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PubMed2000

Computer Modeling in Bone Research.

Computer modeling has had an undoubtedly enormous impact on the field of bone research in recent years. Development of advanced computer based models has permitted researchers to explore a vast area of musculoskeletal science from the complex biophysical stimuli at the cellular level to the mechanical behavior of heterogeneous skeletal structures. Furthermore, computer modeling has given significant impetus to the impressive progress of modern bone implant development. With recent advances in computers, faster hardware and increasingly sophisticated software, the prospects for the future of computer-based bone research appear more exciting than ever.

Journal Article↗
PubMed2006

Synthetic computational models of selective attention.

Computational modeling plays an important role to understand the mechanisms of attention. In this framework, synthetic computational models can uniquely contribute to integrate different explanatory levels and neurocognitive findings, with special reference to the integration of attention and awareness processes. Novel combined experimental and computational investigations can lead to important insights, as in the revived domain of neural correlates of attention- and awareness-related meditation states and traits.

Attention↗
PubMed1983

Evidence for a multiple random coupling mechanism in the alpha-ketoglutarate dehydrogenase multienzyme complex of Escherichia coli: a computer model analysis.

A computer modeling system was used to analyze experimental data for inactivation of the Escherichia coli alpha-ketoglutarate dehydrogenase complex accompanying release of lipoic acid residues by lipoamidase and by trypsin [Stepp, L. R., Bleile, D. M., McRorie, D. K., Pettit, F. H. & Reed, L. J. (1981) Biochemistry 20, 4555-4560]. The results provide insight into the active-site coupling mechanism in the alpha-ketoglutarate dehydrogenase complex. The model studies indicate that the overall activity of the alpha-ketoglutarate dehydrogenase complex is influenced by redundancies and random processes that we describe as a multiple random coupling mechanism. More than one lipoyl moiety services each E1 subunit (alpha-ketoglutarate dehydrogenase, EC 1.2.4.2), and an extensive lipoyl-lipoyl interaction network for exchange of electrons and possibly acyl groups must also be present. The best fit between computed and experimental data was obtained with a model that has two lipoyl moieties servicing each E1 subunit and a lipoyl-lipoyl interaction network that links all lipoyl moieties on the E2 cube (dihydrolipoamide succinyltransferase, EC 2.3.1.61). The single lipoyl moiety on an E2 subunit is assumed to service the coenzyme A-dependent succinyltransferase site of that E2 subunit as well as an E3 subunit (dihydrolipoamide dehydrogenase, EC 1.6.4.3) if the latter is bound to that particular E2 subunit.

Acyltransferases↗
PubMed1993

Vagal-mediated atrial premature beats: a computer model.

A computer algorithm is described that used experimental data to model the arrhythmogenic interaction of phasic vagal stimuli and atrial ectopic pacemakers. The model consisted of a dominant sinus node and a single ectopic pacemaker center separated by conducting atrial tissue. Its primary operation was to predict the timing and incidence of atrial premature beats resulting from transient escape of ectopic automatic impulses when vagal-induced entrance block of the sinus impulse was simulated near the ectopic focus. These predictions were based on a series of experimentally derived phase-response and corrected recovery time curves, describing the modulation of ectopic pacemaker periodicity by vagal input and overdrive suppression, respectively. Depending on the combination of curves tested, the model predicted premature beats to develop only with critically timed vagal stimuli. The coupling intervals of vagal-induced premature beats were > 300 ms and varied as a function of vagal timing and sinus cycle length. The model suggests therefore that phasic vagal stimuli within the atrium may transiently protect ectopic pacemaker foci from conducted sinus impulses and mediate the genesis of atrial extrasystoles with long coupling intervals.

Animals↗
PubMed1986

Possible pathophysiology of torsade de pointes evaluated by a realistic heart computer model.

