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At least 397 records · Page 22Linked to original sources

Computer simulation of FES standing up in paraplegia: a self-adaptive fuzzy controller with reinforcement learning.

Using computer simulation, the theoretical feasibility of functional electrical stimulation (FES) assisted standing up is demonstrated using a closed-loop self-adaptive fuzzy logic controller based on reinforcement machine learning (FLC-RL). The control goal was to minimize upper limb forces and the terminal velocity of the knee joint. The reinforcement learning (RL) technique was extended to multicontroller problems in continuous state and action spaces. The validated algorithms were used to synthesize FES controllers for the knee and hip joints in simulated paraplegic standing up. The FLC-RL controller was able to achieve the maneuver with only 22% of the upper limb force required to stand-up without FES and to simultaneously reduce the terminal velocity of the knee joint close to zero. The FLC-RL controller demonstrated, as expected, the closed loop fuzzy logic control and on-line self-adaptation capability of the RL was able to accommodate for simulated disturbances due to voluntary arm forces, FES induced muscle fatigue and anthropometric differences between individuals. A method of incorporating a priori heuristic rule based knowledge is described that could reduce the number of the learning trials required to establish a usable control strategy. We also discuss how such heuristics may also be incorporated into the initial FLC-RL controller to ensure safe operation from the onset.

Arm↗

Computer simulation as a tool for clinical trial design.

Use of a computer simulation technique as a tool for optimising the design of a clinical trial is described. One of several aspects of trial design facilitated by use of the technique is the estimation of the number of patients required in the trial. The simulation tool provides the basis for structured and disciplined discussion of all the issues to be considered in designing a trial. Copies of the simulation program are available from the author.

Clinical Trials as Topic↗

Extinction as new learning versus unlearning: considerations from a computer simulation of the cerebellum.

Like many forms of Pavlovian conditioning, eyelid conditioning displays robust extinction. We used a computer simulation of the cerebellum as a tool to consider the widely accepted view that extinction involves new, inhibitory learning rather than unlearning of acquisition. Previously, this simulation suggested basic mechanistic features of extinction and savings in eyelid conditioning, with predictions born out by experiments. We review previous work showing that the simulation reproduces behavioral phenomena and lesion effects generally taken as evidence that extinction does not reverse acquisition, even though its plasticity is bidirectional with no site dedicated to inhibitory learning per se. In contrast, we show that even though the sites of plasticity are, in general, affected in opposite directions by acquisition and extinction training, most synapses do not return to their naive state after acquisition followed by extinction. These results suggest caution in interpreting a range of observations as necessarily supporting extinction as unlearning or extinction as new inhibitory learning. We argue that the question "is extinction reversal of acquisition or new inhibitory learning?" is therefore not well posed because the answer may depend on factors such as the brain system in question or the level of analysis considered.

Association Learning↗

Computer simulations of cardiac action potentials in two dimensions.

A novel method of calculation is presented which allows computer simulations of action potentials for a two-dimensional, planar reconstruction of the depolarization phase of a cardiac action potential to be followed through nonuniform tissue. The calculation is explicit in type and assumes an infinite, grounded extracellular region. A 70 by 70 point region is calculated swiftly on a PC/AT. Results show elliptical isochrones when slow and fast directions have different resistivities. The time derivative of Vm is, however, similar in both directions. Insertion of a test region of tissue with high resistance results in wave-like propagation of the A.P. around the 'bad' region.

Action Potentials↗

Investigation of parameter estimator and adaptive controller for assist pump by computer simulation.

The multi-output adaptive controller of a left ventricular assist device (LVAD) was studied by computer simulation. The controller regulated two outputs--mean aortic pressure (mAoP) and mean atrial pressure (mLAP)--by regulating vacuum pressure (input). The autoregressive models were used to describe the circulatory system. The parameters of the models were estimated by the recursive least squares method. Based on the autoregressive models, the vacuum pressure minimizing a performance index was searched. The index used was the weighted summation of the square errors. Responses of the adaptive controller were simulated when the contractility of the left ventricle was decreased at various rates and the peripheral resistance was changed. Both the mAoP and mLAP were controlled to their predicted values in the steady state. The steady-state errors of the mAoP were less than a few mm Hg, and those of the mLAP were lower than 1 mm Hg. Consequently, the estimated parameters can be regarded as true parameters, and the adaptive controller has the potential to control more than two outputs. The multioutput adaptive controller studied is useful in controlling the LVAD according to the change in circulatory condition.

