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Results for “Monte Carlo Method”

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PubMed1993

Lipid-cholesterol interactions in the P beta' phase. Application of a statistical mechanical model.

We describe a statistical mechanical model for lipid-cholesterol mixtures in the P beta' (ripple) phase of lipid bilayers. The model is a simple extension of an earlier model for the ripple phase in pure lipid bilayers. The extension consists of adding a degree of freedom to allow for the occupation of underlying lattice sites by cholesterol molecules, and adding a lipid-cholesterol interaction term to the model Hamiltonian. The interaction term was constructed based on numerical calculations of lipid-cholesterol energies for several different packing juxtapositions of the two molecules. Other than the lipid-cholesterol interactions, the extended model uses the same parameter set as the earlier model, so that comparison of the properties of the extended model with experimental data serves as a test of the validity of the original model. Properties of the model were calculated using the Monte Carlo method. Results are displayed as snapshots of the ripple configurations at different cholesterol concentrations. The spacing of the ripples increases with increasing cholesterol concentration and the rate of increase compares very well with experimental data. The success of this model supports the conclusion drawn earlier that frustration arising from anisotropic packing interactions is responsible for the ripple phase in lipid bilayers. In the extended model these packing interactions are responsible for the selective partitioning of cholesterol in the regions between the ripples.

Animals↗

PubMed1983

Postnatal dendritic development in motoneurons: evaluation by a Monte Carlo technique.

A Monte Carlo method was used to quantitate the dendritic characteristics of horseradish peroxidase-injected lumbar motoneurons (MNs) from kittens 44 to 73 days old (during the postnatal interval when motor cortical input/output linkages mature) and compared with those from adults. All of the 6 MNs analyzed were within the same range of somal sizes (40-61 micron) and dendritic domain volumes. However, two-dimensional distributions of dendritic diameter versus distance from the soma revealed that in the youngest MNs' (44 and 51 days) most dendritic processes (82 and 84%) were less than 2 micron in diameter, and had no dendrites greater than 5 micron. The adult MNs had large dendrites (20 and 24% were greater than 5 mu), while the kittens of intermediate age (66 and 73 days) exhibited both adult-like (6 and 13% greater than 5 micron) and immature (48 and 73% less than 2 micron) characteristics. "Hit probabilities" calculated from the Monte Carlo data suggest that immature MNs' dendrites may present denser targets per unit volume for ingrowing growth cones than adult MNs, and may facilitate the probability of contact with appropriate afferent axons.

Animals↗

PubMed2004

A particle-tracking model for simulating pollutant dispersion in the Strait of Gibraltar.

A particle-tracking model to simulate the dispersion of contaminants in the Strait of Gibraltar has been developed. The model solves the hydrodynamic equations off-line and tidal analysis is carried out to determine tidal constants for the two main constituents. Tidal constants and residuals are stored in files that are read by the dispersion model. A lagrangian approach is used to solve dispersion; diffusion and decay are simulated by a Monte Carlo method. A method for assessing the areas of the Strait with higher probability of being affected by contamination occurring after an accident in the shipping routes is given. Generally speaking, the fate of a pollutant discharge strongly depends on wind conditions. Winds from the east tend to retain contamination into the Strait. As a consequence, transverse mixing occurs and both Spain and Morocco coasts are affected by contamination. Under calm conditions and west winds, contaminants are flushed out of the Strait faster and transverse mixing does not occur. Thus, only part of Morocco coast has a higher probability of being affected by contamination.

Environmental Monitoring↗

PubMed2006

Torsional anharmonicity in the conformational analysis of beta-D-galactose.

Schemes to include a treatment of torsional anharmonicity in the conformational analysis of biological molecules are introduced. The approaches combine ab initio electronic energies and harmonic frequencies with anharmonic torsional partition functions calculated using the torsional path integral Monte Carlo method on affordable potential energy surfaces. The schemes are applied to the conformational study of the monosaccharide beta-d-galactose in the gas phase. The global minimum structure is almost exclusively populated at 100 K, but a large number of conformers are present at ambient and higher temperatures. Both quantum mechanical and anharmonic effects in the torsional modes have little effect on the populations at all temperatures considered, and it is, therefore, expected that standard harmonic treatments are satisfactory for the conformational study of monosaccharides.

Galactose↗

PubMed1999

Testing for multiple species in fossil samples: an evaluation and comparison of tests for equal relative variation.

