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PubMed1988

Algorithms for determining the fate of sites and domain boundaries in computer simulations of recombinant DNA procedures.

Structural and functional features within genomic sequences are best described by their position within the genomic structure. Cleavage sites can be conveniently described by single positions but genomic domains require the position of their two boundaries. The handling of these positions simultaneously to sequence manipulations in computer simulations of recombinant DNA procedures greatly improves the understanding of the resulting recombinant constructs. In addition, the algorithms describing the fate of domain boundaries can be used for the handling of nucleotide sequences in dynamic database environments handled by languages like Prolog which are particularly suitable for artificial intelligence implementations. This communication describes a set of algorithms for the automatic updating of single sites and double domain boundaries in linear and circular models for computer simulation of recombinant DNA procedures.

Algorithms↗
PubMed1988

An analysis of the hyper-sharp phenomenon of myosin diffusion in an F-actin/ATP solution by computer simulation.

The diffusion of myosin molecules was demonstrated using schlieren optics and Rayleigh fringe optics. A hyper-sharp schlieren pattern appeared near the boundary between the upper and lower parts of the diffusion cell at a time when ATP in the lower part had almost been consumed. The mechanism underlying the appearance of the hyper-sharp peak was investigated by means of computer simulations based on random-walk theory. The schlieren pattern with the hyper-sharp peak could be reproduced on the computer with the assumptions that a myosin molecule can be detached from an actin filament only on binding of ATP and that it can then move along actin filaments or diffuse in the aqueous solution. The results of the computer simulations are in good agreement with the experimental data.

Actins↗
PubMed1986

Computer simulations of the kinetics of irreversible enzyme inhibition by an unstable inhibitor.

Computer simulations of the irreversible inhibition of an enzyme by an unstable inhibitor are presented. Data obtained at the end point of reaction are shown to conform poorly in many situations with relationships derived from integrated rate equations by setting t = infinity, and the implications concerning the experimental use of this method to determine kinetic constants describing inactivation are considered. The alternative approach of conducting experiments under conditions of inhibitor excess over enzyme is further discussed, and a graphical procedure is suggested for the description of time courses of reaction of enzyme with unstable inhibitor when an enzyme-inhibitor adsorptive complex is involved.

Computer Simulation↗
PubMed1990

Computer simulation of the hemodynamic determinants of myocardial oxygen supply and demand.

A computer program was developed that uses a mathematical model of the cardiovascular system to predict myocardial oxygen supply and demand as well as cardiac hemodynamics. This model combines the time-varying elastance model of the left ventricle, the modified Windkessel model of the arterial system, and the left ventricular pressure-volume area prediction of myocardial oxygen demand. The computer simulation permits independent control of variables, thus providing the opportunity to design "experiments" and to observe the results. The model predicts that tachycardia leads to reduced myocardial oxygen supply and increased demand. Hypertension caused by increased systemic vascular resistance increases supply more than it increases demand. On the other hand, increased contractility or left ventricular end-diastolic pressure increases demand more than supply, and may cause ischemia in the presence of coronary artery stenosis. The model is an aid in understanding how hemodynamic variables affect the balance between myocardial oxygen supply and demand. It can be used for education and to analyze study protocols prior to animal experimentation.

Animals↗
PubMed1990

Computer simulation in the design of local exhaust hoods for shielded metal arc welding.

Computer simulations were used to examine competing exhaust hood configurations for shielded metal arc welding. The welder's breathing zone concentration appears to be an inverse linear function of the computer-predicted hood capture efficiency. Hood aspect ratio, hood flow, and the welder's position relative to the hood all have a significant effect on the breathing zone concentration. The height of the hood above the welding surface showed no significant effect in reducing breathing zone concentration. Further examination of breathing zone concentration as a function of capture efficiency is needed before reliable design methods can be developed using this parameter.

Air Movements↗
PubMed1990

Computer simulation for optimization of high-performance liquid chromatography of some phenolic pollutants.

