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PubMedDate not supplied

Decomposition and plant-available nitrogen in biosolids: laboratory studies, field studies, and computer simulation.

This research combines laboratory and field studies with computer simulation to characterize the amount of plant-available nitrogen (PAN) released when municipal biosolids are land-applied to agronomic crops. In the laboratory studies, biosolids were incubated in or on soil from the land application sites. Mean biosolids total C, organic N, and C to N ratio were 292 g kg(-1), 41.7 g kg(-1), and 7.5, respectively. Based on CO2 evolution at 25 degrees C and optimum soil moisture, 27 of the 37 biosolids-soil combinations had two decomposition phases. The mean rapid and slow fraction rate constants were 0.021 and 0.0015 d(-1), respectively, and the rapid fraction contained 23% of the total C assuming sequential decomposition. Where only one decomposition phase existed, the mean first order rate constant was 0.0046 d(-1). The mean rate constant for biosolids stored in lagoons for an extended time was 0.00097 d(-1). The only treatment process that was related to biosolids treatment was stabilization by storage in a lagoon. Biosolids addition rates (dry basis) ranged from 1.3 to 33.8 Mg ha(-1) with a mean value of 10.6 Mg ha(-1). A relationship between fertilizer N rate and crop response was used to estimate observed PAN at each site. Mean observed PAN during the growing season was 18.9 kg N Mg(-1) or 37% of the biosolids total N. Observed PAN was linearly related to biosolids total N. Predicted PAN using the computer model Decomposition, actual growing-season weather, actual analytical data, and laboratory decomposition kinetics compared well with observed PAN. The mean computer model prediction of growing-season PAN was 19.2 kg N Mg(-1) and the slope of the regression between predicted and observed PAN was not significantly different from unity. Predicted PAN obtained using mean decomposition kinetics was related to predicted PAN using actual decomposition kinetics suggesting that mean rate constants, actual weather, and actual analytical data could be used in estimation of PAN. There was a linear relationship between predicted N mineralization for the growing season and for the first year. For this study, the mean values for the growing season and year were 27 and 37% of the organic N, respectively.

Agriculture↗
PubMed2000

Dose staggering as a strategy to reduce drug--drug interactions due to reversible enzyme inhibition between orally administered drugs with high first pass effect: a computer simulation study.

A physiological computer model was designed to simulate the metabolic drug-drug interactions between two orally co-administered drugs due to reversible enzyme inhibition using drug concentrations in the portal vein. The extent of interactions was compared at steady-state for the effects of a delay in time between the administration of the substrate and the inhibitor. It was demonstrated that the extent of the interactions can be strongly affected by a time interval between the two drug administrations. By delaying the administration of the inhibitor until after the absorption phase of the substrate, one can significantly reduce the extent of the drug--drug interactions. This is because drug concentrations in the portal vein and the liver are much higher than that in the systemic circulation during the absorption phase. The model also showed that interactions involving substrates with a high extraction ratio (E(H)), i.e., drugs with higher first-pass effect, can be more strongly affected by dose staggering. Substrates with a low absorption rate constant (k(a)) require a longer interval with the inhibitor in order to reduce the extent of the interactions. This observation suggests dose staggering as a simple and cost-effective way to reduce the extent of unwanted drug--drug interactions in clinical practice.

Administration, Oral↗
PubMed2003

The computer simulation of proton transport in biomolecular systems.

A Molecular Dynamics computer simulation model for describing proton transport in biomolecular systems will be reviewed. The development of the underlying computational method which allows us to study the structural and dynamical properties of excess protons in these channels will first be discussed. Several applications of the methodology to study proton transport in channel environments will then be described. In each case, insight will be provided into the atomistic factors which determine the proton transport rate and the underlying mechanism(s) for the proton hopping process. More extensive background and results for the M2 channel in the influenza A virus will also be presented.

Amino Acid Sequence↗
PubMed1986

A computer simulation of nuclear magnetic resonance imaging.

A modular, user-friendly computer simulation of NMR imaging was created for the DEC VAX computer. This simulation is novel in that complex imaging phenomena, such as chemical shifts and flow, may be easily studied. Other features include spin warp and backprojection imaging, movie generation, and simulation of image contrast, composite pulse sequences, motion artifacts, aliasing, selective excitation, field inhomogeneity, noise and signal averaging. The simulation incorporates fast Fourier transform and graphics modules for processing and display of one- and two-dimensional images. Examples which illustrate features of the program are shown. The simulation is a useful tool for both the sophisticated and the beginning user of NMR imaging. It serves as a drawing board for studying MRI phenomena and a teaching program for demonstrating basic techniques.

