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At least 253 records · Page 14Linked to original sources
PubMed1977

Computer simulation of rat heart metabolism after adding glucose to the perfusate.

An experiment where perfused rat hearts receiving no substrate are suddenly given glucose with insulin in the perfusate is simulated with a computer model of cardiac energy metabolism. Mitochondrial metabolism is quantitatively reorganized under cytoplasmic control, with fatty acid oxidation undergoing a two-step decrease. There is an unspanning of the Krebs cycle (different reactions going at different rates) due primarily to slowing of alpha-ketoglutarate dehydrogenase; this ends when cytoplasmic glucose reaches a new steady state. Mitochondria in vitro are known to have higher pH than their surroundings; it is found here that this also holds in situ. Under these conditions, glycolysis is coherently substrate controlled, as is phosphofructokinase, usually considered the typical example of an allosteric enzyme. Limitations on simple methods of analyzing metabolic data of this type, e.g., use of lactate/pyruvate ratios to calculate NADH/NAD ratios, are discussed. Here a large volume of enzyme and other biochemical information has been integrated into a physiologically meaningful system.

Amino Acids↗
PubMed1984

Cardiopulmonary resuscitation by intrathoracic pressure variations--in vivo studies and computer simulation.

The effect of intrathoracic pressure variations on the hemodynamics of dogs with cardiac arrest were studied experimentally and simulated on a computer. High intrathoracic pressure (up to 90 mm Hg) was generated by lung inflation with passive and active modes of external fixation. Abdominal binding was found to be essential for the generation of high intrathoracic pressure. Remarkable Doppler flow signals were detected over the femoral artery with each lung inflation. Blood gases measured after 30 minutes of cardiac fibrillation in dogs together with intrathoracic pressure variations showed well oxygenated arterial blood with metabolic acidosis. A computer model was used to explore the effects of intrathoracic pressure variations over a large range of parameters. For intrathoracic pressure of 50/0 mm Hg. the mathematical model predicted maximal flow of 663 ml/min, occurring at a rate of 115 cpm, with a duty cycle of 58%. The heart showed only minor volume changes during the cycle, indicating its main function as a passive conduit during cardiopulmonary resuscitation. The data show that intrathoracic pressure variation with no direct heart compression can cause systemic blood flow of the magnitude occurring in most cardiopulmonary resuscitation techniques.

Animals↗
PubMed1988

Structural mechanics of the blowout fracture: numerical computer simulation of orbital deformation by the finite element method.

Blowout fractures most frequently involve the orbital floor. The contour of the orbit has been postulated as one of the factors responsible for this phenomenon, but only a few studies have been carried out. The present study was planned to determine the effect of the contour of the orbit when intraorbital pressure is raised to simulate the hydraulic mechanism of blowout fracture. The profile of the orbit was estimated from five dry human skulls, and the measurements were approximated to frame models. The deformation of these models by raised intraorbital pressure was calculated by computer simulation using the finite element method. In all of the orbital models, the deformation of the orbital floor was significantly greater than that of the roof. These findings verified that the orbital roof has a higher resistance than the floor against raised intraorbital pressure. We suspect that this resistance is due to the arched shape of the orbital roof, whereas the floor is rather flat.

Computer Simulation↗
PubMed1992

Neurite branching pattern formation: modeling and computer simulation.

A model for nerve cell pattern formation is proposed in this paper. The model is based on some experimental results and an assumption that there is a kind of inhibitive interaction between growing neurites on the same nerve cell. In this paper, this interaction is termed lateral inhibition. A group of ordinary differential equations are used to describe the elongation of the terminal neurite segments of individual nerve cells. Computer simulation and comparison of it with in vitro studies are also made in this paper.

Animals↗
PubMed1990

A new glucose-clamp algorithm--theoretical considerations and computer simulations.

The commonly used setup of an automatic glucose-clamp was analyzed as a control system, modeling the measuring device and the patient in a simple but effective way. Strict limits in response time, parasitic oscillation amplitude, and accuracy were defined in order to approach the physician's requirements. We developed a new control algorithm and defined the gain coefficients which can lead the system within these limits. Computer simulations with model parameters from literature (patient) and from experimental data (measuring device) are presented. Preliminary in vivo trials are also presented.

Algorithms↗
PubMed1992

Computer simulation analysis of the effects of countermeasures for reentry orthostatic intolerance.

Fluid loading is a countermeasure currently in routine use to improve the g-tolerance of crewmembers during reentry and return of Shuttle flights. However, its effectiveness diminishes with mission duration. Countermeasures that will be effective on long-duration flights are needed and are presently under development. This paper discusses the application of computer simulation in the analysis of the effects of countermeasures for reentry orthostatic intolerance. The results suggest improvements upon the fluid loading countermeasure currently in use.

