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At least 379 records · Page 21Linked 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↗
PubMed1994

Estimation of metabolic flux rates in liver purine catabolism of tumour-bearing mice by computer simulation of radioactive tracer experiments.

Mouse hepatocytes from healthy control mice and from Ehrlich ascites tumour-bearing mice were used for tracer-kinetic studies of purine catabolism of liver cells during different periods of tumour growth. The dynamics of the radioactive tracers were modelled mathematically by a system of differential equations. Computer simulations, i.e. direct fitting of numerical solutions of these equations to the observed time-courses of metabolites and specific radioactivities, enables one to estimate unknown kinetic parameters of a simplified model of pathways of hepatic purine catabolism in tumour-bearing mice. There occurred great differences of metabolic flux rates between control hepatocytes, hepatocytes of mice during the proliferating period of tumour growth (6th day after inoculation of the tumour) and hepatocytes of mice during the resting period of tumour growth (12th day after inoculation of the tumour). The final purine degradation of hepatocytes prepared during the proliferating period was lower in comparison with that of control hepatocytes, but it was markedly higher in hepatocytes prepared during the resting period of tumour growth. The changes in hepatocyte purine catabolism during the proliferating period of tumour growth argue for transitions which aim at the maintenance of high purine nucleotide levels in the liver itself rather than for an increased nucleoside and nucleobase supply for the tumour. This suggestion is in accordance with the increased ATP level of the liver during the proliferating phase of tumour growth.(ABSTRACT TRUNCATED AT 250 WORDS)

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↗
PubMed1993

Computer simulation in sport and industry.

The last several decades have brought decreases in the specific cost of computer memory and increases in processor throughput. As a result simulation has become correspondingly more important as a component of industrial design and as a method for the study of general biomechanics and sports techniques. This paper illustrates, by way of examples, several of the more important aspects of the application of computer simulation to dynamic problems. Topics include (1) the ideas of suitable model complexity and its tradeoff with interpretability; (2) the sequential and iterative nature of model building and the importance of experimental data in the modelling and validation process; (3) the essential role of user-friendly software and graphical interfaces in the interchange of information between simulation programs and the users; and 4) the role of computer simulation in learning feedback loops, both in the field and in the computer laboratory. Most industrial use of simulation is in the design process. A similar approach is equally valid in biomechanics and sport applications through the incorporation of design variables, which may be easily changed in the model experiment.

Biomechanical Phenomena↗
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↗
PubMed1995

A general method for the computer simulation of biological systems interacting with fluids.

At this Symposium on Biological Fluid Dynamics, it is appropriate to ask whether there is any common theme that unites the diverse problems that arise in the study of living systems interacting with fluids. The answer that immediately comes to mind is this: biological fluid dynamics invariably involves the interaction of elastic flexible tissue with viscous incompressible fluid. (In many cases the tissue is not only elastic, it is also active, i.e. capable of doing work on the fluid). This paper describes the immersed boundary method, which is a general framework for the computer simulation of biofluid dynamic systems. This method has already been applied to blood flow in the heart (including the computer-assisted design of prosthetic cardiac valves), platelet aggregation during blood clotting, aquatic animal locomotion, wave propagation along the basilar membrane of the inner ear, and flow in collapsible tubes. In the immersed boundary method, the elastic (and possibly active) biological tissue is treated as a part of the fluid in which additional forces (derived from the tissue stresses) are applied. Because the tissue is represented in terms of its force field, the method remains straightforward, even when the geometry of the biological tissue is complicated, dynamic and not known in advance.

Animals↗
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↗
PubMedDate not supplied

Conformational analysis of the dipeptide taste ligand L-aspartyl-D-2-aminobutyric acid-(S)-alpha-ethylbenzylamide and its analogues by NMR spectroscopy, computer simulations and X-ray diffraction studies.

