SEARCH · PubMed Health

Results for “Computer Simulation”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,495 records · Page 83Linked to original sources

PubMed1997

Computer simulation of the responses of human motoneurons to composite 1A EPSPS: effects of background firing rate.

Two compartmental models of spinal alpha motoneurons were constructed to explore the relationship between background firing rate and response to an excitatory input. The results of these simulations were compared with previous results obtained from human motoneurons and discussed in relation to the current model for repetitively firing human motoneurons. The morphologies and cable parameters of the models were based on two type-identified cat motoneurons previously reported in the literature. Each model included five voltage-dependent channels that were modeled using Hodgkin-Huxley formalism. These included fast Na+ and K+ channels in the initial segment and fast Na+ and K+ channels as well as a slow K+ channel in the soma compartment. The density and rate factors for the slow K+ channel were varied until the models could reproduce single spike AHP parameters for type-identified motoneurons in the cat. Excitatory synaptic conductances were distributed along the equivalent dendrites with the same density described for la synapses from muscle spindles to type-identified cat motoneurons. Simultaneous activation of all synapses on the dendrite resulted in a large compound excitatory postsynaptic potential (EPSP). Brief depolarizing pulses injected into a compartment of the equivalent dendrite resulted in pulse potentials (PPs), which resembled the compound EPSPs. The effects of compound EPSPs and PPs on firing probability of the two motoneuron models were examined during rhythmic firing. Peristimulus time histograms, constructed between the stimulus and the spikes of the model motoneuron, showed excitatory peaks whose integrated time course approximated the time course of the underlying EPSP or PP as has been shown in cat motoneurons. The excitatory peaks were quantified in terms of response probability, and the relationship between background firing rate and response probability was explored. As in real human motoneurons, the models exhibited an inverse relationship between response probability and background firing rate. The biophysical properties responsible for the relationship between response probability and firing rate included the shapes of the membrane voltage trajectories between spikes and nonlinear changes in PP amplitude during the interspike interval at different firing rates. The results from these simulations suggest that the relationship between response probability and background firing rate is an intrinsic feature of motoneurons. The similarity of the results from the models, which were based on the properties of cat motoneurons, and those from human motoneurons suggests that the biophysical properties governing rhythmic firing in human motoneurons are similar to those of the cat.

Cell Membrane↗

PubMed1993

Computer simulations of three-dimensional propagation in ventricular myocardium. Effects of intramural fiber rotation and inhomogeneous conductivity on epicardial activation.

Three-dimensional membrane-based simulations of action potential propagation in ventricular myocardium were performed. Specifically, the effects of the intramural rotation of the fiber axes and inhomogeneous conductivity on the timing and pattern of epicardial activation were examined. Models were built, with approximately 400,000 microscopic elements arranged in rectangular parallelepipeds in each model. Simulations used the nonlinear Ebihara and Johnson membrane equations for the fast sodium current. Constructed models had histological features of ventricular myocardium. All models were anisotropic. In a subset of the models, an abrupt intramural rotation of the fiber axes was included. This feature was also combined with randomly distributed inhomogeneous conductivity and regions of high transverse resistance to represent nonuniform anisotropy in a further subset of the models. Epicardial stimuli were applied for each simulation. Three-dimensional activation patterns and epicardial isochron maps were constructed from the simulations. We noted that the rotation of fiber axes accelerated epicardial activation distant from the stimulus site. The inhomogeneous conductivity caused regional acceleration and deceleration of activation spread. We also noted features of epicardial activation that resulted from the fiber rotation, and the inhomogeneous conductivity corresponded to that observed in maps from experimental animals.

Animals↗

PubMed2004

Impact of truncated area under the curve on failed bioequivalence studies: a computer simulation analysis.

The common measures used in a bioequivalence study are area under the curve (AUC) and the maximum plasma concentration. Estimation of AUC requires frequent blood samples. For long half-life drugs, sampling for long periods of time may become cumbersome. To resolve this issue some investigators have suggested the use of truncated AUC in bioequivalence studies for long half-life drugs. The suggested length of time for the truncated AUC is 72 hours. Many studies have been conducted to show that truncated AUC till 72 hours is a suitable approach. However, the suitability of truncated AUC for failed bioequivalence study has not been demonstrated. This report of simulated plasma concentration versus time data evaluates the suitability of truncated AUC for failed bioequivalence study of two hypothetical drugs. The results of the study indicate that the truncated approach for the estimation of the AUC for long half-life drugs in bioequivalence studies may be useful but it also increases the probability of accepting drugs as being bioequivalent when they are not.

