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PubMed1989

'Last adventure'--a computer simulation package for use in nurse education.

The benefits of using microcomputers in the education of learner nurses is not always apparent. A simulation package called 'Last Adventure' was developed for use by a group of Introductory Course nurse learners. A small scale research project was carried out to assess the educational value of the software, as well as to determine whether any educational benefits occurred as a result of using this piece of computer software, compared with the traditional method of written work. The results indicate that although initially no major differences were noted, there was a more positive feedback to nurse learners using the microcomputer which resulted in a longer retention time of facts tested.

Computer Simulation↗

PubMed1987

Isotachophoretic determination of mobility and pKa by means of computer simulation. V. Evaluation of mo and pKa of twenty-eight dipeptides and assessment of separability.

Isotachophoretic qualitative indices, RE, for twenty-eight dipeptides were measured in the range pH 7.4-9.6. The absolute mobility, mo, and pKa values were evaluated by the use of the least-squares method, utilizing a simulation of the isotachophoretic steady state. The mo values were newly evaluated and the pKa values were in good agreement with literature values. By comparison of the evaluated mo and pKa values of the dipeptides with those of the constituent amino acids, simple relationships were found which may be used to estimate the mo and pKa values of other dipeptides. The separability of the dipeptides was also evaluated by considering the differences between their simulated effective mobilities. It is concluded that isotachophoresis is very convenient for the separation of dipeptides and their constituent amino acids.

Amino Acids↗

PubMed1988

Positional variations in germinal cell growth in pigment-chimeric eyes of Xenopus: posterior half of the developing eye studied in genetic chimerae and in computer simulations.

Growth of germinal cells at different angular positions within the posterior portion of the embryonic frog eye has been examined by orthotopically transplanting small groups of germinal cells from pigmented (stage 30-38) donor embryos into albino (stage 28-36) hosts and then serially photographing the polyclonal-cell progeny domain (typically a black sector) in the pigmented retinal epithelium of the living, growing eye. Far-ventral (6 o'clock) germinal cells formed a narrow sector along the ventral fissure, but ventral germinal cells at a position just posterior to the fissure (7 o'clock on a right eye) were seen to expand rapidly their angular territory on the germinal zone and formed huge sectors that widened toward the front of the older larval eye. Posterior (8, 9, and 10 o'clock) germinal cells were seen to shift their angular positions gradually toward dorsal and formed sectors that appeared to veer dorsalward nearing the front of the older eye. Dorsal (11 o'clock) germinal cells showed attenuative growth, forming sectors that narrowed approaching the front of the older eye. A simulation model of the growth dynamic was used to examine how expansive growth ventrally drives the positional variations in growth. When far-ventral germinal cells were programmed to retain the 6 o'clock position and ventral (7 o'clock) germinal cells were programmed to divide symmetrically at a high probability to produce two daughter germinal cells, not only were the observed ventral chimeric patterns simulated, but also simulated were the attenuative growth of dorsal transplants and the dorsal displacement and veering seen in the growth of posterior transplants.

Animals↗

PubMed2005

Computer simulations of sympatric speciation in a simple food web.

Galapagos finches, have motivated much theoretical research aimed at understanding the processes associated with the formation of the species. Inspired by them, in this paper we investigate the process of sympatric speciation in a simple food web model. For that we modify the individual-based Penna model that has been widely used to study aging as well as other evolutionary processes. Initially, our web consists of a primary food source and a single herbivore species that feeds on this resource. Subsequently we introduce a predator that feeds on the herbivore. In both instances we manipulate directly a basal resource distribution and monitor the changes in the populations. Sympatric speciation is obtained for the top species in both cases, and our results suggest that the speciation velocity depends on how far up, in the food chain, the focus population is feeding. Simulations are done with three different sexual imprinting-like mechanisms, in order to discuss adaptation by natural selection.

Animals↗

PubMed1998

Intrinsic muscle properties facilitate locomotor control - a computer simulation study.

