[Study of kinetic vitreous fluorophotometry with computer simulation. I. Computer simulation of the vitreous fluorescein kinetics].
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Documentation of students' clinical reasoning using a computer simulation.
Computer simulations can provide both a clinical experience for teaching problem solving and a method of documenting a student's clinical reasoning style. The CAMPS simulation consists of approximately 500 items describing a patient's history, physical examination and laboratory results, and treatments. The student has full option to select any item in any order, producing a wide variation of performances. Since all of the students interact with the same clinical problems, the faculty member can make comparisons of that individual student with the class. From the record of the simulation encounter, the person responsible for student evaluations can prepare a narrative that lists the overall performance, the specific omissions and commissions, and comparisons with the class. Experience with a group of 111 students in a basic pediatric course showed that this method of documenting clinical inquiry detected a variety of levels of performances. Comparisons of the results of these tests with the faculty observations showed that 16% of these students who were judged to be very good or excellent in problem solving by the faculty performed at least 1 SD below the class average on the simulations. This project highlights the power of computer simulations to provide documentation of student performance with the additional benefit of a cost of less than $1 per student.
Clinical Competence↗
New approach to analysis of rotational panoramic radiography by computer simulation.
Computer simulation is an effective method for mathematical analysis of the image of rotational panoramic radiography. Conventional simulation methods have been used only for analysis of imaging factors and prediction of the characteristics of the obtained image. This paper describes a new computer simulation method that analyzes the imaging factors and produces the simulated image itself. The simulation is carried out by reproducing the actual image formation process in the computer. The head phantom for simulation, which represents the human dentomaxillofacial structures as a numerical value from 0 to 4, was constructed by scanning a real head phantom from neck to head with an X-ray CT scanner at a slice thickness of 1 mm and at 1 mm slice intervals. The diverging X-ray beam was expressed as a set of straight lines and was moved according to various parameters. The simulated image obtained was satisfactory for image analysis of rotational panoramic radiography.
Computer Simulation↗
Polyhydroxyalkanoate (PHA) granule formation in Ralstonia eutropha cells: a computer simulation.
Computer simulation of polyhydroxyalkanoate (PHA) granule formation in vivo could help to design strategies to optimize the fermentation process and achieve higher yields of PHA. It could also suggest biotechnological approaches to control the granule size and molecular weight of the polymer. A computer program simulating the formation of PHA granules inside a Ralstonia eutropha cell was developed, based on published experimental data. The results are applicable to R. eutropha cells or other microorganisms and transgenic plants, where polyhydroxybutyrate production is made possible by heterologous expression systems. The simulation starts at the outset of the PHA accumulation phase when the cells are small and contain no PHA granules. In the presence of abundant glucose, the cell responds to phosphorus limitation by producing 3-hydroxybutyryl-CoA which undergoes polymerization on the few PHA synthase molecules present in the cytoplasm. The amphiphilic PHA synthase-PHA complex attracts additional PHA synthase molecules and granules begin to grow from these initiation sites. Phosphorus limitation and the appearance of PHA in the cytoplasm also stimulate production of phasin molecules that attach themselves to the growing granules. As the granules grow bigger, they begin to touch each other and move to optimize their packing. The phasin coat prevents the granules from coalescing. The size of the cell increases and its prolate ellipsoid shape becomes closer to spherical. The accumulation process stops either when the supply of glucose is exhausted or when the granules become tightly packed within the cell, so that access to their surface is limited. All important variables, such as cell dimensions, granule size, counts of granule-associated molecules, PHA yield, degree of polymerization of the PHA molecules, etc., are recorded in real time during the simulation. Examples of virtual experiments with the cell and their results are shown.
Acyltransferases↗
Improving toxicology testing protocols using computer simulations.
Computer simulation can be used to integrate existing toxicity information within a biologically realistic framework. Simulation models calculate relevant measures of target tissue dose based on physiological, biochemical and physicochemical properties and readily support the dose, route, species and interchemical extrapolations necessary for human risk assessment. Because these models require very specific information, much of which can be obtained in vitro, they are much less dependent on extensive animal experiments than conventional risk assessment methods. With continuing development, simulation modeling will become an invaluable tool for improving experimental designs, for interpreting animal toxicity tests, and for estimating the importance of the animal toxicity observations for people.
