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PubMed2004

Use of computer simulation for determining endovascular skill levels in a carotid stenting model.

OBJECTIVES: The purpose of this study was to determine whether performance on a simulator model of carotid artery stenting correlates with previous endovascular experience and to assess the effects of repetition and training. METHODS: Participants were stratified to untrained and advanced skill groups on the basis of number of endovascular procedures previously performed. Baseline performance was assessed by means of a pretest, and participants were randomized to practice and no-practice groups. Practice consisted of a 30-minute to 60-minute proctored session before taking a final test; those in the no-practice group proceeded directly to the final test without this session. Primary outcomes were completion of a standardized protocol and the length of time needed to complete all steps. RESULTS: Twenty-nine subjects (16 untrained, 13 advanced) participated fully in the study. Ninety-two percent of participants in the advanced group successfully completed the pretest, versus 63% in the untrained group (P = .09); mean time to successful completion was 29.9 +/- 4.8 (mean +/- SD) versus 48.0 +/- 9.9 minutes, respectively (P < .001). Subjects who received no practice did not significantly improve their completion times between pretest and final test, whereas those who received practice did (novice, 47.9 +/- 7.0 minutes vs 24.5 +/- 2.9 minutes, P < .001; advanced, 29.6 +/- 3.1 minutes vs 20.2 +/- 4.1 minutes, P < .001). The group without previous training had significantly more time improvement from training than did the advanced group. Exit survey results showed that those who had the opportunity to practice more commonly believed that the simulator increased their endovascular skills and interest in vascular surgery (both P < .01 vs untrained group). CONCLUSIONS: Performance on the carotid stenting simulator correlated with previous endovascular experience. Although both novice and advanced groups improved their time after a 30-minute to 60-minute proctored training session, improvement in the novice group was greater than that in the advanced group, which suggests that novices may benefit disproportionately from this type of training.

Blood Vessel Prosthesis Implantation↗

PubMed1986

A molecular dynamics computer simulation of an eight-base-pair DNA fragment in aqueous solution: comparison with experimental two-dimensional NMR data.

The structure and dynamics of an 8-base-pair DNA fragment (dCGCAACGC/dGCGTTGCG) in aqueous solution (14 Na+ ions, 1231 water molecules) have been simulated by using the molecular-dynamics method. Interproton distances have been calculated for various structures and are compared with a set of 174 distances which have been derived from 2D NOE experiments. The averaged MD structures are compared with ideal A-DNA and B-DNA structures in terms of helix parameters, dihedral angles, and so forth. The hydration of various atoms of the DNA fragment and of the Na+ ions is analyzed by calculating coordination numbers and first-neighbor shell residence times.

Base Composition↗

PubMed2005

Structure of a cyclodextrin functionalized anionic clay: XRD analysis, spectroscopy, and computer simulations.

Carboxy-methyl beta-cyclodextrin (CMCD) cavities have been intercalated within the galleries of anionic clay, Mg-Al layered double hydroxide (LDH). The cyclodextrin functionalized LDH has been reported to adsorb neutral and nonpolar guest molecules. X-ray diffraction, IR, and Raman vibrational spectroscopy and (13)C CPMAS NMR have been used to characterize the confined CMCD molecules, whereas molecular dynamics simulations have been used to probe the interlayer arrangement and orientation of the intercalated species. Spectroscopic measurements as well as MD simulations show that there is no significant change in the geometry of the CMCD cavity on intercalation. Within the galleries of the anionic clay, the CMCD anions are arranged as bilayers with the carboxy methyl substituents, located at the narrower opening of the bucket-like cyclodextrin toroid, anchored to the LDH sheet. This arrangement leaves the wider opening of the CMCD anion facing away from the layers allowing the interior of the cyclodextrin cavity to be accessible to guest molecules. Finally, the hydrophobicity of the anchored cyclodextrin cavity has been characterized using fluorescence from pyrene included within it.

Anions↗

PubMed2002

Relationship between the flow of bolus and occlusal condition during mastication--computer simulation based on the measurement of characteristics of the bolus.