A realistic computer model that closely simulates the behaviour of the cardiac conduction system and myocardium in producing electrocardiographic records was used to evaluate some hypotheses of the pathophysiological mechanisms causing torsade de pointes tachycardia. Five different groups of experiments showed that pathological phenomena of different natures can either directly cause the usual pattern of torsade de pointes or contribute to its occurrence. The phenomena investigated were coincidence of two or more pathological foci with slightly changing periods of impulse generation; periodical disturbances of the conduction velocities of the main branches of the conduction system; a single pathological focus changing its position by slowly moving around the whole heart or around a local area of the myocardium; combination of a pathological ventricular tachycardia focus with a one way (ventriculoatrial) direct atrioventricular accessory pathway allowing atrioventricular re-entry; and different repolarisation periods of separate areas of heart muscle in the presence of a pathological ventricular focus with a fixed or oscillating rate of impulse generation. Future extended versions of the model could be used for testing other hypotheses of the origin of torsade de pointes, such as situations in which the intramuscle or local re-entry occurs.

Atrioventricular Node↗
PubMed2003

Associative memory in chronic schizophrenia: a computational model.

We developed a computer model to simulate associative memory recall of patients with chronic schizophrenia. Model inputs consisted of words derived from normative data that differed in terms of connectivity and network size, with the former quantitatively represented by parametric weights and the latter by the specific number of word associates that formed a particular network. Previous behavioral studies of normal subjects indicated better recall for words of high connectivity-small network (HCSN), followed by low connectivity-small network (LCSN), high connectivity-large network (HCLN), and low connectivity-large network (LCLN). This pattern of recall differed from that observed in behavioral studies of schizophrenic patients, which showed better recall for high connectivity words, regardless of network size. Holding constant network size while manipulating connection weights effectively simulated this schizophrenic pattern of recall. That is, manipulation of parametric weights coupled with a slight increase in noise significantly and reliably elicited the response pattern of abnormal connectivity demonstrated in the prior behavioral study of patients with chronic schizophrenia. An increase in noise was a necessary, but insufficient step in modeling the response pattern of abnormal connectivity. These findings provide support for the use of computational models to investigate dynamics of associative word recall in patients with chronic schizophrenia.

Chronic Disease↗
PubMed1996

Control of slow oscillations in the thalamocortical neuron: a computer model.

We investigated computer models of a single thalamocortical neuron to assess the interaction of intrinsic voltage-sensitive channels and cortical synaptic input in producing the range of oscillation frequencies observed in these cells in vivo. A morphologically detailed model with Hodgkin-Huxley-like ion channels demonstrated that intrinsic properties would be sufficient to readily produce 3 to 6 Hz oscillations. Hyperpolarization of the model cell reduced its oscillation frequency monotonically whether through current injection or modulation of a potassium conductance, simulating the response to a neuromodulatory input. We performed detailed analysis of highly reduced models to determine the mechanism of this frequency control. The interburst interval was controlled by two different mechanisms depending on whether or not the pacemaker current, IH, was present. In the absence of IH, depolarization during the interburst interval occurred at the same rate with different current injections. The voltage difference from the nadir to threshold for the low-threshold calcium current, IT, determined the interburst interval. In contrast, with IH present, the rate of depolarization depended on injected current. With the full model, simulated repetitive cortical synaptic input entrained oscillations up to approximately double the natural frequency. Cortical input readily produced phase resetting as well. Our findings suggest that neither ascending brainstem control altering underlying hyperpolarization, nor descending drive by repetitive cortical inputs, would alone be sufficient to produce the range of oscillation frequencies seen in thalamocortical neurons. Instead, intrinsic neuronal mechanisms would dominate for generating the delta range (0.5-4 Hz) oscillations seen during slow wave sleep, whereas synaptic interactions with cortex and the thalamic reticular nucleus would be required for faster oscillations in the frequency range of spindling (7-14 Hz).

Cerebral Cortex↗
PubMed2004

Infant grasp learning: a computational model.

