Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Computer Simulation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 253 records · Page 14Linked to original sources
PubMed2006

Computer simulations of transport through membranes: passive diffusion, pores, channels and transporters.

A key function of biological membranes is to provide mechanisms for the controlled transport of ions, nutrients, metabolites, peptides and proteins between a cell and its environment. We are using computer simulations to study several processes involved in transport. In model membranes, the distribution of small molecules can be accurately calculated; we are making progress towards understanding the factors that determine the partitioning behaviour in the inhomogeneous lipid environment, with implications for drug distribution, membrane protein folding and the energetics of voltage gating. Lipid bilayers can be simulated at a scale that is sufficiently large to study significant defects, such as those caused by electroporation. Computer simulations of complex membrane proteins, such as potassium channels and ATP-binding cassette (ABC) transporters, can give detailed information about the atomistic dynamics that form the basis of ion transport, selectivity, conformational change and the molecular mechanism of ATP-driven transport. This is illustrated in the present review with recent simulation studies of the voltage-gated potassium channel KvAP and the ABC transporter BtuCD.

ATP-Binding Cassette Transporters↗
PubMed1983

Acinar heterogeneity in hepatic transport of dibromosulfophthalein and ouabain studied by autoradiography, normal and retrograde perfusions and computer simulation.

This study is aimed to investigate the relative involvement of periportal (zone 1) and perivenous (zone 3) hepatocytes in the uptake and biliary excretion of the organic anion dibromosulfophthalein (DBSP) and the uncharged cardiac-glycoside ouabain. The localization in the acinus of [35S]BSP (sulfobromophthalein, the tetra-bromo-analogue of DBSP) and [3H]ouabain administered to livers perfused with normal and retrograde flow, was detected by autoradiography. The plasma disappearance and biliary excretion rates of DBSP and [3H]ouabain were determined in normal and retrograde perfusions. In addition, computer simulations were performed to predict the effect of reversal of the perfusate flow on the plasma disappearance and biliary excretion rate curves and on the concentration of label in zones 1 and 3. Autoradiography showed that 2 and 10 min after injection of [35S]BSP to normally and retrogradely perfused livers, the label was uniformly distributed in the liver acinus. The same results were found 30 sec and 10 min after injection of [3H]ouabain to normally and retrogradely perfused livers. The plasma disappearance and biliary excretion rate of DBSP were slightly faster in retrograde perfusions compared to normal perfusions both with and without a basal bile salt infusion of 15 mumole/hr. This could not be explained by an acinar heterogeneity with respect to any of the DBSP transport steps (plasma to liver, liver to plasma, liver to bile) as was shown by computer simulations. The plasma disappearance and biliary excretion rate of ouabain were similar in normal and retrograde perfusions. It is concluded that periportal and perivenous hepatocytes are equally involved in the uptake of (D)BSP and ouabain from the medium. However, due to the particular distribution patterns no conclusions can be drawn from normal and retrograde perfusions about the relative involvement of these cells in biliary excretion, as was shown by computer simulation. The unaffected kinetic behaviour of the retrogradely perfused livers indicated that no liver damage occurs during retrograde perfusion with respect to transport function.

Animals↗
PubMed2004

XSophe-Sophe-XeprView. A computer simulation software suite (v. 1.1.3) for the analysis of continuous wave EPR spectra.