Area Under Curve↗

PubMed1978

A study of the motor unit action potential by means of computer simulation.

In order to study the motor unit action potential a computer stimulation model was developed. It is based on the superposition of single muscle fibre potentials of the fibres belonging to the motor unit. The parameters which characterize each fibre (spatial position, diameter, and a dispersion of arrival time of the potential at the electrode) are chosen from statistical distributions which can be derived from anatomical and physiological data. The electrode type, position and dimensions can be specified. Simulated motor unit action potentials are presented in the time and frequency domain. The stimulation results refer to (1) the influence of the electrode position and dimensions with respect to the motor unit territory, (2) the meaning of this model for the study of pathological phenomena, (3) the variability of some parameters characterizing the motor unit, (4) the selectivity of uni- and bipolar electrodes and finally (5) the influence of the geometrical situation of the motor end-plates within the muscle, on the shape of motor unit action potentials.

Action Potentials↗

PubMed1979

Computer simulation of circumnutations--behaviour under different g's and comparison with experiment.

The influence of different g-forces on helical growth movements--circumnutation--of sunflower seedlings is treated. Predictions from a model, describing the movements as geotropic overshoot movements, are given. Results from tests of the assumptions are given. These results as well as results in the literature do not contradict the model. The need for more precise centrifuge tests under otherwise free fall conditions is emphasized.

Computer Simulation↗

PubMed1994

Computer simulations of cyclic and acyclic cholinergic agonists: conformational search and molecular dynamics simulations.

Molecular dynamics simulations have been performed on aqueous solutions of two chemically similar nicotinic cholinergic agonists in order to compare their structural and dynamical differences. The cyclic 1,1-dimethyl-4-acetylpiperazinium iodide (HPIP) molecule was previously shown to be a strong agonist for nicotinic acetylcholine receptors (McGroddy et al., 1993), while the acyclic N,N,N,N'-tetramethyl-N'-acetylethylenediamine iodide (HTED) derivative is much less potent. These differences were expected to arise from differences in the solution structures and internal dynamics of the two molecules. HPIP was originally thought to be relatively rigid; however, molecular dynamics simulations suggest that the acetyl portion of the molecule undergoes significant ring dynamics on a psec timescale. The less constrained HTED molecule is relatively rigid, with only one transition observed about any of the major dihedrals in four 100 psec simulations, each started from a different conformation. The average structures obtained from the simulations are very similar to the starting minimized structure in each case, except for the HTED simulation where a single rotation about the N-C-C-N(+) backbone occurred. In each case, HTED had three to five more water molecules in its primary solvation shell than HPIP, indicating that differences in the energetics of desolvation before binding may partially explain the increased potency of HPIP as compared to HTED.

Biophysical Phenomena↗

PubMed2006

[Computer simulation model of propagation and impact of undergroud garage noise between buildings in urban residential region].

Aimed at certain types of building dispositions in urban residential region, the noise impacts of the underground garage is analyzed and calculated with the simulation model of random point sound source. The comparison between the predicted results and measured value of noise level shows that the predicted model presents an acceptable degree of accuracy. Adopting this model to predict noise impacts of the underground garage in designed and newly-built residential region will provide scientific basis for effective noise

Computer Simulation↗

PubMed1998

Computer simulation studies of the fully solvated wild-type and mutated GnRH in extended and beta-turn conformations.

The conformational preference of the gonadotropin-releasing hormone (GnRH) and its Lys-8 mutant, studied earlier with a continuum model, was revisited using an explicit solvent model and thermodynamic integration to calculate the solvents contribution to the conformation-dependence of its free energy. In addition, the Proximity Criterion was used to further analyze the effects of conformational changes.

Computer Simulation↗

PubMed2001

Dissecting the superoxide dismutase-ascorbate-glutathione-pathway in chloroplasts by metabolic modeling. Computer simulations as a step towards flux analysis.

