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Results for “Monte Carlo Method”

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PubMedDate not supplied

Ytterbium-169: a promising new radionuclide for intravascular brachytherapy.

PURPOSE: To explore the feasibility of 169Yb (gamma, 93 keV) as a new radionuclide for intravascular brachytherapy (IVBT) in terms of dose distribution, penetration power, and radiation safety features as compared with 125I and 192Ir. METHODS: The dose distributions for catheter-based sources, 169Yb, 125I, and 192Ir, in homogeneous water and in the presence of calcium and a steel stent have been determined and compared using the Monte Carlo method (MCNP4B2 code). The dose rates of the sources were evaluated from 0.02 to 100 cm. RESULTS: In the short distance range (0.02<r<1.0 cm), the dose distributions in homogeneous water are very similar for the three radionuclides when the dose rates are normalized at 2 mm. Between 1 and 20 cm, the relative dose rates fall off similarly for 169Yb and 192Ir, whereas for 125I, it decreases much more rapidly. At a distance further away (r approximately 100 cm), the dose rate of 169Yb is about 10 times lower than that of 192Ir, indicating the cathlab radiation shielding requirement for 169Yb is substantially reduced as compared with 192Ir. Calcified plaques and stents cause a drastic dose reduction in the arterial wall for 125I, but have no effect for 192Ir gamma-rays. Only slight dose reductions were detected for 169Yb beyond a layer of 1.0-mm calcium (2-3%), and behind a steel stent strut (5%). CONCLUSION: 169Yb is a promising new radionuclide for IVBT. It has a much better penetrating power through calcified plaques and stents compared with the low-energy source 125I. It also provides easier radiation protection measures for cardiac cathlab personnel than the high-energy source 192Ir, while preserving a favorable dose distribution in tissues surrounding an arterial vessel.

Brachytherapy↗

PubMed1998

Monte Carlo generated mammograms: development and validation.

We have developed a model using Monte Carlo methods to simulate x-ray mammography. All possible physical processes of interaction of x-rays with matter have been taken into account. A simplified geometry of the mammographic apparatus has been considered along with a software phantom of compressed breast. The phantom may contain inhomogeneities of various compositions and sizes. We have used this model to produce Monte Carlo mammograms under realistic conditions. The validation of the simulation includes both the modelling of physical processes and the production of Monte Carlo mammograms. The first part is accomplished by the demonstration of the coincidence between Monte Carlo and theoretical data, whereas the second is accomplished by the comparison of real mammograms, taken from irradiation of a simplified breast phantom that we have constructed, and Monte Carlo mammograms taken from simulation of the above phantom under the corresponding exposure conditions. The limitations of the model as well as the future use of Monte Carlo mammograms are discussed.

Biophysical Phenomena↗

PubMed2005

Effect of lot variability on ultraviolet radiation inactivation kinetics of Cryptosporidium parvum oocysts.

Numerous studies have demonstrated the efficiency of ultraviolet (UV) radiation for the inactivation of oocysts of Cryptosporidium parvum. In these studies inactivation is measured as reduction in oocysts. A primary goal is to estimate the UV radiation required to achieve a high degree of inactivation. Different lots of Cryptosporidium parvum oocysts are used in these studies, and the inactivation rate may vary depending on the lot of oocysts used. The goal of this paper is to account for the error in estimating the amount of inactivation after exposure to UV radiation, and for the effect of lot variability in determining the required UV radiation. A Bayesian approach is used to simultaneously model the logistic dose-response model and the UV inactivation kinetic model. The oocysts lot variability is incorporated using a hierarchical Bayesian model. Posterior distributions using Markov Chain Monte Carlo method is used to obtain estimates and Bayesian credible interval for the required UV radiation to achieve a given inactivation level of Cryptosporidium parvum oocysts.

Animals↗

PubMedDate not supplied

Differential pencil beam dose computation model for photons.

Differential pencil beam (DPB) is defined as the dose distribution relative to the position of the first collision, per unit collision density, for a monoenergetic pencil beam of photons in an infinite homogeneous medium of unit density. We have generated DPB dose distribution tables for a number of photon energies in water using the Monte Carlo method. The three-dimensional (3D) nature of the transport of photons and electrons is automatically incorporated in DPB dose distributions. Dose is computed by evaluating 3D integrals of DPB dose. The DPB dose computation model has been applied to calculate dose distributions for 60Co and accelerator beams. Calculations for the latter are performed using energy spectra generated with the Monte Carlo program. To predict dose distributions near the beam boundaries defined by the collimation system as well as blocks, we utilize the angular distribution of incident photons. Inhomogeneities are taken into account by attenuating the primary photon fluence exponentially utilizing the average total linear attenuation coefficient of intervening tissue, by multiplying photon fluence by the linear attenuation coefficient to yield the number of collisions in the scattering volume, and by scaling the path between the scattering volume element and the computation point by an effective density.