The XSophe-Sophe-XeprView computer simulation software suite enables scientists to easily determine spin Hamiltonian parameters from isotropic, randomly oriented and single crystal continuous wave electron paramagnetic resonance (CW EPR) spectra from radicals and isolated paramagnetic metal ion centers or clusters found in metalloproteins, chemical systems and materials science. XSophe provides an X-windows graphical user interface to the Sophe programme and allows: creation of multiple input files, local and remote execution of Sophe, the display of sophelog (output from Sophe) and input parameters/files. Sophe is a sophisticated computer simulation software programme employing a number of innovative technologies including; the Sydney OPera HousE (SOPHE) partition and interpolation schemes, a field segmentation algorithm, the mosaic misorientation linewidth model, parallelization and spectral optimisation. In conjunction with the SOPHE partition scheme and the field segmentation algorithm, the SOPHE interpolation scheme and the mosaic misorientation linewidth model greatly increase the speed of simulations for most spin systems. Employing brute force matrix diagonalization in the simulation of an EPR spectrum from a high spin Cr(III) complex with the spin Hamiltonian parameters g(e) = 2.00, D=0.10 cm(-1), E/D = 0.25, A(x) = 120.0, A(y) = 120.0, A(z) = 240.0 x 10 (-4) cm(-1) requires a SOPHE grid size of N = 400 (to produce a good signal to noise ratio) and takes 229.47 s. In contrast the use of either the SOPHE interpolation scheme or the mosaic misorientation linewidth model requires a SOPHE grid size of only N = 18 and takes 44.08 and 0.79 s, respectively. Results from Sophe are transferred via the Common Object Request Broker Architecture (CORBA) to XSophe and subsequently to XeprView where the simulated CW EPR spectra (1D and 2D) can be compared to the experimental spectra. Energy level diagrams, transition roadmaps and transition surfaces aid the interpretation of complicated randomly oriented CW EPR spectra and can be viewed with a web browser and an OpenInventor scene graph viewer.

Journal Article↗
PubMedDate not supplied

Sucrose gradient analysis: computer simulation and measurement of the parameters involved in the sedimentation of DNA molecules.

The Montecarlo method is used to computer simulate a random distribution of molecular lengths generated by inducing T4 DNA fragmentation through the decay of 32P atoms introduced in the molecule. Taking into account the experimental conditions we find that the value of alpha for alkali sucrose gradients is 0.46 +/- 0.02 and does not depend on the running time. Our findings also prove that the computer simulation can be utilized to analyze sedimentation profiles of DNA molecules fragmented in vivo.

Centrifugation, Density Gradient↗
PubMed1993

Computer simulation of normal and pathological copper metabolism in man.

A digital computer simulation of copper metabolism was used to simulate human copper metabolism. The simulation agrees well with the normal data extant. Wilson's disease (hepatolenticular degeneration) and Menkes' disease (steely-hair syndrome) were simulated. Simulation of the unavailability of accumulated liver copper simulated Wilson's disease if it was assumed that the increased urinary excretion was due to induction of an enzymic mechanism for enhanced excretion. This would be consistent with the genetic defect causing only the sequestering of unavailable copper in the liver. Other genetic defects need not be present. Menkes' disease is also a genetic disease affecting the newborn. It was simulated successfully as a defect in absorption of copper from the gastrointestinal tract.

Adult↗
PubMed1996

Experimental basis for realistic large-scale computer simulation of the enteric nervous system.

1. The enteric nervous system is perhaps the most accessible part of the mammalian nervous system in which it is feasible to attempt large scale computer simulation that is based closely on experimentally determined data. Here we summarize the data obtained for simulation of motility reflexes in the guinea-pig small intestine. 2. The chemistry, morphology and connectivity of each type of neuron involved in intrinsic reflexes have been investigated and most classes of neurons are physiologically well characterized. This includes primary sensory neurons, ascending and descending interneurons and motor neurons to circular and longitudinal muscle. 3. The responses of primary sensory neurons and the physiology of synaptic transmission from sensory neurons to interneurons and motor neurons, from interneurons to interneurons and from interneurons to motor neurons have been recorded during reflexes and in some cases the pharmacology of transmission has also been investigated. 4. Computer simulation, in which the activities of up to 30,000 neurons are modelled, produces patterns of activity that closely mimic those recorded in physiological experiments.

Animals↗
PubMed2001

Computer simulations of electrorheological fluids in the dipole-induced dipole model.

We have employed the multiple image method to compute the interparticle force for a polydisperse electrorheological (ER) fluid in which the suspended particles can have various sizes and different permittivities. The point-dipole (PD) approximation, being routinely adopted in the computer simulation of ER fluids, is known to err considerably when the particles approach and finally touch due to multipolar interactions. The PD approximation becomes even worse when the dielectric contrast between the particles and the host medium is large. From the results, we show that the dipole-induced-dipole (DID) model yields very good agreements with the multiple image results for a wide range of dielectric contrasts and polydispersity. As an illustration, we have employed the DID model to simulate the athermal aggregation of particles in ER fluids, both in uniaxial and rotating fields. We find that the aggregation time is significantly reduced. The DID model partially accounts for the multipolar interaction and is simple to use in the computer simulation of ER fluids.