Tests for equal relative variation are valuable and frequently used tools for evaluating hypotheses about taxonomic heterogeneity in fossil hominids. In this study, Monte Carlo methods and simulated data are used to evaluate and compare 11 tests for equal relative variation. The tests evaluated include CV-based parametric bootstrap tests, modifications of Levene's test, and modified weighted scores tests. The results of these simulations show that a modified version of the weighted scores test developed by Fligner and Killeen ([1976] J. Am. Stat. Assoc. 71:210-213) is the only test that maintains an acceptable balance of type I and type II errors, even under conditions where all other tests have extraordinarily high type I error rates or little power.

Animals↗

PubMed2000

Absorbed fractions in a voxel-based phantom calculated with the MCNP-4B code.

A new approach for calculating internal dose estimates was developed through the use of a more realistic computational model of the human body. The present technique shows the capability to build a patient-specific phantom with tomography data (a voxel-based phantom) for the simulation of radiation transport and energy deposition using Monte Carlo methods such as in the MCNP-4B code. MCNP-4B absorbed fractions for photons in the mathematical phantom of Snyder et al. agreed well with reference values. Results obtained through radiation transport simulation in the voxel-based phantom, in general, agreed well with reference values. Considerable discrepancies, however, were found in some cases due to two major causes: differences in the organ masses between the phantoms and the occurrence of organ overlap in the voxel-based phantom, which is not considered in the mathematical phantom.

Algorithms↗

PubMed2004

Stochastic modeling of the tumor volume assessment and growth patterns in hepatocellular carcinoma.

The growth pattern of hepatocellular carcinoma (HCC) arising from cirrhosis is variable and depends on the degree of differentiation and vascularization. Because growth is not constant in the natural history of HCC, prediction of subsequent growth rate based on tumor volume doubling time and correlation with histological and ultrasonographical characteristics at the moment of initial diagnosis are usually unreliable. The aim of our study was to assess the growth patterns of HCC with the aid of stochastic modeling. Thus, we included in our study 27 patients with histologically proven HCC, which had multiple (more than three)follow-up ultrasound studies in a six months interval. The patients did not receive any treatment during the observation period. HCC was visualized by computer aided ultrasound imaging, obtaining both the primary size quantification and the edge-detection enhancement. By a bi-cubic B-spline interpolation of points on the edges (3-D Bezier approximation) we approximated the surfaces shapes, and using the hit or miss Monte Carlo method we accurately estimate the tumor volume. Starting from the previous tumor volumes time series recorded during the first six months of evolution we applied both a linear, exponential and logarithmic smoothing to forecast the future size of the HCC tumor in the next six months. Our conclusion was that a dynamic forecasting model of HCC volumes could be very accurate for the assessment of tumor volume doubling time usually obtained by two discrete volume measurements of the tumor.

Adult↗

PubMed1987

A model for the spatio-temporal organization of DNA replication in mammalian cells.

The spatio-temporal organization of chromosomal DNA replication was analyzed using a model based on a "DNA unit" (or decondensation unit) hypothesis. The model is an extension of the fork movement theory of Huberman & Riggs (1968) and can account for a partially deterministic and partially stochastic order of DNA replication in chromosomes. It presumes that each chromosome is composed of DNA units that are arranged in sequence and that are replicated in parallel. A deterministic wave of chromatin decondensation propagates along the DNA unit continuously and progressively providing a field for the random activation of replication origin. Assignment of replication times to DNA compartments by a Monte Carlo method was programmed based on the model and the program was used to stimulate DNA synthesis rate curves that can be measured by the method of Dolbeare et al. (1983, 1985). The shape of the curve is shown to constrain possible parameter values of the model, which include the rate of fork movement, the fraction of chromatin that is decondensed at the start of S-phase, the initial number of origins activated, the rate at which new origins are activated, etc. The chromosomal organization that controls the molecular level of DNA replication is briefly reviewed and its relevance to the model is also discussed.

Algorithms↗

PubMed1998

Photonuclear production in tissue for different 50 MV bremsstrahlung beams.

Calculations of photonuclear production in "tissue approximation" and the relative heavy particle dose to photon dose at dose maximum in water have been performed. Different 50 MV spectra based on a scanned beam technique to produce flat photon fields were used. These spectra were calculated with the Monte Carlo method and correspond to different target configurations and scan patterns. Photonuclear cross sections of neutron, proton, and alpha production for oxygen, nitrogen, and carbon are taken from the literature. Activation measurements using a HpGe detector have been used to verify the calculations. The relative heavy particle dose to photon dose was found to be 0.30%-0.42%, depending on the spectra used, and the estimated uncertainty was 20%. A relative biological effect (RBE) of 1.01-1.03 in "tissue approximation" for 50 MV were estimated using a RBE for neutron and protons of 2-5 and 4-10 for alpha particles.

