of the subjects tested was perfect, accuracy appears to be within 0.3 degrees-1.0 degrees for all three dimensions. Linearity after all corrections is within 4-9% within a visual field of 60 x 40 degrees (horizontal x vertical).

Computer Graphics↗
PubMed2000

Step-along vergence procedures in stigmatic and astigmatic systems.

The traditional step-along vergence procedure applies to stigmatic systems, that is, systems that are not astigmatic. Computation is disrupted when a focus coincides with a thin lens or refracting surface. A small change to the procedure results in a modified procedure which overcomes the computational problems. The modified procedure is easier to execute than the traditional procedure and allows one to write down useful equations directly. Among the formulae are those for back-vertex power. A step-along vergence procedure also exists for astigmatic systems. It makes use of the dioptric power matrix and the reduced vergence matrix. Computational problems arise when a point or line focus coincides with a thin lens or refracting surface; however they are not overcome by an analogous modification to the procedure. Nevertheless the modified procedure has some advantages including the fact that, as for stigmatic systems, it allows one to write down useful formulae directly. Stepwise calculations of vergence are sometimes performed backward through a system; the advantages and disadvantages described for step-along procedures holds for such step-back procedures as well.

Astigmatism↗
PubMed1992

Conformational regions of Boc-Ala-Aib-Ala-OMe. Sampling with molecular dynamics simulations using time averaging of distance restraints.

The method of time averaging of distance restraints in molecular dynamics simulations is applied to Boc-Ala-Aib-Ala-OMe in order to demonstrate the improved sampling properties of this method compared to conventional distance restraining. Two conformational regions, beta-turn type II and gamma-turn, are seen during MD runs at a simulation temperature of 500 K, while in simulations with conventional distance restraining, no conformational transitions could be observed for temperatures up to 1000 K.

Amino Acid Sequence↗
PubMed1991

Dimensional oscillation. A fast variation of energy embedding gives good results with the AMBER potential energy function.

The structure of the AMBER potential energy surface of the cyclic tetrapeptide cyclotetrasarcosyl is analyzed as a function of the dimensionality of coordinate space. It is found that the number of local energy minima decreases as the dimensionality of the space increases until some limit at which point equipotential subspaces appear. The applicability of energy embedding methods to finding global energy minima in this type of energy-conformation space is explored. Dimensional oscillation, a computationally fast variant of energy embedding is introduced and found to sample conformation space widely and to do a good job of finding global and near-global energy minima.

Computer Simulation↗