The purpose of this study was to investigate, theoretically, to what extent muscle properties could contribute to recovery from perturbations during locomotion. Four models with different actuator properties were created: the FLVT model, which encompassed force-length (FL) and force-velocity (FV) characteristics of human muscles as well as muscle stimulation inputs as functions of time (T); the FLT model, which had muscles without force-velocity characteristics; the FVT model, which had muscles without specific force-length characteristics; and the MT model, which had no muscles but was driven by joint moments (M) as a function of time. Each model was exposed to static and dynamic perturbations and its response was examined. FLVT showed good resistance to both static can dynamic perturbations. FLT was resistant to static perturbation but could not counteract dynamic perturbation, whereas the opposite was found for FVT. MT could not counteract either of the perturbations. Based on the results of the simulations, skeletal muscle force-length-velocity properties, although interactively complex, contribute substantially to the dynamic stability of the musculoskeletal system.

Computer Simulation↗

PubMed1989

[Studies on the computer simulated model of toluene elimination from the brain using HPLC measured urinary hippuric acid and the patient's consciousness level and its medical implications].

Urine specimens were sampled from toluene exposed persons (2 painters, 2 plasterers and 1 addict of organic solvent), who were admitted to the critical care center of our medical school and the urinary hippuric acid (HA; the metabolite of toluene) was monitored every one hour after admission for 10-12 hours and thence-forth every 4 hours for more than 40 hours. The hourly (t) excretion pattern of HA(Y) was simulated with multiexponential functions; Y = sigma Ai.exp(-Bit).....(1), i = 1 to 3. The HA(Y) level during the term before the admission was estimated by equation (eq.) (1) for the respective cases. The consciousness level was evaluated according to the Japan Coma Scale on the following time points; on the telephone call to the emergency center (t1), on the arrival of the ambulance (t2) and on admission (t3). We related the differential change of the consciousness level (w) per time (between t1 and t2); delta w/delta t to one of the regression coefficients (Bi) of eq. (1) expressing the elimination of toluene from the body. A set of Bi whose scale parameter Ai is positive and whose absolute value is the minimum in the individual eq. (1) has the highest correlation coefficient with the value of delta w/delta t (r = -.870, p less than .05). We calculated the toluene elimination equivalent (X) from the brain by applying this Bi to the equation; X = exp(-Bit) on the respective time point, t1, t2 and t3, and related this X to W by simulating a logistic eq.; W = 3.0/[1 + exp[alpha(X - beta]].....(2), as to each respective case. The calculated values by eq. (2) for the occupationally toluene exposed cases revealed that the scale parameter (alpha) and the location parameter (beta) correlated well with the integral HA excretion value for 48 hours computed by eq. (1), and the elimination rate equivalent (Bi), respectively. But the calculated data of the solvent addict using eq. (2) indicated that there is a tolerance mechanism against toluene exposure; the scale parameter is larger and the location parameter is smaller than the respective ones from the painters and the plasterers.

Accidents, Occupational↗

PubMed1987

Computer simulation of fibrillation threshold measurements and electrophysiologic testing procedures.

A finite element model of cardiac conduction was used to simulate two experimental protocols: 1) fibrillation threshold measurements and 2) clinical electrophysiologic (EP) testing procedures. The model consisted of a cylindrical lattice whose properties were determined by four parameters: element length, conduction velocity, mean refractory period, and standard deviation of refractory periods. Different stimulation patterns were applied to the lattice under a given set of lattice parameter values and the response of the model was observed through a simulated electrocardiogram. The studies confirm that the model can account for observations made in experimental fibrillation threshold measurements and in clinical EP testing protocols.

Algorithms↗

PubMed1985

A computer simulation of medical decision strategy performance.