Alpha Particles↗

PubMed2002

Evolving the division of labour: generalists, specialists and task allocation.

The evolutionary dynamics of specialization, in the context of the division of labour, are investigated. Individuals associate in groups in which benefits are shared and costs borne individually; each individual is either a generalist who can perform all the necessary tasks, a specialist who performs a sub-set of the necessary tasks, or a parasite who contributes nothing to the group. The implications of the model are explored analytically and through both numerical and Monte Carlo methods. These methods demonstrate the evolution of populations towards stable arrangements of specialists and generalists. The fittest populations are those that divide tasks fairly and associate in large, highly specialized groups. Generalists have a distinct advantage in small groups, but the presence of generalists, ironically, lowers group fitness. Parasites are able to invade both specialized and non-specialized populations. A basic model for the continuous division of labour is also presented, demonstrating a tendency for populations to evolve increasingly unfair divisions of labour. This last result implies that an evolutionary ratchet favours disparity between the workload of specialist populations.

Animals↗

PubMed2005

Assessing the occupational risk of dust particles in the Kenyan tanning industry using rapid image processing and microscopy techniques.

The purpose of this study was to investigate the occupational hazards within the tanning industry caused by contaminated dust. A qualitative assessment of the risk of human exposure to dust was made throughout a commercial Kenyan tannery. Using this information, high-risk points in the processing line were identified and dust sampling regimes developed. An optical set-up using microscopy and digital imaging techniques was used to determine dust particle numbers and size distributions. The results showed that chemical handling was the most hazardous (12 mg m(-3)). A Monte Carlo method was used to estimate the concentration of the dust in the air throughout the tannery during an 8 h working day. This showed that the high-risk area of the tannery was associated with mean concentrations of dust greater than the UK Statutory Instrument 2002 No. 2677. stipulated limits (exceeding 10 mg m(-3) (Inhalable dust limits) and 4 mg m(-3) (Respirable dust limits). This therefore has implications in terms of provision of personal protective equipment (PPE) to the tannery workers for the mitigation of occupational risk.

Dust↗

PubMed1999

Mass attenuation coefficients of clear-Pb for photons from 125I, 103Pd, 99mTc, 192Ir, 137Cs and 60Co.

The mass attenuation coefficients, mu/rho, for Clear-Pb for photon energies ranging from 10 keV to 10 MeV were determined using Monte Carlo methods and simple equations used to manipulate elemental mass attenuation coefficients. It was determined that the effectiveness of Clear-Pb as a radiation shielding material was greater than plain acrylic for all photon energies, especially those less than 150 keV, and for deep penetration problems where the differences in mu/rho between Clear-Pb and acrylic became more significant. Finally, the usefulness of Clear-Pb as a shielding material when compared with acrylic was determined for the following commonly used radionuclides: 125I, 103Pd, 99mTc, 192Ir, 137Cs, and 60Co.

Cesium Radioisotopes↗

PubMed2002

Modeling the bidirectional reflectance of emissive displays.

The reflection properties of a display device influence the available contrast and affect the perception of subtle detail. The display reflection characteristics of flat-panel displays (FPDs) are appropriately described by a six-dimensional bidirectional reflectance distribution function (BRDF). I describe a Monte Carlo method for modeling the bidirectional reflectance of multilayer emissive structures used in electronic display devices. I estimate the complete BRDF using a one-dimensional angular distribution function of the luminance. I apply the method to model typical high-performance cathode-ray tube and FPD structures. I find that, for the BRDF signatures of cathode-ray tubes characterized by a specular and a quasi-Lambertian components, the estimated values for the specular and diffuse reflection coefficients agree well with low-resolution experimental measurements conducted with a rotation arm and a collimated probe. I show that emissive FPDs with thin-film organic layers on reflective substrates can exhibit a predominant specular peak broadened by short-range light scattering.

Data Display↗

PubMed1996

Speed discrimination of distal stimuli during smooth pursuit eye motion.

