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PubMed1986

3-dimensional computer simulation of depolarization and repolarization processes in the myocardium.

A computer algorithm for 3-dimensional computer simulation of electric phenomena in the human heart has been completed, in which the heart model consists of 50,000 functional cells arranged in the cubic close-packed structure and various waveforms of the action potential have been allotted to these functional cells. The present model allows one to estimate time courses of ECG, VCG, and body surface potential distribution from the P-wave up to the T-wave. It also can simulate electric phenomena in the heart with anomalies in the conduction system and the myocardium.

Action Potentials↗
PubMed2001

Cross-checking of nanoelectrospray ionization mass spectrometry and computer simulation for the evaluation of the interaction strength of non-covalently bound enkephalins in solution.

Nanoelectrospray ionization mass spectrometry (nanoESI-MS) and computer simulation were applied to the characterization of non-covalent interactions of [Leu5]-enkephalin (LE) and its optical isomers, [D-Tyr1, Leu5]-enkephalin (Y-LE), [D-Phe4, Leu5]-enkephalin (F-LE) and [D-Tyr1, D-Phe4, Leu5]-enkephalin (YF-LE). The dimer formation tendencies of the optical isomers of LE were evaluated by nanoESI-MS using quadruply deuterated LE (H2N-Tyr-(2,2-d2)Gly-(2,2-d2)Gly-Phe-Leu-COOH, d4-LE) as an internal standard. The relative interaction strengths of the optical isomers of LE were estimated to be Y-LE < F-LE < LE < YF-LE. Geometry optimization calculations were performed for interactions in vacuo and in water using a semi-empirical SCF method (PM3). The initial coordinate of the dimer structure of LE was taken from that obtained from single-crystalline x-ray diffraction analysis. Estimates of the interaction strengths of the dimer complexes were based on the heats of formation of a dimer complex (Hd) and the corresponding monomers (Hm) using the equation DeltaH = Hd - 2Hm. The values of DeltaH obtained from the calculations for interactions in water decreased in the order Y-LE > F-LE > LE > YF-LE. Since the smaller values of DeltaH correspond to stronger interactions between peptides, the results from computer simulations were qualitatively consistent with those obtained from the nanoESI experiments. The possibility of cross-checking these independent techniques was demonstrated using medium-sized molecules of biological importance. The agreement of the results from the two techniques suggested that nanoESI experiments, at least qualitatively, reflected the relative interaction strengths of non-covalently bound enkephalins in aqueous solution.

Computer Simulation↗
PubMed1965

SOME KINETIC PROPERTIES OF A DETERMINISTIC EPIDEMIC CONFIRMED BY COMPUTER SIMULATION.

Representative epidemic transients were generated by computer by a known, plausible mechanism. Accurate retrieval of the individual rate constants and confirmation of their predictive value resulted from a manual test of the mechanism by which the computer outputs were generated. The method is applicable in principle to any regenerative process opposed by exponential decay.

Computer Simulation↗
PubMed2000

Analyses of insulin-potentiating fragments of human growth hormone by computative simulation; essential unit for insulin-involved biological responses.

