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Results for “Computer Simulation”

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At least 235 records · Page 13Linked to original sources

PubMed1984

On computer simulation methods used to study models of two-component lipid bilayers.

We show that the use of a computer simulation method introduced to calculate the equilibrium thermodynamic properties of a model of a two-component lipid bilayer membrane [Freire, E., & Snyder, B. (1980) Biochemistry 19, 88-94] is incorrect. This is done by comparing the method to that of Metropolis, which has been proven to generate equilibrium distribution of that model, and by showing that back-processes have been omitted in the implicit master equation of Freire and Snyder. We have illustrated this explicitly by first generating distributions according to the method of Freire and Snyder and then allowing the system to relax via the Kawasaki method, which uses the technique of Metropolis. We show that relaxation to a different distribution occurs. We also remark that the cluster distributions generated by the Freire-Snyder method are substantially different from those occurring in equilibrium distributions. Thus, conclusions about equilibrium thermodynamic properties such as specific heats and transition enthalpies or about transport properties or cluster properties at equilibrium cannot be drawn from the results obtained by using this method. Finally, we point out that the method of Freire and Snyder is appropriate to so-called aggregation models, which have been used to study irreversible growth; and we suggest biological systems that might be simulated by their method.

Computers↗

PubMed1991

How many probes are needed for HLA-DPB1 typing with sequence-specific oligonucleotide probes? A theoretical approach using computer simulation.

HLA-DP genotyping with sequence-specific oligonucleotides is used to detect known sequence variations in the polymorphic segments of the DPB1 second exon. This approach is a valuable method replacing the tedious cellular definition of DP polymorphism. We have addressed, by computer simulation, the question: what is the minimum number of probes needed to provide an unambiguous assignment of HLA-DP alleles by genotyping of heterozygous individuals? We were able to reduce the number of probes in a set defining the presently known 22 different alleles and most of the heterozygous combinations to 18 probes. Only two pairs of allelic combinations cannot be distinguished by this method, neither with our optimized set of probes nor with any larger set comprising probes of reasonable length. This is because two pairs of alleles may be the result of a reciprocal genetic exchange. These two pairs, however, could be distinguished by family analysis, direct sequencing, or DNA amplification using specific primers chosen from the polymorphic ends of the DPB1 second exon.

Alleles↗

PubMed1992

Computer simulations of EPSP-spike (E-S) potentiation in hippocampal CA1 pyramidal cells.

Long-term potentiation of hippocampal excitatory synapses is often accompanied by an increase in the probability of spiking to an EPSP of fixed strength (E-S potentiation). We used computer simulations of a CA1 pyramidal neuron to test the plausibility of the hypothesis that E-S potentiation is caused by changes in dendritic excitability. These changes were simulated by adding "hot spots" of noninactivating voltage-sensitive Ca2+ conductance to various dendritic compartments. This typically caused spiking in response to previously subthreshold synaptic inputs. The magnitude of the simulated E-S potentiation depended on the passive electrical properties of the cell, the excitability of the soma, and the relative locations on the dendrites of the synaptic inputs and hot spots. The specificity of the simulated E-S potentiation was quantified by colocalizing the hot spots with a subset (40 of 80) of the synaptic contacts, denoted "tetanized," and then comparing the effects of the hot spots on these and the remaining (untetanized) synaptic contacts. The simulated E-S potentiation tended to be specific to the tetanized input if the untetanized contacts were, on average, electrically closer to the soma than the tetanized contacts. Specificity was also high if the tetanized and untetanized contacts were segregated to different primary dendrites. The results also predict, however, that E-S potentiation by this mechanism will appear to be nonspecific (heterosynaptic) if the synapses of the untetanized input are sufficiently far from the soma relative to the tetanized synapses. Experimental confirmation of this prediction would support the hypothesis that changes in postsynaptic excitability can contribute to hippocampal E-S potentiation.

Animals↗

PubMed1990

A model for computer simulation of P-glycoprotein and transmembrane delta pH-mediated anthracycline transport in multidrug-resistant tumor cells.

Anthracycline resistance in multidrug-resistant (MDR) tumor cells is due in part to a reduced cellular drug accumulation. Using a simple kinetic model and numerical computer simulations, we have analyzed mathematically the following possible mechanisms controlling fluxes of the membrane permeable anthracyclines in MDR cells: (1) active outward transport via a specific drug transporter (P-glycoprotein), (2) exocytotic drug export via the endosomal vesicle system, and (3) pH-gradients across the plasma membrane. Model calculations were based on morphometric and kinetic data previously presented in the literature for daunorubicin transport in wild-type Ehrlich ascites tumor cells (EHR2) and the corresponding daunorubicin (DNR)-resistant cell line EHR2/DNR+. The results confirm the possible importance of the cell-surface pH in controlling DNR accumulation in the cells. With P-glycoprotein as the main efflux pump, a catalytic constant of the protein greater than 40 mol DNR transported/mol protein per min is predicted by the model calculations. Changes in the drug binding affinity of P-glycoprotein (Km = 10(-9)-10(-6) M) is of little importance in influencing its effectiveness to reduce DNR accumulation, which could explain the broad substrate specificity of the MDR efflux pump system. The conditions to evaluate unidirectional fluxes of DNR across the plasma membrane in cells with active P-glycoprotein are defined. An efflux mechanism which relies solely on pH-dependent drug trapping in a pH 5 endosomal compartment by a simple diffusion process followed by exocytosis, appears inadequate to account for the high rate of DNR efflux in EHR2/DNR+ cells.