This paper presents ILGM (the Infant Learning to Grasp Model), the first computational model of infant grasp learning that is constrained by the infant motor development literature. By grasp learning we mean learning how to make motor plans in response to sensory stimuli such that open-loop execution of the plan leads to a successful grasp. The open-loop assumption is justified by the behavioral evidence that early grasping is based on open-loop control rather than on-line visual feedback. Key elements of the infancy period, namely elementary motor schemas, the exploratory nature of infant motor interaction, and inherent motor variability are captured in the model. In particular we show, through computational modeling, how an existing behavior (reaching) yields a more complex behavior (grasping) through interactive goal-directed trial and error learning. Our study focuses on how the infant learns to generate grasps that match the affordances presented by objects in the environment. ILGM was designed to learn execution parameters for controlling the hand movement as well as for modulating the reach to provide a successful grasp matching the target object affordance. Moreover, ILGM produces testable predictions regarding infant motor learning processes and poses new questions to experimentalists.

Computational Biology↗
PubMedDate not supplied

Osmotic forces and gap junctions in spreading depression: a computational model.

In a computational model of spreading depression (SD), ionic movement through a neuronal syncytium of cells connected by gap junctions is described electrodiffusively. Simulations predict that SD will not occur unless cells are allowed to expand in response to osmotic pressure gradients and K+ is allowed to move through gap junctions. SD waves of [K+]out approximately 25 to approximately 60 mM moving at approximately 2 to approximately 18 mm/min are predicted over the range of parametric values reported in gray matter, with extracellular space decreasing up to approximately 50%. Predicted waveform shape is qualitatively similar to laboratory reports. The delayed-rectifier, NMDA, BK, and Na+ currents are predicted to facilitate SD, while SK and A-type K+ currents and glial activity impede SD. These predictions are consonant with recent findings that gap junction poisons block SD and support the theories that cytosolic diffusion via gap junctions and osmotic forces are important mechanisms underlying SD.

Computer Simulation↗
PubMed1992

Effects of myocardial electrotonic interaction on the sequence of excitation and repolarisation and on T wave polarity. Computer modelling experiments.

A computer model of a 3-dimensional rectangular block of myocardial tissue (3969 cells) has been used to investigate the influence on excitation and repolarisation sequences and on the modelled electrocardiographic T wave of (a) electrotonic interaction, (b) intrinsic distribution of refractoriness, and (c) the speed of repolarisation of action potentials. The model allowed electrotonic interactions to be investigated separately during the depolarisation and repolarisation phases. Scales of 14 values of the strength of electrotonic interaction during the depolarisation phase, 14 values of the strength of electrotonic interaction during the repolarisation phase, 3 shapes of action potential, and 5 distributions of tissue refractoriness were selected and all 2940 combinations were examined. In each experiment, the tissue model was artificially excited and the resulting excitation and repolarisation sequences were simulated. The results of the study suggested that electrotonic interactions between excited cells can cause non-uniform speed of propagation which, by means of the phase shifts of action potentials, contributes to the inversion of the repolarisation sequence and to the physiologic orientation of T waves. Experiments with this model did not support the hypothesis that simple electrotonic smoothing of the differences in repolarisation phases due to the excitation phase shift of action potentials reverses the repolarisation sequence and explains T wave polarity.

Action Potentials↗
PubMedDate not supplied

High speed electrophoresis simulation for optimization of continuous flow electrophoresis and high performance capillary techniques: Part I. Computer model.

A computer program for high-speed simulation and optimization of electrophoretic processes has been developed for carrier-free systems of all kinds. The calculations are based on the one-dimensional dynamic (transient-state) model. The three-dimensional geometry of the simulation space can be chosen deliberately. With a highly efficient transport algorithm instead of complicated integration schemes for the transport equations, the calculation time can be effectively spent on various important parameters such as ionic strength, temperature, Joule heat, activity coefficients and concentration changes due to membranes. The parameter set of any carrier free electrophoretic method (i.e., continuous-flow electrophoresis, capillary isotachophoresis and high performance capillary zone electrophoresis) can be imported directly into the computer program by means of a graphic user interface. The program performs overnight-simulation of any electrophoretic system containing up to 15 components.

