The lognormal distribution of the incubation time of exogenous diseases. Genetic interpretations and a computer simulation.
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Computers↗
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Accuracy of distance measurement in the bat Eptesicus fuscus: theoretical aspects and computer simulations.
Behavioral experiments of Simmons [J. Acoust. Soc. Am. 54, 157-173 (1973) and Science 204, 1336-1338 (1979)] on the ranging accuracy in the bat Eptesicus fuscus have led to far-reaching postulates on the existence of optimal and phase-conserving processing mechanisms in the bat. In this paper, the results of computer simulations of these experiments are presented. Two receiver types are investigated: the fully coherent cross-correlation receiver and the cross-correlation receiver with envelope processing (semicoherent). It is shown that Simmons' experiments cannot be treated as a simple estimation of distance, but require at least two (range difference experiment; see Simmons, 1973) or four (range jitter experiment; see Simmons, 1979) echolocation sounds for one decision. The performance of the bat in both experiments is much worse than predicted for a coherent and a semicoherent receiver type. The bat's accuracy in Simmons' range difference experiment is at least 18 dB worse than predicted for an optimal receiver. The results of the jitter experiment cannot be interpreted in a simple way as proof that bats are able to evaluate phase information as in a fully coherent cross-correlation receiver.
Animals↗
Computer simulation of the cellular immune response to malignant lymphoid cells: logic of approach, model design and laboratory verification.
A computer model was constructed to simulate the lymphocyte-mediated destruction of line Ib malignant lymphoid cells (Ib cells) as they circulated through the major tissue compartments of immune syngeneic C58 mice. The technique of discrete-event simulation was used to account for the arterial and venous circulation of blood-borne Ib cells through the lung, spleen, liver, and carcass. Simulation was carried out by means of IBM computer program 360, using the technique of General Purpose System Simulation. The parameters analysed were the mean residence times of viable and killed Ib cells in each tissue compartment, the rate or proliferation of Ib cells, the rate of generation of cytotoxic splenic lymphocytes, the rate of lysis of 51Cr labelled Ib cells, and the organ-specific rate constants for target cell kill. Direct laboratory measurements of these parameters validated the model and made it possible to calibrate computer simulations by the technique of best-fit analysis. The computer modelling technique accurately simulated the growth of viable Ib cells in vivo and the retention times of 51Cr in the spleen, lung, liver and carcass when viable or heat-killed Ib cells were inoculated intravenously (i.v.) into normal and immune mice. Computer simulations quantitatively defined the mean residence times of viable and heat-killed Ib cells in the major tissue compartments and the mean rate constants for target cell lysis in such compartments. The applicability of modelling approach to an analysis of immunological phenomena is discussed.
Animals↗
Computer simulation as a teaching aid in pharmacy management--Part 1: Principles of accounting.
The need for pharmacists to develop management expertise through participation in formal courses is now widely acknowledged. Many schools of pharmacy lay the foundations for future management training by providing introductory courses as an integral or elective part of the undergraduate syllabus. The benefit of such courses may, however, be limited by the lack of opportunity for the student to apply the concepts and procedures in a practical working environment. Computer simulations provide a means to overcome this problem, particularly in the field of resource management. In this, the first of two articles, the use of a computer model to demonstrate basic accounting principles is described.
Accounting↗
Comparison of phantom and computer-simulated MR images of flow in a convergent geometry: implications for improved two-dimensional MR angiography.
The signal loss that occurs in regions of disturbed flow significantly decreases the clinical usefulness of MR angiography in the imaging of diseased arteries. This signal loss is most often attributed to turbulent flow; but on a typical MR angiogram, the signal is lost in the nonturbulent upstream region of the stenosis as well as in the turbulent downstream region. In the current study we used a flow phantom with a forward-facing step geometry to model the upstream region. The flow upstream of the step was convergent, which created high levels of convective acceleration. This region of the flow field contributes to signal loss at the constriction, leading to overestimation of the area of stenosis reduction. A computer program was designed to simulate the image artifacts that would be caused by this geometry in two-dimensional time-of-flight MR angiography. Simulated images were compared with actual phantom images and the flow artifacts were highly correlated. The computer simulation was then used to test the effects of different orders of motion compensation and of fewer pixels per diameter, as would be present in MR angiograms of small arteries. The results indicated that the computational simulation of flow artifacts upstream of the stenosis provides an important tool in the design of optimal imaging sequences for the reduction of signal loss.
Arteriosclerosis↗
Development of frontal impact crashworthy wheelchair seating design criteria using computer simulation.
