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At least 145 records · Page 8Linked to original sources
PubMed1992

Computer simulation of the segmental neural network generating locomotion in lamprey by using populations of network interneurons.

Realistic computer simulations of the experimentally established local spinal cord neural network generating swimming in the lamprey have been performed. Populations of network interneurons were used in which cellular properties, like cell size and membrane conductance including voltage dependent ion channels were randomly distributed around experimentally obtained mean values, as were synaptic conductances (kainate/AMPA, NMDA, glycine) and delays. This population model displayed more robust burst activity over a wider frequency range than the more simple subsample model used previously, and the pattern of interneuronal activity was appropriate. The strength of the reciprocal inhibition played a very important role in the regulation of burst frequency, and just by changing the inhibitory bias the entire physiological range could be covered. At the lower frequency range of bursting the segmental excitatory interneurons provide stability as does the activation of voltage dependent NMDA receptors. Spike frequency adaptation by means of summation of afterhyperpolarization (AHP) serves as a major burst terminating factor, and at lower rates the membrane properties conferred by the NMDA receptor activation. The lateral interneurons were not of critical importance for the burst termination. They may, however, be of particular importance for inducing a rapid burst termination during for instance steering and righting reactions. Several cellular factors combine to provide a secure and stable motor pattern in the entire frequency range.

Animals↗
PubMed1992

Supercoiled DNA energetics and dynamics by computer simulation.

A new formulation is presented for investigating supercoiled DNA configurations by deterministic techniques. Thus far, the computational difficulties involved in applying deterministic methods to supercoiled DNA studies have generally limited computer simulations to stochastic approaches. While stochastic methods, such as simulated annealing and Metropolis-Monte Carlo sampling, are successful at generating a large number of configurations and estimating thermodynamic properties of topoisomer ensembles, deterministic methods offer an accurate characterization of the minima and a systematic following of their dynamics. To make this feasible, we model circular duplex DNA compactly by a B-spline ribbon-like model in terms of a small number of control vertices. We associate an elastic deformation energy composed of bending and twisting integrals and represent intrachain contact by a 6-12 Lennard Jones potential. The latter is parameterized to yield an energy minimum at the observed DNA-helix diameter inclusive of a hydration shell. A penalty term to ensure fixed contour length is also included. First and second partial derivatives of the energy function have been derived by using various mathematical simplifications. First derivatives are essential for Newton-type minimization as well as molecular dynamics, and partial second-derivative information can significantly accelerate minimization convergence through preconditioning. Here we apply a new large-scale truncated-Newton algorithm for minimization and a Langevin/implicit-Euler scheme for molecular dynamics. Our truncated-Newton method exploits the separability of potential energy functions into terms of differing complexity. It relies on a preconditioned conjugate gradient method that is efficient for large-scale problems to solve approximately for the search direction at every step. Our dynamics algorithm is numerically stable over large time steps. It also introduces a frequency-discriminating mechanism so that vibrational modes with frequencies greater than a chosen cutoff frequency are essentially frozen by the method. With these tools, we rapidly identify corresponding circular and interwound energy minima for small DNA rings for a series of imposed linking-number differences. These structures are consistent with available electron microscopy data. The energetic exchange of stability between the circle and the figure-8, in very good agreement with analytical results, is also detailed. Molecular dynamics trajectories at 100 femtosecond time steps then reveal the rapid folding of the unstable circular state into supercoiled forms. Significant bending and twisting motions of the interwound structures are also observed. Such information may be useful for understanding transition states along the folding pathway and the role of enzymes that regulate supercoiling.(ABSTRACT TRUNCATED AT 400 WORDS)

Algorithms↗
PubMed1992

Cardiovascular simulation using a multiple modeling method on a digital computer--simulation of interaction between the cardiovascular system and angiotensin II.