Computer simulation was used to optimize high-performance liquid chromatography of phenol and its chloro and nitro derivatives. On the basis of two linear gradient runs of different steepness (RP-18-water + methanol + 1% acetic acid), several simulated gradient runs allowed the optimum gradient programme and flow-rate to be chosen so that the time of analysis could be considerably shortened. Good agreement between simulated and experimental chromatograms was obtained in spite of changes in experimental conditions.

Air Pollutants↗
PubMedDate not supplied

Using a computer simulation program to assess the decision-making process in child health care.

The purpose of this paper was to describe the development and testing of a computer simulation program designed to assess the decision-making process in the public health nurses' work in child health care. The work was based primarily on theories of problem-solving and decision making; on knowledge of child development, health care, and education; and on the soft systems methodology. An authoring program and two simulations were designed and produced at the University of Turku by a team of two nurse researchers, a computer specialist, and three public health nurses. The simulations presented two typical situations encountered by the public health nurses' work in child health care. A total of 61 public health nurses from 11 health centers in the southwestern part of Finland completed the simulations. The public health nurses responded positively to the simulations and the program worked very well. The results revealed some inconsistencies in the decision-making process of the public health nurses with respect to the needs of the child and the family. The public health nurses' decisions were more closely related to the developmental stage of the child than to the unique needs of each family. The simulation is acting to test the public health nurses' ability to make decisions "here and now" but not about caring it forward. These shortcomings can be corrected by asking them to explain their decisions and thoughts after each stage and by tape recording their answers. The findings gave many answers to the question of how the computer simulation program can be developed.

Computer Simulation↗
PubMed1990

The development of computer simulations of the geometries and thermodynamics of biological molecules.

The historical development of computer simulations of molecular geometry and thermodynamics (molecular mechanics, force field method) is outlined. The advantages and disadvantages of techniques such as energy minimization, molecular dynamics and free energy perturbation are discussed. An example is included that shows how energy minimization studies of dopamine D-2 antagonists have been used to develop an understanding of the three-dimensional pharmacophore necessary for this pharmacological activity.

Computer Simulation↗
PubMed1992

Synthesis and conformational properties of the lanthionine-bridged opioid peptide [D-AlaL2,AlaL5]enkephalin as determined by NMR and computer simulations.

We report the synthesis and conformational analysis by means of NMR and computer simulations of a novel opioid peptide with the sequence [formula: see text], which we write as [formula: see text], abbreviated [D-AlaL2,L-AlaL5]EA, where AlaL denotes each of the lanthionine amino acid ends linked by a monosulfide bridge and EA indicates enkephalinamide. Data from 2D NMR (HOHAHA and ROESY) provide short-range NOEs that are used as constraints in molecular modeling; measurement of coupling constants shows that chi 1 (D-AlaL2) is predominantly in either the t or g- conformation, and temperature coefficient data suggest the participation of the AlaL5 amide proton in an intramolecular hydrogen bond. The use of NOE and hydrogen-bond constraints in a distance-geometry program yields a large number of initial conformations compatible with the data. Energy minimization of these structures using CHARMM results in three families of backbone ring conformations, labled A1, A2, and B. The torsion chi 1 in D-AlaL2 remains close to trans for all three conformations. Molecular dynamics in vacuo at 300 K show that these three families of conformers interconvert, with concerted shifts in two of the three torsions psi(Phe), phi(AlaL5), and chi(AlaL5). The [D-AlaL2,L-AlaL5]EA is superactive in the guinea pig ileum (GPI) and mouse vas deferens (MVD) in vitro tests and also in the rat hot plate test in vivo. At the same time, this analog with a constrained 13-membered ring shows virtually no selectivity with a ratio IC50 (MVD)/IC50 (GPI) of 0.882.

Amino Acid Sequence↗
PubMed1989

Positron emission tomographic measurement of blood-to-brain and blood-to-tumour transport of 82Rb. I: Error analysis and computer simulations.