The present study introduces metabolic modeling as a new tool to analyze the network of redox reactions composing the superoxide dismutase-ascorbate (Asc)-glutathione (GSH) cycle. Based on previously determined concentrations of antioxidants and defense enzymes in chloroplasts, kinetic properties of antioxidative enzymes, and nonenzymatic rate constants of antioxidants with reactive oxygen, models were constructed to simulate oxidative stress and calculate changes in concentrations and fluxes of oxidants and antioxidants. Simulated oxidative stress in chloroplasts did not result in a significant accumulation of O2*- and H2O2 when the supply with reductant was sufficient. Model results suggest that the coupling between Asc- and GSH-related redox systems was weak because monodehydroascorbate radical reductase prevented dehydroascorbate (DHA) formation efficiently. DHA reductase activity was dispensable. Glutathione reductase was mainly required for the recycling of GSH oxidized in nonenzymatic reactions. In the absence of monodehydroascorbate radical reductase and DHA reductase, glutathione reductase and GSH were capable to maintain the Asc pool more than 99% reduced. This suggests that measured DHA/Asc ratios do not reflect a redox balance related to the Asc-GSH-cycle. Decreases in Asc peroxidase resulted in marked H2O2 accumulation without significant effects on the redox balance of Asc/DHA or GSH/GSSG. Simulated loss of SOD resulted in higher H2O2 production rates, thereby affecting all subsequent steps of the Asc-GSH-cycle. In conclusion, modeling approaches contribute to the theoretical understanding of the functioning of antioxidant systems by pointing out questions that need to be validated and provide additional information that is useful to develop breeding strategies for higher stress resistance in plants.

Ascorbic Acid↗

PubMed1992

Computer simulation of periacetabular osteotomy.

A simple static three-dimensional mathematical model of an adult hip in one-legged stance was used to evaluate the mechanical situation after periacetabular osteotomy. We found that the hip joint rotation center shifted as a consequence of the osteotomy. This may have considerable effects on the hip joint resultant force and therefore also on the pressure on the femoral head, which could cause the development of arthrosis.

Acetabulum↗

PubMed1990

Computer simulation of oral fluoride clearance.

The presence of fluoride in saliva and dental plaque is important for prevention of dental caries. The elimination of fluoride from the oral cavity after introduction of a fluoride containing agent is a complicated physiological process. This process was simulated with a Pascal program running under MS-DOS on IBM-compatible microcomputers. The program calculated the fluoride concentration in saliva as a function of time from several input parameters, the most important being the amount of fluoride, salivary stimulation due to the fluoride vehicle, resting salivary flow rate and volume factors. Furthermore, factors such as excretion of fluoride in the saliva following fluoride absorption in the intestinal tract were modeled. The fluoride concentration in dental plaque due to diffusion was also calculated. Output was directed to files which could be processed by a graphics interface. The results of the computations were very similar to findings in vivo.

Algorithms↗

PubMed2006

Effect of continuous arterial blood flow in patients with rotary cardiac assist device on the washout of a stenosis wake in the carotid bifurcation: a computer simulation study.

In recipients of rotary blood pumps for cardiac assist, the pulsatility of arterial flow is considerably diminished. This influences the shear stress patterns and streamlines in the arterial bed, with potential influence on washout and plaque growth. These effects may be aggravated in the recirculation area of stenoses, and therefore, exclude patients with atherosclerosis from the therapy with these devices. A numerical study was performed for the human carotid artery bifurcation with the assumption of a massive stenosis (75% reduction of cross-section area) in the carotid bulb. Four different flow time patterns (no support to full pump support) were applied. Flow patterns and particle residence time within the recirculation region were calculated, once within the relevant volume behind the stenosis and and once within a small region directly at the posterior heel of the stenosis. The flow patterns showed a considerable radial vorticity behind the stenosis. Mean particle residence time in the whole recirculation region was 15% less for high pump support (nearly continuous flow) compared to the natural flow pattern (0.19s compared to 0.22s), and nearly identical for the small heel region (0.28 to 0.27s). The flow simulation demonstrates, that even in the case of a pre-existing stenosis, the local effects of continuous flow on particle residence times are rather minimal (as was shown previously for intact arterial geometries). Therefore, from the point of macroscopic flow field analysis, continuous flow should not enhance the thromboembolic risk in ventricular assist device recipients.

Blood Flow Velocity↗

PubMed1997

Dorfman-Berbaum-Metz method for statistical analysis of multireader, multimodality receiver operating characteristic data: validation with computer simulation.

