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PubMed2000

The use of simulation and post-simulation interview to examine the knowledge involved in community nursing assessment practice.

This paper describes the development of an innovative research approach which used the complementary methods of simulation and post-simulation interview to examine the knowledge-base involved in community nursing assessment practice in the United Kingdom. The study commenced in 1994 and the main phase of data-gathering took place over a 3-week period in 1995. Having outlined the study's aim, context and theoretical background, this paper focuses on the two main methods of data-gathering used. Detailed description of the simulation method and the post-simulation interview and the rationales for their use are followed by critical discussion which identifies their particular strengths and weaknesses. Threats to validity are also considered. It is argued that the combined use of a simulated assessment and a post-simulation structured interview has great potential as a means of exploring the knowledge involved in community nursing assessment practice.

Community Health Nursing↗
PubMed2006

A structure-based simulation approach for electron paramagnetic resonance spectra using molecular and stochastic dynamics simulations.

Electron paramagnetic resonance (EPR) spectroscopy using site-directed spin-labeling is an appropriate technique to analyze the structure and dynamics of flexible protein regions as well as protein-protein interactions under native conditions. The analysis of a set of protein mutants with consecutive spin-label positions leads to the identification of secondary and tertiary structure elements. In the first place, continuous-wave EPR spectra reflect the motional freedom of the spin-label specifically linked to a desired site within the protein. EPR spectra calculations based on molecular dynamics (MD) and stochastic dynamics simulations facilitate verification or refinement of predicted computer-aided models of local protein conformations. The presented spectra simulation algorithm implies a specialized in vacuo MD simulation at 600 K with additional restrictions to sample the entire accessible space of the bound spin-label without large temporal effort. It is shown that the distribution of spin-label orientations obtained from such MD simulations at 600 K agrees well with the extrapolated motion behavior during a long timescale MD at 300 K with explicit water. The following potential-dependent stochastic dynamics simulation combines the MD data about the site-specific orientation probabilities of the spin-label with a realistic rotational diffusion coefficient yielding a set of trajectories, each more than 700 ns long, essential to calculate the EPR spectrum. Analyses of a structural model of the loop between helices E and F of bacteriorhodopsin are illustrated to demonstrate the applicability and potentials of the reported simulation approach. Furthermore, effects on the motional freedom of bound spin-labels induced by solubilization of bacteriorhodopsin with Triton X-100 are examined.

Algorithms↗
PubMed2000

Input and output for surgical simulation: devices to measure tissue properties in vivo and a haptic interface for laparoscopy simulators.

Current efforts in surgical simulation very often focus on creating realistic graphical feedback, but neglect some or all tactile and force (haptic) feedback that a surgeon would normally receive. Simulations that do include haptic feedback do not typically use real tissue compliance properties, favoring estimates and user feedback to determine realism. When tissue compliance data are used, there are virtually no in vivo property measurements to draw upon. Together with the Center for Innovative Minimally Invasive Therapy at the Massachusetts General Hospital, the Haptics Group is developing tools to introduce more comprehensive haptic feedback in laparoscopy simulators and to provide biological tissue material property data for our software simulation. The platform for providing haptic feedback is a PHANToM Haptic Interface, produced by SensAble Technologies, Inc. Our devices supplement the PHANToM to provide for grasping and optionally, for the roll axis of the tool. Together with feedback from the PHANToM, which provides the pitch, yaw and thrust axes of a typical laparoscopy tool, we can recreate all of the haptic sensations experienced during laparoscopy. The devices integrate real laparoscopy toolhandles and a compliant torso model to complete the set of visual and tactile sensations. Biological tissues are known to exhibit non-linear mechanical properties, and change their properties dramatically when removed from a living organism. To measure the properties in vivo, two devices are being developed. The first is a small displacement, 1-D indenter. It will measure the linear tissue compliance (stiffness and damping) over a wide range of frequencies. These data will be used as inputs to a finite element or other model. The second device will be able to deflect tissues in 3-D over a larger range, so that the non-linearities due to changes in the tissue geometry will be measured. This will allow us to validate the performance of the model on large tissue deformations. Both devices are designed to pass through standard 12 mm laparoscopy trocars, and will be suitable for use during open or minimally invasive procedures. We plan to acquire data from pigs used by surgeons for training purposes, but conceivably, the tools could be refined for use on humans undergoing surgery. Our work will provide the necessary data input for surgical simulations to accurately model the force interactions that a surgeon would have with tissue, and will provide the force output to create a truly realistic simulation of minimally invasive surgery.

