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PubMedDate not supplied

Computer model to investigate the effect of eye movements on retinal heating during long-duration fixation on a laser source.

A computer simulation called RHME (Retinal Heating in Moving Eye) is developed to simulate the heating pattern that occurs in the retina during a long-duration exposure to a continuous wave laser beam. The simulation takes into account eye movements that occur during a deliberate fixation. Due to the rapid (millisecond) thermal time scale for heating and cooling, only the area of the retina directly exposed to the laser sustains an increased temperature. Once the laser spot is removed from a particular location of the retina (because of eye movements) that location quickly cools. Points of the retina will therefore have a complex thermal history during a long-duration exposure. Simulation results for a minimal retinal spot size indicate that subjects staring at a helium-neon laser (lambda=632.8 nm) beam producing the small-source maximum permissible exposure (MPE) level corneal irradiance of 1 mW cm(-2) (>10-s exposure) will experience a maximum although transient temperature increase in the retina of less than 2 degrees C during a 50-s fixation trial. The large increase in the International Commission on Non-Ionizing Radiation Protection (ICNIRP) and ANSI Z136.1 safety limits for a long-duration small-source exposure to visible continuous wave lasers that was adopted in 2000 therefore appears appropriate.

Animals↗
PubMed2004

A computer modeling study of the competitive adsorption of water and organic surfactants at surfaces of the mineral scheelite.

Atomistic computer simulation techniques were employed to investigate the interaction of a selection of organic surfactant molecules with a range of scheelite surfaces. The adsorbates coordinate mainly to the surfaces through interaction between their oxygen (or nitrogen) atoms to surface calcium ions, followed by hydrogen-bonded interactions to surface oxygen ions. Bridging between two surface calcium ions is the preferred mode of adsorption, but a bidentate interaction by two adsorbate oxygen ions to the same surface calcium ion is also a stable configuration and multiple interactions between surfaces and adsorbate molecules lead to the largest adsorption energies. All adsorbates containing carbonyl and hydroxy groups interact strongly with the surfaces, releasing energies between approximately 80 and 170 kJ mol(-1), but methylamine containing only the -NH2 functional group adsorbs to the surfaces to a much lesser extent (55-86 kJ mol(-1)). Both hydroxymethanamide and hydroxyethanal adsorb to some surfaces in an eclipsed conformation, which is a requisite for these functional groups. Sorption of the organic material by replacement of preadsorbed water at different surface features is calculated to be mainly exothermic for methanoic acid, but less so for the hydroxymethanamide and hydroxyethanal molecules, whereas methylamine would not replace preadsorbed water at the scheelite surfaces. The efficacy of the surfactant molecules is hence calculated to be carboxylic acids > alkyl hydroxamates > hydroxyaldehydes > alkylamines. The results from this study suggest that computer simulations may provide a route to the identification or even design of particular organic surfactants for use in mineral separation processes.

Journal Article↗
PubMed2003

Estimation of entrainment response using electrograms from remote sites: validation in animal and computer models of reentrant tachycardia.

INTRODUCTION: Studies suggest that entrainment response (ER) of reentrant tachycardia to overdrive pacing can be estimated using signals from sites other than the paced site. METHODS AND RESULTS: A formula for estimation of ER using remote sites against the difference between the postpacing interval (PPI) and tachycardia cycle length (TCL) determined solely from the paced site signal was validated in experimental data and using a simple two-dimensional cellular automata model of reentry. The model also was used to study the behavior and features of entrained surfaces, including the resetting of tachycardia phase by single premature paced stimuli. Experimental results from 1,484 remote sites in 115 pacing sequences showed the average of the median ER estimate error at each pacing site was -2 +/- 5 msec, and the median ER estimate was within 10 msec of PPI-TCL for 94% of pacing sites. From simulation results, ER at the paced site was accurately estimated from >99.8% of 20,764 remote sites during pacing at 24 sites and three paced cycle lengths. Intervals measured from remote electrograms revealed whether the site was activated orthodromically or nonorthodromically during pacing, and results of simulations illustrated that the portion of the surface activated nonorthodromically during pacing increased with distance from the pacing site to the circuit. The phenomenon of nonorthodromic activation of reentrant circuits predicted by modeling was discernible in measurements taken from the animal model of reentrant tachycardia. Results also showed that, for single premature stimuli that penetrated the tachycardia circuit, phase reset of the tachycardia was linearly related to distance between the central obstacle and the paced site. CONCLUSION: The ER is a complex but predictable perturbation of the global activation sequence of reentrant tachycardias. This predictability allows calculations of the response from anywhere on the perturbed surface. These findings suggest new techniques for measurement of the ER, which may lend themselves to computer-based methods for accurate and rapid mapping of reentrant circuits.