Aorta, Thoracic↗

Computer simulation of flagellar movement VIII: coordination of dynein by local curvature control can generate helical bending waves.

Computer simulations have been carried out with a model flagellum that can bend in three dimensions. A pattern of dynein activation in which regions of dynein activity propagate along each doublet, with a phase shift of approximately 1/9 wavelength between adjacent doublets, will produce a helical bending wave. This pattern can be termed "doublet metachronism." The simulations show that doublet metachronism can arise spontaneously in a model axoneme in which activation of dyneins is controlled locally by the curvature of each outer doublet microtubule. In this model, dyneins operate both as sensors of curvature and as motors. Doublet metachronism and the chirality of the resulting helical bending pattern are regulated by the angular difference between the direction of the moment and sliding produced by dyneins on a doublet and the direction of the controlling curvature for that doublet. A flagellum that is generating a helical bending wave experiences twisting moments when it moves against external viscous resistance. At high viscosities, helical bending will be significantly modified by twist unless the twist resistance is greater than previously estimated. Spontaneous doublet metachronism must be modified or overridden in order for a flagellum to generate the planar bending waves that are required for efficient propulsion of spermatozoa. Planar bending can be achieved with the three-dimensional flagellar model by appropriate specification of the direction of the controlling curvature for each doublet. However, experimental observations indicate that this "hard-wired" solution is not appropriate for real flagella.

Animals↗

Computer simulation of the segmental neural network generating locomotion in lamprey by using populations of network interneurons.

Realistic computer simulations of the experimentally established local spinal cord neural network generating swimming in the lamprey have been performed. Populations of network interneurons were used in which cellular properties, like cell size and membrane conductance including voltage dependent ion channels were randomly distributed around experimentally obtained mean values, as were synaptic conductances (kainate/AMPA, NMDA, glycine) and delays. This population model displayed more robust burst activity over a wider frequency range than the more simple subsample model used previously, and the pattern of interneuronal activity was appropriate. The strength of the reciprocal inhibition played a very important role in the regulation of burst frequency, and just by changing the inhibitory bias the entire physiological range could be covered. At the lower frequency range of bursting the segmental excitatory interneurons provide stability as does the activation of voltage dependent NMDA receptors. Spike frequency adaptation by means of summation of afterhyperpolarization (AHP) serves as a major burst terminating factor, and at lower rates the membrane properties conferred by the NMDA receptor activation. The lateral interneurons were not of critical importance for the burst termination. They may, however, be of particular importance for inducing a rapid burst termination during for instance steering and righting reactions. Several cellular factors combine to provide a secure and stable motor pattern in the entire frequency range.

Animals↗

Supercoiled DNA energetics and dynamics by computer simulation.

A new formulation is presented for investigating supercoiled DNA configurations by deterministic techniques. Thus far, the computational difficulties involved in applying deterministic methods to supercoiled DNA studies have generally limited computer simulations to stochastic approaches. While stochastic methods, such as simulated annealing and Metropolis-Monte Carlo sampling, are successful at generating a large number of configurations and estimating thermodynamic properties of topoisomer ensembles, deterministic methods offer an accurate characterization of the minima and a systematic following of their dynamics. To make this feasible, we model circular duplex DNA compactly by a B-spline ribbon-like model in terms of a small number of control vertices. We associate an elastic deformation energy composed of bending and twisting integrals and represent intrachain contact by a 6-12 Lennard Jones potential. The latter is parameterized to yield an energy minimum at the observed DNA-helix diameter inclusive of a hydration shell. A penalty term to ensure fixed contour length is also included. First and second partial derivatives of the energy function have been derived by using various mathematical simplifications. First derivatives are essential for Newton-type minimization as well as molecular dynamics, and partial second-derivative information can significantly accelerate minimization convergence through preconditioning. Here we apply a new large-scale truncated-Newton algorithm for minimization and a Langevin/implicit-Euler scheme for molecular dynamics. Our truncated-Newton method exploits the separability of potential energy functions into terms of differing complexity. It relies on a preconditioned conjugate gradient method that is efficient for large-scale problems to solve approximately for the search direction at every step. Our dynamics algorithm is numerically stable over large time steps. It also introduces a frequency-discriminating mechanism so that vibrational modes with frequencies greater than a chosen cutoff frequency are essentially frozen by the method. With these tools, we rapidly identify corresponding circular and interwound energy minima for small DNA rings for a series of imposed linking-number differences. These structures are consistent with available electron microscopy data. The energetic exchange of stability between the circle and the figure-8, in very good agreement with analytical results, is also detailed. Molecular dynamics trajectories at 100 femtosecond time steps then reveal the rapid folding of the unstable circular state into supercoiled forms. Significant bending and twisting motions of the interwound structures are also observed. Such information may be useful for understanding transition states along the folding pathway and the role of enzymes that regulate supercoiling.(ABSTRACT TRUNCATED AT 400 WORDS)

Algorithms↗

Computer simulation of ribosome editing.

