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At least 109 records · Page 6Linked to original sources
PubMed1989

A new technique in computer modeling of molecules with transparency effect, due to partially stripped surfaces.

Conventional space filling molecular modeling in computers, using the scan method, takes considerable computer time and effort. In depicting the CPK-image on a computer screen, the hidden-point removal is the main task and on such an image, the front-line atoms hide the back-benchers and their whereabouts become completely unknown, in a given view of the picture. While in search of a simple and faster algorithm for producing surface graphics of molecules, we have developed a novel method, which is considerably faster than the conventional one and it has an interesting transparency-effect which would be useful in the various fields of molecular designs.

Algorithms↗
PubMed2003

Developing integrative computational models of pulmonary structure.

Integrative computational modeling of the pulmonary system aims to incorporate interactions between the lung's subsystems by means of a hierarchy of structural and functional models. This requires detailed imaging-based data, along with a wide range of functional information from experiments. Advances in computed tomography imaging technology ensure that high-resolution data are now readily available upon which the structure of these models can be based. We present methods for constructing anatomically realistic finite element models of interrelated pulmonary structures from such data. Segmented human lung lobe data are fit to high-order (cubic Hermite) volume elements. Meshes for the conducting airways and pulmonary arteries and veins are constructed within the lobe mesh, using a combination of fitting to imaging data and a bifurcating-distributive algorithm. The algorithm generates an airway-consistent mesh within a host volume, and this airway mesh is then used as a template for generating blood vessel models. The lung parenchyma is modeled as a space-filling three-dimensional (3D) Voronoi mesh, with generated geometry consistent with the alveolated airway structure. Pulmonary capillaries are generated over the alveolar model, as a 2D Voronoi mesh. These structural models have been compared extensively with morphometric data to verify that their geometry is representative of the pulmonary system. The models are designed to be integrative: they relate multiple structural systems within the same individual, and their use as computational meshes allows application of spatially distributed properties.

Algorithms↗
PubMed2005

Investigation of the relative effects of vascular branching structure and gravity on pulmonary arterial blood flow heterogeneity via an image-based computational model.

RATIONALE AND OBJECTIVES: A computational model of blood flow through the human pulmonary arterial tree has been developed to investigate the relative influence of branching structure and gravity on blood flow distribution in the human lung. MATERIALS AND METHODS: Geometric models of the largest arterial vessels and lobar boundaries were first derived using multidetector row x-ray computed tomography (MDCT) scans. Further accompanying arterial vessels were generated from the MDCT vessel endpoints into the lobar volumes using a volume-filling branching algorithm. Equations governing the conservation of mass and momentum were solved within the geometric model to calculate pressure, velocity, and vessel radius. Blood flow results in the anatomically based model, with and without gravity, and in a symmetric geometric model were compared to investigate their relative contributions to blood flow heterogeneity. RESULTS: Results showed a persistent blood flow gradient and flow heterogeneity in the absence of gravitational forces in the anatomically based model. Comparison with flow results in the symmetric model revealed that the asymmetric vascular branching structure was largely responsible for producing this heterogeneity. Analysis of average results in varying slice thicknesses illustrated a clear flow gradient because of gravity in "lower resolution" data (thicker slices), but on examination of higher resolution data, a trend was less obvious. CONCLUSIONS: Results suggest that although gravity does influence flow distribution, the influence of the tree branching structure is also a dominant factor. These results are consistent with high-resolution experimental studies that have demonstrated gravity to be only a minor determinant of blood flow distribution.

Blood Flow Velocity↗
PubMed1982

Trajectory formation and handwriting: a computational model.

This paper proposes a computational model for different aspects of trajectory formation, from point-to-point movements to handwriting. The proposed model is based on a mechanism of composition of basic curve elements (strokes) which separates the spatial and the temporal aspects of trajectory formation. At the same time, the model suggests a method for storing and describing arm movements, as a list of stroke descriptors. Experimental trajectories were digitized and analyzed with regard to several types of movements: i) point-to-point trajectories, ii) closed trajectories, iii) trajectories with inflection points, iv) spiral-like trajectories, v) handwritten trajectories. Velocity and curvature profiles were computed for the trajectories and the model was fitted to the data. The implications of the model and its "credibility" in the general context of motor control are discussed.

Arm↗
PubMedDate not supplied

Some aspects of computer modelling in cardiac electrophysiology.