A cardiovascular system model that simulates interactive responses to drugs has been developed on a small digital computer. The overall model basically consists of three models. The first is a momentum transport model that represents relations between blood pressure and flow in the cardiovascular system. In this model, the cardiovascular system is divided into 14 components and modeled by using equivalent electrical circuits. The second is a mass transport model comprising 14 compartments corresponding to the respective components of the cardiovascular system. This model represents the distribution of the administered drug in the various cardiovascular components. The third is an interaction model that represents the relationships between the momentum and mass transport models. This model causes variations in the resistance and capacitance parameters of the momentum transport model as a function of the current drug concentrations in the appropriate compartments of the mass transport model. The capacitances representing the ventricles are varied in a time-dependent fashion to simulate the beat of the heart. Simulation is performed by using the Euler method to solve a system of 28 ordinary differential equations governing the momentum and mass transport models on a 32-bit microcomputer, a Macintosh II. The model was assessed by performing two demonstrations of the cardiovascular response to the vasopressor angiotensin II (AT II). They first examined the interaction between the cardiovascular system and AT II. The effect of AT II on the cardiovascular system was incorporated into the interaction model. Administration of AT II as a constant infusion (200 micrograms/hr) resulted in an elevation of mean arterial pressure from approximately 100 to 150 mm Hg.(ABSTRACT TRUNCATED AT 250 WORDS)

Angiotensin II↗
PubMed1990

Effect of sample size on reproducibility of behavioral teratological study results: a computer simulation experiment using data from the Collaborative Behavioral Teratology Study of the National Center for Toxicological Research.

A computer simulation experiment which attempted to examine the effect of sample size on reproducibility of the effect of treatment was performed on the basis of actual data obtained from the Collaborative Behavioral Teratology Study of the National Center for Toxicological Research. The degree of the treatment effect was assessed in terms of the strength of the association (eta square). The results indicate that sample size has a large effect on the reproducibility of results which are assessed with the magnitude of SD for eta squares obtained from replication experiments. Suitable sample sizes to obtain relatively consistent results across studies were discussed, pointing out that not enough attention has been paid to the effect of sample size in the issue of reproducibility of results in some behavioral teratology studies.

Computer Simulation↗
PubMed1991

Clinical decision making of critical care nurses managing computer-simulated tachydysrhythmias.

The purposes of this study were to describe the clinical decision making of critical care nurses managing computer-simulated tachydysrhythmias and to assess the major sources of error related to the management of two tachydysrhythmias: atrial flutter and ventricular tachycardia. In this descriptive study, 142 critical care nurses each completed four computerized clinical simulations (two atrial flutter and two ventricular tachycardia). Simulation performance was measured by proficiency score (comparison with expert performance), patient outcome (cure or die), and amount of data collected before the first intervention. Mean proficiency scores were 51% for atrial flutter and 35% for ventricular tachycardia. Thirteen percent of the atrial flutter and 35% of the ventricular tachycardia simulations ended in patient death. Failure to recognize ventricular tachycardia and unfamiliarity with second- and third-line treatments were major sources of error. Medication errors were the cause of death in 87% of the simulations ending in patient death. These results document the need for emphasis on dysrhythmia management in the critical care curriculum.

Arrhythmias, Cardiac↗
PubMed1987

Computer simulation of the metabolic consequences of the combined deficiency of 6-phosphogluconolactonase and glucose-6-phosphate dehydrogenase in human erythrocytes.

Computer simulation of the human erythrocyte hexose monophosphate shunt was used to investigate whether the severity of hemolysis, caused by deficiency of glucose-6-phosphate dehydrogenase, could be influenced by an accompanying deficiency of 6-phosphogluconolactonase. The known kinetics of the enzymes involved in the oxidative part of the hexose monophosphate shunt suggest that partial deficiency of 6-phosphogluconolactonase would not restrict the rate of reduced nicotinamide-adenine dinucleotide phosphate production significantly. It is therefore concluded that the metabolic consequences of a combined deficiency of the two enzymes are unlikely to be responsible for the interpatient variability of the hematologic response to deficiency of glucose-6-phosphate dehydrogenase.

Carboxylic Ester Hydrolases↗
PubMedDate not supplied

Computer simulation study of Siemens star x-ray image artifacts.

In the Siemens star image, exact determination of the first disappearance frequency, which is used to measure the focal spot size, is difficult since the disappearance band has a finite width and the image also has other artifacts. The origin of these artifacts and their appearance was studied by Siemens star image simulation on a digital computer. The simulated images were manipulated by using many different modulation and phase transfer functions. It is shown that the bending of spokes is not related to zero contrast; exact triplet splitting can occur only at the disappearance frequency, and therefore splitting is a valuable indicator of that frequency.

Computers↗
PubMed1990

Computer simulation of the pentose-phosphate pathway and associated metabolism used in conjunction with NMR experimental data from human erythrocytes.