Bone and Bones↗

PubMed2004

Optical imaging of breast tumor through temporal log-slope difference mappings.

A novel optical temporal log-slope difference mapping approach is proposed for cancerous breast tumor detection. In this method, target tissues are illuminated by near-infrared (700-1000 nm) ultrashort laser pulses from various surface source points, and backscattered time-resolved light signals are collected at the same surface points. By analyzing the log-slopes of decaying signals over all points on the source-detection grid, a log-slope distribution on the surface is obtained. After administration of absorption contrast agents, the presence of cancerous tumors increases the decaying steepness of the transient signals. The mapping of log-slope difference between native tissue and absorption-enhanced cancerous tissue indicates the location and projection of tumors on the detection surface. In this paper, we examine this method in the detection of breast tumors in two model tissue phantoms through computer simulation. The first model has a spherical tumor of 6mm in diameter embedded at the tissue center. The second model is a large tissue phantom embedded with a non-centered spherical tumor 8mm in diameter. Monte Carlo methods were employed to simulate the light transport and signal measurement. It is shown that the tumor in both the tissue models will be accurately projected on the detection surface by the proposed log-slope difference mapping method. The image processing is very fast and does not require any inverse optimization in image reconstruction.

Breast Neoplasms↗

PubMed1997

Two-dimensional scatter integration method for brachytherapy dose calculations in 3D geometry.

In brachytherapy clinical practice, applicator shielding and tissue heterogeneities are usually not explicitly taken into account. None of the existing dose computational methods are able to reconcile accurate dose calculation in complex three-dimensional (3D) geometries with high efficiency and simplicity. We propose a new model that performs two-dimensional integration of the scattered dose component. The model calculates the effective primary dose at the point of interest and estimates the scatter dose as a superposition of the scatter contributions from pyramid-shaped minibeams. The approach generalizes a previous scatter subtraction model designed to calculate the dose for axial points in simple cylindrically symmetric geometry by dividing the scattering volume into spatial regions coaxial with the source-to-measurement point direction. To allow for azimuthal variation of the primary dose, these minibeams were divided into equally spaced azimuthally distributed pyramidal volumes. The model uses precalculated scatter-to-primary ratios (SPRs) for collimated isotropic sources. Effective primary dose, which includes the radiation scattered in the source capsule, is used to achieve independence from the source structure. For realistic models of the 192Ir HDR and PDR sources, the algorithm agrees with Monte Carlo within 2.5% and for the 125I type 6702 seed within 6%. The 2D scatter integration (2DSI) model has the potential to estimate the dose behind high-density heterogeneities both accurately and efficiently. The algorithm is much faster than Monte Carlo methods and predicts the dose around sources with different gamma-ray energies and differently shaped capsules with high accuracy.

Biophysical Phenomena↗

PubMed2002

A Monte Carlo simulation model of mammographic imaging with x-ray sources of finite dimensions.

A simulation model of mammographic x-ray sources with finite size has been developed. The model is based on Monte Carlo methods and it takes into account the electron penetration inside the anode, the anode geometry and material, as well as the resulting heel effect and the spectral and spatial distribution of x-rays. This x-ray source simulation model has been embedded into an earlier developed simulation package of a mammography unit. The main outputs of this model are Monte Carlo generated images that correspond to the irradiation of properly designed phantoms. In this way it is possible to make studies of the influence of x-ray source characteristics on MTF. This paper presents the development of the mammographic x-ray source model, accompanied by a set of simulation studies concerning the influence of magnification effects as well as that of the x-ray spatial and spectral distribution on the mammographic spatial resolution for a certain magnification factor (m = 1.4). The validity level of the model, as well as its limitations and perspectives, rise through comparisons with experimental and theoretical data.

Algorithms↗

PubMed2000

LIAN 3.0: detecting linkage disequilibrium in multilocus data. Linkage Analysis.

