SEARCH · PubMed Health

Results for “Computer Simulation”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 505 records · Page 28Linked to original sources

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↗

PubMed2000

Dynamics of capillary isoelectric focusing in the absence of fluid flow: high-resolution computer simulation and experimental validation with whole column optical imaging.

A 150-component, dynamic electrophoresis simulator was developed and applied to the description of capillary isoelectric focusing (CIEF) of amphoteric substances in quiescent solution. The simulator is shown to be capable of producing high-resolution pH 3-10 focusing data with 140 individual carrier ampholytes (20/pH unit) and at current densities that are used in CIEF, i.e., under conditions that were hitherto unaccessible by dynamic computer simulation. Having a focusing capillary of 5-cm length, the predicted focusing dynamics for amphoteric dyes obtained at a constant voltage of 1500 V (300 V/cm) are shown to qualitatively agree with data obtained by whole-column optical imaging. The simulation data provide detailed insight into the dynamics of the focusing process for the cases with the focusing column being sandwiched between 40 mM NaOH (catholyte) and 100 mM phosphoric acid (anolyte) or having the column ends only permeable for OH- and H+ at cathode and anode, respectively. Simulation data reveal that the number of sample boundaries migrating from the two ends of the column to the focusing positions is always equal to the number of sample components. The number of detectable migrating sample boundaries, however, can be lower. Whole-column optical imaging is demonstrated to be the method of choice for following the approach to equilibrium. With that detection format, transient sample peaks can be recognized and properly identified. This would also be possible with a scanning detector moving rapidly and repeatedly along the column but cannot be accomplished by a stationary detector placed at a specified location. The data presented demonstrate that the model together with imaging monitoring can be used to optimize the CIEF separation conditions.

Coloring Agents↗

PubMedDate not supplied

Surface effects and dipolar correlations of confined and constrained liquids investigated by NMR relaxation experiments and computer simulations.

Local order and molecular dynamics of liquids near surfaces strongly deviate from the behavior in the bulk. This in particular refers to liquid crystals above the bulk isotropization temperature. Transverse relaxation data of 5CB examined in porous glasses with different pore sizes are reported. A strong pore size effect was found. For the interpretation, a simple diffusion-adsorption computer simulation was carried out. Molecules can diffuse from the isotropic bulk part of the pore fluid to the ordered surface layer and vice versa. The residual dipolar correlation function is characterized by a slowly decaying tail owing to repeated returns of molecules to the surface. At each return the molecular orientation correlation is recovered as far as the surface sites visited have orientations correlated to the initial site. That is, molecular orientation is controlled by the "reorientation mediated by translational displacement" process considered in previous papers.

Computer Simulation↗

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↗

PubMed1999

Computer simulation to determine how rapid anesthetic recovery protocols to decrease the time for emergence or increase the phase I postanesthesia care unit bypass rate affect staffing of an ambulatory surgery center.

UNLABELLED: Ambulatory surgery centers (ASC) are implementing new anesthetic techniques and rapid recovery protocols in the postanesthesia care unit (PACU) to achieve earlier discharge after general anesthesia. Using computer simulation, we addressed two questions. First, what is the decrease in an ASC's operating room (OR) staff if the time from which the surgery is finished to the time the patient leaves the OR is decreased? Second, what is the decrease in PACU nursing staffing if patients bypass phase I PACU (i.e., proceed from the OR directly to the phase II PACU)? The decrease in labor costs from rapid emergence or fast-tracking depends on how staff are compensated, how many ORs routinely run concurrently, and what percentage of patients undergo general anesthesia. The results show potential decreases in ASCs' labor costs ($7.39 per case) from technologies (e.g., new anesthetics or Bispectral Index [Aspect Medical Systems, Natick, MA] monitoring) to decrease emergence times or increase the phase I bypass rates. IMPLICATIONS: Decreases in operating room and postanesthesia care unit labor costs resulting from faster emergence and phase I postanesthesia care unit bypass vary depending on the amount of routine overtime, how the staff are compensated, and how many patients are routinely anesthetized each day.

Ambulatory Surgical Procedures↗

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↗

PubMed2000

Computer simulation of primary kinetic isotope effects in the proposed rate-limiting step of the glyoxalase I catalyzed reaction.

