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At least 433 records · Page 24Linked to original sources
PubMed1996

Computer simulations of voltage clamping retinal ganglion cells through whole-cell electrodes in the soma.

1. Computer simulations of voltage-clamp experiments in retinal ganglion cells were implemented to better understand the insights that can be obtained with this physiological approach. 2. Simulation studies of voltage clamping were based on the contemporary approach of using whole-cell recordings with low resistance electrodes attached to the soma. Realistic ganglion cell morphologies were provided by cell staining experiments in the mudpuppy retina; selected cells included small-, medium-, and large-field neurons whose morphologies were entered into a computer through a neuron tracing program. 3. Values for the specific membrane resistance (Rm) varied from 5,000 to 100,000 omega/cm2 to conform to the range of Rm values obtained with intracellular sharp electrodes and whole-cell recordings. 4. Synaptic input currents were simulated by injecting current with and without an underlying conductance change into different regions of the dendritic tree. The time-variant waveform of the current included a combined transient and sustained component similar to the waveform of ON-bipolar activation. 5. Simulations were base on 1) intact structures, which included the soma and the entire dendritic tree, and 2) a more limited cell geometry that included representation of the soma, but only part of the dendritic tree, to represent the restricted morphology that might be rendered after cutting the retina into 150-microns cross sections for retinal slice experiments. 6. The results of this study indicate that voltage clamping from the soma, with optimal, low resistance electrodes and series resistance compensation, provides an error-free voltage clamp for slow signals that are generated within a small electrotonic distance from the soma (approximately 0.1 lambda). 7. The ideal voltage-clamp conditions are optimized when synaptic conductances are small and nonlinear membrane elements are minimally activated: small-field neurons best approximate these conditions, but clamping errors are evident in these cells when more distal branches are activated. The degree of error in voltage clamping was much greater when medium-and large-field neurons were evaluated. 8. It was not possible to clamp action potentials (nonpropagating) even when they were generated near the soma in any of the three model cells examined. 9. Experimental paradigms were developed to demonstrate that inadequate voltage clamping can lead to errors in the interpretation of experimental data when relevant variables are not taken into consideration. Suggestions are made for determining and optimizing favorable clamp conditions.

Action Potentials↗
PubMed1999

Computer simulation of the interaction of non-steroidal anti-inflammatory drugs: indoprofen and NS398 with cyclooxygenase.

We have applied computer simulation technique to study interaction of two anti-inflammatory drugs (NSAIDs) indoprofen and NS398 with cyclooxygenase (COX-1 and COX-2) enzymes. We have also investigated conformational flexibility of the two drugs by systematic search and simulated annealing molecular dynamics (SAMD) methods. Both the drugs were docked in the cyclooxygenase channel using in house docking program IMF1. The complexes were energy minimised by molecular mechanics (MM) method. These were heated for 30 picoseconds (ps), equilibrated for 110 ps at 300K and subjected to 'production simulation' for 110 ps by molecular dynamics (MD) method using Sanderís module of AMBER 5.0 package and united atom force field mostly from PARM96.DAT. Integration was carried out with time step of 0.001 ps, distance dependent di-electric constant with scaling factor 2.0 for 1-4 interaction and cut-off distance for non-bonded pair-list equal to 8A. The non-bonded pair-list was upgraded after every 20 cycles. The coordinate output from MD trajectories is analysed using analysis package of AMBER 5.0, MOLMOL, P-CURVES 3.0 and in house packages: ANALMD, ANALP1. We have observed perturbative changes in COX-1 and COX-2 structures due to indoprofen and NS398. In case of indoprofen specific changes between COX-1 and COX-2 were noted in helix D, H6, S6 and helix H8 in the cyclooxygenase cavity. In case of NS398 these were in helix B in membrane binding domain, helix H6, S8 and S10 in cyclooxygenase cavity and helices H14-H16 in small lobe close to haem binding region. Implications of these results in enzyme selectivity by NSAIDs is discussed here.

Anti-Inflammatory Agents, Non-Steroidal↗
PubMed2006

Evaluation of a prostate biopsy strategy for cancer detection using a computer simulation system with virtual needle biopsy for three-dimensional prostate models.

