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At least 1,063 records · Page 59Linked to original sources
PubMed2000

Computer simulation for the simultaneous optimization of any two variables and any chromatographic procedure.

Computer software that allows the simulation of any chromatographic separation as a function of simultaneous changes in any one or two variables that can affect sample separation order (selectivity) is described. For one example, an application is described for the simultaneous variation of the mobile phase pH and gradient time in reversed-phase liquid chromatography. The accuracy of such predictions is examined for a sample mixture of 17 substituted benzoic acids and anilines, and requirements for an acceptable predictive accuracy are summarized. In a second example, the separation of three peptides by capillary electrophoresis is optimized.

Benzoates↗
PubMed1991

A deterministic computer simulation model of life-cycle lamb and wool production.

A deterministic mathematical computer model was developed to simulate effects on life-cycle efficiency of lamb and wool production from genetic improvement of performance traits under alternative management systems. Genetic input parameters can be varied for age at puberty, length of anestrus, fertility, precocity of fertility, number born, milk yield, mortality, growth rate, body fat, and wool growth. Management options include mating systems, lambing intervals, feeding levels, creep feeding, weaning age, marketing age or weight, and culling policy. Simulated growth of animals is linear from birth to inflection point, then slows asymptotically to specified mature empty BW and fat content when nutrition is not limiting. The ME intake requirement to maintain normal condition is calculated daily or weekly for maintenance, protein and fat deposition, wool growth, gestation, and lactation. Simulated feed intake is the minimum of availability, DM physical limit, or ME physiological limit. Tissue catabolism occurs when intake is below the requirement for essential functions. Mortality increases when BW is depressed. Equations developed for calculations of biological functions were validated with published and unpublished experimental data. Lifetime totals are accumulated for TDN, DM, and protein intake and for market lamb equivalent output values of empty body or carcass lean and wool from both lambs and ewes. These measures of efficiency for combinations of genetic, management, and marketing variables can provide the relative economic weighting of traits needed to derive optimal criteria for genetic selection among and within breeds under defined industry production systems.

Animals↗
PubMedDate not supplied

Proteins in vacuo: denaturing and folding mechanisms studied with computer-simulated molecular dynamics.

Mounting evidence from experiments suggests that the native fold in solution is metastable in dehydrated proteins. Results from a number of experiments that use mass spectrometry indicate also that folding-unfolding transitions take place in protein ions even in the absence of water. These observations on anhydrous proteins call for a re-evaluation of our understanding of the folding transition. In this context, computer-assisted simulations are an important complementary tool. Here, we provide an overview of recent progress on the simulation of proteins in vacuo. In particular, we discuss the response of proteins and protein ions to perturbations that trigger unfolding and re-folding transitions. By comparing the general patterns emerging from theory and experiment, we propose a series of new measurements that could help to validate, and improve, current simulation models.

Algorithms↗
PubMed1979

Computer simulation of ventricular tachyarrhythmias during coronary artery ligation and release.

A computer (PDP-10) simulation model was constructed using rapid, simultaneous measurements of effective refractory period (ERP), ERP dispersion (RPD), premature ventricular beat (PVB) thresholds, and multi-directional conduction times during coronary artery ligations and release in the anesthetized dog. In addition, estimates of currents of injury between ischemic and non-ischemic electrodes were included based on published data from electromagnetic recordings in dogs. Propagated PVB's were inscribed by the model when criteria for excitation, dispersion, and conduction were met based on known electrophysiological characteristics of heart muscle. The model correctly predicts high vulnerability to arrhythmias at three to seven minutes of ligation, stabilization at 10 to 15 minutes of ligation, and decreased vulnerability by lidocaine during ischemia. There was no arrhythmia when ischemic thresholds were increased by the drug before significant RPD and conduction prolongation developed. Vulnerability to arrhythmias was also predicted by the model after release of short (five minute) and long (15 minute) ligation. Since (experimentally) arrhythmias occurred much more frequently after long ligations, additional yet unknown factors other than those considered in the model must be operative in the genesis of reperfusion arrhythmias. This conclusion is supported by the observations that high ischemic thresholds induced by lidocaine returned to normal slowly after ligation release, and despite this protective effect, experimentally, lidocaine failed to abolish reperfusion arrhythmias.

Animals↗
PubMed1989

[New results in computer simulation of the spread of excitation in the myocardium].