Animals↗
PubMed1996

A computer model of processes of binocular vision in the cerebral cortex.

Fundamentals and options of modeling cortical processes of binocular vision are dealt with in this paper. Physiologically characterized cell types of the visual cortex are modelled and used as basis of a network implementing a simulation of the binocular vision. An attempt is made to establish correlations between typical activity patterns of visual cortical cells and the network incorporating them.

Animals↗
PubMedDate not supplied

Computer-modeling-based QSARs for analyzing experimental data on biotransformation and toxicity.

Over the past decades the description of quantitative structure-activity relationships (QSARs) has been undertaken in order to find predictive models and/or mechanistic explanations for chemical as well as biological activities. This includes QSAR studies in toxicology. In an approach beyond the classical QSAR approaches, attempts have been made to define parameters for the QSAR studies on the basis of quantum mechanical computer calculations. The conversion of relatively small xenobiotics within the active sites of biotransformation enzymes can be expected to follow the general rules of chemistry. This makes the description of QSARs on the basis of only one parameter, chosen on the basis of insight in the mechanism, feasible. In contrast, toxicological endpoints can very often be the result of more than one physico-chemical interaction of the compound with the model system of interest. Therefore the description of quantitative structure-toxicity relationships often does not follow a one-descriptor mechanistic approach but starts from the other end, describing QSARs by multi-parameter approaches. The present paper focuses on the possibilities and restrictions of using computer-based QSAR modeling for analyzing experimental toxicological data, with emphasis on examples from the field of biotransformation and toxicity.

Animal Testing Alternatives↗
PubMed1993

A computational model of echo processing and acoustic imaging in frequency-modulated echolocating bats: the spectrogram correlation and transformation receiver.

The spectrogram correlation and transformation (SCAT) model of the sonar receiver in the big brown bat (Eptesicus fuscus) consists of a cochlear component for encoding the bat's frequency modulated (FM) sonar transmissions and multiple FM echoes in a spectrogram format, followed by two parallel pathways for processing temporal and spectral information in sonar echoes to reconstruct the absolute range and fine range structure of multiple targets from echo spectrograms. The outputs of computations taking place along these parallel pathways converge to be displayed along a computed image dimension of echo delay or target range. The resulting image depicts the location of various reflecting sources in different targets along the range axis. This series of transforms is equivalent to simultaneous, parallel forward and inverse transforms on sonar echoes, yielding the impulse responses of targets by deconvolution of the spectrograms. The performance of the model accurately reproduces the images perceived by Eptesicus in a variety of behavioral experiments on two-glint resolution in range, echo phase sensitivity, amplitude-latency trading of range estimates, dissociation of time- and frequency-domain image components, and ranging accuracy in noise.

Animals↗
PubMed2003

Computer model for recognition of functional transcription start sites in RNA polymerase II promoters of vertebrates.