Computer Simulation↗
PubMed1997

[A quality assurance program of simulators in radiation therapy. 2. Extent and results of long-term quality assurance test on a therapy simulator].

BACKGROUND: Since 1990 we follow a quality assurance program with periodical tests of functional performance values of a 16-year-old simulator. MATERIAL AND METHOD: For this purpose we adopted and modified German standards for quality assurance on linear accelerators and international standards elaborated for simulators (International Electrotechnical Commission). The tests are subdivided into daily visual checks (light field indication, optical distance indicator, isocentre-indicating devices, indication of gantry and collimator angles) and monthly and annually tests of relevant simulator parameters. Some important examples demonstrate the small variation of parameters over 6 years: position of the light field centre when rotating the collimator, diameter of the isocentre circle when rotating the gantry, accuracy of the isocentre indication device, and coincidence of light field and simulated radiation field. RESULTS: As an important result we can state, that by these rigid periodic tests it was possible to detect and compensate deteriorations of simulators quality rapidly. CONCLUSIONS: Technical improvements and specific calling-in of maintenance personnel whenever felt appropriate provided performance characteristics of our old simulator which are required by international recommendations as a basis for modern radiotherapy.

Germany↗
PubMed2004

Simulation of roller compaction using a laboratory scale compaction simulator.

A method for simulation of the roller compaction process using a laboratory scale compaction simulator was developed. The simulation was evaluated using microcrystalline cellulose as model material and ribbon solid fraction and tensile strength as key ribbon properties. When compacted to the same solid fractions, real and simulated ribbons exhibited similar compression behavior and equivalent mechanical properties (tensile strengths). Thus, simulated and real ribbons are expected to result in equivalent granulations. Although the simulation cannot account for some roller compaction aspects (non-homogeneous ribbon density and material bypass) it enables prediction of the effects that critical parameters such as roll speed, pressure and radius have on the properties of ribbons using a fraction of material required by conventional roller compaction equipment. Furthermore, constant ribbon solid fraction and/or tensile strength may be utilized as scale up and transfer factors for the roller compaction process. The improved material efficiency and product transfer methods could enable formulation of tablet dosage forms earlier in drug product development.

Cellulose↗
PubMed1999

Spatial and stochastic simulation to evaluate the impact of events and control measures on the 1997-1998 classical swine fever epidemic in The Netherlands. I. Description of simulation model.

The simulation model InterCSF was developed to simulate the Dutch Classical Swine Fever (CSF) epidemic of 1997-98 as closely as possible. InterCSF is a spatial, temporal and stochastic simulation model. The outcomes of the various replications give an estimate of the variation in size and duration of possible CSF-epidemics. InterCSF simulates disease spread from an infected farm to other farms through three contact types (animals, vehicles, persons) and through local spread up to a specified distance. The main disease-control mechanisms that influence the disease spread in InterCSF are diagnosis of the infected farms, depopulation of infected farms, movement-control areas, tracing, and pre-emptive slaughter. InterCSF was developed using InterSpread as the basis. InterSpread was developed for foot-and-mouth disease (FMD). This paper describes the process of modifying InterSpread into InterCSF. This involved changing the assumptions and mechanisms for disease spread from FMD to CSF. In addition, CSF-specific control measures based on the standard European Union (EU) regulations were included, as well as additional control measures that were applied during the Dutch epidemic. To adapt InterCSF as closely as possible to the Dutch 1997/98 epidemic, data from the real epidemic were analysed. Both disease spread and disease-control parameters were thus specifically based on the real epidemic. In general, InterSpread turned out to be a flexible tool that could be adapted to simulate another disease with relative ease. The most difficult were the modifications necessary to mimic the real epidemic as closely as possible. The model was well able to simulate an epidemic with a similar pattern over time for number of detected farms as the real outbreak; but the absolute numbers were (despite many relevant modifications) not exactly the same--but were within an acceptable range. Furthermore, the development of InterCSF provided the researchers with a better insight into the existing knowledge gaps. In part II (see the final paper in this issue), InterCSF was used to compare various control strategies as applied to this epidemic.