This study demonstrates a computer model which can be used to compare the effects of errors in probability and utility estimation on the performance of Bayesian and alternative medical decision strategies. The model task requires choosing one of three treatments for a patient with one of three diseases based on the patient's state with respect to five binary cues and estimates of the prior probabilities of disease, the conditional probabilities of the cues and the utilities of the treatments. A classic decision analytic strategy uses Bayes' formula to calculate posterior probabilities of disease and chooses treatments based on maximization of expected value. Alternative strategies use likelihood ratios to calculate disease scores for each patient state and choose the treatment with highest payoff for the disease with the highest score. Two strategies with different cutoffs for the ratios are compared with a random strategy and a classic decision analytic strategy. The simulation results show that the payoffs for all strategies except the random strategy decline with increasing estimation error. The decision analytic strategy has the highest mean payoff at all levels of error. The differences between this optical strategy and the alternatives, however, decrease as estimation error increases, and the frequency with which the strategies based on simple diagnostic scoring rules outperform the formal Bayesian strategy increases.

Bayes Theorem↗

PubMed2003

Computer simulations of enzyme catalysis: methods, progress, and insights.

Understanding the action of enzymes on an atomistic level is one of the important aims of modern biophysics. This review describes the state of the art in addressing this challenge by simulating enzymatic reactions. It considers different modeling methods including the empirical valence bond (EVB) and more standard molecular orbital quantum mechanics/molecular mechanics (QM/MM) methods. The importance of proper configurational averaging of QM/MM energies is emphasized, pointing out that at present such averages are performed most effectively by the EVB method. It is clarified that all properly conducted simulation studies have identified electrostatic preorganization effects as the source of enzyme catalysis. It is argued that the ability to simulate enzymatic reactions also provides the chance to examine the importance of nonelectrostatic contributions and the validity of the corresponding proposals. In fact, simulation studies have indicated that prominent proposals such as desolvation, steric strain, near attack conformation, entropy traps, and coherent dynamics do not account for a major part of the catalytic power of enzymes. Finally, it is pointed out that although some of the issues are likely to remain controversial for some time, computer modeling approaches can provide a powerful tool for understanding enzyme catalysis.

Catalysis↗

PubMed1996

Computer simulation of landing movement in downhill skiing: anterior cruciate ligament injuries.

Anterior cruciate ligament (ACL) injuries typically occur in high-speed downhill skiing during the landing phase following a jump. A direct dynamics simulation model was developed which allows investigation of possible ACL injury mechanisms without the need to use actual skiers in a potentially dangerous environment. The model included multibody dynamics, muscle dynamics and a model for ski-snow interaction. The model's ability to reproduce an actual landing movement was investigated by minimizing the differences between measured and stimulated landing movements as a function of constant muscle stimulation levels. The remaining difference was mainly due to noise in the measurements. A small balance disturbance was induced to simulate an injury condition. This disturbance caused the modeled skier to fall slightly backwards. A recovery attempt was made by maximal activation of the quadriceps and iliopsoas muscles. Peak resultant shear force at the knee joint in ACL direction was substantially higher in the injury simulation (1001 N) when compared to the simulated normal landing movement (589 N). Taking into account quadriceps contraction and orientation of the ACL with respect to tibial plateau, peak ACL force during the injury simulation was estimated to be 1350 N, which is within the range of failure loads for this ligament. The external forces were mainly (75%) responsible for this loading. The contribution of the fully activated quadriceps muscles was only 25%. It was concluded that the model could reproduce a typical landing movement and is therefore considered to be sufficiently realistic. Second, the simulation results suggest that external forces are the main cause for ACL injuries during landing movements in downhill skiing.

Anterior Cruciate Ligament Injuries↗

PubMed1994

Investigation of shape variations in the antibody binding site by molecular dynamics computer simulation.

Molecular dynamics simulations have been used to investigate the flexibility and variations in the shape of the binding site of an antibody against human Rhinovirus serotype 2 (HRV2) and its complex with a 15 amino acid oligopeptide, the structure of which has been recently determined by X-ray crystallography. During the simulation of the unbound antibody the binding site, defined in terms of the hypervariable regions or complementarity determining regions (CDRs), shows significant fluctuations in shape. For the complex such variations in the shape of the binding site were reduced. The largest fluctuations in the unbound antibody occurred within the CDR-H3. The largest differences between the bound and unbound crystal structures are also associated with CDR-H3. The relative displacements of the loops have been analysed in terms of internal distortions, rigid body motions of the loops and changes with respect to the framework regions. The degree to which the motions of the loops are correlated and the variation in the volume of the binding pocket during the simulation have also been examined.

