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At least 1,207 records · Page 67Linked to original sources
PubMed1985

Induced self-motion in central vision.

Previous research on visually induced self-motion found that stimulation of the central visual field (up to 30 degrees in diameter) results in perceived object motion while self-motion requires peripheral stimulation. In the present study, perceived self-motion was induced with a radially expanding pattern simulating observer motion through a space filled with dots, with visual angles of 7.5 degrees, 10.6 degrees, 15 degrees, and 21.2 degrees. Speed and texture density were also varied. The duration of reported self-motion (a) decreased with increased speed, (b) failed to increase with increased visual angle, and (c) decreased with visual angle at the highest speed level. In a second experiment, subjects rated the perceived depth of the displays. The speed and speed/area interaction effects on judged depth matched those found for induced self-motion. These results suggest an extension of the focal/ambient theory: In addition to a more primitive ambient processing mode that requires peripheral vision, there is a higher level system concerned with ambient processing that functions in the central visual field and uses more complex stimulus information, such as internal depth represented in a radially expanding pattern.

Depth Perception↗
PubMed2004

Thermodynamics of lattice heteropolymers.

We calculate thermodynamic quantities of hydrophobic-polar (HP) lattice proteins by means of a multicanonical chain-growth algorithm that connects the new variants of the Pruned-Enriched Rosenbluth Method and flat histogram sampling of the entire energy space. Since our method directly simulates the density of states, we obtain results for thermodynamic quantities of the system for all temperatures. In particular, this algorithm enables us to accurately simulate the usually difficult accessible low-temperature region. Therefore, it becomes possible to perform detailed analyses of the low-temperature transition between ground states and compact globules.

Algorithms↗
PubMed2001

Artefacts in multi-echo T2 imaging for high-precision gel dosimetry: III. Effects of temperature drift during scanning.

In high-precision 3D gel dosimetry, long MR measurement times together with a high amount of RF energy being absorbed by the phantom are very common, and result in a spatially dependent temperature rise in the gel. As T2 of the dosimeter gel is temperature dependent, dose estimation will be affected. In this study we assess the temperature rise in the dosimeter gel by use of MR temperature mapping and computer modelling. It is shown that in conventional MR sequences. where linear k-space sampling is used, a temperature rise of 3 C results in a dose underestimation of 10% over the whole dose map. To correct for these dose errors, a compensation method involving centric k-space ordering is suggested. Computer simulations have been performed to analyse the robustness of the proposed method. Applying the compensated sequence, a temperature rise of 3 C leads to a narrow dose artefact of the order of 3% for a 'worst case' situation in which a single pixel dose gradient is assumed. Negligible deviations are found in the rest of the dose map.

Acrylamide↗
PubMed2002

A Monte Carlo dose calculation tool for radiotherapy treatment planning.

A Monte Carlo user code, MCDOSE, has been developed for radiotherapy treatment planning (RTP) dose calculations. MCDOSE is designed as a dose calculation module suitable for adaptation to host RTP systems. MCDOSE can be used for both conventional photon/electron beam calculation and intensity modulated radiotherapy (IMRT) treatment planning. MCDOSE uses a multiple-source model to reconstruct the treatment beam phase space. Based on Monte Carlo simulated or measured beam data acquired during commissioning, source-model parameters are adjusted through an automated procedure. Beam modifiers such as jaws, physical and dynamic wedges, compensators, blocks, electron cut-outs and bolus are simulated by MCDOSE together with a 3D rectilinear patient geometry model built from CT data. Dose distributions calculated using MCDOSE agreed well with those calculated by the EGS4/DOSXYZ code using different beam set-ups and beam modifiers. Heterogeneity correction factors for layered-lung or layered-bone phantoms as calculated by both codes were consistent with measured data to within 1%. The effect of energy cut-offs for particle transport was investigated. Variance reduction techniques were implemented in MCDOSE to achieve a speedup factor of 10-30 compared to DOSXYZ.

Computer Simulation↗
PubMed2001

Model-based administration of inhalation anaesthesia. 1. Developing a system model.

This paper is the first of a series of reports on a system model for the administration of inhalation anaesthesia. We present the development and basic testing of the model. It is a multiple-gas model; it covers fresh-gas flow rates from basal to more than total ventilation and includes an actual, not an idealized, circle-absorber breathing system featuring a standing bellows ventilator. Kinetics of nitrogen, oxygen, carbon dioxide, nitrous oxide, inhaled anaesthetic agents and helium are described. Their partial pressures sum to the total pressure. Ventilation and cardiac output are treated as continuous, not cyclical. The model of the breathing system was empirically matched to the chosen one (a GMS absorber and 7850 ventilator (Datex-Ohmeda)). Predictions for the wash-in of isoflurane and the uptake of desflurane and isoflurane agree well with observed data. The results obtained by continuously checking total gas pressures, calculating mass balances and simulating the measurement of alveolar space by the closed-circuit helium dilution method support the mathematical credibility of the model. It thus merits further exploration.

Algorithms↗
PubMed2002

Mathematical models of vaccination.