The purpose of the present study was to clarify the relationship between the flow of a bolus and occlusal condition during mastication. First, the characteristics of a bolus under mastication was measured in subjects having different occlusal conditions. Secondly, the flow of a bolus between the upper and lower first molars under mastication was simulated using finite element non-linear dynamic analysis. Measurement of the elasticity of the bolus clarified the phenomenon of its communition. The measurement of the viscosity of the bolus clarified the phenomenon of its mixing with saliva. In addition, a relationship between the elasticity and the viscosity of the bolus at the point of just before swallowing was investigated. The flow of the bolus under mastication was revealed to vary according to the occlusal condition. These results suggest a close relationship between the occlusal condition, the flow of the bolus and its characteristics.

Adult↗

PubMed2003

Multisampling suprathreshold perimetry: a comparison with conventional suprathreshold and full-threshold strategies by computer simulation.

PURPOSE: To compare a multisampling suprathreshold strategy with conventional suprathreshold and full-threshold strategies in detecting localized visual field defects and in quantifying the area of loss. METHODS: Probability theory was applied to examine various suprathreshold pass criteria (i.e., the number of stimuli that have to be seen for a test location to be classified as normal). A suprathreshold strategy that requires three seen or three missed stimuli per test location (multisampling suprathreshold) was selected for further investigation. Simulation was used to determine how the multisampling suprathreshold, conventional suprathreshold, and full-threshold strategies detect localized field loss. To determine the systematic error and variability in estimates of loss area, artificial fields were generated with clustered defects (0-25 field locations with 8- and 16-dB loss) and, for each condition, the number of test locations classified as defective (suprathreshold strategies) and with pattern deviation probability less than 5% (full-threshold strategy), was derived from 1000 simulated test results. RESULTS: The full-threshold and multisampling suprathreshold strategies had similar sensitivity to field loss. Both detected defects earlier than the conventional suprathreshold strategy. The pattern deviation probability analyses of full-threshold results underestimated the area of field loss. The conventional suprathreshold perimetry also underestimated the defect area. With multisampling suprathreshold perimetry, the estimates of defect area were less variable and exhibited lower systematic error. CONCLUSIONS: Multisampling suprathreshold paradigms may be a powerful alternative to other strategies of visual field testing. Clinical trials are needed to verify these findings.

Computer Simulation↗

PubMed1992

Computer simulation on creep of amalgam in Class I cavity.

The creep behavior of amalgam in Class I cavity was simulated by an axi-symmetric elastic creep finite element method. In this procedure, the stress and time dependencies of the creep strain of amalgam were incorporated. Exponents of stress and time dependencies were postulated as 2.0 and 1.0, respectively. Amalgam with 1.0% of creep value (tested by American Dental Association Specification No. 1) were selected for the material to calculate. Simulation was conducted for the occlusal force of 40, 100, and 150 N, respectively, on the caps of enamel and vertical direction to the axis of the tooth. Results show that creep strain of amalgam in the cavity did not increase linearly with time because the amalgam deformed to become stress-free and creep rate was a function of the stress. It was concluded that elastic deformation of the crown with no filling material in its cavity is an important factor in determining the creep strain and the gap between the cavity and the restorative material.

Biomechanical Phenomena↗

PubMed1992

Hydrogen peroxide plays a key role in the oxidation reaction of myoglobin by molecular oxygen. A computer simulation.

The stability properties of the iron(II)-dioxygen bond in myoglobin and hemoglobin are of particular importance, because both proteins are oxidized easily to the ferric met-form, which cannot be oxygenated and is therefore physiologically inactive. In this paper, we have formulated all the possible pathways leading to the oxidation of myoglobin to metmyoglobin with each required rate constant in 0.1 M buffer (pH 7.0) at 25 degrees C, and have set up six rate equations for the elementary processes going on in a simultaneous way. By using the Runge-Kutta method to solve these differential equations, the concentration progress curves were then displayed for all the reactive species involved. In this complex reaction, the primary event was the autoxidation of MbO2 to metMb with generation of the superoxide anion, this anion being converted immediately and almost completely into H2O2 by the spontaneous dismutation. Under air-saturated conditions (PO2 = 150 Torr), the H2O2 produced was decomposed mostly by the metMb resulting from the autoxidation of MbO2. At lower pressures of O2, however, H2O2 can act as the most potent oxidant of the deoxyMb, which increases with decreasing O2 pressures, so that there appeared a well defined maximum rate in the formation of metMb at approximately 5 Torr of oxygen. Such examinations with the aid of a computer provide us, for the first time, with a full picture of the oxidation reaction of myoglobin as a function of oxygen pressures. These results also seem to be of primary importance from a point of view of clinical biochemistry of the oxygen supply, as well as of pathophysiology of ischemia, in red muscles such as cardiac and skeletal muscle tissues.