We analyzed the structural features of insulin-potentiating fragments of human growth hormone by computative simulations. The peptides were designated from the N-terminus sequences of the hormone positions at 1-15 (hGH(1-15); H2N-Phe1-Pro2-Thr3-Ile4-Pro5-Leu6-Ser7-Arg8-L eu9-Phe10-Asp11-Asn12-Ala13-Met14-Leu15 -COOH), 6-13 (hGH(6-13)), 7-13 (hGH(7-13)) and 8-13 (hGH(8-13)), which enhanced insulin-producing hypoglycemia. In these peptide molecules, ionic bonds were predicted to form between 8th-arginyl residue and 11th-aspartic residue, and this intramolecular interaction caused the formation of a macrocyclic structure containing a tetrapeptide Arg8-Leu9-Phe10-Asp11. The peptide positions at 6-10 (hGH(6-10)), 9-13 (hGH(9-13)) and 10-13 (hGH(10-13)) did not lead to a macrocyclic formation in the molecules, and had no effect on the insulin action. Although beta-Ala13hGH(1-15), in which the 13th-alanine was replaced by a beta-alanyl residue, had no effect on insulin-producing hypoglycemia, the macrocyclic region (Arg8-Leu9-Phe10-Asp11) was observed by the computative simulation. An isothermal vibration analysis of both of beta-Ala13hGH(1-15) and hGH(1-15) peptide suggested that beta-Ala13hGH(1-15) is molecule was more flexible than hGH(1-15); C-terminal carboxyl group of Leu15 easily accessed to Arg8 and inhibited the ionic bond formation between Arg8 and Asp11 in beta-Ala13hGH(1-15). The peptide of hGH(8-13) dose-dependently enhanced the insulin-involved fatty acid synthesis in rat white adipocytes, and stabilized the C6-NBD-PC (1-acyl-2-[6-[(7-nitro-2,1,3benzoxadiazol-4-yl)amino]-caproyl]-sn- glycero-3-phosphatidylcholine) model membranes. In contrast, hGH(9-13) had no effect both on the fatty acid synthesis and the membrane stability. In the same culture conditions as the fatty acid synthesis assay, hGH(8-13) had no effect on the transcript levels of glucose transporter isoforms (GLUT 1, 4) and hexokinase isozymes (HK I, II) in rat white adipocytes. Judging from these results we considered that the macrocyclic structure in human growth hormonal peptides is regarded with the modification of insulin action, and hGH(8-13) is an essential sequence for the modification of insulin action. This hGH(8-13) peptide modifies the insulin action via stabilizing the cell membrane, and does not directly act on the insulin-involved glucose metabolism.

Adipocytes↗
PubMed2005

A study of hominin dispersal out of Africa using computer simulations.

A study of hominin dispersal out of Africa using computer simulations is presented. Attention is focused on the joint probability of the colonization of Western Europe later than 1 Ma and that of Eastern Asia prior to 1.6 or 1.8 Ma, as current archaeological estimates suggest. We found that the determinant factor to hominin dispersal is the mode of hominin movement. If the movement of all populations is uniform and their number great enough, greater than 300 in our models, then such movement favors the colonization of Eastern Asia and Western Europe at more or less the same time. On the other hand, the colonization acquires prominent probabilistic features if the number of populations migrating is small enough, smaller than 10 in our models, or when all hominin populations may move but there are only a few with much higher mobility. In this case, the joint probability for the earliest dispersals of hominins in Western Europe after 1 Ma and Eastern Asia prior to 1.6 Ma ranges from 0.02 to 0.05. The single probability of colonization of Western Europe after 1 Ma is very high, about 0.5 for the majority of the colonization routes, whereas the corresponding probability of the colonization of Eastern Asia prior to 1.6 Ma is ten times lower, about 0.05. The least probable event is the earliest colonization of Java prior to 1.6 Ma, to which our simulation attributes a probability of ca 0.01. Deserts, mountains, and mountain ranges may delay the arrival at a certain location; nevertheless, their effect on the joint probability is very small.

Africa↗
PubMed2002

Evaluation in health informatics: computer simulation.

The evaluation of complex medical informatics applications involves not only the information system, but also its impact on the organizational environment in which it is implemented. In instances where these applications cannot be evaluated with traditional experimental methods, computer simulation provides a flexible approach to evaluation. The construction of a computer simulation model involves the development of a model that represents important aspects of the system under evaluation. Once validated, the model can be used to study the effects of variation in system inputs, differences in initial conditions and changes in the structure of the system. Three examples are discussed, namely, a wide-area health care network, physician order entry into a hospital information system, and the use of an information system designed to prevent medical errors that lead to adverse drug events in hospitals.

Computer Simulation↗
PubMed2006

Achieving plane-wise uniform B1 amplitude in a 3D volume for high-field MRI: a computer simulation study.