AIM: We evaluated a prostate biopsy strategy for cancer detection using a computer simulation system with virtual needle biopsy for three-dimensional (3D) prostate models. METHODS: Two 3D prostate models with a volume of 25 cc or 50 cc were constructed from computed tomographic images of radical prostatectomy specimens. The peripheral zone (PZ) and transition zone (TZ) were arranged in the prostate models according to the anatomical information. Four thousand patterns of cancer lesions were automatically inserted into each prostate model with a proportion of 75% in PZ and 25% in TZ. Average hit rates (AHR) in prostate models were evaluated both with an increased number of biopsy cores and various angles of virtual needle biopsy. The influence of adding secondary tumors for hit rates was also evaluated. RESULTS: For both sizes, the laterally angled biopsy in 4-8 core biopsy schemes showed higher AHR than the vertical plane biopsy, while the vertical plane biopsy in 10-18 core biopsy schemes showed higher AHR than the laterally angled biopsy. A higher number of biopsy cores increased the AHR of secondary tumors. CONCLUSIONS: Our results suggest that it is important in prostate cancer detection to change the needle placement according to the number of biopsy cores and the size of the prostate.

Biopsy, Needle↗
PubMed1996

Progress toward chemical accuracy in the computer simulation of condensed phase reactions.

We describe a procedure for the generation of chemically accurate computer-simulation models to study chemical reactions in the condensed phase. The process involves (i) the use of a coupled semiempirical quantum and classical molecular mechanics method to represent solutes and solvent, respectively; (ii) the optimization of semiempirical quantum mechanics (QM) parameters to produce a computationally efficient and chemically accurate QM model; (iii) the calibration of a quantum/classical microsolvation model using ab initio quantum theory; and (iv) the use of statistical mechanical principles and methods to simulate, on massively parallel computers, the thermodynamic properties of chemical reactions in aqueous solution. The utility of this process is demonstrated by the calculation of the enthalpy of reaction in vacuum and free energy change in aqueous solution for a proton transfer involving methanol, methoxide, imidazole, and imidazolium, which are functional groups involved with proton transfers in many biochemical systems. An optimized semiempirical QM model is produced, which results in the calculation of heats of formation of the above chemical species to within 1.0 kcal/mol (1 kcal = 4.18 kJ) of experimental values. The use of the calibrated QM and microsolvation QM/MM (molecular mechanics) models for the simulation of a proton transfer in aqueous solution gives a calculated free energy that is within 1.0 kcal/mol (12.2 calculated vs. 12.8 experimental) of a value estimated from experimental pKa values of the reacting species.

Journal Article↗
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↗
PubMedDate not supplied

[Computer simulation of protein molecular dynamics].

A review of the works on the computer simulation of the globular protein dynamics is given. Methodological aspects of the simulation procedure are outlined briefly. Main peculiarities of protein dynamics revealed in the course of simulation of pancreatic trypsin inhibitor and cytochrome c are presented. The causes of "anomalous" processes, inherent in the simulated behaviour of model proteins are discussed. These "anomalous" processes are: continuous drift of the structure and its deviation from the experimental one, determined by X-ray analysis. Both processes are supposed to be the consequence of the reduced conformational rigidity of the model protein in comparison to the real one. Among the possible reasons for this reduced rigidity absence of the water molecules, hydrating peptide groups in the real protein, may be mentioned. Analogy between "anomalous" processes in the simulated protein dynamics and some phenomena observed in the real proteins during their functioning is drawn.

Computers↗
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↗
PubMed2003

Computer simulation and experimental studies of implanted 210Po in glass resulting from radon exposure.

Retrospective radon exposure measurements rely on an understanding of how the depth distribution of the implanted activity in glass is influenced by processes such as implantation, diffusion, corrosion, and cleaning. In this study, the implantation depth of 210Po was found by step-wise etching with two different etchants to obtain the depth distribution. The depth profiles are compared with results from simulations using the SRIM computer program. Theoretically estimated distributions showed good agreement with experimental 210Pb (or 210Po) activity depth profiles obtained by sequential etching. The maximum depth of implanted activity was about 100 nm, and activity deeper than about 70 nm is associated with the second alpha decay from 214Po activity previously implanted in the glass matrix. However, there was no depth interval where the activity was solely due to a single decay from the surface. The results also show that measurement of the depth profile for both "old" and controlled 222Rn exposure

Air Pollutants, Radioactive↗
PubMed2001

Development of a space radiation Monte Carlo computer simulation based on the FLUKA and ROOT codes.