We evaluated the hypothesis that smooth pursuit eye movements affect speed discrimination thresholds of distal stimuli because they alter the retinal image speed. Subjects judged speed differences of sine-wave gratings while they simultaneously pursued a superimposed moving bar. Speed discrimination thresholds were measured, under conditions of controlled eye movements, for grating speeds of 0.5 and 2.0 deg/sec across a range of eye velocities. Thresholds were stimulated using a Monte Carlo method based on the retinal speed hypothesis, and the simulation predictions were compared to the psychophysically determined thresholds. The simulation results provided a good match to the psychophysical data for conditions where the eye moved at a slower speed than the grating, regardless of whether the eye moved in the same or opposite direction. However, when the eye moved at a faster speed than the grating in the same direction, the psychophysical thresholds were significantly higher than predicted by the simulation. Control experiments and analyses rule out explanations based on relative motion cues, saccadic involvement, and attentional demands.

Differential Threshold↗

PubMed1989

Monte Carlo simulation of the power of a test for the exponential distribution of survival times.

An illustrative analysis is presented demonstrating the use of the Monte Carlo method in estimating the power of a test to detect deviations from distributional form. New estimates of power are obtained for the WE0 test, a statistical test used to assess a set of observed survival times for deviation from the exponential distribution. An IBM PC/AT was used to process a series of simulations, in which samples of survival times were drawn from a series of populations whose survival was distributed according to the gamma distribution. Each sample was then tested for difference from the exponential to see how often the WE0 test would correctly classify the sample as drawn from a non-exponential population.

Computer Simulation↗

PubMed1996

A computer program for sample size and power calculations in the design of multi-arm and factorial clinical trials with survival time endpoints.

This paper presents a computer program for use in the design of long-term clinical trials with multiple treatment arms in which the primary outcome variables are censored survival times. The treatment arms may be structured as a one-way or multi-way factorial design. It is assumed that patients are entered and randomized to a treatment arm during an accrual period. The patients are then followed for a fixed period during which there may be dropouts. Various distributional assumptions can be used to model the survival times. These include an option in which there is an effect of treatment duly after a lag or delay time. The program then computes the power of various statistical tests of hypotheses concerning treatment differences, interactions and trends. The power computations are "exact" in that they use the Monte Carlo method to obtain Type I and II error probabilities. However the program also outputs the normal approximations for comparison, although they are typically not accurate in these situations. Fisher's LSD method is used to adjust for the multiple comparisons. By comparing the power for various sets of design parameters, such as sample size, numbers of factor levels, patient accrual rate, and length of follow-up, an appropriate design can be constructed. Two examples are provided. The first is a simple one-way layout with multiple treatment arms; the second a two-way factorial design for a proposed large scale cancer chemoprevention trial.

Clinical Trials as Topic↗

PubMed1994

Interparticle interactions and structure in nonideal solutions of human serum albumin studied by small-angle neutron scattering and Monte Carlo simulation.

Moderately or highly concentrated nonideal solutions of macromolecules are very important systems e.g. in biology and in many technical processes. In this work we have used the small-angle neutron scattering technique (SANS) to study the interactions and interparticle structure in solutions of human serum albumin (HSA) up to a concentration of 0.26 g/cm3 in 1.08 M NaCl. In order to obtain a model for the interactions we have combined the SANS data with results obtained by Monte Carlo simulations where we calculate the structure factor S(Q) and the pair correlation function g(r). The advantage of using the Monte Carlo method is that completely general models for the particle shape and the interactions can be considered. It is found that the SANS data can be explained by a model where the shape of the HSA molecule is approximated by an ellipsoid of revolution with semiaxes a = 6.8 nm and b = c = 1.9 nm. The interaction potential between the HSA molecules consists of two parts: (a) the molecules are hard and impenetrable and (b) the molecules are surrounded by a spherically symmetric repulsive potential which can be expressed by an empirical formula containing the HSA concentration and the centre-centre distances as the only variables.

Humans↗

PubMed1985

Stopping-power ratio for a photon spectrum as a weighted sum of the values for monoenergetic photon beams.

Stopping-power ratios for water to air, Sw,air, have been calculated for 60Co and thin-target bremsstrahlung beams. The Monte Carlo method was used to generate depth-dependent Sw,air values and depth-absorbed-dose distributions in water for monoenergetic photon beams covering the energy range 0.1-50 MeV. An averaging procedure has been developed to derive the stopping-power ratios for a photon spectrum from the monoenergetic data. Values of the Spencer-Attix ratio for delta = 10 keV, SSAw,air (delta = 10 keV), and the Bragg-Gray ratio, SBGw,air, evaluated using the new I values and two different sets of values for the density effect correction, are given at the reference depths recommended in the dosimetry protocols.

Humans↗