Amino Acid Sequence↗

PubMed2003

The effect of graft stiffness on knee joint biomechanics after ACL reconstruction--a 3D computational simulation.

OBJECTIVE: The objective was to determine the effect of varying graft stiffness and initial graft tension on knee kinematics and graft tension after anterior cruciate ligament reconstruction. DESIGN: A 3D computational knee model was used. BACKGROUND: Many factors influencing the biomechanical outcome of anterior cruciate ligament reconstruction have been investigated. However, there are no reports on the effect of variations in graft stiffness on knee behavior. METHODS: A 3D computational knee model was used to simulate anterior cruciate ligament reconstruction using three different grafts with stiffnesses similar to the anterior cruciate ligament (graft 1), a 10mm bone-patellar tendon-bone graft (graft 2), and a 14 mm bone-patellar tendon-bone graft (graft 3). The initial graft tension was set to 0 or 40 N with the knee at 30 degrees of flexion. A 134 N anterior tibial drawer load and a 400 N quadriceps load were applied to the knee, and kinematics and graft tension were calculated. RESULTS: When fixed with no initial tension, graft 1 was found to under-constrain the knee, while graft 2 slightly over-constrained the knee, and graft 3 over-constrained the knee when compared to the intact knee. When an initial graft tension of 40 N was used, all of the reconstructed knees were more constrained than when an initial tension of 0 N was used. CONCLUSIONS: This study suggests that graft stiffness has a direct impact on knee biomechanics after anterior cruciate ligament reconstruction. An optimal anterior cruciate ligament reconstruction can be achieved if the anterior cruciate ligament is replaced by a graft with similar structural stiffness. RELEVANCE: This study showed that if the graft material and fixation sites are selected such that the anterior cruciate ligament structural stiffness is retained, normal knee kinematics can be restored.

Aged↗

PubMed2003

Comfort climate evaluation with thermal manikin methods and computer simulation models.

With increasing demand for acceptable environment in the modern workplace is it necessary, already in the construction phase, to estimate what effect different environmental factors have on the occupants. Thermal sensation is affected by many factors in the work place environment, especially thermal factors and effects from air movement caused by different ventilation principles. A series of full scale measurements as well as numerical calculations have been carried out in order to investigate whether Computational Fluid Dynamics (CFD) calculations and measurements with a thermal manikin are able to predict the perceived thermal climate. When human thermal sensation is linked together in measurements and calculations, the thermal situation in the work place environment is visualized. The results show relatively good agreement with the measurements made in the real environment. However, numerical and experimental methods need to be further developed. Evaluation methods of this type, will enable engineers to make better predictions and early decisions in the design and construction process. This also opens possibilities to use results from a number of full scale tests providing means to improve the comfort, health and productivity in working life.

Air Movements↗

PubMed1993

Computer-simulated neural networks: an appropriate model for motor development?

The idea of an artificial neural network is introduced in a historical context, and the essential aspect of it, viz., the modifiable synapse, is compared to the aspect of plasticity in the natural nervous system. Based on such an artificial neural network, a model is presented for the way in which (the path along which) the connectivity in the spinal cord is modified during the period that a newborn 'learns' to control the movement of his forearm. In this way an automatic calibration of the receptors and the antagonists' recruitment of motor units is represented. The learning process is described in non-mathematical terminology. The model is then shown to be able after learning to reach target angles outside the training set of angles, and to be able to relearn when an important receptor has been made inoperative. In this way it is shown that the model is able to generalize, and that it is robust against at least some damage.

Computer Simulation↗

PubMed2001

Strategies to decrease tuberculosis in us homeless populations: a computer simulation model.