This paper introduces a new computer system for recognition of functional transcription start sites (TSSs) in RNA polymerase II promoter regions of vertebrates. This system allows scanning complete vertebrate genomes for promoters with significantly reduced number of false positive predictions. It can be used in the context of gene finding through its recognition of the 5' end of genes. The implemented recognition model uses a composite-hierarchical approach, artificial intelligence, statistics, and signal processing techniques. It also exploits the separation of promoter sequences into those that are C+G-rich or C+G-poor. The system was evaluated on a large and diverse human sequence-set and exhibited several times higher accuracy than several publicly available TSS-finding programs. Results obtained using human chromosome 22 data showed even greater specificity than the evaluation set results. The system has been implemented in the Dragon Promoter Finder package, which can be accessed at http://sdmc.krdl.org.sg:8080/promoter/.

Animals↗
PubMed1988

Characterization of five epitopes of human renin from a computer model.

Antigenic determinants in proteins have been found to coincide with surface regions accessible to a large probe of 1-nm radius, which approximates the size of an antibody binding domain. To predict epitopes of human renin, a computer algorithm was used to calculate the accessibility of a model of the three-dimensional structure of human renin to a 1-nm probe. Of the 17 segments predicted to be epitopes or parts of epitopes, 6 were synthesized and tested for their recognition by 11 polyclonal antibodies prepared against pure human renin. Four peptides, Y-133-144, C-180-188, Y-211-224, and Y-300-310, were bound by some polyclonal anti-renin antibodies when tested in both a solution assay and an enzyme-linked immunosorbent assay (ELISA), and one peptide, C-290-296-G, was bound only in an ELISA. Of the five epitopes identified, peptide Y-211-224 seems dominant, since it was bound by all antisera in the solution assay and by 8 of the 11 in the ELISA. This peptide contains a disulfide loop, and the corresponding linear peptide obtained after reduction of the disulfide was not recognized by any anti-renin antisera in the solution assay. This suggests that the epitope is conformationally dependent and that a disulfide bridge linking cysteines-217 and -221 is present in the native structure of human renin. Purified immunoglobulins raised to peptides Y-133-144 and Y-211-224 (located near, but not at, the catalytic site) were found to inhibit the cleavage of human angiotensinogen by purified human renin but not the cleavage of a tetradecapeptide substrate representing the N-terminal region of angiotensinogen.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1990

A computer model for the evaluation of the effect of corneal topography on optical performance.

We developed a method that models the effect of irregular corneal surface topography on corneal optical performance. A computer program mimics the function of an optical bench. The method generates a variety of objects (single point, standard Snellen letters, low contrast Snellen letters, arbitrarily complex objects) in object space. The lens is the corneal surface evaluated by a corneal topography analysis system. The objects are refracted by the cornea by using raytracing analysis to produce an image, which is displayed on a video monitor. Optically degraded images are generated by raytracing analysis of selected irregular corneal surfaces, such as those from patients with keratoconus and those from patients having undergone epikeratophakia for aphakia.

Computer Simulation↗
PubMed1998

Computational modelling of optic flow selectivity in MSTd neurons.

In neurophysiological experiments examining the selectivity of MSTd neurons to visual motion components of optic flow stimuli in monkeys, Duffy and Wurtz (1991) reported cells with double-component (plano-radial and plano-circular) and triple-component (plano-radial-circular) selectivities, while Graziano et al (1994) reported neurons selective to a continuum of optic flow stimuli including spiral motion. Here, we address these reported findings under simulated experimental conditions by examining the development of optic flow selectivity in the hidden units of a two-layer back-propagation network. We also examine network motion sensitivity during simulated psychophysical tests via the addition of a competitive decision layer. Network analysis with neurophysiological stimuli identified a majority of hidden units whose position invariance and motion selectivity were consistent with MSTd responses to the visual motion components of optic flow stimuli reported by Duffy and Wurtz and Graziano et al. Furthermore, the hidden units developed a continuum of optic flow selectivities independent of the biases associated with the specification of the motion selectivity in the output layer. During psychophysical testing, network responses showed motion sensitivities which met or exceeded human performance. Within the limitations imposed by the learning algorithm, the psychophysical results were consistent with a model of global motion perception via local integration along complex motion trajectories.