Administration, Inhalation↗
Determination of DNA structures by NMR and distance geometry techniques: a computer simulation.
Computer simulations have been performed to determine how accurately and precisely structures of DNA oligomers can be generated from distance data obtained from two-dimensional NMR experiments. A hexamer fragment d(CGAATT) of the Dickerson dodecamer [Drew, H.R., Wing, R.M., Takano, T., Broka, C., Tanaha, S., Itakura, K. & Dickerson, R.E. (1981) Proc. Natl. Acad. Sci. USA 78, 2179-2183] was used as the model structure in these simulations. Protons were added to the coordinates of the original x-ray structure, which was then subjected to a regularization procedure to minimize deviations from standard bond lengths and bond angles. The proton-proton distances normally observed in NMR experiments were measured from this regularized target structure and used as input for a distance geometry algorithm. Distance geometry structures were generated from two distance sets, one with essentially exact distances (+/- 0.005 A) and one set with a precision (+/- 0.2 A) that simulates an optimal NMR experiment. The results of these calculations were used to judge how accurately and precisely the following helical parameters could be reproduced from this simulated NMR distance data: helical twist, helical rise, dislocation, roll, tilt, glycosidic angle, delta torsion angle, and pseudorotation angle. These data provide a basis from which to judge the quality of DNA structures produced from real NMR experiments.
Base Sequence↗
Molecular dynamics of rhodopsin and free opsin: computer simulation.
Computer simulation was used to perform a comparative study of the molecular dynamics of rhodopsin containing the chromophore group (11-cis-retinal) and free opsin. The molecular dynamics were followed over a time interval of 3000 psec; a total of 3 x 10(6) discrete conformational states of rhodopsin and opsin. The presence of the chromophore group in the chromophore center of opsin was shown to have significant effects on the immediate protein environment of the chromophore and the conformational state of the cytoplasmic domain, but to have virtually no effect on the conformational state of the intradisk domain. The simulation results are used to discuss the possible intramolecular mechanism by which rhodopsin is maintained as a G-protein-coupled receptor in the inactive state, i.e., the function of the chromophore as an effective antagonist ligand.
Animals↗
Branch geometry in Cornus kousa (Cornaceae): computer simulations.
Computer simulations similar to actual trees were constructed using simple branching rules. Branch orientation with respect to the direction of gravity was a fundamental consideration. In Cornus kousa BUERG. ex HANCE, several types of branches develop from winter buds, varying from orthotropic shoots to plagiotropic ones. Based on actual observations and measurements of branching structures with a wide range of orientations, we made a flexible geometrical model consisting of five forking branches that varied in outgrowth depending on the direction of the shoot with respect to gravity. Repetition of the branching by computer generated a realistic tree pattern, which was close to the shape of a young C. kousa tree. Reproductive shoots seem to be under a branching rule that was a modification of vegetative branching, although the reproductive branch size was considerably smaller than the vegetative one, and reproductive branching was bifurcated instead of five-forked. We conclude that all branchings in orthotropic and plagiotropic shoots in the vegetative phase and shoots in the reproductive phase are formed under the same branching rule, but each has different parameter values.
Computer Simulation↗
Ventricular energetics during mechanical ventilation and intraaortic balloon pumping--computer simulation.
Computer simulation of a cardiovascular system enabled us to predict the effects of simultaneous application of mechanical ventilation (MV) and intraaortic ballon pumping (IABP) on ventricular energetics. External work (EW), pressure-volume area (PVA), potential energy (PE) and cardiac mechanical efficiency (CME) were calculated. Nummerical simulation showed that changes of positive intrathoracic pressure have a considerable effect on left and right ventricular EW, PE, PVA and CME, whether IABP is used or not. The right ventricular energetics was much less influenced by systemic resistance (Ras) changes than the left ventricular one. Simultaneous application of IABP and MV showed a remarkable effect on left ventricular EW. The net result was reversed sensitivity to pulmonary resistance (Rap) and reduced sensitivity to Ras. PVA was generally reduced, while CME is increased by simultaneous presence of IABP and MV. The sensitivity of CME to Rap and Ras variation was diminished in this situation.