Animal Husbandry↗
PubMed2006

Single chain in mean field simulations: quasi-instantaneous field approximation and quantitative comparison with Monte Carlo simulations.

The description of fluctuations by single chain in mean field (SCMF) simulations is discussed and the results of this particle-based self-consistent field technique are quantitatively compared to Monte Carlo simulations of the same discretized Edwards-Hamiltonian providing exact reference data. In SCMF simulations one studies a large ensemble of noninteracting molecules subjected to real, external fields by Monte Carlo simulations. The external fields approximate nonbonded, instantaneous interactions between molecules. In the self-consistent mean field theory the external fields are static and fluctuation effects are ignored. In SCMF simulations, the external fields fluctuate since they are frequently recalculated from the instantaneous density distribution of the ensemble of molecules. In the limit of infinitely high density or instantaneous update of the external fields, the SCMF simulation method accurately describes long-wavelength fluctuations. At high but finite updating frequency the accuracy depends on the discretization of the model. The accuracy is illustrated by studying the single chain structure and intermolecular correlations in polymer melts, and fluctuation effects on the order-disorder transition of symmetric diblock copolymers.

Journal Article↗
PubMed1987

Simulation of genetic control of reproduction in beef cows. I. Simulation model.

A stochastic computer simulation model was constructed to predict the reproductive performance of beef cows as a function of the postpartum interval from calving to first estrus and the single-service conception rate. Phenotypic values for single-service conception rate were obtained by truncation of an assumed underlying normal phenotypic distribution at a point corresponding to a cumulative frequency of conception of .70. The underlying phenotypic distribution was derived as the sum of independent, normally-distributed additive genetic, permanent environmental and temporary environmental effects. The phenotypic frequency distribution for postpartum interval has been shown to be skewed toward large intervals. This distribution was simulated by combining normal distributions of additive genetic and permanent environmental effects with a strongly skewed Pearson III gamma distribution of temporary environmental effects. The simulated management system involved a 63-d breeding season, thereby allowing females up to three opportunities to conceive. The reproductive outputs that were simulated from postpartum interval and single-service conception rate included date of first service, first-service conception rate, number of services received, annual conception rate, calving date and postpartum interval. A normally-distributed 205-d weaning weight was also simulated and converted to an actual weaning weight by adjustment for calving date. General simulation results in terms of frequencies, means and standard deviations were compared with values found in the literature and found to provide a reasonable model of bovine reproductive performance.

Animals↗
PubMedDate not supplied

Simulating soft data to make soft data applicable to simulation.

BACKGROUND: Biomedical processes are often influenced by measures considered "non-crisp", "soft" or "subjective". Despite the growing awareness of the importance of such measures, they are rarely considered in biomedical simulation. This study introduces an input generator for soft data (input generator SD) that makes soft data applicable to simulation. MATERIALS AND METHODS: Machine learning approaches and standard regression techniques were applied to simulate odour intensity ratings. RESULTS: The performance of all the applied methods was satisfactory and the results can be used to modify systems biological mathematical models. CONCLUSION: Soft data should no longer be discounted in systems biological simulations. Exemplarily, it can be demonstrated that the input generator SD produces results that are similar to those that the simulated system can generate. Machine learning and/or appropriate conventional mathematical approaches may be applied to simulate noncrisp processes that can be used to modify mathematical models of any granularity.