PURPOSE: To demonstrate the possibility of achieving plane-wise uniform B(1) field amplitude for human head imaging with an array coil configuration by using computer simulations. MATERIALS AND METHODS: We considered the use of an excitation array coil that employed composite excitation elements. Each composite excitation element consisted of three small current loops centered close to each other with axes along the x, y, and z directions, respectively. The excitation elements were distributed to surround a model human head. The vector B(1) field from each current loop was calculated using the FDTD numerical method at 170 MHz. Analytical target RF field patterns with plane-wise uniform B(1) field amplitude were derived and approximately constructed from the fields of individual current loops through a least-squares procedure. RESULTS: The RF field patterns generated by the computer simulations closely followed the target field patterns. Highly uniform B(1) field amplitude was obtained within parallel sagittal planes or parallel axial-to-coronal oblique planes in the brain with the expected plane-to-plane variations. CONCLUSION: In principle, patterns of B(1) amplitude distribution with a high degree of plane-wise homogeneity can be achieved simultaneously in multiple parallel planes in a 3D volume.

Brain↗
PubMed2004

Computer simulation as a component of catheter-based training.

INTRODUCTION: Computer simulation has been used in a variety of training programs, ranging from airline piloting to general surgery. In this study we evaluate the use of simulation to train novice and advanced interventionalists in catheter-based techniques. METHODS: Twenty-one physicians underwent evaluation in a simulator training program that involved placement of a carotid stent. Five participants were highly experienced in catheter-based techniques (>300 percutaneous cases), including carotid angioplasty and stenting (CAS); the remaining 16 participants were interventional novices (<5 percutaneous cases). The Procedicus VIST simulator, composed of real-time vascular imaging simulation software and a tactile interface coupled to angiographic catheters and guide wires, was used. After didactic instruction regarding CAS and use of the simulator, each participant performed a simulated CAS procedure. The participant's performance was supervised and evaluated by an expert interventionalist on the basis of 50 specific procedural steps with a maximal score of 100. Specific techniques of guide wire and catheter manipulation were subjectively assessed on a scale of 0 to 5 points based on ability. After evaluation of the initial simulated CAS procedure, each participant received a minimum of 2 hours of individualized training by the expert interventionalist, with the VIST simulator. Each participant then performed a second simulated CAS procedure, which was graded with the same scale. After completion, participants assessed the training program and its utility via survey questionnaire. RESULTS: The average simulated score for novice participants after the training program improved significantly from 17.8 +/- 15.6 to 69.8 +/- 9.8 (P < .01), time to complete simulation decreased from 44 +/- 10 minutes to 30 +/- 8 minutes (P < .01), and fluoroscopy time decreased from 31 +/- 7 minutes to 23 +/- 7 minutes ( P < .01). No statistically significant difference in score, total time, or fluoroscopy time was noted for experienced interventionalists. Improvement was noted in guide wire and catheter manipulation skills in novices. Analysis of survey data from experienced interventionalists indicated that the simulated clinical scenarios were realistic and that the simulator could be a valuable tool if clinical and tactile feedback were improved. Novices also thought the simulated training was a valuable experience, and desired further training time. CONCLUSIONS: An endovascular training program using the Procedicus VIST haptic simulator resulted in significant improvement in trainee facility with catheter-based techniques in a simulated clinical setting. Novice participants derived the greatest benefit from simulator training in a mentored program, whereas experienced interventionalists did not seem to derive significant benefit.

Blood Vessel Prosthesis Implantation↗
PubMed1989

Computer simulation of liquid crystals.

We review recent progress in the computer simulation of liquid crystals, with special emphasis on hard particle models. Surprisingly, the simplest molecular models, taking account only of molecular size and shape, are sufficient to generate a wide variety of liquid crystalline phases, closely analogous to those observed in real life. Thermodynamic stability of different phases is very sensitive to shape, and presumably will also be sensitive to further details of intermolecular interactions as they are incorporated into the model. Realistic atom-atom potential models of liquid crystals are available, but the associated simulations are quite expensive. Thus, while idealized models may be used to study quite general, fundamental properties of mesophases, the modelling of specific liquid crystal systems in a realistic way remains a great challenge. Progress continues to be made on both these fronts.