Unidirectional blood-to-brain and blood-to-tumour transport rate constants (K1) for 82Rb (half-life 76 s) and plasma water volume per unit mass of brain/tumour tissue (Vp) can be estimated in vivo using dynamic positron emission tomography (PET). The accuracy of these estimates depends upon the accuracy of PET measurements of regional brain/tumour radioactivity and scintillation well detector measurements of whole-blood radioactivity, which, in turn, depend upon the time course of arterial blood radioactivity. A two-compartmental model has been employed to derive estimates for K1, k2 (efflux rate constant) and Vp from 82Rb/PET data. Errors in these parameter estimates have been studied (1) qualitatively using sensitivity function analysis and (2) quantitatively using computer simulations. The effect of adding a third irreversible compartment and its unidirectional rate constant, k3, has also been investigated. The advantages and disadvantages of bolus injection vs continuous infusion protocols are discussed. Precision in estimated parameters from actual patient data is compared to that obtained from computer simulations in part II of this paper.

Blood↗
PubMed1975

Analysis of expert diagnosis of a computer simulation of congenital heart disease.

Analysis of data from five expert cardiologists indicates substantial agreement on the first step to be taken in response to an emergency case of computer-simulated congenital heart disease. There was little or no agreement among these same subjects on the specific steps undertaken following their initial response. The problem was solved in 11, 10, 8, and 6 steps by four of the cardiologists. The problem-solving sequence employed by one expert resulted in the patient's death. It is concluded that while the behavior of experts in the hospital and clinic is the primary means of evaluating successful student performance, computer simulations of patient cases offer the opportunity to use expert data in the calibration of student error.

Computers↗
PubMed1987

Computer simulations of the diffusion of a substrate to an active site of an enzyme.

Computer simulations of the diffusion of a substrate to an enzyme active site were performed. They included the detailed shape of the protein and an accurate description of its electrostatic potential. Application of the method to the diffusion of the superoxide anion to the protein superoxide dismutase revealed that the electric field of the enzyme enhances the association rate of the anion by a factor of 30 or more. Calculated changes in the association rate as a function of ionic strength and amino acid modification paralleled the observed behavior. Design principles of superoxide dismutase are considered with respect to insights provided by the simulations. A possible means of enhancing the enzyme turnover rate through site-directed mutagenesis is proposed.

Binding Sites↗
PubMed1991

Computer simulation of surface-induced aggregation of ferritin.

Models are presented describing the transient mass-transport limited adsorption and cluster growth of ferritin at a solid surface. Computer simulations are carried out on a hexagonal lattice using a computer model that can be characterized as a two-dimensional stochastic cellular automaton allowing different rules regarding association, lateral interaction and dissociation to be incorporated in the model. The fractal dimensions of individual clusters were extracted from simulated aggregates and for similar rules found to be consistent with literature values on reversible diffusion-limited aggregation in two dimensions. The distribution of clusters versus free surface were shown to be affected by neighbor-dependent association probability. Low fractal dimension clusters were generated by a combination of strong lateral cohesion and neighbor-dependent dissociation to the bulk. By comparing computer simulated aggregation to experimental electron micrographs of adsorbed ferritin layers it is suggested that neighbor-dependent association, neighbor-dependent dissociation and lateral interactions are important factors in the complex dynamics of adsorbed protein layers.

Computer Simulation↗
PubMed1991

Computer simulations of cell-target encounter including biased cell motion toward targets: single and multiple cell-target simulations in two dimensions.