A computer-based model of the metabolism of sugar phosphates by human erythrocytes has been developed to assist in the understanding of the biochemical transformations occurring in the pentose phosphate pathway. These transformations are reflected in the changes, with time, of the relative intensities of the metabolite peaks apparent in 1H, 13C and 31P NMR spectra. The deterministic model consists of 79 reactions interconnected in a defined structure and characterized by 155 rate constants. It also includes 17 different enzymes, 69 enzyme forms, 32 metabolites, and initial value of time and concentration of each of the reactants. The differential equations describing the time-dependence of the concentrations of the reactants are generated and then solved by using the computer program BIOSSIM, which is designed to solve arrays of "stiff" differential equations. We synthesized [1-13C]D-ribose 5-phosphate and used 13C and 31P NMR to monitor its transformation into various intermediates of the pentose phosphate pathway, after the addition of diluted haemolysates which had previously been depleted of nicotinamide- and adenine-nucleotides. The concentrations of several of the reactants were able to be quantified, while other peaks in both the 13C and 31P spectra are yet to be assigned with confidence. There was reasonable qualitative agreement between some aspects of the computer simulation of the proposed metabolic system and the experimental data.

Biotransformation↗
PubMed1988

Computer simulations of nuclear reactions induced by incident protons in the energy range of 100 to 500 MeV in a human body.

Computer simulations of nuclear reactions induced by protons in a human body were carried out in the incident energy range from 100 to 500 MeV. Nuclear reactions by secondary particles produced at primary interactions are included. Nuclides produced by the secondary particles increase smoothly with increasing incident proton energy and they are about 15 and 45% of those produced by the primary protons at 150 and 500 MeV, respectively. The yield of product nuclides by the primary protons is approximately constant in the proton energy range above 150 MeV but drops sharply below 150 MeV.

Computer Simulation↗
PubMed1987

Movements of molluscs by computer simulation.

The movements of two kinds of molluscs (Paludina viviparus and Heliosoma (taphius) Nigricans) (in Argentina Biomphalaria tenagophila) performing feeding activities have been simulated by a digital computer. Successive positions of the organisms were determined by a computer program which was based on Rashevsky's (1973) Principle of Adequate Design.

Animals↗
PubMed1990

Computer simulation (based on a linear-elution-strength approximation) as an aid for optimizing separations by programmed-temperature gas chromatography.

If the dependence of retention on temperature is specified for the various components of a sample in isothermal gas chromatography (GC), it is possible to predict retention, bandwidth, and resolution for programmed-temperature GC separations as a function of experimental conditions. The use of a linear-elution-strength (LES) approximation for isothermal retention allows these predictions to be carried out more easily and conveniently, in turn facilitating rapid simulations with a personal computer. This approach to GC method development appears promising, especially if segmented-temperature programs are used. The LES approximation also provides added insight into how different factors affect separation in programmed-temperature GC.

Chromatography, Gas↗
PubMed1985

Fine structure of wide and narrow vertebrate muscle Z-lines. A proposed model and computer simulation of Z-line architecture.

A model of the structure of vertebrate Z-lines and Z-line analogs is introduced and supported by evidence from electron microscope studies of wide Z-lines (rat and feline soleus, and feline and canine cardiac muscles), narrow Z-lines (guppy, newt and frog skeletal muscles), and Z-rods (from a patient with nemaline myopathy and from cardiac muscles of aged dog). The model is based on a pair of Z-filaments (termed a Z-unit), which are linked near their centers at a 90 degrees angle and form bridges between neighboring antipolar thin (actin) filaments. A square lattice of four Z-filament pairs (the basic structure of the Z-line, termed a Z-line unit) defines the geometrical position of the I-square unit. In this native state of the Z-line, small square and large square net forms appear in cross-section. Other cross-sectional patterns of Z-lines, including basket-weave and diagonal-square net patterns, can be explained by detachment of the Z-filament from the Z-filament binding region within each Z-filament pair due to chemical or physical stress. Dissection of Z-lines and Z-line analogs with calcium-activated neutral protease provides evidence that the width of all wide Z-line structures is determined by the amount of overlap of antipolar thin filaments from adjacent sarcomeres. Longitudinal patterns of narrow and wide Z-lines are shown and described in relation to the model. To test the proposed model, the dynamics of the Z-line unit structure were computer-simulated. An attempt was made to correlate longitudinal (z direction) and cross-sectional (x and y directions) patterns and to determine the amount of movement of thin or Z-filaments that is required to explain the diversity observed in cross-sectional patterns of Z-lines. The computer simulations demonstrated that the structural transitions among the small square, and therefore large square net, as well as basket-weave and diagonal-square net forms seen in cross-sections could be caused by movements of thin filaments less than 10 nm in any direction (x, y or z).(ABSTRACT TRUNCATED AT 400 WORDS)

Actins↗
PubMed1990

Computer simulation of zinc finger motifs from cellular nucleic acid binding protein and their interaction with consensus DNA sequences.