Computer Simulation↗

PubMed2006

Computer simulation of polypeptides in a confinement.

A coarse-grained model of polypeptide chains confined in a slit formed by two parallel impenetrable surfaces was studied. The chains were flexible heteropolymers (polypeptides) built of two kinds of united atoms-hydrophobic and hydrophilic. The positions of the united atoms were restricted to the vertices of a [310] lattice. The force field consisted of a rigorous excluded volume, a long-distance potential between a pair of amino-acid residues and a local preference for forming secondary structure (helices). The properties of the chains were studied at a wide range of temperatures from good to bad solvent conditions. Monte-Carlo simulations were carried out using the algorithm based on the chain's local changes of conformation and employing the Replica Exchange technique. The influence of the chain length, the distances between the confining surfaces, the temperature and the force field on the dimension and the structure of chains were studied. It was shown that the presence of the confinement chain complicates the process of the chain collapse to low-temperature structures. For some conditions, one can find a rapid decrease of chain size and a second transition indicated by the rapid decrease of the total energy of the system.

Computer Simulation↗

PubMed2004

Computer simulation of leachate quality by recirculation in a sanitary landfill bioreactor.

Sanitary Landfills are the most widely used method of solid waste disposal around the world. Modern sanitary landfills are designed with impervious liners, and leachate collection, removal, and treatment systems to minimize the potential for groundwater contamination. Leachate recycle through the landfill is an effective method of leachate treatment, and to enhance solid waste stabilization. A mathematical model is developed to simulate the release of contaminants from solid wastes, and their movement into the percolating liquid. Two differential equations are used that express the mass balance of the contaminants in the percolating water and those in the solid wastes. These simultaneous linear differential equations are solved numerically using a fourth-order Runge-Kutta algorithm with many physical and process parameters. The model results are used to estimate the active life of landfill with and without leachate recirculation. Such information is valuable in the operation, maintenance, and closure plan of a sanitary landfill.

Bioreactors↗

PubMed1993

[The acetabular prosthesis: detection of a migration using ruler and pencil? Measurements on a pelvic phantom in comparison with a 3D computer simulation].

Conventional X-ray films were made with varying degrees of tilt of a pelvic phantom containing an acetabular prosthesis. The position of the prosthesis was then reconstructed graphically. The measurement errors were calculated and an estimate was made for the tilt. There is a linear correlation between the measurement error and the tilt of the prosthesis. Therefore a tilt dependent maximum error can be calculated. This error is very small for small degrees of tilt, so that acetabular migration can in this instance be evaluated with greater confidence than with other graphical methods. The error also correlates with the determination of the selected region of the acetabulum, but not with the position of the central focus spot or image magnification.

Acetabulum↗

PubMedDate not supplied

Computer simulation of hydrodynamic properties of semiflexible macromolecules: randomly broken chains, wormlike chains, and analysis of properties of DNA.

The translational and rotational diffusion coefficients and the intrinsic viscosity of semiflexible, randomly broken, and wormlike chains have been obtained by Monte Carlo simulation in the context of the rigid-body treatment. Both approximate and rigorous rigid-body hydrodynamics are used, so that the error introduced by the approximate methods can be evaluated. A randomly broken chain and a wormlike chain having the same contour length and persistence length have the same radius of gyration but different values for any of the hydrodynamic properties. The two types of chains are compared in this regard. Considering that the cross section of the chain is represented by a cylinder better than by a string of spheres, we devise a cylindrical correction to be applied to the results simulated for chains of beads. Application is made to the analysis of experimental data for the translational and rotational coefficients of DNA fragments with up to 10(3) base pairs, obtaining the persistence length for each model. The values for the wormlike chain agree well with model-independent values obtained from radii of gyration and with other literature data at varying ionic strength. The randomly broken chain is equally able to reproduce the experimental length dependence of the properties, but the resulting persistence length may be too high.