Chemical Phenomena↗
PubMed1999

Computer simulation of protein-protein association kinetics: acetylcholinesterase-fasciculin.

Computer simulations were performed to investigate the role of electrostatic interactions in promoting fast association of acetylcholinesterase with its peptidic inhibitor, the neurotoxin fasciculin. The encounter of the two macromolecules was simulated with the technique of Brownian dynamics (BD), using atomically detailed structures, and association rate constants were calculated for the wild-type and a number of mutant proteins. In a first set of simulations, the ordering of the experimental rate constants for the mutant proteins was correctly reproduced, although the absolute values of the rate constants were overestimated by a factor of around 30. Rigorous calculations of the full electrostatic interaction energy between the two proteins indicate that this overestimation of association rates results at least in part from approximations made in the description of interaction energetics in the BD simulations. In particular, the initial BD simulations neglect the unfavourable electrostatic desolvation effects that result from the exclusion of high dielectric solvent that accompanies the approach of the two low dielectric proteins. This electrostatic desolvation component is so large that the overall contribution of electrostatics to the binding energy of the complex is unlikely to be strongly favourable. Nevertheless, electrostatic interactions are still responsible for increased association rates, because even if they are unfavourable in the fully formed complex, they are still favourable at intermediate protein-protein separation distances. It therefore appears possible for electrostatic interactions to promote the kinetics of binding even if they do not make a strongly favourable contribution to the thermodynamics of binding. When an approximate description of these electrostatic desolvation effects is included in a second set of BD simulations, the relative ordering of the mutant proteins is again correctly reproduced, but now association rate constants that are much closer in magnitude to the experimental values are obtained. Inclusion of electrostatic desolvation effects also improves reproduction of the experimental ionic strength dependence of the wild-type association rate.

Acetylcholinesterase↗
PubMed1999

Computer simulations of the mechanical properties of metals.

Atomic-scale computer simulations can be used to gain a better understanding of the mechanical properties of materials. In this paper we demonstrate how this can be done in the case of nanocrystalline copper, and give a brief overview of how simulations may be extended to larger length scales. Nanocrystline metals are metals with grain sizes in the nanometre range, they have a number of technologically interesting properties such as much increased hardness and yield strength. Our simulations show that the deformation mechanisms are different in these materials than in coarse-grained materials. The main deformation is occurring in the grain boundaries, and only little dislocation activity is seen inside the grains. This leads to a hardening of the material as the grain size is increased, and the volume fraction of grain boundaries is decreased.

Computer Simulation↗
PubMed1994

Computer simulation of protein-induced structural changes in closed circular DNA.

The effect of protein-induced wrapping on overall DNA folding is studied using Monte Carlo computer simulation techniques. A new modeling scheme is devised to represent configurations of closed circular DNA containing fragments of the double helix partially wrapped around a core of proteins. The DNA consists of two regions, a fragment wrapped in a left-handed superhelical path around a 'phantom' protein core and a free connecting loop. The loop has at least one single-stranded scission so that it can assume a torsionally relaxed state. The configuration of the loop is varied during the course of the computer simulations and the three-dimensional spatial arrangements of lowest total energy are identified. The axis of the DNA loop is represented by a finite three-dimensional Fourier series perturbation of an initial Bézier curve, making it possible to fix the position and orientation of the chain ends as well as the contour length of the free loop. The energy is approximated by elastic terms for the bending and twisting of the DNA and an excluded volume contribution that prevents the self-intersection of sequentially distant chain segments. The proportions of the protein-DNA complex, the number of superhelical turns, the chain length and the imposed linking number difference of the closed DNA are varied in the calculations. The resulting minimum energy structures are consistent with physical models and suggest new ways to think about how proteins add and remove supercoils from DNA. Of special note in this regard is the sudden collapse of three-dimensional structure that accompanies small incremental wrapping of the DNA around the idealized protein core. These observations offer new structural insight into the mechanisms of action of proteins which add or remove supercoils from DNA and provide a first step in thinking about the activity of such systems at the chemical level whereby small fluctuations in local molecular structure are translated into large-scale macromolecular changes. The configurations identified in the simulations can also be examined in the context of the well known "linking number paradox" associated with nucleosome formation on closed circular plasmids. The findings bear relevance to DNA with natural curvature as well as to protein-induced bending and deformations of the double helix.