Adult↗
PubMed1999

Multiple-task performance on a computer-simulated life support system during a space mission simulation.

This paper presents an experiment which examined the effects of isolation and confinement during a simulation of a short-term space mission. During the 7-day spaceflight simulation, four Canadian astronauts were tested daily on a 30-min performance task. The task, CAMS (Cabin Air Management System), represents a computer-based simulation of a generic life support system. As a multiple-task environment, it allows the measurement of a wide range of task management variables such as primary and secondary task performance, and system control activities. Measures of subjective state variables were also taken. The results did not show any evidence of serious performance decrements for any crew member. The analysis revealed different adjustment patterns with which crew members responded as a function of mission duration and variations in workload. Among the secondary tasks employed, prospective memory was found to be more sensitive than reaction time to increases in workload. The paper concludes with a discussion of the utility of spaceflight simulations and computer-based simulations of space work.

Adaptation, Psychological↗
PubMed2005

Framework-based design of a new all-purpose molecular simulation application: the Adun simulator.

Here we present Adun, a new molecular simulator that represents a paradigm shift in the way scientific programs are developed. The traditional algorithm centric methods of scientific programming can lead to major maintainability and productivity problems when developing large complex programs. These problems have long been recognized by computer scientists; however, the ideas and techniques developed to deal with them have not achieved widespread adoption in the scientific community. Adun is the result of the application of these ideas, including pervasive polymorphism, evolutionary frameworks, and refactoring, to the molecular simulation domain. The simulator itself is underpinned by the Adun Framework, which separates the structure of the program from any underlying algorithms, thus giving a completely reusable design. The aims are twofold. The first is to provide a platform for rapid development and implementation of different simulation types and algorithms. The second is to decrease the learning barrier for new developers by providing a rigorous and well-defined structure. We present some examples on the use of Adun by performing simple free-energy simulations for the adiabatic charging of a single ion, using both free-energy perturbation and the Bennett's method. We also illustrate the power of the design by detailing the ease with which ASEP/MD, an elaborated mean field QM/MM method originally written in FORTRAN 90, was implemented into Adun.

Algorithms↗
PubMed1990

The simulation of aerial movement--IV. A computer simulation model.

A computer simulation model of human airborne movement is described. The body is modelled as 11 rigid linked segments with 17 degrees of freedom which are chosen with a view to modelling twisting somersaults. The accuracy of the model is evaluated by comparing the simulation values of the angles describing somersault, tilt and twist with the corresponding values obtained from film data of nine twisting somersaults. The maximum deviations between simulation and film are found to be 0.04 revolutions for somersault, seven degrees for tilt and 0.12 revolutions for twist. It is shown that anthropometric measurement errors, from which segmental inertia parameters are calculated, have a small effect on a simulation, whereas film digitization errors can account for a substantial part of the deviation between simulation and film values.

Anthropometry↗
PubMed2004

Simulation of size-exclusion chromatography distribution coefficients of comb-shaped molecules in spherical pores comparison of simulation and experiment.

Simulations of the distribution coefficients of linear polymers and regular combs with various spacings between the arms have been performed. The distribution coefficients were plotted as a function of the number of segments in order to compare the size exclusion chromatography (SEC)-elution behavior of combs relative to linear molecules. By comparing the simulated SEC-calibration curves it is possible to predict the elution behavior of comb-shaped polymers relative to linear ones. In order to compare the results obtained by computer simulations with experimental data, a variety of comb-shaped polymers varying in side chain length, spacing between the side chains and molecular weights of the backbone were analyzed by SEC with light-scattering detection. It was found that the computer simulations could predict the molecular weights of linear molecules having the same retention volume with an accuracy of about 10%, i.e. the error in the molecular weight obtained by calculating the molecular weight of the comb-polymer based on a calibration curve constructed using linear standards and the results of the computer simulations are of the same magnitude as the experimental error of absolute molecular weight determination.