A stochastic model of protein synthesis was modified by including the process of dissociating peptidyl-tRNA from ribosomes. To simulate ribosome editing, the probability of dissociation was assumed to be high if the peptidyl-tRNA was erroneous; that is, if it resulted from transfer of a peptide to an aminoacyl-tRNA that was inappropriate relative to the mRNA codon. The effects of amino acid starvation on protein synthesis were simulated both by increasing the probability of such erring at and by reducing the conditional probability of elongation at "hungry" codons, those whose correct amino acid was in short supply. These probabilities were varied systematically to simulate tryptophan limitation during synthesis of coat protein from bacteriophage MS2. Significant reduction, during starvation, in the synthesis of complete coat protein required large reductions in the probability of elongation at hungry codons but only small increases in the probability of erring. Enhanced dissociation of peptidyl-tRNA during starvation, followed rapidly by dissociation of ribosomes from mRNA, led to reductions in mean polysome size, a result that had been interpreted by others as due to some effect of starvation on the initiation of protein synthesis. Results from experiments by Goldman (1982) on the cell-free synthesis of MS2 coat protein during tryptophan starvation could be mimicked in detail by the computer simulations. A simple competition between correct and erroneous amino acids was sufficient to explain the tryptophan dependence of complete coat protein and internal peptide syntheses. Values for the Michaelis constants were derived from the computer simulations.

Codon↗

16-detector multislice CT: dosimetry estimation by TLD measurement compared with Monte Carlo simulation.

Computer simulations are widely used to estimate effective doses from CT examinations. The raw data often used in their estimations were obtained some years ago and made certain assumptions regarding CT unit design. At that time multidetector CT units were unavailable. Changes in design will limit the accuracy of computer simulated dosimetry on these machines. We therefore estimated CT dose on a 16-detector unit directly using thermoluminescent dosemeters (TLDs) and an anthropomorphic phantom. We found that the dose measured directly was 18% higher than the computer simulated dosimetry, in keeping with the previously recognised underestimation by computer simulation techniques compared with TLD measurements.

Computer Simulation↗

Computer simulation analysis of Sartwell's incubation period model for diseases with uncertain etiology. The effect of competing risk.

Computer simulation was applied to Sartwell's model to examine the impact of competing risks of death on the underlying assumptions and the power to reject both uniform and normal incubation period distributions. Exponential and nonparametric survival functions were imposed onto lognormal, uniform, and normal distributions to create random samples reflecting competing risk. These random samples were evaluated with the Shapiro-Wilk's test to determine the proportion for which the lognormal distribution was rejected. The simulations indicated that competing causes of death do not significantly alter the lognormal distribution of incubation periods. In only approximately 5% of the samples drawn from a lognormal distribution was a lognormal hypothesis rejected with a goodness-of-fit test when sample size varied from 20 to 500. There was generally good power (> 80%) to reject a lognormal distribution if the random samples were generated from a uniform distribution of incubation times, but not when they were generated from a normal distribution, particularly with increasing ages at disease onset. Varying the standard deviation did not significantly change the simulation results if the random samples came from a lognormal or uniform distribution. These conclusions were further supported by application of Sartwell's model to published data on the ages of onset for several chronic diseases.

Adult↗

Cardiovascular simulation using a multiple modeling method on a digital computer--simulation of interaction between the cardiovascular system and angiotensin II.

