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 1,783 records · Page 99Linked to original sources

PubMed2006

Direct computational simulations and experiments for film condensation inside tubes and channels.

This article presents accurate numerical solutions of the full 2D governing equations for steady and unsteady laminar/laminar internal condensing flows of pure vapor (FC-72 and R-113) inside a vertical tube and a channel. The film condensation is on the inside wall of a tube or one of the walls of a channel (the lower wall in case of a downward sloping channel). Both experiments and simulations find that exit condition specifications are important. The computations are able to predict whether or not a steady flow exists with a well-defined and steady natural exit condition. If well-defined natural steady/quasi-steady flows exist-as is shown to be the case for gravity-dominated or strong shear-dominated condensate flows that remain parabolic up to the exit location-the computations are able to predict both the natural exit condition and any point of transition (from stable to unstable or smooth to wavy behavior) that may exist within this zone. Compared to gravity-driven cases, shear-driven cases (zero gravity or horizontal cases) tend to destabilize easily. It is found that only for gravity-driven cases interfacial waves are able to cause a concurrent enhancement in heat transfer rates along with an enhancement in interfacial shear. Also it is found that this enhancement in interfacial wave energy is significant if the condensing surface noise is in resonance with the intrinsic waves.

Journal Article↗

PubMed1988

Computer simulation of high-performance liquid chromatographic separations of peptide and protein digests for development of size-exclusion, ion-exchange and reversed-phase chromatographic methods.

A computer program, called Pro Digest-LC, has been developed which assists scientists in devising methods of size-exclusion, cation-exchange and reversed-phase high-performance liquid chromatography for the analytical separation and purification of biologically active peptides and peptide fragments from enzymatic and chemical digests of proteins. Pro Digest-LC accurately predicts the retention behaviour of peptides of known composition, containing 2-50 amino acid residues, and simulates the elution profiles in all three modes of chromatography. In addition, Pro Digest-LC is a user-friendly program, designed as a teaching aid for both students and researchers in selecting the correct conditions for chromatography, that is, the mode of chromatography, column selection, mobile-phase selection, and has the ability to examine the effects of flow-rate, gradient-rate, and sample size on the separation. We have designed a set of peptide standards for each mode of chromatography to aid the researcher in eliminating non-specific interactions, to standardize retention behaviour on the user's columns, to monitor column performance and to compare packing materials. In the development of each prediction mode, experimental peak heights, peak widths, and retention times from model synthetic peptide standards were incorporated directly into the program and can be used as default values. Pro Digest-LC is an interactive program, in that researchers can run peptide standards on their particular columns and enter the peak width at half-height, peak height, retention time and quantity injected to adjust the simulation to their particular column. The simulated experiments eliminate the time-consuming trial-and-error methods used to suitable separation or purification procedures. The researcher would perform the actual experiment only after predicting the optimized conditions, thereby saving valuable sample and research time. The general concepts of the program along with representative separations of protein digests are displayed.

Animals↗

PubMed1990

Analysis of the gel electrophoresis of looped protein-DNA complexes by computer simulation.

The theory of mass transport coupled to reversible interactions under chemical kinetic control forms the basis of a numerical model that has been applied to systems such as lac repressor-lac operator DNA, in which a protein binds in two different modes to linear DNA carrying two specific binding sites. Three complexes may be formed: (1) a linear 1:1 complex with one protein molecule bound to one site on the DNA molecule; (2) a 1:1 complex in which a single protein molecule is bound to both sites simultaneously, thereby inducing a large DNA loop; and (3) a 2:1 linear complex in which two protein molecules are bound in tandem, each occupying a single site. The computational model affords a quantitative numerical simulation of the observed gel electrophoretic patterns produced by titration of the DNA with protein and provides new insights into the shape and nature of the patterns. In particular, the patterns may represent unimodal or bimodal reaction zones. Nevertheless, analysis of the peaks in the patterns obtained at low DNA and high protein concentration provides essential information as to the stoichiometry of the complexes and satisfactory estimates of association constants. The theory thus provides the experimenter with guidelines for quantitative evaluation of the results of gel retardation assays of the particular system under investigation, once protein-induced DNA (or RNA) loops have been established by independent physical or chemical methods. It is suggested that these insights might also find application to systems involving the binding of two or three different proteins to DNA with loop formation.

Binding Sites↗

PubMed1983

Computer simulation of metabolism in palmitate-perfused rat heart. I. Palmitate oxidation.