Animals↗

PubMed1991

Applications of a computer simulation model of the natural history of CD4 T-cell number in HIV-infected individuals.

Data from the Multicenter AIDS Cohort Study (MACS) of 1637 gay men, recruited in 1984 and 1985 in Los Angeles and followed at 6-monthly intervals, are used to develop a computer simulation model of the typical pattern of CD4 T-cell number changes in HIV-infected AIDS-free subjects. The empirical model incorporates the following features: (1) within-person and between-person variability in CD4 measurements; (2) variation in the rates of decline of CD4 values; (3) variation in the level of CD4 at which clinical AIDS is diagnosed, and (4) greater absolute variation in CD4 values in men with high CD4 levels compared with men with low CD4 values. Three applications of the model to assist in the design and interpretation of clinical trials are given. Further applications to clinical trials and to estimate the current and future spectrum of HIV-mediated immunological disease in the USA, as measured by the CD4 values, are discussed.

Biomarkers↗

PubMed1991

Computer simulation analysis of morphological patterns in human melanocytic skin tumours.

Tumour cell proliferation and particularly tumour cell motility are considered to be essential pre-requisites for invasive tumour growth. Despite abundant in vitro data on tumour cell motility, the behaviour of tumour cells in complex human tumour tissues is yet unknown. In this study, estimates of proliferation and motility are statistically derived from morphological tumour patterns in human melanocytic skin tumours. Two-dimensional, discrete, random computer simulations of tumour growth were carried out in order to determine the influence of tumour cell proliferation and motility on morphological patterns. A set of binary morphological criteria turned out to facilitate a significant estimate of the relative probabilities of motility and proliferation (CART analysis). When the same morphological criteria were applied to H & E stained slides of 45 melanocytic skin tumours, benign common nevi showed a predominance of motility, whereas primary and metastatic malignant melanoma revealed a predominance of proliferation. The direct assessment of the number of proliferating cells by Ki-67 staining shows a steep increase from benign nevi to primary and metastatic melanoma. These data provide first evidence that in benign common nevi the overall motility exceeds the very low degree of proliferation, whereas in malignant melanocytic tumours proliferation considerably exceeds tumour cell motility.

Cell Division↗

PubMed1990

[Basic study on criteria for the reactivity of non-stress tests by means of computer simulation].

The non-stress test has become one of the most popular tests for antenatal surveillance in modern obstetrics. However, the fact that there are so many criteria for 'reactivity' in this test has made it rather difficult to interpret the results of these tests and compare them with each other. Using computer simulation of the occurrence of acceleration in fetal heart beats, the sensitivity and specificity of eight criteria which are in general use were studied. Diagnosis by Brown's criteria produced the best results for both sensitivity and specificity, but the long time necessary for this test is a drawback. However, the predictive value positive (probability of poor fetal outcome with nonreactivity) is only 62% even according to Brown's criteria when the test is done for antenatal care screening of an unrestricted population. The results of the test are far more convincing when it is reactive because the predictive value negative is more than 96%, even when strictly interpreted.

Computer Simulation↗

PubMedDate not supplied

[Teaching medical diagnosis by computer simulation].

A program of computer-assisted teaching, called AEDM, has been developed to simulate, with a conversational type terminal, the natural process of medical decision making. This system rests on two softwares, 'teaching' and 'inquiring', with 10 000 PASCAL instructions and the database of a computer-assisted diagnostic system (about 100 MO). The study describes the objectives and the characteristics of a system based on a simulation program; using natural procedures and non-specialized software is useful to develop computer-assisted teaching concerning different fields of pathology.

Computer-Assisted Instruction↗

PubMed1989

Computer simulation and experimental validation of the electrophoretic behavior of proteins.

A mathematical model of the electrophoretic behavior of proteins is presented. The Debye-Hückel-Henry theory is used for the description of protein mobility, which has the important result of making net mobility a function of ionic strength. A net charge vs pH relationship and a diffusion coefficient are required to describe a specific protein. The model is employed for the computer simulation of three distinct electrophoretic modes: isoelectric focusing, isotachophoresis, and zone electrophoresis. The validity of the model is tested by comparing simulation with experimental data. Excellent qualitative agreement was found.

Computer Simulation↗

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↗