The paper presents the results from three series of simulation experiments performed by means of a realistic computer model of activation propagation in the myocardium. Simulation of two types of hypertrophy showed that hypertrophy of the ventricles without their simultaneous dilatation leaves the parameters of the cardioelectric field virtually unchanged. Change in the activation rate in the layer of elements formed by the intraventricular surface of the cavities, compared to the rate in the other elements of the heart, considerably affects the magnitude and orientation of cardiac vectors during the middle and terminal phase of activation. Rotation of the model heart around its longitudinal axis induces similar changes in the time course of the cardiac vector as are observed in some types of hypertrophy and in volume load of the ventricles.

Cardiomegaly↗
PubMed1992

Visual increment and decrement threshold curves as a function of luminance range and noise in simulated computed tomographic scans.

OBJECTIVES: The effect of luminance range compression on the visual threshold of a target in a computed tomographic (CT) scan was investigated in eight experiments. METHODS: Both visual increment thresholds of a hot target and visual decrement thresholds of a cold target were obtained. Realistic noisy CT images simulating a scan reconstruction and partial volume blurring were tested as representative of complex medical images. Negative versions, high luminance versions, and noise-free versions of these CT images also were tested. RESULTS AND CONCLUSIONS: In all the noisy images, as the luminance range of the image was compressed, proportionately smaller physical luminance differences between the target and its local background were needed to reach visual threshold. However, the thresholds were the same in terms of the difference in CT numbers between target and background. Noise in terms of CT numbers sets the threshold for a wide range of display conditions. In the noise-free CTs, as the luminance range was compressed, the luminance differences between the target and background needed to reach threshold also decreased, but only marginally. However, in terms of CT numbers, the thresholds were increased.

Analysis of Variance↗
PubMed1991

Computer simulation of the heart magnetic field dynamics.

A personal-computer based model, which enables the investigation of the correlation between the temporal dynamics of the magnetic field distribution and electrophysiological processes during ventricular depolarisation, has been tested. The activation sequence following a stimulus to the atrioventricular node or directly to the ventricular myocardium can be simulated in isotropic conditions and visualised in a three-dimensional presentation. The corresponding behaviour of the distribution of the normal component of the magnetic field is calculated using a simple algorithm. Colour animation is used to observe the simulated magnetic field dynamics and to compare them with measured data.

Computer Simulation↗
PubMed1996

Neural network computer simulation of medical aerosols.

Preliminary investigations have been conducted to assess the potential for using artificial neural networks to simulate aerosol behaviour, with a view to employing this type of methodology in the evaluation and design of pulmonary drug-delivery systems. Details are presented of the general purpose software developed for these tasks; it implements a feed-forward back-propagation algorithm with weight decay and connection pruning, the user having complete run-time control of the network architecture and mode of training. A series of exploratory investigations is then reported in which different network structures and training strategies are assessed in terms of their ability to simulate known patterns of fluid flow in simple model systems. The first of these involves simulations of cellular automata-generated data for fluid flow through a partially obstructed two-dimensional pipe. The artificial neural networks are shown to be highly successful in simulating the behaviour of this simple linear system, but with important provisos relating to the information content of the training data and the criteria used to judge when the network is properly trained. A second set of investigations is then reported in which similar networks are used to simulate patterns of fluid flow through aerosol generation devices, using training data furnished through rigorous computational fluid dynamics modelling. These more complex three-dimensional systems are modelled with equal success. It is concluded that carefully tailored, well trained networks could provide valuable tools not just for predicting but also for analysing the spatial dynamics of pharmaceutical aerosols.

Aerosols↗
PubMed1988

Computer simulation of the binding of quinocarcin to DNA. Prediction of mode of action and absolute configuration.

Computer-based models were derived for the covalent and noncovalent binding of the antitumor antibiotic quinocarcin to a representative DNA segment, d(ATGCAT)2. They showed that a mode of action, involving opening of the oxazolidine ring to give an iminium ion, followed by initial noncovalent binding in the minor groove and subsequent alkylation of the 2-amino group of guanine, was rational and attended by favorable interaction energies in each step. The best model had the aryl ring of quinocarcin lying in the 3' direction from the covalent binding site and an R configuration at the carbon involved in covalent bond formation. It also showed that the preferred absolute configuration for quinocarcin was the reverse of that arbitrarily assigned in the literature.

Computer Simulation↗
PubMedDate not supplied

Computational simulation of biomechanics in e-PTFE and venous Miller's cuffs: implications for intimal hyperplasia.