A dipeptide taste ligand L-aspartyl-D-2-aminobutyric acid-(S)-alpha-ethylbenzylamide was found to be about 2000 times more potent than sucrose. To investigate the molecular basis of its potent sweet taste, we carried out conformational analysis of this molecular and several related analogues by NMR spectroscopy, computer simulations and X-ray crystallographic studies. The results of the studies support our earlier model that an L-shape molecular array is essential for eliciting sweet taste. In addition, we have identified an aromatic group located between the stem and the base of the L-shape, which is responsible for enhancement of sweetness potency. In this study, we also assessed the optimal size of the essential hydrophobic group (X) and the effects of the chirality of the second residue toward taste.

Aminobutyrates↗
PubMed1997

Exactness of source analysis of biomagnetic signals of epileptiform spikes by the method of spatial filtering: a computer simulation.

On the basis of spatial covariance it is found that, by spatial filtering the localisation of a single dipole source, both parallel and perpendicular to the measurement plane (assuming a signal-noise ratio of 5:1), can be performed with an accuracy of < 0.5 mm. When the signal-noise ratio is increased to 30:1, the resolution of temporally independent current sources separated by 2 mm becomes practicable. This resolution study is carried out by means of a pair of unity current dipoles with the dipole distance as a varying source model parameter. The conclusions, drawn from the results of computer simulation and supported by statistical calculations, refer to the spherical model of the volume conductor of the brain.

Computer Simulation↗
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↗
PubMed1994

Sources of errors in different single-electrode voltage-clamp techniques: a computer simulation study.

The use of voltage clamp with a single electrode has been useful in estimating kinetic parameters for a number of ionic whole-cell currents. There are two main types of such a technique: discontinuous voltage clamp (dSEVC) (Brennecke and Lindemann, 1974), and continuous voltage clamp (cSEVC) (Hamill et al., 1981). We have studied, by means of computer simulations, the performance of both types of clamp on estimating activation kinetics parameters of a typical neuronal Ca2+ current. Deviations from the theoretical values are shown to be sensitive on both set-up and cell properties. Both types of clamp are shown to lose voltage control when either access resistance or absolute membrane conductance are increased. In contrast, changes in membrane capacitance affect differently to the estimates obtained by the two types of clamp. Cell size is also shown to affect cSEVC performance but not that of dSEVC. The nature and magnitude of errors obtained by using both types of clamp in different situations are discussed.

Amplifiers, Electronic↗
PubMed1996

Functional significance of the outer dense fibers of mammalian sperm examined by computer simulations with the geometric clutch model.

The flagella of mammalian sperm possess certain structural characteristics that distinguish them from simple flagella. Most notable of these features are the sheath (surrounding the axoneme), the outer dense fibers of ODFs (that are attached to the outer doublets), and the connecting piece (which anchors the ODFs at the base of the flagellum). In this study, the significance of these specialized axonemal elements is explored. Their impact on microtubule sliding and force production within the axoneme is specifically analyzed. A working hypothesis is developed based on the premise that forces produced by interdoublet sliding are transferred to the ODFs. In this way, the torque required to bend the flagellum is developed between the ODFs, which are anchored in the connecting piece. This working hypothesis was incorporated into the pre-existing "geometric clutch" model that earlier simulated only cilia and simple flagella. The characteristic length and stiffness of bovine sperm flagella were specified as modelling parameters. Additionally, the inter-ODF spacing of bull sperm was incorporated to calculate doublet sliding and bending torque. The resultant computer-simulated pattern of flagellar beating possesses many of the attributes of the beat of a live bull sperm flagellum. Notably, this life-like simulation can be produced using parameters for the central axonemal "motor" that are comparable to those effective in modelling a simple flagellum. In the proposed scheme, the accessory structures of the mammalian sperm axoneme provide increased stiffness while at the same time providing a means to proportionately raise the bending torque to overcome that additional flexural rigidity. This capacity is due to the inter-ODF distances being larger than the corresponding interdoublet spacings. If force is transmitted to the flagellar base by way of the ODFs, then the larger effective diameter generates both a greater bending torque and increased interdoublet sliding. This has the interesting effect of consolidating the energy from more dynein cross-bridges into the production of a single bend. Consequently. greater bending torque development is permitted than would be possible in a simple flagellum. In This way, the same 9 + 2 organization of a simple flagellum can power a much larger (and stiffer) version than would otherwise be possible.

Animals↗
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↗