RATIONALE AND OBJECTIVES: The authors examined the relationship between the critical P value (alpha) and the empirical type I error rate when using the Dorfman-Berbaum-Metz (DMB) method for analysis of variance in multireader, multimodality receiver operating characteristic (ROC) data. METHODS: The authors developed a linear mixed-effect model to generate continuous, normally distributed random decision variables containing multiple sources (components) of variation. A range of magnitudes for these variance components was used to stimulate experiments in which multiple readers (three or five) read imaged obtained with two modalities from the same set of cases with no re-reading. Three binormal population ROC curves, with areas of 0.962, 0.855, and 0.702, were included. Case-sample sizes ranged from 50 to 400, and either 50% or 10% of cases were actually positive. For each experiment, 2,000 data sets were analyzed by the computer program, and the proportion of 2,000 modality differences that was found to be statistically significant at an alpha level of .05 was tubulated. RESULTS: The test for modality difference performed well for the low and intermediate ROC curves, even with small case samples. For the high ROC curve, the small-sample results were conservative. No relationship between observed type I error rate and the magnitude of data correlation was evident. CONCLUSION: For typical ROC curves, the DBM method is robust in testing for modality effects in the null case, given a sufficient sample size. Instructions for obtaining a free copy of the software are given.

Analysis of Variance↗

PubMed1998

Computer simulation of magnetic resonance spectra employing homotopy.

Multidimensional homotopy provides an efficient method for accurately tracing energy levels and hence transitions in the presence of energy level anticrossings and looping transitions. Herein we describe the application and implementation of homotopy to the analysis of continuous wave electron paramagnetic resonance spectra. The method can also be applied to electron nuclear double resonance, electron spin echo envelope modulation, solid-state nuclear magnetic resonance, and nuclear quadrupole resonance spectra.

Computer Simulation↗

PubMed1992

Symptoms related to abnormal tonic state: experimental results and computer simulations.

There have been numerous attempts to relate tonic accommodation and tonic vergence and their adaptive capabilities to a variety of parameters in vision science and clinical optometry. In this paper, investigations attempting to correlate the tonic state with nearwork symptoms will be reviewed. Results suggest that tonic vergence is more closely linked to near symptoms than is tonic accommodation. The results will be discussed in terms of a steady-state model of accommodation and vergence.

Accommodation, Ocular↗

PubMed2005

Assessment of strategies to control BVDV spread in a dairy herd using computer simulation.

The efficiency of a test-and-cull programme to control BVDV spread within a dairy herd was assessed using a stochastic model. A single virus introduction by a non-PI dam carrying a PI foetus was simulated in a typical western-France dairy herd. Herd monitoring in test-and-cull programme enabled us to detect virus spread within 1 year after introduction in 87% of the replications. The test-and-cull programme reduced the length of the virus persistence. The extent of infection was moderately reduced.

Animals↗

PubMed2006

Solution NMR and computer simulation studies of active site loop motion in triosephosphate isomerase.

Solution NMR spin relaxation experiments and classical MD simulations are used to study the dynamics of triosephosphate isomerase (TIM) in complex with glycerol 3-phosphate (G3P). Three regions in TIM exhibit conformational transitions on the micros-ms time scale as detected by chemical exchange broadening effects in NMR spectroscopy: residue Lys 84 on helix C, located at the dimeric interface; active site loop 6; and helix G. The results indicate that the conformational exchange process affecting the residues of loop 6 is the correlated opening and closing of the loop. Distinct processes are responsible for the chemical exchange linebroadening observed in the other regions of TIM. MD simulations confirm that motions of individual residues within the active site loop are correlated and suggest that the chemical exchange processes observed for residues in helix G arise from transitions between 3(10)- and alpha-helical structures. The results of the joint NMR and MD study provide global insight into the role of conformational dynamic processes in the function of TIM.

Binding Sites↗

PubMed1996

Motor unit recruitment patterns during reflex compensation of muscle yield investigated by computer simulations.

An important function of the stretch reflex in the soleus muscle in the decerebrate cat preparation is to compensate for the tendency of muscle suddenly to yield during ramp increases in length. As the level of background (i.e. pre-stretch) force increases, there is a systematic change in the curvature of the force trajectory during this reflex compensation, from concave to convex with respect to increasing force. The hypothesis that this change in curvature was due to background force-dependent changes in the recruitment pattern of motor units was investigated with a combined computer simulation/experimental technique. The simulation consisted of 20 model motor units for the soleus muscle, each based on a distributed moment muscle model. The timing of recruitment of the motor units was optimized to allow the simulation outputs to fit a set of experimental data records on the reflex response to stretch initiated at five different levels of pre-stretch force. The resulting recruitment patterns showed that a tendency for recruitment to be concentrated progressively in the early portion of the stretch as pre-stretch force increased could account for the changes in reflex force curvature. These results are consistent with the skewed distribution of intrinsic electrical thresholds of motoneurons, in which low-threshold units are much more frequent than high-threshold ones. Therefore the changes in recruitment pattern and reflex force curvature may be due primarily to the intrinsic properties of motoneurons.

Animals↗