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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↗
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↗
PubMed2004

Advanced fitness landscape analysis and the performance of memetic algorithms.

Memetic algorithms (MAs) have demonstrated very effective in combinatorial optimization. This paper offers explanations as to why this is so by investigating the performance of MAs in terms of efficiency and effectiveness. A special class of MAs is used to discuss efficiency and effectiveness for local search and evolutionary meta-search. It is shown that the efficiency of MAs can be increased drastically with the use of domain knowledge. However, effectiveness highly depends on the structure of the problem. As is well-known, identifying this structure is made easier with the notion of fitness landscapes: the local properties of the fitness landscape strongly influence the effectiveness of the local search while the global properties strongly influence the effectiveness of the evolutionary meta-search. This paper also introduces new techniques for analyzing the fitness landscapes of combinatorial problems; these techniques focus on the investigation of random walks in the fitness landscape starting at locally optimal solutions as well as on the escape from the basins of attractions of current local optima. It is shown for NK-landscapes and landscapes of the unconstrained binary quadratic programming problem (BQP) that a random walk to another local optimum can be used to explain the efficiency of recombination in comparison to mutation. Moreover, the paper shows that other aspects like the size of the basins of attractions of local optima are important for the efficiency of MAs and a local search escape analysis is proposed. These simple analysis techniques have several advantages over previously proposed statistical measures and provide valuable insight into the behaviour of MAs on different kinds of landscapes.

Algorithms↗
PubMed2004

Automatic generation of controllers for embodied legged organisms: a Pareto evolutionary multi-objective approach.

In this paper, we investigate the use of a self-adaptive Pareto evolutionary multi-objective optimization (EMO) approach for evolving the controllers of virtual embodied organisms. The objective of this paper is to demonstrate the trade-off between quality of solutions and computational cost. We show empirically that evolving controllers using the proposed algorithm incurs significantly less computational cost when compared to a self-adaptive weighted sum EMO algorithm, a self-adaptive single-objective evolutionary algorithm (EA) and a hand-tuned Pareto EMO algorithm. The main contribution of the self-adaptive Pareto EMO approach is its ability to produce sufficiently good controllers with different locomotion capabilities in a single run, thereby reducing the evolutionary computational cost and allowing the designer to explore the space of good solutions simultaneously. Our results also show that self-adaptation was found to be highly beneficial in reducing redundancy when compared against the other algorithms. Moreover, it was also shown that genetic diversity was being maintained naturally by virtue of the system's inherent multi-objectivity.

Algorithms↗