A computer model simulating the electrical activity of the heart is described. The model is designed for use in clinical cardiological research. Its implementation is based on the methods of discrete process simulation. The simulation program is written in FORTRAN, has approximately 12,000 lines and requires 160 kilobytes of memory to run. The whole heart is modelled, including a realistic description of the conduction system and a 'hollow shell' structure with a central plane representing the atrial, ventricular and septal components of the cardiac musculature. The myocardium itself is represented by simple hexagonal elements, which are pieced together to form the 'hollow shell'. The ideas used to develop the model are briefly described, but emphasis is given to clinical applications. The model is first validated by examining its output under well-known pathological conditions. Clinical applications, including predictive value, testing of hypotheses, and evaluation of pacemaker function, are then described, results being presented in the form of orthogonal lead projections.

Computers↗
PubMed1993

Gas uptake from an unventilated area of lung: computer model of absorption atelectasis.

A computer model of gas uptake from an area of nonventilated lung, such as a pulmonary lobe with an occluded bronchus or an alveolus with an occluded airway, is presented. Previous analyses have assumed that when an inert gas is present, equilibration of O2 and CO2 with mixed venous blood is sufficiently rapid to be treated as instantaneous. This is valid for insoluble gases such as N2 or He when the fractional concentration of inspired O2 (FIO2) is < or = 0.6 but is invalid for a relatively soluble gas such as N2O. When a mixture of O2 and an inert gas is breathed, the time for an area of unventilated lung to collapse depends on the solubility of the inert gas and FIO2. When the solubility is low (N2 or He), collapse takes longer than when 100% O2 is breathed, and the lower the FIO2 the longer the time to collapse. When the gas is more soluble (N2O) and FIO2 is > 0.3, collapse is more rapid than when 100% O2 is breathed.

Absorption↗
PubMed1996

A computer model of major haemorrhage and resuscitation.

An interactive computer model is described which uses 'blood volume deficit' and 'bleeding duration' together with rates of infusion to simulate the first two hours of haemorrhage. It allows multiple infusions of various fluids to be specified and includes an estimation of the volumes added by the transcapillary refill mechanism. The output is expressed graphically in terms of blood pressure and haematocrit at intervals of one minute. This computer model has proved useful for assessing the effects of a range of variables in hypovolaemic shock. It has considerable potential for investigating the relative efficacy of various clinical protocols and could provide an alternative to animal experimentation which has so far been the primary method of obtaining data on acute haemorrhage. It is also a useful teaching aid.

Animals↗
PubMed1998

Computer modelling of spinal cord stimulation and its contribution to therapeutic efficacy.

An overview of computer models developed since the late seventies, which enable the simulation of the primary effects of spinal cord stimulation (SCS) on nerve fibres, is presented. These models consist of a 3-dimensional volume conductor model, representing anatomical structures and their electrical conductivities, and cable models representing the electrical behaviour of nerve fibres. The characteristics of these models and their relation to anatomy and physiology, as well as the calculation of stimulation-induced electrical fields and their effect on nerve fibre models, are reviewed. It is shown that most characteristics of SCS as predicted by computer modelling correspond well with empirical data. Accordingly, a theoretical framework describing the relations between relevant parameters in SCS is presented. Finally, it is shown how theory and computer modeling are applied to improve the efficacy of SCS by the optimization of its technique, primarily by the design of new epidural electrodes.

Computer Simulation↗
PubMed1985

Membrane resistivity estimated for the Purkinje neuron by means of a passive computer model.

A multicompartment passive electrotonic computer model is constructed for the cerebellar Purkinje cell of the guinea-pig. The model has 1089 coupled compartments to accurately represent the morphology of the Purkinje cell. In order that the calculated behavior of the model fit the published electrophysiological observations of somatic and dendritic input conductance, the neural membrane resistivity must be spatially non-uniform. The passive electrical parameter values for which the model best fits the observations of input conductances, pulse attenuation and current-clamp voltage transients are rm,dend = 45,740 omega cm2, rm,soma = 760 omega cm2, ri = 225 omega cm and cm = 1.16 microF/cm2 (the membrane and cytoplasm specific resistivities and membrane specific capacitance, respectively). The model with these parameter values is electrically compact, with electrotonic length X = 0.33 and dendritic dominance ratio p = 0.44. Analysis of the calculated voltage transient of the multicompartment model by the methods of equivalent-cylinder cable theory is shown to result in very different and unreliable conclusions. The significance for neuronal function of the estimated electrical parameter values is discussed. The possible effect of active conductances on these conclusions is assessed.

Animals↗
PubMed2004

A computational model for periodic pattern perception based on frieze and wallpaper groups.