Animals↗
PubMed1986

A computer model for the study of segregation in reciprocal translocation carriers: application to 20 new cases.

We report on a computer program that, given the breakpoints and the chromosomes involved in a translocation, generates all the possible imbalanced gametes, calculates their corresponding imbalances, and arranges them in order of increasing imbalance. When compared to current, more cumbersome criteria from the literature, both methods agreed on 196 cases of 199 (greater than 98%). When compared to observed data from families with aneuploid offspring, both our program and the other reported methods yield a rate of accurate prediction of 87%. The use of the program is illustrated in 20 new translocations from our laboratory. The possible influence of crossing over in meiosis I in altering the gamete that is most likely to be passed to aneuploid live births is discussed.

Abortion, Habitual↗
PubMed2004

A three-dimensional computer model of the human mandible in two simulated standard trauma situations.

PURPOSE: A three-dimensional finite element model of the human mandible was developed to simulate and analyse biomechanical behaviour in two standard trauma situations. This computer-based study was made to assess the stress patterns within human mandibles generated by impact forces. MATERIAL AND METHODS: The mandibular model was generated using 7.073 nodes and 30.119 tetrahedra. A commercial finite element solver was then applied to this mesh to compute stresses generated in standard trauma situations (a blow in the symphysis region and another one to the body of the mandible). RESULTS: The results indicate that following a blow to the symphysis region, maximum stress areas were located at the symphysis, retromolar and condylar regions. In the case of a blow to the mandibular body, the maximum stress areas were located at the contralateral angle, the ipsilateral body and the ipsilateral condylar neck regions. CONCLUSION: The main application of this study was the prediction of fractures as a consequence of known forces.

Biomechanical Phenomena↗
PubMed1986

Modification of human hemoglobin by glutathione. III. Perturbations of hemoglobin conformation analyzed by computer modeling.

The perturbations of the conformation of human deoxyhemoglobin induced by the covalent attachment of glutathione at cysteine beta 93 have been investigated by computer simulation in conjunction with molecular graphics. In the first phase of the analysis, a systematic search was carried out of the conformational space of glutathione attached to deoxyhemoglobin. In this search, the conformation of the hemoglobin molecule was held constant, while the relative energies of a series of 186,624 glutathione conformations involving systematic variation of six dihedral angels were calculated. From this search, the most favorable conformation was selected as the starting conformation for energy minimization of the glutathionyl hemoglobin molecule as a function of all Cartesian coordinates. In order to provide a reference state, an independent minimization by the same procedures was carried out for deoxyhemoglobin in the absence of glutathione. Comparison of the minimized structures with and without glutathione attached revealed a number of significant differences. The most conspicuous difference in the protein moiety concerned the salt bridge between aspartate beta 94 and histidine beta 146 which is destabilized upon minimization of the glutathionyl-hemoglobin complex due to interactions of the aspartate residue with the glycyl NH group of glutathione. Other observed differences in the minimized structures are located at the alpha 1-beta 2 interface and include displacement of the carboxyl group of aspartate beta 99. In the minimized complex, the glutathione portion assumes a quasi-cyclic conformation stabilized through interactions between the free (gamma-glutamyl) amino and (glycyl) carboxyl ends of the tripeptide and between this carboxyl end and the epsilon amino group of lysine alpha 40. In a parallel conformational study of glutathione alone, a similar structure was found as the lowest energy form. These quasi-cyclic conformations contrast with the extended structures reported by Wright (Wright, W.B. (1955) Acta Crystallogr. 11, 632-642) for crystals of glutathione where interactions between molecules play a major role. The conclusions of our analysis are in agreement with the experimental investigations reported in the two preceding papers and permit, moreover, a coherent interpretation of the observed functional and structural changes in deoxyhemoglobin induced by glutathione.

Binding Sites↗