Computer Simulation↗
An examination of refractive error through computer simulation.
Computer simulation is used to investigate the distribution of refractive error, generating two models based on corneal power, anterior chamber depth, lens power, and axial length for several samples (N = 1000). Discrepancies between simulated and observed data indicate that emmetropization is a more complex process than is accounted for by intercorrelations among components.
Computers↗
Psoriasis and cell cycle: a computer simulation.
Computer simulation using a two-phase model of the cell cycle has demonstrated that a transitory shift in the normal balance between the rate of cell flow to the differentiated and that to the proliferative compartment is sufficient to cause a permanent increase in the germinative population, thus resembling the alteration found in psoriasis. This shows the coherence of the hypothesis that cell kinetic parameters need not necessarily be expected to differ in psoriasis as compared with normal epidermis. This theoretical demonstration raises the possibility that the psoriagenic agent need not necessarily be present as long as the symptoms of psoriasis persist. From a therepeutic point of view this has implications that are sifficiently evident to warrant communication of this work.
Cell Cycle↗
Radical initiated polymerization in a bifunctional mixture via computer simulation.
Computer simulations are performed to study the polymerization behavior in a mixture of bifunctional groups such as olefins (A) and acrylates (B) in an effective solvent (a coarse description for vegetable oil derived macromonomers (VOMMs) in solution) on a cubic lattice. A set of interactions between these units and solvent (S) constituents and their relative concentrations (p(A), p(B), and p(S)) are considered. Samples are equilibrated with Metropolis algorithm to model the perceived behavior of VOMMs. The covalent bonding between monomeric units is then implemented via reaction pathways initiated by stochastic motion of free radicals (a very small fraction). The rate of reaction shows decay patterns with the time steps (t) with power laws (i.e., R(ab)alphat(-r), r congruent with 0.4-0.8), exponential decays (i.e., R(ab)alphae(-0.001t)), and their combination. Growth of A-B bonding is studied as a function of polymer concentration p=p(A)+p(B) for four different model systems appropriate for VOMMs. The data from the free radical initiated simulations are compared to the original simulations with homopolymerization. While most of the data are consistent with experimental observations, the variations are found to be model dependent.
Journal Article↗
Interplay of water, extra-framework cations and framework atoms in the structure of low-silica zeolites: the case of the natural zeolite Goosecreekite as studied by computer simulation.
Computational methods are described that model accurately the structure of hydrated Ca-bearing zeolites. Using Goosecreekite as a model system we probe the influence of framework ordering, cation siting and hydration of pores on the structure and its stability. We develop a methodology which allows the location of Al within the framework to be determined together with the position of extra-framework cations, in a stepwise fashion, progressing from an anhydrous model, via a dielectric continuum model, to finally, a fully atomistic model of the water in the intrazeolite pore space. Our methods reveal the complex interplay of short- and long-range interactions on the optimal structure of such materials.
Cations↗
[Computer simulation and pharmacoeconomics. Computer simulation as an aid for the analysis of operating room efficiency: an example].
In this study we compared operating room (OR) efficiency of total intravenous anaesthesia (TIVA) with remifentanil and propofol and balanced anaesthesia (BAL) with fentanyl and isoflurane in cataract surgery using computersimulation. We simulated patient flow for one OR and for three ORs. Time intervals of patient flow were randomly generated from the results of a prospective, randomized trial. Both for one and for three ORs, the postanaesthesia care unit (PACU) finished earlier and one additional case per OR and per day could be performed when TIVA was used for the procedures. Overtime in the PACU was less after TIVA. With a workload of 13 or 15 operations per day in three ORs, monitoring equipment for an additional patient in the PACU was required when BAL was used. TIVA with remifentanil and propofol was associated with more OR efficiency than balanced anaesthesia with fentanyl and isoflurane when given for cataract surgery.