When designing wheelchairs for use as motor vehicle seats, special design criteria must be followed to assure the crash safety of the wheelchair user. Failure of seating system components under crash loading conditions could lead to serious injury or fatality. In this study, seat and seat-back loading in a frontal crash are explored using computer simulation techniques. A previously validated simulation model consisting of a powerbase wheelchair and a seated 50th-percentile male test dummy subjected to a 20g/30mph frontal impact were used for the study. Since such a wide range of seating systems are available, parametric analyses were conducted to evaluate the influence of surface stiffness and seat-back angle on wheelchair seat and back loading. Seat loading varied with stiffness, ranging from 819-3,273 lb., while seat-back loading was found to be between 1,427-2,691 lb., depending upon back stiffness and recline angle.
Accidents, Traffic↗
Computer simulation of the breakdown of carrot particles during human mastication.
There are two separable aspects of the mastication of food particles. One aspect describes the probability of the selection of particles for fracture (selection); the other describes the manner of fragmentation of the particles (breakage). Definitions of these concepts were used to produce an approximate equation for food breakdown, which can be solved by iteration in a computer. Values for the selection and breakage functions, obtained from 10 human subjects using carrot as a test food, were used in a computer program which modelled mastication. The model assumed (1) that selection depended only on particle size (2) that fragmentation (range of fractions or sub-particles produced) was similar for all particles, whatever their size. Good agreement was found between the actual particle-size distributions produced by mastication and those distributions generated by the computer. Simulations predicted that the initial particle size of the carrot before mastication could be varied substantially, so producing similar particle-size distributions after 15 chews.
Computers↗
Applications of simulator computed tomography number for photon dose calculations during radiotherapy treatment planning.
PURPOSE: To study the variation of computed tomography (CT) number from a simulator-based scanner and the effect of this variation on photon-dose calculations. METHOD AND MATERIALS: CT images of a cylindrical phantom with multiple inserts were obtained using a commercially-available simulator-CT (Ximatron: Varian, Palo Alto, CA). The linear correlation coefficient and Chi-square methods were used to determine the X-ray effective energy in a phantom. CT numbers in Hounsfield units (HU) were measured as a function of phantom size, orientation, field of view (FOV), distance from the center, and time for various inserts. The change of dose calculations due to the CT number variations was then determined using the equivalent path-length (EPL) and collapsed cone convolution methods. RESULTS AND DISCUSSION: A significant beam-hardening effect was observed for the simulator-CT. Consequently, the CT number from the sim-CT was more sensitive to the size of the phantom than those from a conventional CT. The sim-CT number is not sensitive to the locations within the phantom and is stable over a 6-week period. It is important to use the proper FOV for sim-CT studies; scanning a small polystyrene phantom using a large FOV may result in an increase of l20 HU in CT number at the center of the field. However, the dose-calculation variations, due to the CT number uncertainty, do not exceed 2-3% for 6-18 MV photon beams. CONCLUSION: The simulator CT images were acquired with patients in the treatment position, and these CT numbers are useful for CT-based dose calculations.
Algorithms↗
A blood ordering strategy for hospital blood banks derived from a computer simulation.
The ultimate goal of a hospital blood bank inventory control programs is to reduce wastage of blood products and unnecessary use of laboratory services without jeopardizing patient safety. The development of a practical blood ordering policy at the hospital level is an integral part of any such program. In order to explore various blood ordering options in detail, a computer simulation of a hospital blood inventory was used to assess the impact on blood band performance measures of reductions in group O and non-group-O levels from baseline levels, assuming both a 21-day and 35-day shelf life. On the basis of data derived from this study showing that such inventory reductions accompanied by partial protection of the group O inventory will not result in significant shortages, a practical strategy was developed for establishing optimal target inventory levels for a hospital on an empirical basis. These target levels can serve as a guide for subsequent blood ordering. A step-by-step approach for analyzing a hospital blood inventory control program is then suggested, accompanied by an action plan for implementing change which incorporates the experimentally-derived blood ordering strategy. Adherence to this plan should result in a low outdate rate, a reduction in unnecessary cross-matching, and greater availability of blood for those patients with a legitimate need for it.
ABO Blood-Group System↗
Computer simulation study of the global phase behavior of linear rigid Lennard-Jones chain molecules: comparison with flexible models.