A cardiovascular system model that simulates interactive responses to drugs has been developed on a small digital computer. The overall model basically consists of three models. The first is a momentum transport model that represents relations between blood pressure and flow in the cardiovascular system. In this model, the cardiovascular system is divided into 14 components and modeled by using equivalent electrical circuits. The second is a mass transport model comprising 14 compartments corresponding to the respective components of the cardiovascular system. This model represents the distribution of the administered drug in the various cardiovascular components. The third is an interaction model that represents the relationships between the momentum and mass transport models. This model causes variations in the resistance and capacitance parameters of the momentum transport model as a function of the current drug concentrations in the appropriate compartments of the mass transport model. The capacitances representing the ventricles are varied in a time-dependent fashion to simulate the beat of the heart. Simulation is performed by using the Euler method to solve a system of 28 ordinary differential equations governing the momentum and mass transport models on a 32-bit microcomputer, a Macintosh II. The model was assessed by performing two demonstrations of the cardiovascular response to the vasopressor angiotensin II (AT II). They first examined the interaction between the cardiovascular system and AT II. The effect of AT II on the cardiovascular system was incorporated into the interaction model. Administration of AT II as a constant infusion (200 micrograms/hr) resulted in an elevation of mean arterial pressure from approximately 100 to 150 mm Hg.(ABSTRACT TRUNCATED AT 250 WORDS)

Angiotensin II↗

[Relationship between the reproductive capability of a subdivided population and its genetic structure: computer simulation, the simplest multilocus model].

An original computer model, simulating joint genetic and demographic dynamics of subdivided populations, is proposed. The model accounts for the reverse effect of the genetic structure on the reproductive capability of a population, which is based on a postulated limited set of biallelic loci, controlling variation in an adaptive quantitative trait. The model allows to simulate spreading of the population, originating from a single small colony, which involves genetic and demographic equilibrium (a normal population-genetic process) and reorganization of the genetic structure of the subdivided population upon anthropogenic pressure, associated with a decrease in its reproductive capability (an adverse population-genetic process).

Alleles↗

Chromosome-based method for rapid computer simulation in human genetic linkage analysis.

Computer-based simulation has been an important method in human linkage analysis for a long time. Typically, such analyses have been performed by simulating a set of linked markers according to the intermarker recombination fractions, under the assumption of no genetic interference. A novel approach is proposed in which such simulations can be performed using chromosome-based methods, rather than traditional recombination fraction-based methods. We propose simulating pedigree data using a crossover formation (CF) process to generate the number of crossovers and their locations in Morgans along the entire length of a chromosome. By this method, one can generate simulated multilocus data for any number of loci on a chromosome much more efficiently than with the currently available methods like those used in the SLINK or SIMLINK programs. Further, interference can be incorporated directly in this method, which is not possible with existing packages.

Chromosome Mapping↗

Contact pressure models for spiral phyllotaxis and their computer simulation.

We present a simple, biologically motivated model for the creation of phyllotactical patterns in capitula and their computer simulation. An in-depth investigation of Ridley's contact pressure model is performed and a refinement of contact pressure between primordia on the basis of local centroidal Voronoi relaxation is presented. Using this method in combination with Hofmeisters rule for placing new primordia creates stable patterns with Fibonacci spirals of high degree for a large range of initial conditions.

Cell Communication↗

Effect of sample size on reproducibility of behavioral teratological study results: a computer simulation experiment using data from the Collaborative Behavioral Teratology Study of the National Center for Toxicological Research.

A computer simulation experiment which attempted to examine the effect of sample size on reproducibility of the effect of treatment was performed on the basis of actual data obtained from the Collaborative Behavioral Teratology Study of the National Center for Toxicological Research. The degree of the treatment effect was assessed in terms of the strength of the association (eta square). The results indicate that sample size has a large effect on the reproducibility of results which are assessed with the magnitude of SD for eta squares obtained from replication experiments. Suitable sample sizes to obtain relatively consistent results across studies were discussed, pointing out that not enough attention has been paid to the effect of sample size in the issue of reproducibility of results in some behavioral teratology studies.

Computer Simulation↗

Improving outpatient clinic staffing and scheduling with computer simulation.

Patient flow in an appointment-based, outpatient internal medicine clinic involving multiple, sequential providers-registrar, triage nurse, physician, and discharger-was studied using computer simulation. Provider task time distributions were obtained through a time-motion study and then input into the computer program, which simulated the clinic situation well. Time interval and sensitivity analyses yielded insights into staffing levels, appointment times, and clinic dynamics. A bottleneck provider was shown, and patient time in the clinic was related to the time of appointment and was slowed by having too many doctors in the clinic. Subsequent operational changes significantly decreased the average observed patient total time in clinic from 75.4 (SD 34.2) minutes to 57.1 (SD 30.2) minutes (p < .001, t test).

Appointments and Schedules↗