Mathematical models of epidemics have a long history of contributing to the understanding of the impact of vaccination programmes. Simple, one-line models can predict target vaccination coverage that will eradicate an infectious agent, whilst other questions require complex simulations of stochastic processes in space and time. This review introduces some simple ordinary differential equation models of mass vaccination that can be used to address important questions about the predicted impact of vaccination programmes. We show how to calculate the threshold vaccination coverage rate that will eradicate an infection, explore the impact of vaccine-induced immunity that wanes through time, and study the competitive interactions between vaccine susceptible and vaccine resistant strains of infectious agent.

Child↗
PubMed2004

A robust measure of HIV-1 population turnover within chronically infected individuals.

A simple nonparameteric test for population structure was applied to temporally spaced samples of HIV-1 sequences from the gag-pol region within two chronically infected individuals. The results show that temporal structure can be detected for samples separated by about 22 months or more. The performance of the method, which was originally proposed to detect geographic structure, was tested for temporally spaced samples using neutral coalescent simulations. Simulations showed that the method is robust to variation in samples sizes and mutation rates, to the presence/absence of recombination, and that the power to detect temporal structure is high. By comparing levels of temporal structure in simulations to the levels observed in real data, we estimate the effective intra-individual population size of HIV-1 to be between 10(3) and 10(4) viruses, which is in agreement with some previous estimates. Using this estimate and a simple measure of sequence diversity, we estimate an effective neutral mutation rate of about 5 x 10(-6) per site per generation in the gag-pol region. The definition and interpretation of estimates of such "effective" population parameters are discussed.

Evolution, Molecular↗
PubMed2000

Constructing side chains on near-native main chains for ab initio protein structure prediction.

Is there value in constructing side chains while searching protein conformational space during an ab initio simulation? If so, what is the most computationally efficient method for constructing these side chains? To answer these questions, four published approaches were used to construct side chain conformations on a range of near-native main chains generated by ab initio protein structure prediction methods. The accuracy of these approaches was compared with a naive approach that selects the most frequently observed rotamer for a given amino acid to construct side chains. An all-atom conditional probability discriminatory function is useful at selecting conformations with overall low all-atom root mean square deviation (r.m.s.d.) and the discrimination improves on sets that are closer to the native conformation. In addition, the naive approach performs as well as more sophisticated methods in terms of the percentage of chi(1) angles built accurately and the all-atom r. m.s.d., between the native and near-native conformations. The results suggest that the naive method would be extremely useful for fast and efficient side chain construction on vast numbers of conformations for ab initio prediction of protein structure.

Amino Acids↗
PubMed1990

Validation of photosynthate production in ECOPHYS, an ecophysiological growth process model of Populus.

A model of photosynthate production is the central component of a larger whole-tree ecophysiological growth process model for Populus (ECOPHYS). This photosynthesis model was validated by comparing predicted photosynthate production values for individual leaves and the total tree with hourly field measurements collected on four days spaced throughout a growing season. Simulated trees had identical numbers of leaves and leaf areas as the sample trees studied in the field, and hourly weather data collected on the plantation site were supplied as a model input. Total production for the four sample days ranged between 200 and 4900 mg CO(2) tree(-1) day(-1). Model predictions of total daily photosynthate production were within 12% of the observed rates for three of the four sampling days. Diurnal variations in stomatal conductance and ambient CO(2) concentrations and seasonal variations in area leaf weight were the primary sources of error. Total leaf area, proportion of sunlit leaf area, and photosynthetic efficiency were the most important factors influencing carbon dioxide exchange rates.

Journal Article↗
PubMed2002

Wave front propagation failure in an inhomogeneous discrete Nagumo chain: theory and experiments.

The phenomenon of wave propagation failure in a discrete inhomogeneous Nagumo equation is investigated. It is found that the propagation failure occurs not only for small coupling coefficients but as well for an abrupt change of the interelement coupling. The investigation includes the study of the phase space of the system, numerical simulations, and real experiments with a nonlinear electrical lattice.

Journal Article↗
PubMed2002

First-order transition of tethered membranes in three-dimensional space.

We study a model of phantom tethered membranes, embedded in three-dimensional space, by extensive Monte Carlo simulations. The membranes have hexagonal lattice structure where each monomer is interacting with six nearest-neighbors (NN). Tethering interaction between NN, as well as curvature penalty between NN triangles are taken into account. This model is new in the sense that NN interactions are taken into account by a truncated Lennard-Jones potential including both repulsive and attractive parts. The main result of our study is that the system undergoes a first-order crumpling transition from low-temperature flat phase to high-temperature crumpled phase, in contrast with early numerical results on models of tethered membranes.

Journal Article↗
PubMed2000

Growth and form of planetary seedlings: results from a microgravity aggregation experiment.

The outcome of the first stage of planetary formation, which is characterized by ballistic agglomeration of preplanetary dust grains due to Brownian motion in the free molecular flow regime of the solar nebula, is still somewhat speculative. We performed a microgravity experiment flown onboard the space shuttle in which we simulated, for the first time, the onset of free preplanetary dust accumulation and revealed the structures and growth rates of the first dust agglomerates in the young solar system. We find that a thermally aggregating swarm of dust particles evolves very rapidly and forms unexpected open-structured agglomerates.