This NASA funded project is proceeding to develop a Monte Carlo-based computer simulation of the radiation environment in space. With actual funding only initially in place at the end of May 2000, the study is still in the early stage of development. The general tasks have been identified and personnel have been selected. The code to be assembled will be based upon two major existing software packages. The radiation transport simulation will be accomplished by updating the FLUKA Monte Carlo program, and the user interface will employ the ROOT software being developed at CERN. The end-product will be a Monte Carlo-based code which will complement the existing analytic codes such as BRYNTRN/HZETRN presently used by NASA to evaluate the effects of radiation shielding in space. The planned code will possess the ability to evaluate the radiation environment for spacecraft and habitats in Earth orbit, in interplanetary space, on the lunar surface, or on a planetary surface such as Mars. Furthermore, it will be useful in the design and analysis of experiments such as ACCESS (Advanced Cosmic-ray Composition Experiment for Space Station), which is an Office of Space Science payload currently under evaluation for deployment on the International Space Station (ISS). FLUKA will be significantly improved and tailored for use in simulating space radiation in four ways. First, the additional physics not presently within the code that is necessary to simulate the problems of interest, namely the heavy ion inelastic processes, will be incorporated. Second, the internal geometry package will be replaced with one that will substantially increase the calculation speed as well as simplify the data input task. Third, default incident flux packages that include all of the different space radiation sources of interest will be included. Finally, the user interface and internal data structure will be melded together with ROOT, the object-oriented data analysis infrastructure system. Beyond the benefits of 'objectivity', ROOT's incorporation will also provide a graphical user interface with powerful tools for input prior to the calculation, as well as for data analysis and visualization of the results.

Computer Simulation↗
PubMed2005

Effect of the drug-excipient ratio in matrix-type-controlled release systems: computer simulation study.

The main objective of this work is to study the drug release behavior from inert matrix systems by using computer simulation. This study allowed us to propose a new statistical method to evaluate the drug percolation threshold as a function of the exposed surface area of the device. The matrix system was simulated as a simple cubic lattice. The sites of the lattice were randomly occupied at various drug-excipient ratios. By simulating a diffusive process, the drug was delivered from the matrix system. The obtained release profiles were fitted to two different models: near the excipient percolation threshold, the square root of the time was well fitted, whereas close to (but above) the drug percolation threshold, the power law described accurately the release data. A relationship between the initial drug load and the amount of drug trapped inside the matrix system at infinite time was found. This relationship was conveniently described by an error function. Percolation thresholds in the matrix systems were determined from the latter relationship by using a nonlinear regression method. The assessment of percolation thresholds depends on the exposed surface area of the matrix systems. Moreover, estimated percolation thresholds were in agreement with the predicted values stated in the percolation theory.

Algorithms↗
PubMedDate not supplied

[Validity of computer simulation in closed circuit anesthesia].

Developing a computer program to simulate the uptake, distribution, and elimination of inhalational anesthetics allow the anesthesiologist to address specific problems, but intense skills are required to translate the involved process first into a set of mathematical equations and then into a satisfactory computer program. The first step is facilitated by solutions offered in the literature. The second step by personal computer program now currently available as Gus, this program simulates anesthetic uptake and distribution using a numerical model with 12 compartments. Transport of anesthetic agents among the compartment occurs via convection of gas and blood during discrete iteration of the simulation. As initial clinical validation of the linear 12 compartment basic model the current study examined the predictive performance in 20 patients by comparing quantitatively the predicted and the measured alveolar concentration-time profiles after achievement of end tidal concentration of isoflurane (C-alv%) injected into a heated chamber (75 degrees) and then transported in closed circuit system during mechanical ventilation. With regard to the use of isoflurane 20 patients were adequately anesthetized with only 88 ml of liquid isoflurane and that is the same in simulation achieved by computer.