Chemical Phenomena↗

PubMed1996

In vitro studies and computer simulations to assess the use of a diode laser (850 nm) for laser-induced thermotherapy (LITT).

BACKGROUND AND OBJECTIVE: This study investigated the feasibility of 850 nm diode laser-induced thermotherapy (LITT), a new procedure providing local hyperthermia and photocoagulation, a minimally invasive treatment of tumors, and other disorders such as benign prostate hyperplasia. STUDY DESIGN/MATERIAL AND METHODS: An improved fiber optic diffuser inserted through a catheter was used to irradiate prostate, liver, and kidney tissue in-vitro. Experimental results were compared with predictions from mathematical simulations based on measured optical tissue parameters. RESULTS: After 10 minutes of irradiation with 2-4.6 W CW laser power, sizable coagulation diameters had been achieved. In prostate and kidney tissue, temperature rises and coagulation diameters after laser irradiation were found to be smaller than in liver tissue. Those tissues also had a higher threshold for carbonization, thus reducing the risk of damage to the delivery system. CONCLUSION: The data suggest that a low power diode laser can be recommended for use in LITT to treat prostate and kidney tissue.

Animals↗

PubMedDate not supplied

Comblike poly(alpha-alkyl gamma-glutamate)s: computer simulation studies of an intermediate thermal phase.

Monte Carlo (MC) simulations have been used to study the structure of an intermediate thermal phase of poly(alpha-octadecyl gamma,D-glutamate). This is a comblike poly(gamma-peptide) able to adopt a biphasic structure that has been described as a layered arrangement of backbone helical rods immersed in a paraffinic pool of polymethylene side chains. Simulations were performed at two different temperatures (348 and 363 K), both of them above the melting point of the paraffinic phase, using the configurational bias MC algorithm. Results indicate that layers are constituted by a side-by-side packing of 17/5 helices. The organization of the interlayer paraffinic region is described in atomistic terms by examining the torsional angles and the end-to-end distances for the octadecyl side chains. Comparison with previously reported comblike poly(beta-peptide)s revealed significant differences in the organization of the alkyl side chains.

Calorimetry↗

PubMed1999

Comparison of the Bayesian approach and a limited sampling model for the estimation of AUC and Cmax: a computer simulation analysis.

OBJECTIVES: To compare two limited sampling methods (Bayesian and the limited sampling model) for the estimation of AUC and Cmax following a single oral dose of a hypothetical drug. METHODS: The plasma concentration vs time data sets for 50 subjects using a linear one- or two-compartment pharmacokinetic model were generated by simulation. The limited sampling model (LSM) was developed using samples from 10 subjects using one or two time points. The simulated plasma concentrations were also used for Bayesian evaluation. Bayesian analysis was performed on Non-Mem and mean pharmacokinetic parameters used for simulation were assumed as population pharmacokinetic parameters. In addition a test drug was also used to compare the predicted AUC and Cmax for the two approaches. RESULTS: Both methods were validated in 40 subjects for the hypothetical drug and in 12 subjects for the test drug. Both methods provided good estimates of AUC and Cmax. CONCLUSION: The results indicate that the LSM is similar to the Bayesian method and may be used in lieu of the Bayesian approach in estimating AUC and Cmax using one or two samples in clinical settings without detailed pharmacokinetic studies.

Area Under Curve↗

PubMed1997

A comparative computer simulation study of three different sparse-sampling methods for the estimation of steady-state area under the concentration-time curve (AUC) and maximum concentration (Cmax) in toxicokinetics.

A limited-sampling method is proposed to estimate the area under the curve (AUC) of concentration versus time and maximum concentration (Cmax) following single or multiple oral doses of a hypothetical drug. The plasma concentration versus time data sets for 50 animals were generated by simulation. The limited-sampling model (LSM) was developed with samples from 10 animals at a single time point. The model was validated in another 40 animals who received either a 500-mg single dose or multiple doses orally. The model provided good population mean estimates of AUC and Cmax. The proposed method was compared with the existing two methods; they are, naive sampling (five time points) and optimal sampling (three time points). The method described here may be useful in estimating AUC and Cmax with one or two samples in toxicokinetic studies following single or multiple oral dosing without detailed pharmacokinetic studies.