Journal Article↗
PubMed2002

Evaluation of protective shielding thickness for diagnostic radiology rooms: theory and computer simulation.

This work presents the development and evaluation using modern techniques to calculate radiation protection barriers in clinical radiographic facilities. Our methodology uses realistic primary and scattered spectra. The primary spectra were computer simulated using a waveform generalization and a semiempirical model (the Tucker-Barnes-Chakraborty model). The scattered spectra were obtained from published data. An analytical function was used to produce attenuation curves from polychromatic radiation for specified kVp, waveform, and filtration. The results of this analytical function are given in ambient dose equivalent units. The attenuation curves were obtained by application of Archer's model to computer simulation data. The parameters for the best fit to the model using primary and secondary radiation data from different radiographic procedures were determined. They resulted in an optimized model for shielding calculation for any radiographic room. The shielding costs were about 50% lower than those calculated using the traditional method based on Report No. 49 of the National Council on Radiation Protection and Measurements.

Calibration↗
PubMed1978

Computer simulation of Gumboro disease outbreak. II. Results obtained with models G-1 and G-2.

The authors conducted a computer simulation with their Models G-1 and G-2 for Gumboro disease ten times in each of the following initial conditions: (1) size of population, 50, 100, and 1,000 chickens; (2) age of housing, 1, 7, 14, and 21 days; (3) nine levels of parentally conferred immunity in one-day-old chicks; (4) four levels of virus contamination; and (5) three steps of coefficient for aggravating morbid status. Every simulation was operated up to the age when all the birds of a flock turned to be insusceptible so as to yield the daily numbers of chickens (1) susceptible, (2) diseased, (3) immunized, and (4) removed, and (5) the accumulation of diseased chickens. The innate resistance, parentally conferred immunity, virus contamination, and morbid status were expressed in such values that they could be compared with one another. As a result, Model G-2 produced a more realistic epizootic pattern than Model G-1, but both models concealed the effect of differences in size of population and in age of housing. Notwithstanding the incompleteness of the models, the computer simulation gave valuable information for a further advancement in this series of studies.

Animals↗
PubMed1999

Determination of optimal data placement for psychometric function estimation: a computer simulation.

Psychometric functions are used to relate the responses of a subject to physical stimuli in a variety of psychophysical tasks. However, it is time consuming to obtain data to determine a psychometric function if many stimulus levels and many trials are required. A computer simulation was conducted to determine the minimum number of data points needed for such a determination. The computer simulation also determined the optimal placements of the stimuli and the number of trials per datum point for psychometric function determinations. Results indicate that a 2-point sampling method with 30-50 trials per point at optimal locations can produce a psychometric function with accurate spread and threshold estimates in a yes-no paradigm. However, the 4-point sampling method yields statistically smaller variances of the estimates. For the 2-alternative forced-choice paradigm, at least 120 trials per point are needed for the 2-point sampling method's estimated parameters to differ from the known parameter values by less than 5%. The simulation results suggest that 3-alternative or 4-alternative forced-choice is preferable to 2-alternative. Furthermore, when a criterion-free paradigm is not required, the yes-no paradigm is a better procedure than m-alternative forced-choice for obtaining the corresponding psychometric function because of smaller standard deviation of the estimates and smaller number of trials/point required.

Computer Simulation↗
PubMedDate not supplied

Cytoskeletal mechanics of neurulation: insights obtained from computer simulations.

The morphogenetic movements associated with the process of neurulation have been the subject of much investigation during the last one hundred years. A plethora of experimental evidence has been generated regarding the forces that drive this seemingly simple process, and many theories about the mechanics of the process have been proposed. Recent computer simulations have proved useful for evaluating these theories from a mechanical perspective. In this work, computer simulations are used to investigate several theories about the forces that drive neurulation. A simplified version of a formulation previously presented by the authors provides the mathematical foundation for these simulations. The simulations confirm that forces generated by circumferential microfilament bundles (CMB's) in conjunction with notochord forces can produce the rolling motions characteristic of amphibian neurulation. They also support the notion that redundancies exist in the systems of forces available to drive neurulation shape changes. The shape changes that occur following a variety of surgical and teratogenic interventions are also simulated. These simulations corroborate the role of circumferential microfilament bundles as a primary force generator.

Computer Simulation↗
PubMed1987

Optical diffraction intensity of computer-simulated muscle fibers.