Computer Simulation↗
PubMedDate not supplied

Pathways of coronary care--a computer-simulation model of the potential for health gain.

A computer-simulation model of the need for cardiology services is described. The model simulates the potential for health gain, in terms of a fall in mortality, determining the effect of alterations in prevention and treatment rates. The model was initially developed from a pathways-of-care flow chart, which originated from a working group consisting of a consultant cardiac surgeon, cardiologists, and public-health physicians, together with statisticians and an operational-research analyst. The original purpose of the model was as a communication tool, to help nonclinicians to have a better understanding of how and why doctors work as they do, but it has since been developed for use in setting and meeting health targets. It enables quantification of the effects of changing different combinations of key variables over time. It is designed to answer 'what if?' questions of the type 'What would the effect of a 10% reduction in the incidence of angina be on the number of deaths, angiograms, angioplasties, and coronary-artery bypass grafts. The model has been made available in a form which only requires a Lotus 123 spreadsheet package to enable it to run, and it is designed to be easy to use with the assistance of simple two-key commands throughout. The model has been used by district health authorities to calculate the response required in their own local areas to achieve targets for the year 2000.

Adult↗
PubMed2005

Computer simulation study of intermolecular voids in unsaturated phosphatidylcholine lipid bilayers.

Computer simulation of the liquid crystalline phase of five different hydrated unsaturated phosphadidylcholine (PC) lipid bilayers, i.e., membranes built up by 18:0/18:1omega9cis PC, 18:0/18:2omega6cis PC, 18:0/18:3omega3cis PC, 18:0/20:4omega6cis PC, and 18:0/22:6omega3cis PC molecules have been performed on the isothermal-isobaric ensemble at 1 atm and 303 K. (The notation n:domegapcis specifies the lipid tails: n refers to the total number of carbon atoms in the chain, d is the number of the methylene-interrupted double bonds, p denotes the number of carbons between the chain terminal CH(3) group and the nearest double bond, and cis refers to the conformation around the double bonds.) The characteristics of the free volume in these systems have been analyzed by means of a generalized version of the Voronoi-Delaunay method [M. G. Alinchenko et al., J. Phys. Chem. B 108, 19056 (2004)]. As a reference system, the hydrated bilayer of the saturated 14:014:0 PC molecules (dimyristoylphosphatidylcholine) has also been analyzed. It has been found that the profiles of the fraction of the free volume across the membrane exhibit a rather complex pattern. This fine structure of the free volume fraction profiles can be interpreted by dividing the membrane into three separate major zones (i.e., zones of the aqueous, polar, and apolar parts of the membrane) and defining five subzones within these zones according to the average position of various atomic groups in the membrane. The fraction of the free volume in the middle of the membrane is found to increase with increasing unsaturation of the sn-2 chain of the lipid molecule. This is due to the fact that with increasing number of methylene-interrupted double bonds the lipid tails become more flexible, and hence they do not extend to the middle of the membrane. It is found that there are no broad enough preformed channels in the bilayers through which small penetrants, such as water molecules, can readily go through; however, the existing channels can largely facilitate the permeation of these molecules.

Computer Simulation↗
PubMed1995

Indo-European origins: a computer-simulation test of five hypotheses.