We present a computational model for periodic pattern perception based on the mathematical theory of crystallographic groups. In each N-dimensional Euclidean space, a finite number of symmetry groups can characterize the structures of an infinite variety of periodic patterns. In 2D space, there are seven frieze groups describing monochrome patterns that repeat along one direction and 17 wallpaper groups for patterns that repeat along two linearly independent directions to tile the plane. We develop a set of computer algorithms that "understand" a given periodic pattern by automatically finding its underlying lattice, identifying its symmetry group, and extracting its representative motifs. We also extend this computational model for near-periodic patterns using geometric AIC. Applications of such a computational model include pattern indexing, texture synthesis, image compression, and gait analysis.

Algorithms↗
PubMed1997

Interpreting open- and closed-loop transfer relations between cardiorespiratory parameters: lessons learned from a computer model of beat-to-beat cardiovascular regulation.

A computer model of cardiovascular control has been developed based on the response characteristics of cardiovascular control components derived from experiments in animals and humans. Results from the model were compared to those obtained experimentally in humans, and the similarities and differences were used to identify both the strengths and inadequacies of the concepts used to form the model. Findings were confirmatory of some concepts but contrary to some which are firmly held in the literature, indicating that understanding the complexity of cardiovascular control probably requires a combination of experiments and computer models which integrate multiple systems and allow for determination of sufficiency and necessity.

Computer Simulation↗
PubMed1991

A computational model of levodopa pharmacodynamics in Parkinson's disease.

A series of computational models were developed to better understand basal ganglia functions and the effects of levodopa pharmacodynamics in Parkinson's disease. The models employed a relatively new computational approach known as a neural network, which is a small number of simple processing units interconnected with designated constraints. A key difference from traditional computational modeling is that the networks are "trained" rather than programmed with experimental input and output data. After training, only a limited number of these models, could explain the pharmacodynamic data observed by Mouradian et al. in different groups of Parkinsonian patients. These successful models strongly argue for at least two pharmacologic mechanisms to explain the antiparkinsonian effect and dyskinesia tendency for the different classes of Parkinson's patients: never-treated, stable, wearing-off, and on-off. They suggest different roles for the striatal units by examining predictions of motor and dyskinesia tendency through theoretical blockade of each kind of unit. The models show that the antiparkinsonian effect in Parkinson's disease cannot be explained by the action of dopaminergic neurons on striatal neurons alone. Although the models necessarily oversimplify basal ganglia function, they provide a useful quantitative insight into how motor and dyskinesia behaviors may develop in different Parkinsonian subgroups.

Basal Ganglia↗
PubMed1987

Interlaboratory proficiency-testing programs: a computer model to assess their capability to correctly characterize intralaboratory performance.

We developed a computer model of an interlaboratory survey program to study the ability of proficiency testing (PT) programs to detect intralaboratory errors (total, random, and systematic). It uses a base interlaboratory PT population of 400 laboratories and one test laboratory each with uniquely defined intralaboratory characteristics, i.e., mean, standard deviation (SD), and bias. A gaussian random-number generator uses these parameters to simulate 401 test results analogous to the analysis of one PT sample by each laboratory. The test laboratory's intralaboratory error is expressed as various combinations of bias and coefficient of variation (CV); its simulated survey result is evaluated by a performance criterion derived from the group statistics. To eliminate statistical artifacts, the computer model repeats the complete simulation process 400 times and determines the percentage of the test laboratory's results that fail to meet a specified performance criterion. The computer model can use assigned values or actual intralaboratory data.

Computer Simulation↗
PubMed2005

Evaluation of two computational models of amplitude modulation coding in the inferior colliculus.

Two computational models replicating amplitude-modulation encoding in the inferior colliculus (IC) are presented and compared. Neurons in this nucleus are modeled as point neurons using Mc Gregor equations, and receive depolarizing currents from action potentials delivered by stellate cells (chopper units) in the cochlear nucleus (CN). Stellate cells are modeled using modified Hodgkin-Huxley equations and receive inputs from a peripheral auditory model. The CN models of the two proposed architectures are characterized by an important dispersion of cellular characteristics, and therefore by various cellular best modulation frequencies (BMFs) ranging from 60 to 300 Hz. In contrast with the previous model proposed by [M.J. Hewitt, R. Meddis, A computer model of amplitude-modulation sensitivity of single units in the inferior colliculus, J. Acoust. Soc. Am. 95 (1994) 2145], each IC cell model receives convergent input from stellate cells with various BMFs. This approach assumes therefore minimal constraints on the model architecture and cell characteristics. The two models differ in terms of the neuronal structure of the IC, composed of 1 or 2 layers of point neurons acting as coincidence detectors. Each model is evaluated using two metrics: mean firing rate and modulation gain. Rate and temporal modulation transfer functions (r-MTFs and t-MTFs, respectively) are simulated and compared with physiological data. Simulations reveal that (i) an important dispersion of BMFs in the CN cells providing input to IC cells yields plausible IC cells responses to AM stimuli, (ii) the 2-layer IC structure yields the best approximation of IC responses measured in vivo.