A computer program which calculates the Fraunhofer diffraction intensity of a simulated skeletal muscle fiber is described. The intensity calculation contains several adjustable parameters. Some of the parameters are related to the myofibrillar arrangement within the muscle fiber and the angle of incident light. The variations of the left and right first-order diffraction intensities with different incident angles are determined. Their profiles exhibit features related to Bragg reflections from planes formed by the myofibrils. The calculations provide the relationship between the observed intensity profile and the myofibrillar arrangement in a real muscle fiber.

Animals↗
PubMed1999

Computer simulation of spacecraft/environment interaction.

This report presents some examples of a computer simulation of spacecraft interaction with space environment. We analysed a set data on electron and ion fluxes measured in 1991 1994 on geostationary satellite GORIZONT-35. The influence of spacecraft eclipse and device eclipse by solar-cell panel on spacecraft charging was investigated. A simple method was developed for an estimation of spacecraft potentials in LEO. Effects of various particle flux impact and spacecraft orientation are discussed. A computer engineering model for a calculation of space radiation is presented. This model is used as a client/server model with WWW interface, including spacecraft model description and results representation based on the virtual reality markup language.

Computer Simulation↗
PubMed1991

Computer simulation of blood flow patterns in arteries of various geometries.

The purpose of this study is to illustrate the application of computer simulation to the study of blood flow through arteries and to demonstrate the relationship between geometry of the vessels and local flow patterns. A finite element computer program was developed to simulate steady and pulsatile blood flow by solving the continuity and Navier-Stokes equations. The accuracy of the computational method has been confirmed by comparing the numeric results to analytic solutions and to published experimental data from physical models. The results are presented as plots of the velocity vectors, streamlines, and pressure contours. The computational model has been applied to illustrate flow patterns in the following situations: pulsatile flow in a cylindric artery and an artery with an axisymmetric stenosis, steady flow in cylindric arteries with stenoses of varying severity and with different flow rates, steady flow in an artery containing a fusiform aneurysm, steady flow in a two-dimensional model of a symmetric Y-shaped bifurcation, and steady flow in a two-dimensional model of the carotid bifurcation. Regions that are commonly associated with arterial disease often coincide with zones of reversed or stagnant flow. In conclusion, the versatility and feasibility of computational simulation of blood flow is illustrated by this study. Although this mathematic model is a simplification of the real flow phenomena, it yields results that provide useful insights into the understanding of local blood flow patterns for a variety of complex geometries.

Aneurysm↗
PubMed2002

Benzimidazole derivatives. 3. 3D-QSAR/CoMFA model and computational simulation for the recognition of 5-HT(4) receptor antagonists.

A three-dimensional quantitative structure-affinity relationship study (3D-QSAR), using the comparative molecular field analysis (CoMFA) method, and subsequent computational simulation of ligand recognition have been successfully applied to explain the binding affinities for the 5-HT(4) receptor (5-HT(4)R) of a series of benzimidazole-4-carboxamides and carboxylates derivatives 1-24. The K(i) values of these compounds are in the range from 0.11 to 10 000 nM. The derived 3D-QSAR model shows high predictive ability (q(2) = 0.789 and r(2) = 0.997). Steric (contribution of 43.5%) and electrostatic (50.3%) fields and solvation energy (6.1%) of this novel class of 5-HT(4)R antagonists are relevant descriptors for structure-activity relationships. Computational simulation of the complexes between the benzimidazole-4-carboxamide UCM-21195 (5) and the carboxylate UCM-26995 (21) and a 3D model of the transmembrane domain of the 5-HT(4)R, constructed using the reported crystal structure of rhodopsin, have allowed us to define the molecular details of the ligand-receptor interaction that includes (i) the ionic interaction between the NH group of the protonated piperidine of the ligand and the carboxylate group of Asp(3.32), (ii) the hydrogen bond between the carbonyl oxygen of the ligand and the hydroxyl group of Ser(5.43), (iii) the hydrogen bond between the NH group of Asn(6.55) and the aromatic ring of carboxamides or the ether oxygen of carboxylates, (iv) the interaction of the electron-rich clouds of the aromatic ring of Phe(6.51) and the electron-poor hydrogens of the carbon atoms adjacent to the protonated piperidine nitrogen of the ligand, and (v) the pi-sigma stacking interaction between the benzimidazole system of the ligand and the benzene ring of Tyr(5.38). Moreover, the noticeable increase in potency at the 5-HT(4)R sites, by the introduction of a chloro or bromo atom at the 6-position of the aromatic ring, is attributed to the additional electrostatic and van der Waals interaction of the halogen atom in a small cavity located between transmembrane domains 5 and 6.