A computer model of the fatty acid oxidation pathway in perfused rat heart was constructed. It includes uptake, activation, and beta-oxidation of fatty acids, triglyceride synthesis and hydrolysis, and carnitine-dependent transport of acyl groups across the mitochondrial membrane under pseudosteady state conditions. Fatty acid utilization may be limited by beta-oxidation in hypoxia or ischemia but probably not in aerobic conditions. Nonesterified fatty acids bound to proteins are found to be metabolically available. The model predicts that stearate, but not palmitate, can support the highest observed respiration rate for perfused rat heart without supplementation by other substrates. Fatty acids are preferentially oxidized rather than being stored as triglycerides because the cystosolic acyl CoA level is lower than the Km for triglyceride synthesis. It is suggested that feedback inhibition of triglyceride lipase regulates utilization of triglycerides as fuel in aerobic hearts.

3-Hydroxyacyl CoA Dehydrogenases↗

PubMed1979

Computer simulation of metabolism in pyruvate-perfused rat heart. I. Model construction.

A computer model of energy metabolism was constructed for the pyruvate-perfused rat heart subjected to a sudden increase in work load. The model construction techniques are explained and justified. Hypotheses defining a plausible sequence of physiological events resulting in the observed behavior of the organ were arrived at from the measured metabolite time profiles. There is a lag in increasing pyruvate utilization following the work-jump. A transient increase in fatty acid oxidation is required to account for the observed respiration rate. The observed increase in lactate production of this preparation is due to a transient "burst" of glycogenolysis after which the remaining lactate is imported from the interstitium and oxidized, reversing lactate dehydrogenase and hence the alpha-ketoglutarate-malate portion of the malate-aspartate shuttle.

Animals↗

PubMed1978

Interaction of microtubules and the mechanism of chromosome movement (zipper hypothesis). 3 Theoretical analysis of energy requirements and computer simulation of chromosome movement.

A theoretical analysis of the energy requirements and a computer analysis of a special case (symmetrical pull in one plane during anaphase), of the zipper model for chromosome movement (Bajer, 1973a,b) is presented. The conclusions are general, however, and can be applied to any stage of mitosis. It is assumed that the movement is due to a series of short lateral interactions (called 'zips') between microtubules, and it is shown that a particular zip could begin if the bending energy requirement for two microtubules is met, and could terminate when a strain restriction is exceeded. The series of zips ends when the energy requirements for initiation of a particular zip are not met. In such conditions, certain predictions concerning the behaviour of microtubules in the spindle can be made (see Conclusions). It is shown that hydrolysis of ATP or GTP can yield sufficient energy to bend microtubules as specified by the model, that insignificant quantities of the triphosphate would be utilized, and that the linearity of chromosome movement predicted by the model is consistent with the linearity observed in vitro.

Adenosine Triphosphate↗

PubMed1991

Selectivity of ionic channels: as seen through computer simulation.

A theoretical approach has been attempted to study the selectivity of ionic channels in membranes. We predict the channel to behave as an allosteric enzyme and have different conformational states that can bind strongly or weakly to a particular ion. The kinetic equation derived for the channel has few empirical parameters like the allostery factor, the probability factor, binding affinity factor and the transporting rate factor, the later two giving an idea of the ion-ion interactions and ion-channel interactions. The equation is programmed for an IBM compatible personal computer in MS-FORTRAN and the simulation data has been analysed to explain selectivity of the channels to particular ion. The simulation results show that the ions smaller than the permeable ions tend to act as inhibitors, the amplitude depending on the concentrations of the ions and comparative transport rate of the ion in the channel. The program helps easy study of the different parameters on the conducting rate of the permeable ion through the channel which otherwise would demand intricate experimental set-ups.

Computer Simulation↗

PubMed2004

Computer simulations of localized small polarons in amorphous polyethylene.

We use a simple mean field scheme to compute the polarization energy of an excess electron in amorphous polyethylene that allows us to study dynamical properties. Nonadiabatic simulations of an excess electron in amorphous polyethylene at room temperature show the spontaneous formation of localized small polaron states in which the electron is confined in a spherically shaped region with a typical dimension of 5 A. We compute the self-trapping energy to be -0.06+/-0.03 eV, with a lifetime on the time scale of a few tens of picoseconds.

Journal Article↗

PubMed1985

Computer simulation of dual chamber pacemaker algorithms using a realistic heart model.