Adipose Tissue↗
PubMed1976

Cardiac Na+, K+-adenosine triphosphatase inhibition by ouabain and myocardial sodium: a computer simulation.

The major evidence against the hypothesis that Na+, K+-adenosine triphosphatase (Na+, K+-ATPase) inhibition is the mechanism of the positive inotropic action of digitalis is that the myocardial sodium content does not increase at the time of the inotropic response. In order to understand the relationship between sodium pump inhibition and myocardial sodium content, a computer simulation of the intracellular sodium concentration ([Na+]i) during a cycle of myocardial function was performed. The model for the computer simulation is a small compartment adjacent to the inner surface of the sarcolemma. The change in [Na+]i in this compartment is determined by the rate of sodium influx (published data utilized) and the rate of active sodium transport was estimated from the activities of partially purified dog heart Na+, K+-ATPase preparations assayed with various concentrations of sodium and ouabain. The initial rapid sodium influx results in maximal sodium pump activation, but the pump activity decreases with time as the [Na+]i decreases. Thus, the sodium pump functions at a rate close to its maximal velocity during the initial phase of each cycle but at reduced rates during the later phase. Inhibition of Na+, K+-ATPase by ouabain decreases the maximal velocity during the intiial phase of each cycle but at reduced rates during the later phase. Inhibition of Na+, K+-ATPase by ouabain decreases the maximal velocity of the sodium pump but increases the time in each cycle at which the sodium pump operates at its highest possible rate under these conditions, i.e., a rate close to the inhibited maximal velocity. A 40% inhibition of Na+, K+-ATPase activity, caused by inotropic concentrations of ouabain, increases the peak [Na+]i but fails to cause intracellular sodium accumulation since [Na+]i approaches control levels before the beginning of the next cardiac cycle. With greater enzyme inhibition, caused by arrhythmic concentrations of ouabain, [Na+]i fails to return to the precycle level and thus each subsequent cycle causes a progressive accumulation of myocardial sodium. Computer simulation predicts that a positive inotropic concentration of ouabain causes a myocardial sodium accumulation at a high heart rate but not at a lower heart rate. This was confirmed by experiments with Langendorff preparations of guinea-pig hearts. It is concluded that a moderate sodium pump inhibition by inotropic concentrations of ouabain enhances the intracellular sodium transient (a transient increase in intracellular sodium concentration associated with each membrane excitation) but does not cause a significant myocardial sodium accumulation at normal heart rates. A progressive myocardial sodium accumulation occurs only when the degree of Na+, K+-ATPase inhibition exceeds a critical magnitude.

Adenosine Triphosphatases↗
PubMed1993

Quantitative effects of intercellular signals on computer-simulated tumor patterns.

The behavior of tumor cells within a particular in vivo microenvironment is considered to be regulated by intercellular signals. Previous studies of computer simulations of tumor growth demonstrated a qualitative effect of autocrine and paracrine signaling factors on the resulting morphologic patterns. We investigated the quantitative effect of these intercellular signals when the evolving patterns were evaluated by a set of pattern analysis procedures, yielding 18 quantitative morphologic features. The results show that both autocrine and paracrine factors regulating either tumor cell proliferation, motility or death influenced at least 10 of the 18 features significantly (linear regression analysis; n = 50 for each experiment; P = < .01). Furthermore, multivariate analysis of 600 simulated patterns also demonstrated highly significant relationships between intercellular signals and quantitative features of the evolving pattern (P = < .001). The study showed that various pattern measurement features indicate a direct influence of intercellular signals on tumor patterns in computer simulations.

Cell Communication↗
PubMed1992

Computer simulation as a tool for the rapid optimization of the high-performance liquid chromatographic separation of a tryptic digest of human growth hormone.

Computer simulation was used to optimize the separation of a tryptic digest of recombinant human growth hormone using reversed-phase high-performance liquid chromatography in a gradient mode. DryLab G/plus software modelled the retention behavior of the complex tryptic digest mixture as a function of gradient conditions, based on data from two experimental gradient runs. The theoretical optimum separation conditions were rapidly obtained and reproduced experimentally. Resolution did not simply increase as gradient steepness was decreased, rather, an intermediate gradient time provided maximum sample resolution. The simulation results also indicate that the method is reasonably rugged, with little change in the separation expected for different high-performance liquid chromatography systems, and changes in the separation can be compensated by a change in the gradient steepness. Computer simulation can also be useful to quickly reoptimize conditions for a new column, if it fails to provide the same separation.

Chromatography, High Pressure Liquid↗
PubMed1996

Conformational study of two linear hexapeptides by two-dimensional NMR and computer-simulated modeling: implication for peptide cyclization in solution.