The proposed rate-limiting step of the glyoxalase I catalyzed reaction is the proton abstraction from the C1 carbon of the substrate by Glu(172). Here we examine primary kinetic isotope effects and the influence of quantum dynamics on this process by computer simulations. The calculations utilize the empirical valence bond method in combination with the molecular dynamics free energy perturbation technique and path integral simulations. For the enzyme-catalyzed reaction a H/D kinetic isotope effect of 5.0 +/- 1. 3 is predicted in reasonable agreement with the experimental result of about 3. Furthermore, the magnitude of quantum mechanical effects is found to be very similar for the enzyme reaction and the corresponding uncatalyzed process in solution, in agreement with other studies. The problems associated with attaining the required accuracy in order for the present approach to be useful as a diagnostic tool for the study of enzyme reactions are also discussed.

Catalysis↗

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↗

PubMed2002

Computational simulation of the docking of Prochlorothrix hollandica plastocyanin to potosystem I: modeling the electron transfer complex.

We have used several docking algorithms (GRAMM, FTDOCK, DOT, AUTODOCK) to examine protein-protein interactions between plastocyanin (Pc)/photosystem I (PSI) in the electron transfer reaction. Because of the large size and complexity of this system, it is faster and easier to use computer simulations than conduct x-ray crystallography or nuclear magnetic resonance experiments. The main criterion for complex selection was the distance between the copper ion of Pc and the P700 chlorophyll special pair. Additionally, the unique tyrosine residue (Tyr(12)) of the hydrophobic docking surface of Prochlorothrix hollandica Pc yields a specific interaction with the lumenal surface of PSI, thus providing the second constraint for the complex. The structure that corresponded best to our criteria was obtained by the GRAMM algorithm. In this structure, the solvent-exposed histidine that coordinates copper in Pc is at the van der Waals distance from the pair of stacked tryptophans that separate the chlorophylls from the solvent, yielding the shortest possible metal-to-metal distance. The unique tyrosine on the surface of the Prochlorothrix Pc hydrophobic patch also participates in a hydrogen bond with the conserved Asn(633) of the PSI PsaB polypeptide (numbering from the Synechococcus elongatus crystal structure). Free energy calculations for complex formation with wild-type Pc, as well as the hydrophobic patch Tyr(12)Gly and Pro(14)Leu Pc mutants, were carried out using a molecular mechanics Poisson-Boltzman, surface area approach (MM/PBSA). The results are in reasonable agreement with our experimental studies, suggesting that the obtained structure can serve as an adequate model for P. hollandica Pc-PSI complex that can be extended for the study of other cyanobacterial Pc/PSI reaction pairs.

Algorithms↗

PubMed1993

VNTR allele frequency distributions under the stepwise mutation model: a computer simulation approach.

Variable numbers of tandem repeats (VNTRs) are a class of highly informative and widely dispersed genetic markers. Despite their wide application in biological science, little is known about their mutational mechanisms or population dynamics. The objective of this work was to investigate four summary measures of VNTR allele frequency distributions: number of alleles, number of modes, range in allele size and heterozygosity, using computer simulations of the one-step stepwise mutation model (SMM). We estimated these measures and their probability distributions for a wide range of mutation rates and compared the simulation results with predictions from analytical formulations of the one-step SMM. The average heterozygosity from the simulations agreed with the analytical expectation under the SMM. The average number of alleles, however, was larger in the simulations than the analytical expectation of the SMM. We then compared our simulation expectations with actual data reported in the literature. We used the sample size and observed heterozygosity to determine the expected value, 5th and 95th percentiles for the other three summary measures, allelic size range, number of modes and number of alleles. The loci analyzed were classified into three groups based on the size of the repeat unit: microsatellites (1-2 base pair (bp) repeat unit), short tandem repeats [(STR) 3-5 bp repeat unit], and minisatellites (15-70 bp repeat unit). In general, STR loci were most similar to the simulation results under the SMM for the three summary measures (number of alleles, number of modes and range in allele size), followed by the microsatellite loci and then by the minisatellite loci, which showed deviations in the direction of the infinite allele model (IAM). Based on these differences, we hypothesize that these three classes of loci are subject to different mutational forces.

Alleles↗