The global phase behavior (i.e., vapor-liquid and fluid-solid equilibria) of rigid linear Lennard-Jones (LJ) chain molecules is studied. The phase diagrams for three-center and five-center rigid model molecules are obtained by computer simulation. The segment-segment bond lengths are L = sigma, so that models of tangent monomers are considered in this study. The vapor-liquid equilibrium conditions are obtained using the Gibbs ensemble Monte Carlo method and by performing isobaric-isothermal NPT calculations at zero pressure. The phase envelopes and critical conditions are compared with those of flexible LJ molecules of tangent segments. An increase in the critical temperature of linear rigid chains with respect to their flexible counterparts is observed. In the limit of infinitely long chains the critical temperature of linear rigid LJ chains of tangent segments seems to be higher than that of flexible LJ chains. The solid-fluid equilibrium is obtained by Gibbs-Duhem integration, and by performing NPT simulations at zero pressure. A stabilization of the solid phase, an increase in the triple-point temperature, and a widening of the transition region are observed for linear rigid chains when compared to flexible chains with the same number of segments. The triple-point temperature of linear rigid LJ chains increases dramatically with chain length. The results of this work suggest that the fluid-vapor transition could be metastable with respect to the fluid-solid transition for chains with more than six LJ monomer units.
Journal Article↗
Displacement of the diaphragmatic echo by hepatic cysts: a new explanation with computer simulation.
Previous demonstrations of distal displacement of interfaces deep to cystic structures have been based on only the slower speed of sound through the cystic structure, which has been postulated to cause an apparent discontinuity in the echo from the diaphragm deep to a cyst. The authors found cysts whose identification could not be explained by this theory because they were too small or the diaphragm was displaced in such a manner that the explanation would not hold true. They propose that, in addition to the slowing of the speed of sound through the cyst, refraction at the edge of the cyst can cause the apparent discontinuity. Since the machine does not distinguish the sound beam as having been refracted, the echo is displayed at the appropriate distance along the vector in the direction in which the transducer was pointing at the time. A computer simulation is used to confirm this theory.
Computers↗
Turning field size and its effects upon computer-simulated klinotactic orientation.
The turning field is defined in the context of klinotaxis as the angular region(s) into which an organism may direct itself at any point in time and space while orienting within a stimulus gradient. The turning field size determines the size distribution of turns an organism can make during klinotaxis. Changes in turning field size affect the efficiency of klinotactic source location as measured by computer simulations of ideal behaviors. The optimal field size lies between 90 and 150 degrees. Turning field size also affects the appearance of search paths made by organisms locating an attractant source. The significance of turning field size is discussed and the described klinotactic model is proposed as a predictive model for orientation research.
Animals↗
Computational simulations of stem-cell factor/c-kit receptor interaction.
Stem-cell factor (SCF) is a noncovalent homodimeric cytokine that exhibits profound biological function in the early stages of hematopoiesis by binding to a cell surface tyrosine kinase receptor that is encoded by the c-Kit proto-oncogene. The results obtained from a combined implementation of homology-based molecular modeling and computational simulations in the study of species-specific SCF/ c-Kit interactions are reported. The structural models of the human and rat SCF ligands are based on the close structural similarity to the cytokine M-CSF, whose C alpha structure has recently become available. The constant domains of the human Fc fragment are used as a template for the ligand binding domains of the c-Kit receptor. The factors responsible for the stabilization of the SCF quaternary structure and the molecular determinants for ligand recognition and ligand specificity have been identified by assessing the conformational, topographical, and dynamic features of the isolated ligands and of the ligand-receptor complexes.
Animals↗
Computer simulation of an ideal lateral inhibition function.
A model for lateral inhibition is presented in the context of the auditory channel. The mechanical analyzing system of the inner ear cannot alone account for the frequency resolution of hearing. Some additional mechanism, possibly lateral inhibition located in the auditory neural network, is needed to achieve the frequency selectivity observed in electrophysiological and psychoacoustical experiments. In a computer simulation study, the shape of an ideal lateral inhibition function was obtained. Such a function is applicable to all sensory modalities. In hearing, this function permits the sharpest possible frequency resolution as it can completely remove the frequency desharpening effect of the mechanical properties of the basilar membrane. In vision, it can compensate for abberations caused by the imperfections of the optical system of the eye.
Animals↗
On investigating the statistical properties of the populous path algorithm by computer simulation. Counterconclusions to those of Tateno and Nei.