Computer Simulation↗
PubMed2000

Peak blood alcohol prediction: an empirical test of two computer models.

OBJECTIVE: Two computer programs (Computerized Blood Alcohol Calculator and Blood Alcohol Content Estimator) were compared for reliability in predicting peak blood alcohol concentration (BAC). METHOD: Subjects were middle-aged volunteers (N = 40; 20 men, 20 women) who each consumed a constant amount of alcohol (40 ml of 95% alcohol or 30 g ethanol) prior to undergoing breath testing to determine peak BAC. The observed BACs were compared with the predicted BACs obtained with each of the computer programs. RESULTS: The Computerized Blood Alcohol Calculator provided marginally better BAC predictions than did the Blood Alcohol Content Estimator. However, both computer models seriously underestimated the peak BACs for this group of subjects. CONCLUSIONS: Results are discussed with particular reference to the need for additional studies of age, gender, and body composition in predicting peak BACs for heterogeneous subject groups.

Adult↗
PubMed1999

The hemodynamic effects of double-orifice valve repair for mitral regurgitation: a 3D computational model.

OBJECTIVES: A 3D computational model has been implemented for the evaluation of the hemodynamics of the double orifice repair. Critical issues for surgical decision making and echo-Doppler evaluation of the results of the procedure are investigated. METHODS: A parametric 3D computational model of the double-orifice mitral valve based on the finite elements model has been constructed from clinical data. Nine different geometries were investigated, corresponding to three total inflow areas (1.5, 2.25 and 3 cm2) and to three orifice configurations (two equal orifices, two orifices of different areas, i.e. one twice as much the other one, and a single orifice). The simulations were performed in transit; the fluid was initially quiescent and was accelerated to the maximum flow rate with a cubic function. For each case, some characteristic values of velocity and pressure were determined: velocities were calculated downstream of each orifice, at the centre of it (Vcen1, Vcen2). The maximum velocity was also determined for each orifice (Vmax1, Vmax2). Maximum pressure drops (deltap(max)) across the valve were compared with the estimations (deltap(Bernoulli)) based on the Bernoulli formula (4 V2). RESULTS: In each simulation, no notable difference was observed between Vcen1 and Vcen2, and between Vmax1 and Vmax2, regardless of the valve configuration. Maximum velocity and deltap(max) were related to the total orifice area and were not influenced by the orifice configuration. Deltap(Bernoulli) calculated with Vmax was well correlated with the deltap(max) obtained throughout the simulations (y = 0.9126x + 0.3464, r = 0.996); on the contrary the pressure drops estimated using Vcen underestimated (y = 0.6757x + 0.3073, r = 0.999) the actual pressure drops. CONCLUSIONS: The hemodynamic behaviour of a double orifice mitral valve does not differ from that of a physiological valve of same total area: pressure drops and flow velocity across the valve are not influenced by the configuration of the valve. Echo Doppler estimation of the maximum velocities is a reliable method for the calculation of pressure gradients across the repaired valve.

Blood Flow Velocity↗
PubMed1989

Effect of placental resistance, arterial diameter, and blood pressure on the uterine arterial velocity waveform: a computer modeling approach.

A computer model was used to simulate velocity waveforms that can be visualized in the human uterine artery using Doppler ultrasound. It was found that increasing uteroplacental vascular resistance from normal caused an increase in the systolic/diastolic velocity ratio (S/D) and pulsatility index (PI) of the waveform. Increasing uteroplacental resistance also caused the appearance of a dicrotic notch. Reducing the uterine artery radius increased the S/D and PI and this effect was accentuated at high placental resistance. In contrast, increasing mean arterial pressure in the uterine artery had little effect on S/D and PI. Results suggest that waveform shape abnormalities observed in obstetric patients with pregnancy-induced hypertension are primarily caused by high uteroplacental vascular resistance and a reduced uterine arterial diameter.