Anesthesia, Intravenous↗
Application of the primary hydration shell approach to locally enhanced sampling simulated annealing: computer simulation of thyrotropin-releasing hormone in water.
A unified model of simulated annealing with locally enhanced sampling (LES) in a primary hydration shell (PHS) aqueous environment is developed and tested by predicting the structure of the tripeptide thyrotropin-releasing hormone (TRH) in solution. The model extends the formulation of the restraining force in the PHS method as a function of temperature, number of copies in the LES method, and shell thickness. The dependence of the restraining force on temperature can be shown to follow the relationship c(1)T - c(2), which can be derived from the expression for kinetic energy in molecular dynamics simulations. The calibration of the restraining force for different simulation conditions reveals the dependence of c(1) and c(2) on the number of copies in the LES method and the thickness of the PHS. The predicted structure of TRH is in very good agreement with results from NMR experiments and from a 10-ns PHS simulation at 300 K. The method promises to be useful in predicting structure of peptides and proteins in an aqueous environment.
Calibration↗
Interactive simulation training: computer simulated standardized patients for medical diagnosis.
SIMmersion LLC is a software development company that creates human interactive training simulations. SIMmersion produces PC-based simulations of people with whom trainees are able to hold conversations. Trainees communicate with simulated characters in face-to-face conversations, using voice recognition technology. Topics that would match well with SIMmersion's simulation capabilities include diagnosis of depression, alcoholism, or drug use, grievance counseling, marriage counseling, suicide intervention, and first responder training for biological terrorism. SIMmersion's technology could be integrated with modeling technology to create a speech-interactive, mannequin-based patient simulation system for healthcare training and assessment. Systems currently being developed involve early detection of smallpox as a result of a biological attack.
Computer Simulation↗
Mechanical properties of brain tissue in-vivo: experiment and computer simulation.
Realistic computer simulation of neurosurgical procedures requires incorporation of the mechanical properties of brain tissue in the mathematical model. Possible applications of computer simulation of neurosurgery include non-rigid registration, virtual reality training and operation planning systems and robotic devices to perform minimally invasive brain surgery. A number of constitutive models of brain tissue, both single-phase and bi-phasic, have been proposed in recent years. The major deficiency of most of them, however, is the fact that they were identified using experimental data obtained in vitro and there is no certainty whether they can be applied in the realistic in vivo setting. In this paper we attempt to show that previously proposed by us hyper-viscoelastic constitutive model of brain tissue can be applied to simulating surgical procedures. An in vivo indentation experiment is described. The force-displacement curve for the loading speed typical for surgical procedures is concave upward containing no linear portion from which a meaningful elastic modulus might be determined. In order to properly analyse experimental data, a three-dimensional, non-linear finite element model of the brain was developed. Magnetic resonance imaging techniques were used to obtain geometric information needed for the model. The shape of the force-displacement curve obtained using the numerical solution was very similar to the experimental one. The predicted forces were about 31% lower than those recorded during the experiment. Having in mind that the coefficients in the model had been identified based on experimental data obtained in vitro, and large variability of mechanical properties of biological tissues, such agreement can be considered as very good. By appropriately increasing material parameters describing instantaneous stiffness of the tissue one is able, without changing the structure of the model, to reproduce experimental curve almost perfectly. Numerical studies showed also that the linear, viscoelastic model of brain tissue is not appropriate for the modelling brain tissue deformation even for moderate strains.
Animals↗
Computer simulation techniques.
Computer simulation models can be extremely valuable for teaching and for understanding real world processes. The discipline of creating a model forces the investigator to carefully define each relationship and test the result. Even simple models can be fundamentally unpredictable. Models are typically comprised of systems of differential equations and are solved by numerical integration with computer programs. Spreadsheets, simulation software and custom programs may be used to calculate the numerical solution, draw graphs and animate the result.
Computer Simulation↗