We report here a computer simulation of the three-dimensional structures of seven zinc finger motifs from cellular nucleic acid binding protein involved in negative feedback inhibition of cholesterol biosynthesis. The structures are optimised using steric constraints imposed by tetrahedral coordination of the zinc ion with Cys and His residues, by molecular mechanics technique. We have also optimised the structure of a finger-I with GpT sequence. The model for the interaction of seven fingered protein with single-stranded d(GTGCGGTG) from sterol regulatory element (SRE) is given on the basis of these results. We also propose a scheme for recognition of a multifingered regulatory protein with small single-stranded DNA fragments.

Amino Acid Sequence↗
PubMed1977

Computer-simulated clinical encounter. II. Case flow and program content.

The completed computer-simulated case study provides the student with a written model of all components and steps involved in providing nutritional care to a patient. The completed study provides the instructor with a written record of the student's knowledge, her/his response to the patient's inquiries, and her/his organization of the clinical encounter and patient counseling. It is through this written record that student and instructor can analyze and strengthen the student's clinical skills.

Clinical Competence↗
PubMed1975

Computer simulation of immunochemical interactions.

A computer model for simulation of the interactions between a macromolecular antigen and its corresponding IgG has been developed. The model takes all possible immune complexes into account, and it calculates the most probable immune complex distribution patterns on the basis of basic thermodynamic principles from the valences and initial concentrations of antigen and antibody, respectively, together with an association constant assumed to be common to all mutual interactions. In antigen excess small antigen-rich complexes are predicted. At or near equivalence a rich variety of relatively small complexes is predicted, while in antibody excess complexes of the type AgAbn are found to be the most probable. By further assuming that the precipitate consists of antibody excess complexes, a precipitin curve can be calculated. The agreement between calculated results and experimentally obtained data is found to be good. It is of special interest that this theory implies that the outcome of immunochemical interactions depend equally well on the concentrations of antigen and of antibody.

Animals↗
PubMed1975

Computer simulation of flagellar movement. III. Models incorporating cross-bridge kinetics.

A computer simulation procedure is used to analyze the generation of propagated bending waves by flagellar models in which active sliding is generated by a cycle of cross-bridge activity. Two types of cross-bridge cycle have been examined in detail. In both cycles, cross-bridge attachment is followed immediately by a configurational change in the cross-bridge, which transfers energy to a stretched elastic element and generates a shearing force between the filaments. In the first model, which has cross-bridge behavior close to current ideas about cross-bridge behavior in muscle, cross-bridge attachment is proportional to curvature of the flagellum and detachment is an exponential decay process. The configurational change is equivalent to an angular deviation of pi/5 radians. In the second type of cross-bridge cycle, cross-bridge attachment occurs rapidly when a critical curvature is reached, and detachment occurs when a critical curvature in the opposite direction is reached. With this cycle, an unrealistically large angular deviation of the cross-bridges, equivalent to 3.0 radians, is required to obtain bending waves of normal amplitude. Both models generate bending wave patterns similar to those obtained in earlier work. However, the behavior of the second type of cross-bridge model more closely matches the actual behavior of flagella under experimental conditions: the chemical turnover rate per beat cycle remains constant as the viscosity is increased, and reduction in the number of active cross-bridges can cause a reduction in beat frequency, with little change in amplitude or wavelength.

Binding Sites↗
PubMed1992

[The effects of fear on individual and group escape in a computer simulated maze].

UNLABELLED: The purpose is to compare the effects of fear on escape behavior of individual and group conditions, in a computer-simulated maze. CRT display did not provide a bird's eye view of the maze, to the subjects, but only cues, what they would see, if they were actually inside of the maze. In the group escape condition, bodies and behaviors of other people were also shown in the maze. Subjects often got too close each other and collided with each other. THE RESULTS: Fear increased the time and locomotion required to reach the exit, because of the occurrence of a "traffic jam" in the group escape condition, however, fear reduced time in the individual escape condition. In addition, fear influenced types of escape behavior, depending on the form of maze.

Adult↗