Goodman et al.'s (1974) populous path algorithm for estimating hidden mutational change in protein evolution is designed to be used as an adjunct to the maximum parsimony method. When the algorithm is so used, the augmented maximum parsimony distances, far from being overestimates, are underestimates of the actual number of nucleotide substitutions which occur in Tateno and Nei's (1978) computer simulation by the Poisson process model, even when the simulation is carried out at two and a half times the sequence density. Although underestimates, our evidence shows that they are nevertheless more accurate than estimates obtained by a Poisson correction. In the maximum parsimony reconstruction, there is a bias towards overrepresenting the number of shared nucleotide identities between adjacent ancestral and descendant nodal sequences with the bias being stronger in those portions of the evolutionary tree sparser in sequence data. Because of this particular property of maximum parsimony reconstructed sequences, the conclusions of Tateno and Nei concerning the statistical properties of the populous path algorithm are invalid. We conclude that estimates of protein evolutionary rates by the maximum parsimony--populous path approach will become more accurate rather than less as larger numbers of closely related species are included in the analysis.
Biological Evolution↗
Kinetics of protein-protein association explained by Brownian dynamics computer simulation.
Protein-protein bond formations, such as antibody-antigen complexation or aggregation of protein monomers into dimers and larger aggregates, occur with bimolecular rate constants on the order of 10(6) M-1.s-1, which is only 3 orders of magnitude slower than the diffusion-limited Smoluchowski rate. However, since the protein-protein bond requires rotational alignment to within a few angstroms of tolerance, purely geometric estimates would suggest that the observed rates might be 6 orders of magnitude below the Smoluchowski rate. Previous theoretical treatments have not been solved for the highly specific docking criteria of protein-protein association--the entire subunit interface must be aligned within 2 A of the correct position. Several studies have suggested that diffusion alone could not produce the rapid association kinetics and have postulated "lengthy collisions" and/or the operation of electrostatic or hydrophobic steering forces to accelerate the association. In the present study, the Brownian dynamics simulation method is used to compute the rate of association of neutral spherical model proteins with the stated docking criteria. The Brownian simulation predicts a rate of 2 x 10(6) M-1.s-1 for this generic protein-protein association, a rate that is 2000 times faster than that predicted by the simplest geometric calculation and is essentially equal to the rates observed for protein-protein association in aqueous solution. This high rate is obtained by simple diffusive processes and does not require any attractive or steering forces beyond those achieved for a partially formed bond. The rate enhancement is attributed to a diffusive entrapment effect, in which a protein pair surrounded and trapped by water undergoes multiple collisions with rotational reorientation during each encounter.
Computer Simulation↗
REM sleep and depression: further use of computer simulation to test the phase-advance hypothesis.
A phase advance of the circadian rhythm of rapid eye movement (REM) sleep propensity relative to the sleep-wake cycle has been proposed to account for the abnormalities of REM sleep commonly found in depressed patients. One implication of this hypothesis is that a phase delay of sleep in normal subjects should produce the same abnormalities of REM sleep. The hypothesis was tested by computer simulation using equations based on data derived from normal subjects who had experienced phase shifts of their bedtime. At phase delays of between 4 and 6 hours (an estimate of the putative phase advance in depressed patients), the mean REM latency and the mean duration of the first REM period predicted by the equations did not differ significantly from those observed in depressed patients. The findings with respect to the distribution of REM latency were more equivocal.
Adult↗
Computer Simulation of Flocculation Processes: The Roles of Chain Conformation and Chain/Colloid Concentration Ratio in the Aggregate Structures.
The flocculation of colloidal particles in the presence of adsorbing polymers is a key process in colloid science, as well as in the chemical and biological regulation of aquatic systems. Polymers can influence important physical properties of colloidal aggregates such as their densities and settling velocities, as well as their chemical properties, affecting the probability that two colloidal particles will stick together when they collide. The presence of polymers usually makes more difficult the application of a coagulation theory to colloidal suspensions and the interpretation of experimental observations. Knowledge of floc structures is a key factor in the understanding of flocculation processes, and simulation may provide useful insights required to interpret the results of experimental studies and elaborate new theoretical models. Although modeling leaves much room for more progress, researchers now find it indispensible from a fundamental point of view and for environmental applications. In this paper, we report a computer simulation study of a two- and three- dimensional model for bridging flocculation between large linear polymer chains and comparatively small colloidal particles. The floc structures are investigated as a function of chain/particle concentration ratio, chain conformation, and space dimension. The values of the sticking probabilities are chosen to emphasize colloid-chain interactions compared to colloid-colloid or chain-chain interactions. The results suggest that the floc morphology is strongly dependent on the chain conformation and to a slight extent on the chain/particle concentration ratio. In particular, colloid interactions with linear rods result in a network characterized by fractal dimensions significantly higher than those obtained on the basis of the Cluster-Cluster Aggregation models of colloids only, or by flocculation of colloids with coiled chains. Copyright 1998 Academic Press.
Journal Article↗