Two linear peptides, D-leucyl-L-prolyl-L-isoleucyl-L-valyl-L-alanyl-beta-alanine (I) and D-leucyl-L-prolyl-L-isoleucyl-L-valyl-N-methyl-L-alanyl-beta-alanine (II), whose sequences were designed from protodestruxin and desmethyldestruxin B by replacing D-leucic acid with D-leucine, two cyclic hexadepsipeptides with insecticidal and immunodepressant activities, have been found to be cyclized in unusually high yields (>85%). In order to gain insight into the conformation and the relative flexibility of different constituent residues in these linear peptides, we have applied various techniques of 2D-NMR spectroscopy coupled with dynamic simulated annealing by computer modeling to establish the solution conformations of these two linear peptides. Based on the derived structures, it is found that the distances between N- and C-terminal residues of both peptides are short enough to facilitate the cyclization, thus collaborating the observation of favorable cyclization yields for both linear peptides.

Amino Acid Sequence↗
PubMed1994

Influence of obstacles on lipid lateral diffusion: computer simulation of FRAP experiments and application to proteoliposomes and biomembranes.

Fluorescence Recovery After Photobleaching experiments were simulated using a computer approach in which a membrane lipid leaflet was mimicked using a triangular lattice obstructed with randomly distributed immobile and non-overlapping circular obstacles. Influence of the radius r and area fraction c of these obstacles and of the radius R of the observation area on the relative diffusion coefficient D* (Eq. (1)) and mobile fraction M was analyzed. A phenomenological equation relating D* to r and c was established. Fitting this equation to the FRAP data we obtained with the probe NBD-PC embedded in bacteriorhodopsin/egg-PC multilayers suggests that this transmembrane protein rigidifies the surrounding lipid phase over a distance of about 18 A (approximately equal to two lipid layers) from the protein surface. In contrast, analysis of published diffusion constants obtained for lipids in the presence of gramicidin suggests that in terms of lateral diffusion, this relatively small polypeptide does not significantly affect the surrounding lipid phase. With respect to the mobile fraction M, and for point obstacles above the percolation threshold, an increase in R led to a decrease in M which can be associated with the existence of closed domains whose average size and diffusion properties can be determined. Adaptation of this model to the re-interpretation of the FRAP data obtained by Yechiel and Edidin (J Cell Biol (1987) 115:755-760) for the plasma membrane of human fibroblasts consistently leads to the suggestion that the lateral organization of this membrane would be of the confined type, with closed lipid domains of approximately equal to 0.5 microns 2 in area.

Bacteriorhodopsins↗
PubMed1994

Computer simulation of propagated activation in different types of left ventricular enlargement.

An increase of the left ventricular mass does not always have an unambiguous effect on the electro- or vectorcardiographic image of ventricular activation. To analyse this phenomenon, three types of left ventricular enlargement were simulated by a computer model of propagated activation in cardiac ventricles. These were obtained from the reference (normal) left ventricle by an increase of its wall thickness either centripetally or centrifugally, as well as by increase of the ventricular cavity dimensions (dilatation). Two different degrees of mentioned changes, corresponding to an increase of the value of the respective parameters by 50% or 100% of reference left ventricular wall thickness, were analysed. In the case of a centrifugal increase of left ventricular wall thickness, the magnitude of instantaneous cardiac vectors increased only during the last two-thirds of ventricular activation time. A centripetal increase of the wall thickness resulted in a decrease of the resultant cardiac vector magnitudes during the first half of ventricular activation followed by their slight increase. In dilatation of the left ventricle the cardiac vectors were enhanced during the whole activation time.

Action Potentials↗
PubMed1978

Computer simulation of aggregation in Dictyostelium discoideum.

The aggregation phase of development of the cellular slime mould Dictyostelium discoideum is simulated on a computer. The simulation is performed in 2 dimensions, and produces animated graphical output similar to time-lapse films. It is based on observations of cell behaviour as expressed by a set of rules for each cell, involving cell movement and release of and response to chemical signals. Following these rules, the simulation has reproduced many observed aggregation patterns: propagating waves of cell movement; formation of branching streams; entrainment of slower centres; and spiral centre formation. The simulation has proved to be an important adjunct to experimental work.

Cell Aggregation↗
PubMedDate not supplied

Effect of intracellular unstirred layer on apparent reflection coefficient for urea in inner medullary collecting duct: a computer simulation.