Blood Volume↗
PubMed1989

Interactive NMR and computer simulation studies of lanthionine-ring structures.

We report progress in elucidating the structure of nisin, a naturally occurring peptide antibiotic. Nisin contains five rings constrained by lanthionine or methyllanthionine bridges, as well as alpha, beta-unsaturated amino acids. We have determined conformations for two model compounds of ring A and a derivative of ring B through interactive nmr and computer simulation studies. High-resolution nmr techniques provides structural information, which was further refined through molecular dynamics simulations. These methods are being applied to the remaining constrained fragments of the molecule. This conformational information will be employed in an aufbau approach to determining the structure of the entire molecule.

Alanine↗
PubMed1976

Active enzyme gel chromatography: II. Computer simulations.

The behavior of an enzyme undergoing reaction while on a gel chromatography column has been studied by computer simulation using the steady state assumtion for a system with a single enzyme-substrate complex. The profiles of the enzyme-substrate complex, product, and substrate were examined varying the parameters of kcat, flow rate, partition coefficient dispersion, and time. These investigations confirm that much information about both the active enzyme and the product may be obtained by examining the product profile alone, varying the power of applying scanning gel chromatography to active enzyme systems.

Binding Sites↗
PubMed1991

A mathematical model and computer simulation study of insulin receptor regulation.

A homeomorphic mathematical model of cell surface insulin receptor regulation is developed. The overall structure of the model is based on molecular mechanisms suggested by in vivo and in vitro experimental evidence from many different cell types. Model parameters correspond to cellular processes which are constrained by known boundry value conditions. As an example, computer simulation results are compared with published data from BC3H-1 myocytes in culture. With appropriate parameter choice, this model is able to simulate data from other cell types. Cellular processes which are explicitly represented in the model include: bound and unbound receptor endocytosis, receptor recycling, intracellular receptor degradation, and state-dependent receptor synthesis. Most of these processes are represented as first-order events. Using more complex representations of the model structure with higher order rate constants or saturable pathways does not qualitatively improve simulation results. Simulations are able to reproduce ligand-induced down and up regulation of receptors as well as the initial spontaneous display of surface insulin receptors. To demonstrate the behavior of our model and illustrate its utility for explaining insulin receptor regulation for a variety of conditions, simulations for which experimental data is unavailable for direct comparison are also shown. We believe the structure of our model is sufficient to explain insulin receptor regulation in a wide variety of cell types. In addition our model may aid in understanding the receptor component of insulin resistance (decreased sensitivity or responsiveness to insulin) seen in pathological states such as obesity and diabetes mellitus. Finally, this model may be applicable to the study of the regulation of other polypeptide hormone receptors.

Cell Membrane↗
PubMed1990

Conformational studies by circular dichroism, 1H NMR, and computer simulations of bombolitins I and III in aqueous solution containing surfactant micelles.

The heptadecapeptides bombolitin I and bombolitin III are two members of a series of biologically active peptides postulated to be membrane active. In order to understand the effects of the membrane on the secondary structure of the peptides, we have carried out the conformational characterization of bombolitins I and III in the presence of SDS micelles using circular dichroism, nuclear magnetic resonance, and computer simulations. The characteristic bands in the circular dichroism spectra indicate an alpha-helix content of approximately 60% in bombolitin III and 70% in bombolitin I. The observation of NOE's quite distinctive for such secondary structure strongly supports the CD results. The conformational preferences of the two bombolitins derived from CD and NMR were then energetically refined with molecular dynamics simulations. The results from the spectroscopic examination were utilized as input for the simulations, the CD results for generation of the initial structure, and the NOE's as constraints during the simulations. The results from the different techniques employed are in complete agreement.

Amino Acid Sequence↗
PubMed1995

Adults' responses to self-injurious behavior. An experimental analysis using a computer-simulation paradigm.

The behavior of staff who care for people with mental retardation has been identified as a significant factor in the development and maintenance of challenging behaviors. In a recent analysis, Hastings and Remington (1994a) suggested that both environmental contingencies and rules from other people may affect staff actions. The present study tested this analysis by asking participants to respond to a computer simulation of a work situation involving the care of two individuals who engaged in self-injurious behavior. Fifty participants "interacted" with an attention-seeker and a social-avoider on a simulated teaching task. Results showed that rules were the main factor governing performance. The aversive nature of the contingencies between the self-injury and participants' "attending" behavior also appeared to be influential. The implications of these results for work with care staff, the analysis of challenging behaviors, and experimental research on rule-governed behavior are discussed.

Adolescent↗
PubMed1991

A stochastic model for predator-prey systems: basic properties, stability and computer simulation.