Single and dual chamber pacing algorithms have been incorporated into a realistic computer model of cardiac electrical activation. The model enables different pacemaker algorithms to be tested, it allows prediction of their behavior, and it produces a simulated ECG record for each case. The computer model has been used to test eight different modifications of a simple DDD mode to prevent or terminate pacemaker-mediated "endless loop" tachycardia: (1) constant prolongation of the atrial channel refractory period; (2) prolongation of the atrial refractory period after a ventricular premature beat (VPB); (3) atrial pacing synchronously with a VPB; (4) simple rate control; (5) rate control in which the VA counter is not reset; (6) no ventricular pacing after an atrial premature beat; (7) rate limitation of atrial sensing; and (8) a combination of DDD and high frequency atrial stimulation modes. These modifications were tested with VPBs, atrial premature beats, atrial stimulation without capture, and accelerating sinus tachycardia. Only the pacemaker designed not to pace the ventricles following an atrial premature beat behaves satisfactorily in all four circumstances. Further possibilities for the development and use of a pacemaker-oriented computer heart model are discussed.

Computers↗

PubMed1998

Computer simulation of post-spike facilitation in spike-triggered averages of rectified EMG.

When the spikes of a motor cortical cell are used to compile a spike-triggered average (STA) of rectified electromyographic (EMG) activity, a post-spike facilitation (PSF) is sometimes seen. This is generally thought to be indicative of direct corticomotoneuronal (CM) connections. However, it has been claimed that a PSF could be caused by synchronization between CM and non-CM cells. This study investigates the generation of PSF using a computer model. A population of cortical cells was simulated, some of which made CM connections to a pool of 103 motoneurons. Motoneurons were simulated using a biophysically realistic model. A subpopulation of the cortical cells was synchronized together. After a motoneuron discharge, a motor unit action potential was generated; these were summed to produce an EMG output. Realistic values were used for the corticospinal and peripheral nerve conduction velocity distribution, for slowing of impulse conduction in CM terminal axons, and for the amount of cortical synchrony. STA of the rectified EMG from all cortical neurons showed PSF; however, these were qualitatively different for CM versus non-CM cells. Using an epoch analysis to determine reliability in a quantitative manner, it was shown that the onset latency of PSF did not distinguish the two classes of cells after 10,000 spikes because of high noise in the averages. The time of the PSF peak and the peak width at half-maximum (PWHM) could separate CM from synchrony effects. However, only PWHM was robust against changes in motor unit action-potential shape and duration and against changes in the width of cortical synchrony. The amplitude of PSF from a CM cell could be doubled by the presence of synchrony. It is proposed that, if a PSF has PWHM < 7 ms, this reliably indicates that the trigger is a CM cell projecting to the muscle whose EMG is averaged. In an analysis of experimental data where macaque motor cortical cells facilitated hand and forearm muscle EMG, 74% of PSFs fulfilled this criterion. The PWHM criterion could be applied to other STA studies in which it is important to exclude the effects of synchrony.

Action Potentials↗

PubMed2004

Estimating use-dependent synaptic gain in autonomic ganglia by computational simulation and dynamic-clamp analysis.

Biological gain mechanisms regulate the sensitivity and dynamics of signaling pathways at the systemic, cellular, and molecular levels. In the sympathetic nervous system, gain in sensory-motor feedback loops is essential for homeostatic regulation of blood pressure and body temperature. This study shows how synaptic convergence and plasticity can interact to generate synaptic gain in autonomic ganglia and thereby enhance homeostatic control. Using a conductance-based computational model of an idealized sympathetic neuron, we simulated the postganglionic response to noisy patterns of presynaptic activity and found that a threefold amplification in postsynaptic spike output can arise in ganglia, depending on the number and strength of nicotinic synapses, the presynaptic firing rate, the extent of presynaptic facilitation, and the expression of muscarinic and peptidergic excitation. The simulations also showed that postsynaptic refractory periods serve to limit synaptic gain and alter postsynaptic spike timing. Synaptic gain was measured by stimulating dissociated bullfrog sympathetic neurons with 1-10 virtual synapses using a dynamic clamp. As in simulations, the threshold synaptic conductance for nicotinic excitation of firing was typically 10-15 nS, and synaptic gain increased with higher levels of nicotinic convergence. Unlike the model, gain in neurons sometimes declined during stimulation. This postsynaptic effect was partially blocked by 10 microM Cd2+, which inhibits voltage-dependent calcium currents. These results support a general model in which the circuit variations observed in parasympathetic and sympathetic ganglia, as well as other neural relays, can enable functional subsets of neurons to behave either as 1:1 relays, variable amplifiers, or switches.

Animals↗

PubMed1983

Computer simulations of learning in neural systems.