Animals↗
PubMed2002

Interactive computer simulations of knee-replacement surgery.

OBJECTIVE: Current surgical training programs in the United States are based on an apprenticeship model. This model is outdated because it does not provide conceptual scaffolding, promote collaborative learning, or offer constructive reinforcement. Our objective was to create a more useful approach by preparing students and residents for operative cases using interactive computer simulations of surgery. Total-knee-replacement surgery (TKR) is an ideal procedure to model on the computer because there is a systematic protocol for the procedure. Also, this protocol is difficult to learn by the apprenticeship model because of the multiple instruments that must be used in a specific order. We designed an interactive computer tutorial to teach medical students and residents how to perform knee-replacement surgery. We also aimed to reinforce the specific protocol of the operative procedure. Our final goal was to provide immediate, constructive feedback. DESCRIPTION: We created a computer tutorial by generating three-dimensional wire-frame models of the surgical instruments. Next, we applied a surface to the wire-frame models using three-dimensional modeling. Finally, the three-dimensional models were animated to simulate the motions of an actual TKR. The tutorial is a step-by-step tutorial that teaches and tests the correct sequence of steps in a TKR. The student or resident must select the correct instruments in the correct order. The learner is encouraged to learn the stepwise surgical protocol through repetitive use of the computer simulation. Constructive feedback is acquired through a grading system, which rates the student's or resident's ability to perform the task in the correct order. The grading system also accounts for the time required to perform the simulated procedure. We evaluated the efficacy of this teaching technique by testing medical students who learned by the computer simulation and those who learned by reading the surgical protocol manual. Both groups then performed TKR on manufactured bone models using real instruments. Their technique was graded with the standard protocol. The students who learned on the computer simulation performed the task in a shorter time and with fewer errors than the control group. They were also more engaged in the learning process. DISCUSSION: Surgical training programs generally lack a consistent approach to preoperative education related to surgical procedures. This interactive computer tutorial has allowed us to make a quantum leap in medical student and resident teaching in our orthopedic department because the students actually participate in the entire process. Our technique provides a linear, sequential method of skill acquisition and direct feedback, which is ideally suited for learning stepwise surgical protocols. Since our initial evaluation has shown the efficacy of this program, we have implemented this teaching tool into our orthopedic curriculum. Our plans for future work with this simulator include modeling procedures involving other anatomic areas of interest, such as the hip and shoulder.

Arthroplasty, Replacement, Knee↗
PubMed2002

Computer simulation studies of model biological membranes.

This Account is focused on computer simulation studies of model biological membrane systems with potential applications in biomedical research. In the past decade, classical molecular dynamics has provided novel insights into the properties of model biomembrane systems, including the nature of the DNA-lipid interactions, the effect of pore-forming transmembrane peptides on the lipid environment, and the partitioning of volatile anesthetic molecules. Such simulations, employing full atomic detail, are typically restricted to systems of dimensions less than approximately 10 nm. Simplified models of the coarse-grain type have been intended to bridge the gap between full atomistic detail and the mesoscopic (micron) regime. The use of such models is illustrated with the example of anesthetics in a phospholipid bilayer.

Anesthetics↗
PubMed1990

Computational simulation method of intraluminal velocity profile proved by laser Doppler velocimeter.

Measurement of the intraluminal velocity profile within an artery may provide insight into predicting the prognosis of arterial reconstruction. To confirm the results of the computer simulation method a laser Doppler velocimeter using an optical fiber was applied to canine femoral arteries with good or poor runoff, and the intraluminal velocity profile was measured directly. Under normal flow conditions, remarkable fluctuation was obtained at the layer adjacent to the wall, whereas under poor runoff conditions, stagnation of flow was seen at the layer adjacent to the wall. These results showed that our computational simulation method which calculates the intraluminal velocity profile was a reliable, valid method of on-line analysis of the intraluminal velocity profile.

Animals↗