Allele frequency distributions were generated by computer simulation of five models of microevolution in European populations. Genetic distances calculated from these distributions were compared with observed genetic distances among Indo-European speakers. The simulated models differ in complexity, but all incorporate random genetic drift and short-range gene flow (isolation by distance). The best correlations between observed and simulated data were obtained for two models where dispersal of Neolithic farmers from the Near East depends only on population growth. More complex models, where the timing of the farmers' expansion is constrained by archaeological time data, fail to account for a larger fraction of the observed genetic variation; this is also the case for a model including late Neolithic migrations from the Pontic steppes. The genetic structure of current populations speaking Indo-European languages seems therefore to largely reflect a Neolithic expansion. This is consistent with the hypothesis of a parallel spread of farming technologies and a proto-Indo-European language in the Neolithic. Allele-frequency gradients among Indo-European speakers may be due either to incomplete admixture between dispersing farmers, who presumably spoke proto-Indo-European, and pre-existing hunters and gatherers (as in the traditional demic diffusion hypothesis), or to founder effects during the farmers' dispersal. By contrast, successive migrational waves from the East, if any, do not seem to have had genetic consequences detectable by the present comparison of observed and simulated allele frequencies.

Alleles↗
PubMed1998

A computer simulation study of cortical imaging from scalp potentials.

In this paper, computer simulation studies were conducted to test the feasibility of imaging brain electrical activity from the scalp electroencephalograms. The inhomogeneous three-concentric-sphere head model was used to represent the head volume conductor. Closed spherical dipole layers, consisting of several thousand uniformly distributed dipoles, were used to reconstruct the cortical potential maps corresponding to neuronal sources located inside the brain. Simulation results indicate that the present procedure can image both cortical and deep sources, and for the cortical sources, a spatial resolution as high as 1.2 cm can be achieved.

Brain↗
PubMed1999

Computer Simulation Modeling for Recreation Management: A Study on Carriage Road Use in Acadia National Park, Maine, USA.

/ The number of visits to outdoor recreation areas has increased dramatically in the last three decades, leading managers and researchers to wonder if there is a limit to the amount of use a resource such as a park can accommodate. One of the difficulties in addressing this carrying capacity-related question has been the complex nature of visitor travel patterns on often extensive networks of roads and trails. Systematic direct observation is often impractical and anecdotal information is usually inadequate. This study explores the utility of computer simulation as a tool for describing visitor travel by building a dynamic model of visitor travel on the carriage roads of Acadia National Park, Maine, USA. The simulation model uses empirical inputs such as travel routes and travel speeds to generate simulated recreation days on the carriage roads. Data on persons-per-viewscape (PPV) conditions were then gathered from multiple model runs and incorporated into the National Park Service's visitor experience and resource protection (VERP) planning process. Results show that PPV conditions under present-day use levels do not violate proposed standards of quality. Results also show likely PPV conditions under scenarios of increasing use and in different areas within the carriage road system. Goodness-of-fit validity tests indicate the model is an accurate representation of the actual system. The findings of this study suggest that computer simulation is useful for estimating current carrying capacity conditions, predicting future conditions, and guiding related research. KEY WORDS: Computer simulation modeling; Carrying capacity; Recreation management; Acadia National Park

Journal Article↗
PubMed2002

Behavioral observations and computer simulations of blue crab movement to a chemical source in a controlled turbulent flow.

The behavior of crabs tracking odor in turbulent chemical plumes was compared to the performance of computer simulations of search behavior operating in similar chemical signal environments. The movement of blue crabs (Callinectes sapidus) towards a source of food odor was studied in controlled flow conditions in a flume. The evolving chemical stimulus field of a similar chemical source in an equivalent flow environment was captured by recording concentration patterns of a fluorescent tracer. Hypotheses about the sensory mechanisms employed by the crabs were tested by computer simulation using the recorded fluorescence as the stimulus. The results demonstrate that a simple model combining chemotropotaxis (simultaneous, spatial comparisons of chemical signals) and odor-stimulated upstream movement (rheotaxis) is sufficient to explain the efficient movements towards the source displayed by foraging crabs. Spatial integration around each sensor improves performance significantly, but the number of sensors does not have a large impact on performance. The weighting of information from chemical versus flow signals can substantially change simulation performance, resulting in more or less congruence between the behavior of simulations and that of crabs, which suggests the general importance of both sources of information for successful odor-guided navigation.

Animals↗