In the vasopressin-stimulated inner medullary collecting duct (IMCD), urea is transported through a pathway which is distinct from a water channel. Therefore, no frictional interaction between urea and water should occur at the membrane level, and the reflection coefficient for urea must be close to unity. However, the presence of unstirred layers in the vicinity of membranes causes solute concentration polarization, leading to an underestimation of the reflection coefficient (apparent reflection coefficient). When the value is determined across the perfused renal tubular wall, the intracellular space also constitutes an unstirred layer. The profile of solute and water transport across the system consisting of two membranes and the interposed intracellular space was simulated by a computer to examine the effect of unstirred layer on the value of apparent reflection coefficient. The model demonstrated that the imposed osmotic gradient across the tubular epithelial is decreased at each membrane interface. Under conditions of minimal unstirred layers in the bathing fluid, the existence of the intracellular constraints to diffusion cause considerable underestimation of the reflection coefficient. The higher the membrane permeability of urea and the smaller the diffusion coefficient of urea in the intracellular space, the greater becomes the magnitude of the underestimation. Thus, the measured apparent reflection coefficient for urea may become significantly less than the estimated value, leading to a reduction of the effective transmural osmotic driving force.

Animals↗
PubMed1987

Computer simulations of neural information processing and the schizophrenia-mania dichotomy.

Recent developments in artificial intelligence use computer simulations of complex neural systems to model associative memory and gestalt-seeking during cognition. Perturbations imposed on such computer simulations caused catastrophic breakdowns of neural functioning. The resulting cognitive disturbances assumed two forms, one "schizophreniclike" and the other "maniclike." The former was induced by memory overload and resulted in misperceptions, loose associations, and also parasitic processing states that pathologically controlled the flow of associations. The latter was caused by increased randomness of neural activity, which induced "jumps" from one gestalt to another. The relationship between this differential model of psychotic disturbances and other studies of schizophrenia and mania were explored.

Arousal↗
PubMed1994

A computer simulation of radio-frequency ablation of the endocardium.

A computer simulation of radio-frequency (RF) ablation of the endocardium is performed. The objective is to quantify some of the parameters affecting lesion growth, and to obtain theoretical data which can be used as a guide to maximize the lesions obtained with the procedure. The model under consideration consists of a block of heart tissue with the catheter electrode making contact at a right angle on one side (endocardium) and a large grounded electrode on the other side. An RF electrical current flows between the electrodes, heating the tissue. The simulations provide information on the time evolution of the tissue temperature, lesion dimension and tissue resistance. A first set of calculations is based on an applied RF voltage that maintains the maximum tissue temperature at 100 degrees C. The results reveal that: 1) the lesions achievable by RF ablation are considerably larger than those obtained with a hot-tip catheter of the same size; 2) increasing the electrode radius enlarges the lesion because of an associated increase in contact surface area; 3) an increase in electrode length also enlarges the lesion because of the larger convective losses to the blood flow; 4) a large difference in temperature may exist between the electrode and the tissue because of the cooling effect of the blood flow; and 5) the lesions grow as long as power is applied. Other simulations in which the RF voltage is constant show that the lesions can be enlarged by lowering the applied voltage while increasing the duration. Agreement and discrepancies between the simulations and reported experimental results are identified.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗
PubMed2003

Systematic review of the use and value of computer simulation modelling in population health and health care delivery.

BACKGROUND: The objective of the review was to evaluate the extent, quality and value of computer simulation modelling in population health and health care delivery. METHODS: A narrative systematic review was carried out of world literature from 1980 to 1999, searching Medline, INSPEC, Embase, HealthSTAR, Science Citation Index, CINAHL, MathSci, INFORMS Online and SIGLE databases, and researchers in the field were contacted. Papers were included if they contained a computer simulation model of individuals in a stochastic system and the topic or setting related to population health or health service delivery. RESULTS: A total of 182 papers met the inclusion criteria. Simulation modelling has been undertaken in a wide range of health care topic areas, including hospital scheduling and organization, communicable disease, screening, costs of illness and economic evaluation. However, the quality of published papers was variable and few reported on the outcomes of implementation of models, so that the value of modelling could not be assessed. CONCLUSION: Simulation modelling is a powerful method for modelling both small and large populations to inform policy makers in the provision of health care. It has been applied to a wide variety of health care problems. Although the number of modelling papers has grown substantially over recent years, further research is required to assess the value of modelling.

Communicable Disease Control↗
PubMed1981

Two-compartment pharmacokinetic models: computer simulations of their characteristics and clinical consequences.

Computer simulations of two-compartment models of drug disposition were made. These simulations show how variations in each of the three intercompartmental rate constants are related to altered blood and tissue concentrations. Various simulations following rapid injection or continuous infusion are presented to demonstrate the general behavior of such a pharmacokinetic model. A system of drug classification based on comparative values of a drug's intercompartmental rate constants is proposed, and characteristics and consequences of each class are discussed in terms of possible therapeutic results.

Ampicillin↗