Recent experiments have shown that, in some cases, strengths of synaptic ties are being modified in learning. However, it is not known what the rules that control those modifications are, especially what determines which synapses will be modified and which will remain unchanged during a learning episode. Two postulated rules that may solve that problem are introduced. To check their effectiveness, the rules are tested in many computer models that simulate learning in neural systems. The simulations demonstrate that, theoretically, the two postulated rules are effective in organizing the synaptic changes. If they are found to also exist in biological systems, these postulated rules may be an important element in the learning process.

Animals↗

PubMed2004

Computer simulation of a liquid-crystal anchoring transition.

We present a study of the effects of confinement on a system of hard Gaussian overlap particles interacting with planar substrates through the hard-needle-wall potential. Using geometrical arguments to calculate the molecular volume absorbed at the substrates, we show that both planar and homeotropic arrangements can be obtained using this model. Monte Carlo simulations are then used to perform a systematic study of the model's behavior as a function of the system density and the hard-needle-wall interaction parameter. As well as showing the homeotropic to planar anchoring transition, the anchoring phase diagrams computed from these simulations indicate regions of bistability. This bistable behavior is examined further through the explicit simulation of field-induced two-way switching between the two arrangements.

Journal Article↗

PubMed1997

Computer simulation of the enteric neural circuits mediating an ascending reflex: roles of fast and slow excitatory outputs of sensory neurons.

Recent electrophysiological studies of the properties of intestinal reflexes and the neurons that mediate them indicate that the intrinsic sensory neurons may transmit to second order neurons via either fast (30-50 ms duration) or slow (10-60 s duration) excitatory synaptic potentials or both. Which of these possible modes of transmission is involved in the initiation of motility reflexes has not been determined and it is not clear and what the consequences of the different forms of synaptic transmission would be for the properties of the reflex pathways. In the present study, this question has been addressed by the use off a suite of computer programs, Plexus, which was written to simulate the activity of the neurons of the enteric nervous system during intestinal reflexes. The programs construct a simulated enteric nerve circuit based on anatomical and physiological data about the number, functions and interconnections of neurons involved in the control of motility. The membrane potentials of neurons are calculated individually from physiological data about the reversal potentials and membrane conductances for Na+, K+ and Cl-. Synaptic potentials are simulated by changes in specific conductances based on physiological data. The results of each simulation are monitored by recording the membrane potentials of up to 16 separate defined neurons and by recording the summed activity of whole classes of neurons as a function of time and location in the stimulated network. The present series of experiments simulated the behaviour of a network consisting of 18,898 sensory neurons and 3708 ascending interneurons after 75% of the sensory neurons lying in the anal 10 mm of a 30 mm long segment of small intestine were stimulated once. The results were compared with electrophysiological data recorded from myenteric neurons during ascending reflexes evoked either by distension or mechanical stimulation of the mucosa. When transmission from sensory neurons to ascending interneurons was via fast excitatory synaptic potentials, the latencies and durations of the simulated responses were too brief to match the electrophysiologically recorded responses. When transmission from sensory neurons was via slow excitatory synaptic potentials, the latencies were very similar to those recorded physiologically, but the durations of the stimulated responses were much longer than seen in physiological experiments. The latencies and durations of simulated and physiologically recorded responses matched only when the firing of ascending interneurons was limited to the beginning of a slow excitatory synaptic (in this study by limiting the duration of the decrease in K+ conductance). The simulation provided several physiologically testable predictions, indicating that Plexus is an important tool for the investigation of the properties and behaviour of the enteric nervous system.

Computer Simulation↗

PubMed2004

Computational simulations of airflow in an in vitro model of the pediatric upper airways.

In order to understand mechanisms of gas and aerosol transport in the human respiratory system airflow in the upper airways of a pediatric subject (male aged 5) was calculated using Computational Fluid Dynamic techniques. An in vitro reconstruction of the subject's anatomy was produced from MRI images. Flow fields were solved for steady inhalation at 6.4 and 8 LPM. For validation of the numerical solution, airflow in an adult cadaver based trachea was solved using identical numerical methods. Comparisons were made between experimental results and computational data of the adult model to determine solution validity. It was found that numerical simulations can provide an accurate representation of axial velocities and turbulence intensity. Data on flow resistance, axial velocities, secondary velocity vectors, and turbulent kinetic energy are presented for the pediatric case. Turbulent kinetic energy and axial velocities were heavily dependant on flow rate, whereas turbulence intensity varied less over the flow rates studied. The laryngeal jet from an adult model was compared to the laryngeal jet in the pediatric model based on Tracheal Reynolds number. The pediatric case indicated that children show axial velocities in the laryngeal jet comparable to adults, who have much higher tracheal Reynolds numbers than children due to larger characteristic dimensions. The intensity of turbulence follows a similar trend, with higher turbulent kinetic energy levels in the pediatric model than would be expected from measurements in adults at similar tracheal Reynolds numbers. There was reasonable agreement between the location of flow structures between adults and children, suggesting that an unknown length scale correlation factor could exist that would produce acceptable predictions of pediatric velocimetry based off of adult data sets. A combined scale for turbulent intensity as well may not exist due to the complex nature of turbulence production and dissipation.