Adult↗
PubMed2006

[A computer simulation research for the effects of dragon's blood and its component loureirin B on sodium channel in dorsal root ganglion cells].

Using patch clamp technique the effects of dragon's blood and its component loureirin B on tetrodotoxin-sensitive sodium channel currents in dorsal root ganglion cells were observed. The experimental data were simulated with Hodgkin-Huxley model and the corresponding parameters were estimated. In addition, computer-simulated neuron action potentials in the absence and presence of drugs were produced using Hodgkin-Huxley model. The results show that the conductance of tetrodotoxin-sensitive sodium channel was fitted with m3h model well, the half-activated potentials of the sodium channel in the presence of drugs were shifted to the depolarizing direction and the threshold intensity of the cells in the presence of drugs was increased. These results demonstrate that dragon's blood and loureirin B did not resemble the tetrodotoxin which inhibited tetrodotoxin-sensitive sodium channel currents completely. Perhaps the analgesic effects of dragon's blood were partly caused by loureirin B affecting the activation, blocking the action potential generation and interfering with the transmission of painful signals into the central nervous system.

Action Potentials↗
PubMed2005

Evaluating changes of writhe in computer simulations of supercoiled DNA.

We compute changes in the writhe of a polygonal space curve when one of the vertices is displaced. The resulting expressions can be used in simulations of supercoiled DNA. For Brownian dynamics simulations, the expressions can be used to eliminate the explicit twisting degree of freedom. For Monte Carlo simulations, they can be used in fast local moves. Preliminary Monte Carlo simulations using only such fast local moves show that these can be used to efficiently simulate small DNA supercoils.

Algorithms↗
PubMed1994

Computer simulation of a model network for the erythrocyte cytoskeleton.

The geometry and mechanical properties of the human erythrocyte membrane cytoskeleton are investigated by a computer simulation in which the cytoskeleton is represented by a network of polymer chains. Four elastic moduli as well as the area and thickness are predicted for the chain network as a function of temperature and the number of segments in each chain. Comparisons are made with mean field arguments to examine the importance of steric interactions in determining network properties. Applied to the red blood cell, the simulation predicts that in the bilayer plane the membrane cytoskeleton has a shear modulus of 10 +/- 2 x 10(-6) J/m2 and an areal compression modulus of 17 +/- 2 x 10(-6) J/m2. The volume compression modulus and the transverse Young's modulus of the cytoskeleton are predicted to be 1.2 +/- 0.1 x 10(3) J/m3 and 2.0 +/- 0.1 x 10(3) J/m3, respectively. Elements of the cytoskeleton are predicted to have a mean displacement from the bilayer plane of 15 nm. The simulation agrees with some, but not all, of the shear modulus measurements. The other predicted moduli have not been measured.

Computer Simulation↗
PubMed2000

Life-expectancy projection by modelling and computer simulation (UKPDS 46).

A method is described for estimating the life-expectancy of cohorts of type 2 diabetic patients, based on computer simulation from a parametric model. The method can be used where non-parametric methods, such as the Kaplan-Meier estimate, fail due to lack of the data. The simulation algorithm combines observed and modelled information to estimate the life-expectancy implications of event rates observed within a study. The use of bootstrap methods to estimate confidence intervals is discussed. The methods are illustrated with results that have been previously published, without derivation, in a health economic analysis of tight blood pressure (BP) control in the UK Prospective Diabetes Study (UKPDS), and the application to other health economic analyses of UKPDS data is discussed.

Algorithms↗
PubMed1995

Prevention of mandibular fractures by using constructional design principles. I. Computer simulation of human mandibular strength after segmental resections.

A study was carried out on mechanical stress at the resection site in mandibles undergoing segmental resections. A computer simulation model was used to study particularly the effect of various radii of the posterior resection corners and the effect of elimination of muscle action. It was found that an enlarged radius of the resection corner in conjunction with coronoid process resection on the ipsilateral side offers the best condition to prevent fracture of the mandible.

Biomechanical Phenomena↗