Algorithms↗
PubMed1994

Computer simulations of cyclic and acyclic cholinergic agonists: conformational search and molecular dynamics simulations.

Molecular dynamics simulations have been performed on aqueous solutions of two chemically similar nicotinic cholinergic agonists in order to compare their structural and dynamical differences. The cyclic 1,1-dimethyl-4-acetylpiperazinium iodide (HPIP) molecule was previously shown to be a strong agonist for nicotinic acetylcholine receptors (McGroddy et al., 1993), while the acyclic N,N,N,N'-tetramethyl-N'-acetylethylenediamine iodide (HTED) derivative is much less potent. These differences were expected to arise from differences in the solution structures and internal dynamics of the two molecules. HPIP was originally thought to be relatively rigid; however, molecular dynamics simulations suggest that the acetyl portion of the molecule undergoes significant ring dynamics on a psec timescale. The less constrained HTED molecule is relatively rigid, with only one transition observed about any of the major dihedrals in four 100 psec simulations, each started from a different conformation. The average structures obtained from the simulations are very similar to the starting minimized structure in each case, except for the HTED simulation where a single rotation about the N-C-C-N(+) backbone occurred. In each case, HTED had three to five more water molecules in its primary solvation shell than HPIP, indicating that differences in the energetics of desolvation before binding may partially explain the increased potency of HPIP as compared to HTED.

Biophysical Phenomena↗
PubMed2002

Theoretical simulation of oxygen tension measurement in the tissue using a microelectrode: II. Simulated measurements in tissues.

BACKGROUND AND PURPOSE: The objectives of this study were to make a computer simulation of tissues with different vascular structures and to simulate measurements of oxygen tension using an Eppendorf-like electrode in these tissues and to compare the response to radiation of the tissues with the real oxygen distributions (called input distribution) with the response to radiation of the tissues in which the oxygen distribution is given by the results of the simulated measurements (called output distribution). MATERIALS AND METHODS: The structure of various tissues and the measurements of oxygen tension using a microelectrode were simulated using a computer program. The mathematical model used combines the description of a gradient of tissue oxygenation and the electrode absorption process. RESULTS: We have compared the oxygen distributions resulting from diffusion (input) with those obtained from a simulation of measurements (output) for various tissues in the same points. Because the electrode measurement is an averaging process, the calculated oxygen distributions are different from the expected ones and the extreme high and low values are not detected. We have then calculated the survival curves describing the response to radiation if there is a small fraction of truly hypoxic cells (expected values) or a large fraction of cells at intermediate values (observed results) in order to determine the differences between them. CONCLUSIONS: The results of our study show that oxygen electrode measurements do not give the true distribution of pO(2) values in the tissue. However, our results do not contradict the numerous empirical correlations between the Eppendorf measurements of tumour oxygenation and the outcome of treatments. Measurement results will be misleading for modelling purposes since they do not reflect the actual distributions of oxygen tensions in the measured tissue. Decisions based on such modelling could be very dangerous, especially with respect to the clinical response of tumours to new treatments.

Cell Hypoxia↗
PubMedDate not supplied

Comparison of a virtual reality simulator and simulated limbs for phlebotomy training.

The current study compared the CathSim virtual reality simulator with simulated limbs for phlebotomy training. In the first experiment, medical students completed two 1-hour training sessions using 1 of the 2 methods. Afterward, the students' performance was assessed with both simulated limbs and genuine patients. The results showed that students trained with the simulated limbs achieved higher scores on both the posttest and the field test with actual patients than those trained on the CathSim system. In the second study, graduate students practiced with the CathSim system for 5 hours. The results showed a significant improvement in scores from pretest to posttest for these students. However, even after extended practice, their final scores did not differ from those of the medical students in the first experiment. Critical differences in design characteristics between the 2 systems may explain these findings. Although the authors observed a clear advantage for simulated limbs over the CathSim system, neither system faithfully represents all of steps needed to perform the procedure. Thus, training decisions may require that the unique advantages afforded by each system be considered.

Adult↗