A simple stochastic description of a model of a predator-prey system is given. The evolution of the system is described by means of Itô's stochastic differential equations (SDEs), which are the natural stochastic generalization of the Lotka-Volterra deterministic differential equations. Since these SDEs do not satisfy the usual conditions for the existence and uniqueness of the solution, we state a theorem of existence; moreover we study the stability of the equilibrium point and perform a computer simulation to study the behaviour of the trajectories of solutions with given initial data and to estimate first and second moments.

Animals↗
PubMed1986

Cross-correlation analysis of intracellularly recorded synaptic activities: an evaluation of the method through computer simulation.

Cross-correlation of 'spontaneous' synaptic activities intracellularly recorded from pairs of neurons may be used to detect shared synaptic input, which could remain hidden in the raw data by the non-synchronized postsynaptic potentials (PSPs); besides, if a normalized cross-correlation function is adopted, the fraction of synchronized activity may be quantitatively estimated. To evaluate power and limits of this method, computer-simulated synaptic activities of pairs of neurons, in which a given percentage of PSPs were simultaneous, were subjected to this type of analysis. It was shown that percentages of shared activities as low as 4% and in some cases 2% could be revealed, with a conspicuity which was influenced by the types of associated PSPs.

Action Potentials↗
PubMedDate not supplied

The initiator titration model: computer simulation of chromosome and minichromosome control.

The initiator titration model was formulated to explain the initiation control of the bacterial chromosome. In particular, features concerning the replication behaviour of minichromosomes, such as their high copy number and Escherichia coli's ability to coinitiate chromosome and many minichromosome origins, were considered during the formulation of the model. The model is based on the initiator protein DnaA and its binding sites, DnaA boxes, in oriC, in the dnaA promoter and at other positions on the chromosome. Another important factor in the model is the eclipse period created by the hemimethylation of a new oriC which makes it refractory to initiation. The model was analysed by computer simulations using a stochastic approach varying the different input parameters, and the resulting computer cells were compared with data on living E. coli cells. Here we present the outcome of a few of these simulations concerning the eclipse period, in silico-shift experiments blocking initiation or elongation of replication, and introduction of minichromosomes into the computer cells. We also discuss the synthesis of DnaA protein in the computer cells. From our simulations, we conclude that, whether true or not, the model can mimic the in vivo initiation control of E. coli.

Bacterial Proteins↗
PubMed1991

Protein-protein interaction: an analysis by computer simulation.

A survey of protein-protein interactions in structures derived by X-ray crystallography of protease-inhibitor and antigen-antibody complexes shows that they form close-packed interfaces from which water is excluded. The interfaces are of almost constant size, and they contain about ten hydrogen bonds. These features account for the stability of the complexes. To test whether they also account for specificity, we designed a computer simulation that searches for complementary surfaces on two protein molecules. In all cases tested, the simulation finds a number of complexes having interfaces and hydrogen bonds equivalent to those of the native complexes. These artificial complexes might represent secondary specificities, which can be detected when normal association is prevented by mutation or other means.

Computer Simulation↗
PubMed1990

[The computer simulation of orthodontic tooth movements].

A personal computer programme is presented which allows the prediction of orthodontic tooth movement under the influence of any given force and moment. The changes in position of the front teeth caused by the chosen forces appear on the monitor as a three-dimensional diagram and as a movie-like picture sequence.

Computer Simulation↗
PubMed1990

Restoring unassisted natural gait to paraplegics via functional neuromuscular stimulation: a computer simulation study.

Functional neuromuscular stimulation (FNS) of paralyzed muscles has enabled spinal-cord-injured patients to regain a semblance of lower-extremity control, for example to ambulate while relying heavily on the use of walkers. Given the limitations of FNS, specifically low muscle strengths, high rates of fatigue, and a limited ability to modulate muscle excitations, it remains unclear, however, whether FNS can be developed as a practical means to control the lower extremity musculature to restore aesthetic, unsupported gait to paraplegics. A computer simulation of FNS-assisted bipedal gait shows that it is difficult, but possible to attain undisturbed, level gait at normal speeds provided the electrically-stimulated ankle plantarflexors exhibit either near-normal strengths or are augmented by an orthosis, and at least seven muscle-groups in each leg are stimulated. A combination of dynamic programming and an open-loop, trial-and-error adjustment process was used to find a suboptimal set of discretely-varying muscle stimulation patterns needed for a 3-D, 8 degree-of-freedom dynamic model to sustain a step. An ankle-foot orthosis was found to be especially useful, as it helped to stabilize the stance leg and simplified the task of controlling the foot during swing. It is believed that the process of simulating natural gait with this model will serve to highlight difficulties to be expected during laboratory and clinical trials.

Computer Simulation↗