Area Under Curve↗

PubMed2001

Computer simulation of ion chromatography separation: an algorithm enabling continuous monitoring of anion distribution on an ion-exchange chromatography column.

A computer algorithm for the calculation of ion chromatography separation is presented. It is based on the calculation of equilibrium concentrations of present analyte in discrete column segments. The continuous column is treated as a number of discrete cells or segments where the equilibration process between the stationary phase and the eluent is simulated. The ion-exchange equilibration process is supposed to be instantaneous and quantitative. The continuous flow of the eluent is rendered by discrete transfers. The size of each transfer of the eluent corresponds to a portion of the volume contained in one column segment. The equilibrium calculations in all column segments are repeated for each transfer of the eluent, through all the stages of the chromatographic process. The distribution of the analytes between the stationary phase and the eluent can be monitored at any step and in any column segment which means that the described algorithm provides the spatial and time concentration profiles. The simulated chromatogram is acquired as a time-concentration profile in the last column segment. The obtained chromatograms are in good agreement with the experimental ones. The distribution of ions between the stationary phase and the eluent in the early stages of the ion chromatographic process can thus be studied with confidence.

Algorithms↗

PubMedDate not supplied

Computer simulation of broad-beam and narrow-beam attenuation in lead for diagnostic x-ray energies.

Significant differences between broad- and narrow-beam transmission measurements for lead protective barriers have been noted for x-ray beams in the diagnostic energy range. Work reported in this paper indicates that these differences in transmitted exposure between broad- and narrow-beam geometry measurements are primarily the result of two independent interaction processes; the transmission of K-characteristic photons produced in the barrier, and coherently scattered photons. The magnitude of these effects was studied for x-ray spectra between 70 and 150 kVp. The K-characteristic component was found to be maximal at 150 kVp, while the coherently scattered contribution was found to be maximal for thick barriers and at lower energies. The effect of beam field size on relative transmitted intensities was also studied and found to increase with increasing field size up to 30 cm. A detector-to-barrier distance of 10 cm was found to maximize the K-characteristic component. For a typical diagnostic x-ray potential of 100 kVp, the K-characteristic component was found to be less than 7% of the total transmitted beam. Voltage wave form considerations were found to be significant as has been previously reported. The contribution of K-characteristic photons has been mathematically modeled and a computer program written to allow the rapid computation of broad beam transmission exposures for lead barriers, once the appropriate beam specifications have been entered.

Biophysical Phenomena↗

PubMed1988

Domain interaction in rabbit muscle pyruvate kinase. II. Small angle neutron scattering and computer simulation.

The effects of ligands on the structure of rabbit muscle pyruvate kinase were studied by small angle neutron scattering. The radius of gyration, RG, decreases by about 1 A in the presence of the substrate phosphoenolpyruvate, but increases by about the same magnitude in the presence of the allosteric inhibitor phenylalanine. With increasing pH or in the absence of Mg2+ and K+, the RG of pyruvate kinase increases. Hence, there is a 2-A difference in RG between two alternative conformations. Length distribution analysis indicates that, under all experimental conditions which increase the radius of gyration, there is a pronounced increase observed in the probability for interatomic distance between 80 and 110 A. These small angle neutron scattering results indicate a "contraction" and "expansion" of the enzyme when it transforms between its active and inactive forms. Using the alpha-carbon coordinates of crystalline cat muscle pyruvate kinase, a length distribution profile was calculated, and it matches the scattering profile of the inactive form. These observations are expected since the crystals were grown in the absence of divalent cations (Stuart, D. I., Levine, M., Muirhead, H., and Stammers, D. K. (1979) J. Mol. Biol. 134, 109-142). Hence, results from neutron scattering, x-ray crystallographic, and sedimentation studies (Oberfelder, R. W., Lee, L. L.-Y., and Lee, J.C. (1984) Biochemistry 23, 3813-3821) are totally consistent with each other. With the aid of computer modeling, the crystal structure has been manipulated in order to effect changes that are consistent with the conformational change described by the solution scattering data. The structural manipulation involves the rotation of the B domain relative to the A domain, leading to the closure of the cleft between these domains. These manipulations resulted in the generation of new sets of atomic (C-alpha) coordinates, which were utilized in calculations, the result of which compared favorably with the solution data.

Algorithms↗