In order for immune cells to carry out many of their functions, including clearance of infectious agents from tissue, they must first encounter their targets in the tissue. This encounter process is often the rate-limiting step in the overall function. Most immune cells exhibit chemotactic ability, and previous continuum models for encounter rates and dynamics have shown that chemotaxis can be a great advantage to cells by greatly increasing encounter rates relative to those for randomly moving cells. This paper describes computer simulations of discrete cell-target encounter events in two dimensions, for the two cases considered by the continuum models: where only a single cell and a single target are present, and where many cells and targets are present. The results of these simulations verify our previous model predictions that a small amount of chemotactic bias dramatically decreases the encounter time, while further increases in the amount of bias have a much smaller effect. Chemotactic ability is shown to be an important determinant of the kinetics of target clearance, and its effects depend on the initial cell-target ratio and the initial distributions of cells and targets. To the best of our knowledge, this work provides the first computer simulations of particle-target encounter in which there is biased motion of particles toward their targets, and is therefore of general interest beyond specific application to immune cell function.

Animals↗
PubMed1988

A computer simulation of simultaneous heat and oxygen transport during heterogeneous three dimensional tumor hyperthermia.

Hyperthermia is a developing modelity for the treatment of cancer. This therapy is occasionally used by itself, however, usually it is used as an adjuvate with chemo or radiation therapy. The mechanism for this treatment is based on the fact that cancer cells are heated preferentially by heat application due to lower vascularity in the tumor tissue as compared with the surrounding normal tissue and that, when used with radiation therapy or chemo therapy, higher oxygen partial pressure in the tumor results in increased tumor cell damage. Appropriate mathematical models and their real time prediction of oxygen and temperature profiles could be very helpful in achieving optimal results via hyperthermia and to avoid possible danger which might occur during the treatment. Because of the complexity and the heterogeneous nature of physiological system, it is necessary to include heterogeneous properties in the mathematical models for them to be useful for biomedical calculations. Of course, it is much more difficult to solve mathematically the heterogeneous system than the homogeneous one. In this paper, the importance of the implementation of heterogeneities in the heat and mass transport for biological system mathematical modelling is discussed. Results of a three dimensional computer simulation of mass and heat transfer in tumor tissue with different capillary geometries during hyperthermia are demonstrated. The method used for the computer simulation is a deterministic/probabilistic technique, Williford-Bruley calculational strategy.

Animals↗
PubMed1977

Computer-simulated clinical encounters. I. Development, utilization, and evaluation of a program.

Positive findings from the two-year pilot study indicated no significant difference in academic learning and clinical performance when students substituted computer-simulated experiences for hospital-based clinical experiences. There was also strong evidence that the time spent by students in fewer hospital-based clinical experiences was more decisively monitored by faculty. Based on these positive findings, the computer-simulated clinical encounters are being continued as part of the established curriculum in the coordinated undergraduate program in dietetics at The Ohio State University.

Clinical Competence↗
PubMed1992

Molecular details of the activation of soluble phospholipase A2 on lipid bilayers. Comparison of computer simulations with experimental results.

The initial rate of hydrolysis of large unilamellar vesicles of dipalmitoylphosphatidylcholine by phospholipase A2 from the venom of Agkistrodon piscivorus piscivorus is small and elevates gradually until it suddenly increases by a factor of 10 to 1000 depending on the experimental conditions. This abrupt onset of high enzyme activity appears to be correlated to a specific mole fraction of reaction product at which point a cooperative compositional phase transition in the bilayer occurs. Five models that describe the activation process in terms of its being coupled to the putative product-induced lipid transition are presented. These models include one in which the lipid structure enhances the affinity of enzyme binding to the bilayer surface, two in which the equilibrium position between an active and an inactive form of the enzyme-substrate complex is altered, and two in which the rate of a quasi-irreversible spontaneous activation process is increased. Whether the active form of the enzyme is a monomer or dimer is also considered in the last two pairs of models. Computer simulations of time courses for the different models show how a set of four experimental observables distinguishes qualitatively among them. Comparison of the experimental behavior with the computer-simulated behavior of the observables for each model indicates that activation of phospholipase A2 on the lipid surface involves formation of an enzyme dimer which spontaneously converts to an active form. The active enzyme persists in the active state as it exchanges between vesicles. This model of activation is similar to that proposed previously for activation of porcine pancreatic phospholipase A2.

Computer Simulation↗