CONTEXT: The rate of tuberculosis (TB) among US homeless persons may be 20 times that of the general adult population. Studies suggest that the majority of urban homeless TB cases are attributable to ongoing transmission of TB. Optimal TB-control strategies in both chronically and transiently homeless populations are not known. OBJECTIVE: To examine the effects of TB-control strategies on projected TB cases and deaths in US homeless populations using a computer-based simulation model. DESIGN, SETTING, AND POPULATION: The US general population and a theoretical population of 2 million homeless individuals in 1995 were divided into 18 clinical states based on the risk for or presence of TB and human immunodeficiency virus (HIV) infection in a semi-Markov model. MAIN OUTCOME MEASURES: Prevalence of transiently and chronically homeless individuals with active TB and deaths from TB as a function of public health measures taken to control and eliminate TB, including improvement of treatment effectiveness, improvement in access to treatment, and vaccination with BCG. RESULTS: A 10% increase in access to treatment among homeless persons with active TB produced larger declines in predicted TB cases and deaths after 10 years (cases and deaths among chronically homeless persons decreased 12.5% and 19.8% and among transiently homeless persons dropped 35.9% and 32.4%, respectively) than improvements in the effectiveness of treatment programs (cases and deaths among chronically homeless persons declined 7.2% and 3.1% and among transiently homeless persons dropped 10.9% and 4.1%, respectively). A 10% increase in access to treatment among homeless persons with latent TB infection led to a 6.7% decline in TB among chronically homeless persons and a 5.7% decline among transiently homeless persons, while a 10% improvement in effectiveness of treatment for latent TB infection was associated with declines of 3.0% and 3.3%, respectively. When treatment for latent TB infection was modeled to be the same in vaccinated and nonvaccinated populations, BCG vaccination led to TB case declines of 15.4% and 21.5% in chronically and transiently homeless populations, respectively. CONCLUSIONS: Overcoming barriers faced by homeless individuals in accessing TB treatment programs will be crucial to reducing the burden of TB in this high-risk group. Increased treatment access, improvement in the effectiveness of treatment programs, and BCG vaccination of HIV-negative homeless individuals have the best chance to markedly decrease TB morbidity and mortality.

Antitubercular Agents↗

PubMed1989

Preliminary computer simulation of the effects of radial keratotomy.

We created a computerized mathematical model of the eye for the simulation of refractive surgery. This model used a slightly prolate shape for a moderately myopic eye and an idealized aspheric profile for the cornea. The finite element method and the nonlinear Mooney-Rivelin law were used to analyze stress-strain relationships. Radial keratotomy changes stress distribution in the cornea and the anterior sclera, with major changes at the paracentral and peripheral ends of the incisions. The model predicted that there would be a flattening of the central cornea with a posterior displacement, which increased with an increase in intraocular pressure. A change in the length of the incision of 0.5 mm produced a significant change in correction. For small clear zones (3 to 4 mm), incisions of equal length produced comparable changes in refraction. We found that the effect of the corneal radius of curvature on the amount of refractive change was negligible. We studied the effect of elasticity coefficients and corneal anisotropia.

Biomechanical Phenomena↗

PubMed1976

Computer simulation of movement-generating cross-bridges.

A stochastic computational method was developed to study properties of cross-bridge models for muscle contraction, by following the time history of individual cross-bridge model of Andrew Huxley (1957) and a modified two-state model with more realistic behavior during steady stretching are used as examples. The method can readily compute steady-state force during shortening and stretching and force-transients following rapid changes in length. Computations of velocity with a steady load and of velocity transients are more sensitive to the randomness inherent in the stochastic method.

Computers↗

PubMed2003

Vpu from HIV-1 on an atomic scale: experiments and computer simulations.

Vpu is an 81 amino acid protein encoded by HIV-1. Its role is to amplify viral release by two mechanisms: (i) docking to CD4 with the consequence of targeting CD4 for ubiquitine-mediated degradation, and (ii) formation of ion channels to enhance particle release. The intensive research on its in vivo function, combined with structural investigations, makes this viral membrane protein one of the better characterised membrane proteins. The wealth of structural information enables the use of computational methods to elucidate the mechanisms of function on an atomic scale. The discovery of Vpu and the development of structural models in a chronological order is summarised and first efforts on investigating the mechanics are outlined.

Amino Acid Sequence↗