Computational Biology↗
PubMed2000

Computational model of dot-pattern selective cells.

A computational model of a dot-pattern selective neuron is proposed. This type of neuron is found in the inferotemporal cortex of monkeys. It responds strongly to groups of dots and spots of light intensity variation but very weakly or not at all to single dots and spots that are not part of a pattern. This non-linear behaviour is quite different from the spatial frequency filtering behaviour exhibited by other neurons that react to spot-shaped stimuli, such as neurons with centre-surround receptive field profiles found in the lateral geniculate nuclei and layer 4Cbeta of V1. It is implemented in the proposed computational model by using an AND-type non-linearity to combine the responses of centre-surround cells. The proposed model is capable of explaining the results of neurophysiological experiments as well as certain psychophysical observations.

Animals↗
PubMed2002

The effect of dysfunctional voiding on the costs of treating vesicoureteral reflux: a computer model.

PURPOSE: We created a computer model for evaluating the effect of dysfunctional voiding on the costs of managing vesicoureteral reflux in children. MATERIALS AND METHODS: The literature on vesicoureteral reflux was reviewed to create a set of assumptions regarding the epidemiology, likelihood of resolution, need for operative intervention, risk of infection and appropriate regimen for nonoperative surveillance. Recent literature describing the effect of dysfunctional voiding on the clinical course of vesicoureteral reflux was included in the model to compare the costs of treating vesicoureteral reflux in children with and without dysfunctional voiding. A 5-year management period was considered. RESULTS: Dysfunctional voiding in children with vesicoureteral reflux increased the cost of treatment per patient by 51.2%. The cost per patient increased with increasing grade in those with and without dysfunctional voiding. The difference in costs in the 2 groups increased from 18.7% for grade 1 reflux to 62.1% for grade 5. Sensitivity analysis was performed, in which the risk of urinary tract infection, rate of surgical resolution, incidence of dysfunctional voiding and discount rate varied. The cost in children with dysfunctional voiding remained higher in all scenarios studied, showing the robustness of the model. CONCLUSIONS: Dysfunctional voiding substantially increases the costs of treating children with vesicoureteral reflux due to the higher rate of urinary tract infection in children with dysfunctional voiding. Methods that would decrease the rate of urinary tract infection in children with dysfunctional voiding and vesicoureteral reflux would lead to a significant saving of health care dollars.

Child↗
PubMed2004

Carbohydrate-fat interactions and obesity examined by a two-compartment computer model.

OBJECTIVE: A systems dynamics computer model was developed to examine how the interactions between carbohydrate and fat metabolism influence body weight regulation. It reflects the operation of a two reservoir-system: one representing the body's limited glycogen, and the other, its large fat reserves. The outflows from the reservoirs correspond to the oxidation of glucose and fat, whose relative contributions are affected by the size of the prevailing glycogen and fat reserves. Together, they meet the body's energy expenditure. Replenishments occur three times per day, in portions restoring total glycogen content to specific levels. A parameter mimicking the action of insulin is necessary to create realistic responses. RESEARCH METHODS AND PROCEDURES: The model was run for 125-day periods to establish the degree of adiposity for which rates of fat oxidation become commensurate with fat intake and the influence thereon of various dietary, environmental, lifestyle, and inherited variables. RESULTS: Equivalent degrees of adiposity can be sustained under a variety of conditions. For instance, the impact on steady-state body fat contents of a 10% increase or decrease in the energy provided by dietary fat is offset by a 26-gram decrease or increase in mean glycogen levels. DISCUSSION: Environmental factors such as food diversity, palatability, and availability can be expected to raise the range within which glycogen levels are habitually maintained. This restrains fat oxidation, until expansion of the fat mass is sufficient to promote fat oxidation to a rate commensurate with dietary fat intake. This metabolic leverage can explain why increased food offerings tend to raise the prevalence of obesity.

Adipose Tissue↗