Air↗

PubMedDate not supplied

Computational simulation of platelet deposition and activation: I. Model development and properties.

To better understand the mechanisms leading to the formation and growth of mural thrombi on biomaterials, we have developed a two-dimensional computational model of platelet deposition and activation in flowing blood. The basic formulation is derived from prior work by others, with additional levels of complexity added where appropriate. It is comprised of a series of convection-diffusion-reaction equations which simulate platelet-surface and platelet-platelet adhesion, platelet activation by a weighted linear combination of agonist concentrations, agonist release and synthesis by activated platelets, platelet-phospholipid-dependent thrombin generation, and thrombin inhibition by heparin. The model requires estimation of four parameters to fit it to experimental data: shear-dependent platelet diffusivity and resting and activated platelet-surface and platelet-platelet reaction rate constants. The model is formulated to simulate a wide range of biomaterials and complex flows. In this article we present the basic model and its properties; in Part II (Sorensen et al., Ann. Biomed. Eng. 27:449-458, 1999) we apply the model to experimental results for platelet deposition onto collagen.

Antithrombin III↗

PubMed1989

Computer simulation of the neural discharge carried by the abducens nerve during eye fixation in the cat.

The neural signal carried by the abducens nerve during eye fixations was simulated. The neural discharge was defined by the number of spikes carried by the abducens nerve within each ms. Calculations were based on real neurophysiological data. The computed neural signal showed frequency histograms and variance/mean ratios typical of a Poisson distribution. A peak was obtained in the power spectral density function of the simulated neural signal. This peak appeared in the frequency range corresponding to the firing rate of single motoneurons for each eye position. It remained as a broad spectral peak after filtering by a second-order differential equation simulating the ocular mechanics. The obtained spectra are similar to the described power spectral density function of eye position recordings. Present results add evidence of a possible neural basis for ocular tremor.

Abducens Nerve↗

PubMed1999

How many myeloid post-progenitor cells have to be transplanted to completely abrogate neutropenia after peripheral blood progenitor cell transplantation? Results of a computer simulation.

Although hematopoietic recovery following high-dose chemotherapy (HD-CT) and peripheral blood progenitor cell (PBPC) transplantation is rapid, there is still a 5- to 7-day period of severe neutropenia which, theoretically, might be abrogated by an additional transplantation of more differentiated myeloid post-progenitor cells (MPPC). However, both the number of MPPC required to abrogate neutropenia as well as the optimum scheduling of MPPC infusions are currently unknown. Therefore, these questions were addressed by applying a computer model of human granulopoiesis. First, model calculations simulating varying levels of chemotherapy dose intensity were performed and compared with typical clinical neutrophil recovery curves. Using this approach, the data for HD-CT without PBPC transplantation could be reproduced by assuming a reduction of stem cells, committed granulopoietic progenitors and proliferating precursors to about 0.001% of normal. PBPC-supported HD-CT was reproduced by increasing the starting values to at least 0.1%, which corresponded to about 1 to 2 x 10(5)/kg transplanted CFU-GM. Interestingly, reproduction of PBPC-supported HD-CT data could be observed for a wide range of starting values (0.1%-10% of normal), thus confirming the clinical observation that hematopoietic recovery after PBPCT cannot be improved by increasing the dose of transplanted cells over a certain threshold. Using the same simulation model, we then studied the effects of an additional MPPC transplantation. The results showed, that at least 5.7 X 10(8) MPPC/kg have to be provided in addition to the normal PBPC graft to avoid neutropenia <100/microL, and that MPPC are best transplanted on days 0 and 6 after HD-CT. Assuming a 100- to 120-fold cellular ex-vivo expansion rate and MPPC representing about 70% of total expanded cells, 5.7 X 10(8) MPPC/kg could be generated starting from 1 to 2 leukapheresis preparations with about 7 to 8 x 10(6) CD34+ PBPC/kg. Considering furthermore, that only a fraction of ex-vivo generated cells will seed and effectively produce neutrophils in-vivo, the required number of MPPC is most likely even higher and, therefore, might be difficult to be achieved clinically. However, the validity of the model results remains to be proven in appropriate clinical studies.

Antineoplastic Combined Chemotherapy Protocols↗