Arteries↗
PubMed2003

Defining forces that are associated with shoulder dystocia: the use of a mathematic dynamic computer model.

OBJECTIVE: A computer model was modified to study the impact of maternal endogenous and clinician-applied exogenous delivery loads on the contact force between the anterior fetal shoulder and the maternal symphysis pubis. STUDY DESIGN: Varying endogenous and exogenous loads were applied, and the contact force was determined. Experiments also examined the effect of pelvic orientation and the direction of load application on contact force behind the symphysis pubis. RESULTS: Exogenous loading forces (50-100 N) resulted in anterior shoulder contact forces of 107 to 127 N, with delivery accomplished at 100 N of applied load. Higher contact forces (147-272 N) were noted for endogenously applied loads (100-400 N), with delivery occurring at 400 N of maternal force. Pelvic rotation from lithotomy to McRoberts' positioning resulted in reduced contact forces. Downward lateral flexion of the fetal head led to little difference in contact force but required 30% more exogenous load to achieve delivery. CONCLUSION: Compared with clinician-applied exogenous force, larger maternally derived endogenous forces are needed to clear the impacted anterior fetal shoulder. This is associated with >2 times more contact force by the obstructing symphysis pubis. McRoberts' positioning reduces shoulder-symphysis pubis contact force. Lateral flexion of the fetal head results in the larger forces that are needed for delivery but has little effect on contact force. Model refinements are needed to examine delivery forces and brachial plexus stretching more specifically.

Delivery, Obstetric↗
PubMed1987

Capnography and the Bain circuit II: Validation of a computer model.

Validation of a computer model is described. The behavior of this model is compared both with mechanical ventilation of a test lung in a laboratory setup that uses a washout method and with manual ventilation. A comparison is also made with results obtained from a volunteer breathing spontaneously through a Bain circuit and with results published in the literature. This computer model is a multisegment representation of the Bain circuit and connecting tubing. For each segment, gas pressure, gas volume flow, and partial pressure of carbon dioxide are calculated for any number of breaths wanted. As a result, the time course of these variables can be generated for any location or, conversely, the carbon dioxide distribution in the system can be calculated for any time instant. A test lung, the human lungs, the ventilator bellows, and the reservoir bag are each represented by a single segment. The shapes of pressure and flow curves and of the capnograms taken at different locations in the Bain tubing are in good agreement. The washout study permits measurement of the time delay between the first expiration and the arrival of carbon dioxide at a particular location. The carbon dioxide level in the test lung decreases during inspiration and is stable during expiration. Quantitative agreement between model and experimental transport delays and carbon dioxide levels is such that the differences can be explained by the inaccuracy of the measurement. This is concluded from a sensitivity analysis. The study of the effect of segment size shows an almost optimal agreement between model behavior and experimental results for a 36-segment model. Execution of a thorough validation is imperative before such models can be used for clinical management and decision making or for teaching.

Airway Resistance↗
PubMed2000

Computational modeling of entorhinal cortex.

Computational modeling provides a means for linking the physiological and anatomical characteristics of entorhinal cortex at a cellular level to the functional role of this region in behavior. We have developed detailed simulations of entorhinal cortical neurons and networks, with an emphasis on the role of acetylcholine in entorhinal cortical function. Computational modeling suggests that when acetylcholine levels are high, this sets appropriate dynamics for the storage of stimuli during performance of delayed matching tasks. In particular, acetylcholine activates a calcium-sensitive nonspecific cation current which provides an intrinsic cellular mechanism which could maintain neuronal activity across a delay period. Simulations demonstrate how this phenomena could underlie entorhinal cortex delay activity as described in previous unit recordings. Acetylcholine also induces theta rhythm oscillations which may be appropriate for timing of afferent input to be encoded in hippocampus and for extraction of individual stored sequences from multiple stored sequences. Lower levels of acetylcholine may allow sharp wave dynamics which can reactivate associations encoded in hippocampus and drive the formation of additional traces in hippocampus and entorhinal cortex during consolidation.

Acetylcholine↗