Models, Theoretical↗
PubMed2004

Observation of many coherent oscillations for MeV protons transmitted through stacking faults.

High spatial resolution, high-contrast transmission channeling images of stacking faults in silicon have been produced using a beam of 2 MeV protons focused to a spot size of 60 nm. Over a narrow range of beam tilts to the (011) planes, up to ten periodic intensity oscillations are observed, providing evidence of a long-range coherency of the planar channeled trajectories. This behavior is characterized using Monte Carlo computer simulations, and a phase-space model of planar channeled ion interactions with stacking faults is developed which incorporates all observed channeling and blocking phenomena.

Journal Article↗
PubMed2005

Langevin trajectories between fixed concentrations.

We consider the trajectories of particles diffusing between two infinite baths of fixed concentrations connected by a channel, e.g., a protein channel of a biological membrane. The steady state influx and efflux of Langevin trajectories at the boundaries of a finite volume containing the channel and parts of the two baths is replicated by termination of outgoing trajectories and injection according to a residual phase space density. We present a simulation scheme that maintains averaged fixed concentrations without creating spurious boundary layers, consistent with the assumed physics.

Biophysics↗
PubMed1979

Firing behaviour in a stochastic nerve membrane model based upon the Hodgkin-Huxley equations.

A nerve membrane model with a two-state pore system was investigated by computer simulation in the uniform (space-clamped) case. Both sodium and potassium conducting pores were modelled, each pore having four independent gates which switched randomly between the open and the closed position, governed by the assumed rate constants. Each pore conducted only when all the gates were open. The model was based upon the Hodgkin-Huxley equations for the giant axon in squid, and in the limit of an infinite number of pores it was identical to these. The firing behaviour of this model as a function of the number of pores and the injected current were investigated. The mean firing frequency and the distribution of interspike intervals were mainly used in the presentation of the results. It was found that for pore numbers less than about 20 000 the main effects due to a finite number of pores were a lowering of the current threshold for firing and a more linear frequency current relationship relative to that of the original H-H equations. For higher pore numbers an increase in the current threshold and a pronounced burst firing close to the threshold were found.

Animals↗
PubMed2006

Anthropogenic and natural influences in the evolution of lower stratospheric cooling.

Observations reveal that the substantial cooling of the global lower stratosphere over 1979-2003 occurred in two pronounced steplike transitions. These arose in the aftermath of two major volcanic eruptions, with each cooling transition being followed by a period of relatively steady temperatures. Climate model simulations indicate that the space-time structure of the observed cooling is largely attributable to the combined effect of changes in both anthropogenic factors (ozone depletion and increases in well-mixed greenhouse gases) and natural factors (solar irradiance variation and volcanic aerosols). The anthropogenic factors drove the overall cooling during the period, and the natural ones modulated the evolution of the cooling.

Journal Article↗
PubMed1991

Computed myocardial PO2 histograms: effects of various geometrical and functional conditions.

A model of myocardial oxygenation was developed that allows calculation of Po2 histograms under varying conditions. The model consists of parallel tissue cylinders with varying radii, simulating the heterogeneity of capillary spacing, in agreement with our previous experimental results. The facilitated diffusion of O2 by myoglobin, an additional resistance to diffusion at the capillary level, and the Michaelis-Menten type of O2 consumption were also incorporated. The shape of the histograms depends on input data. When no additional barrier to O2 transport is included, the histograms resemble those obtained with Po2 surface electrodes, and they are strongly dependent on heterogeneity in capillary spacing and capillary blood flow. On the other hand, an inclusion of an additional capillary barrier combined with the Michaelis-Menten type of O2 consumption can generate Po2 histograms similar to those derived from myoglobin cryospectroscopy. In this case, the Po2 histograms are relatively independent of heterogeneity of capillary spacing and blood flow. The facilitation of O2 diffusion by myoglobin has only a modest effect on the form of the histograms in all situations considered.

Animals↗
PubMed1999

Multipoint linkage analysis. A cautionary note.

Multipoint linkage analysis is commonly used to evaluate linkage of a disease to multiple markers in a small region. Multipoint analysis is particularly powerful when the IBD relations of family members at the trait locus are ambiguous. The increased power arises because, unlike single-marker analyses, multipoint analysis uses haplotype information from several markers to infer the IBD relations. We wish to temper this advantage with a cautionary note: multipoint analysis is sensitive to power loss due to misspecification of intermarker distances. Such misspecification is especially problematic when dealing with closely spaced markers. We present computer simulations comparing the power of single-point and multipoint analyses, both when IBD relations are ambiguous, and when the intermarker distances are misspecified. We conclude that when evaluating markers in a small region to confirm or refute previous findings, a situation in which p values of modest statistical significance are important, single marker analyses may provide more reliable measures of the strength of support for linkage than multipoint statistics.

Computer Simulation↗