A computational distal end-to-side Miller's cuff anastomotic model was used to analyse the possible difference in intimal hyperplasia (IH) formed between e-PTFE and venous cuffs. A large strain FEA model was used to compute the strain after physiological loading and the deformed geometries used as wall boundaries for CFD analysis. Regression analysis was performed to investigate relationships between mechanical factors and prior IH. The results showed that the venous Miller's cuff anastomosis deformed twice as much as the e-PTFE cuff and that the expansion of both cuffs generated elevated strains in the artery floor while the fluid shear indices were qualitatively similar in each case. In the e-PTFE cuff, the strain and OSI correlated with IH in a proportional and equivalent manner; however, these regressions grossly over-estimated the predicted IH in the vein cuff. Thus, biomechanical effects may be important in synthetically cuffed anastomoses, but do not account for the reduced IH in venous cuffed anastomoses.

Anastomosis, Surgical↗
PubMed1995

Molecular modelling of glycoproteins by homology with non-glycosylated protein domains, computer simulated glycosylation and molecular dynamics.

OBJECTIVES: This study aims to visualise glycoproteins by computer graphics molecular modelling in order to research the dynamics of the oligosaccharide chains, determine their affects on protein conformation, antigenicity and function and to characterise oligosaccharide recognition determinants. With respect to the last, the modelling included the sialylpolylactosamine of thymocyte Thy-l and the sialyl Le(x)/Le(a) determinant present on brain Thy-l. METHODS: The following techniques were used: 1) database searching for homologies with non-glycosylated protein domains; 2) protein modelling on the basis of homology and secondary structure prediction techniques; 3) oligosaccharide construction using a simulated annealing approach utilising the AMBER forcefield with appropriate parameters in the Biosyn software environment; 4) creation of glycoprotein conjugates for further investigation by energy minimisation and molecular dynamics. RESULTS: This approach was successful in providing models of Thy-l and the carboxy terminus 27.5 kD of HIV-1 gp 120, by homology with immunoglobulin light chain folds and in one case (Thy-l) adding the oligosaccharide chains, phosphatidylinositol glycan anchor and lipid membrane and, in the other, adding additional highly glycosylated domains, and domains which folded by molecular dynamics. Significant affects on protein conformation were shown in the presence or absence of the lipid anchor and simulated membrane, but not by the N-linked oligosaccharide chains. CONCLUSIONS: The highly glycosylated molecules Thy-l and gp120, which are not expected to crystallise in their native state, were modelled by computer graphics simulated annealing or molecular dynamics from which interactions could be predicted which agree with experimental data on antibody binding and in vitro activity.

Carbohydrate Conformation↗
PubMed1978

Electron paramagnetic resonance in biochemistry. Computer simulation of spectra from frozen aqueous samples.

Two computer programs are described; they can be used to simulate e.p.r. spectra of effective spin-1/2 systems in frozen aqueous samples. One program is written in BASIC and the other in FORTRAN IV. Both programs are deposited as a Supplementary Publication (SUP 50082; 27 pages) at the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7QB, U.K. References are given to the applications of these programs in biochemical work.

Computers↗
PubMed2005

Tomographic bioluminescence imaging by use of a combined optical-PET (OPET) system: a computer simulation feasibility study.

The feasibility and limits in performing tomographic bioluminescence imaging with a combined optical-PET (OPET) system were explored by simulating its image formation process. A micro-MRI based virtual mouse phantom was assigned appropriate tissue optical properties to each of its segmented internal organs at wavelengths spanning the emission spectrum of the firefly luciferase at 37 degrees C. The TOAST finite-element code was employed to simulate the diffuse transport of photons emitted from bioluminescence sources in the mouse. OPET measurements were simulated for single-point, two-point and distributed bioluminescence sources located in different organs such as the liver, the kidneys and the gut. An expectation maximization code was employed to recover the intensity and location of these simulated sources. It was found that spectrally resolved measurements were necessary in order to perform tomographic bioluminescence imaging. The true location of emission sources could be recovered if the mouse background optical properties were known a priori. The assumption of a homogeneous optical property background proved inadequate for describing photon transport in optically heterogeneous tissues and led to inaccurate source localization in the reconstructed images. The simulation results pointed out specific methodological challenges that need to be addressed before a practical implementation of OPET-based bioluminescence tomography is achieved.

Computer Simulation↗