SUMMARY: LIAN is a program to test the null hypothesis of linkage equilibrium for multilocus data. LIAN incorporates both a Monte Carlo method as well as a novel algebraic method to carry out the hypothesis test. The program further returns the genetic diversity of the sample and the pairwise distances between its members.

Chromosome Mapping↗

PubMed1984

The use of cadmium telluride detectors for the qualitative analysis of diagnostic x-ray spectra.

A method is introduced for the evaluation of x-ray spectra from x-ray machines operating in the range 50-100 kVp using a cadmium telluride (CdTe) detector with low detection efficiency. The pulse height distribution obtained with this kind of detector does not represent the true photon spectra owing to the presence of K-escape, Compton scattering, etc.; these effects were evaluated using a Monte Carlo method. A stripping procedure is described for implementation on a Univac 1100/82 computer. The validity of our method was finally tested by comparison with experimental results obtained with a Ge detector and with data from the literature; the results are in good agreement with published data.

Cadmium↗

PubMed2005

Mapping quantitative trait loci using naturally occurring genetic variance among commercial inbred lines of maize (Zea mays L.).

Many commercial inbred lines are available in crops. A large amount of genetic variation is preserved among these lines. The genealogical history of the inbred lines is usually well documented. However, quantitative trait loci (QTL) responsible for the genetic variances among the lines are largely unexplored due to lack of statistical methods. In this study, we show that the pedigree information of the lines along with the trait values and marker information can be used to map QTL without the need of further crossing experiments. We develop a Monte Carlo method to estimate locus-specific identity-by-descent (IBD) matrices. These IBD matrices are further incorporated into a mixed-model equation for variance component analysis. QTL variance is estimated and tested at every putative position of the genome. The actual QTL are detected by scanning the entire genome. Applying this new method to a well-documented pedigree of maize (Zea mays L.) that consists of 404 inbred lines, we mapped eight QTL for the maize male flowering trait, growing degree day heat units to pollen shedding (GDUSHD). These detected QTL contributed >80% of the variance observed among the inbred lines. The QTL were then used to evaluate all the inbred lines using the best linear unbiased prediction (BLUP) technique. Superior lines were selected according to the estimated QTL allelic values, a technique called marker-assisted selection (MAS). The MAS procedure implemented via BLUP may be routinely used by breeders to select superior lines and line combinations for development of new cultivars.

Alleles↗

PubMed2006

A practical method for assessment of dose conversion coefficients for aquatic biota.

Radiological impact assessment for flora and fauna requires adequate dosimetric data. Due to the variability of habitats, shapes, and masses of the non-human biota, assessment of doses is a challenging task. External and internal dose conversion coefficients for photons and electrons have been systematically calculated by Monte Carlo methods for spherical and ellipsoidal shapes in water medium. An interpolation method has been developed to approximate absorbed fractions for elliptical shape organisms from absorbed fractions for spherical shapes with reasonable accuracy. The method allows an evaluation of dose conversion coefficients for arbitrary ellipsoids for photon and electron sources with energies from 10 keV to 5 MeV, and for organism masses in the range from 10(-6) to 10(3) kg. As an example of the application of the method, a set of dose coefficients for aquatic organisms discussed as reference animals and plants in a draft of an up-coming publication of the International Commission on Radiological Protection has been determined.

Animals↗

PubMed1988

A program for predicting significant RNA secondary structures.

We describe a program for the analysis of RNA secondary structure. There are two new features in this program. (i) To get vector speeds on a vector pipeline machine (such as Cray X-MP/24) we have vectorized the secondary structure dynamic algorithm. (ii) The statistical significance of a locally 'optimal' secondary structure is assessed by a Monte Carlo method. The results can be depicted graphically including profiles of the stability of local secondary structures and the distribution of the potentially significant secondary structures in the RNA molecules. Interesting regions where both the potentially significant secondary structures and 'open' structures (single-stranded coils) occur can be identified by the plots mentioned above. Furthermore, the speed of the vectorized code allows repeated Monte Carlo simulations with different overlapping window sizes. Thus, the optimal size of the significant secondary structure occurring in the interesting region can be assessed by repeating the Monte Carlo simulation. The power of the program is demonstrated in the analysis of local secondary structures of human T-cell lymphotrophic virus type III (HIV).

Algorithms↗

PubMed1988

Bayesian interval estimation of genetic relationships: application to paternity testing.

Using genetic marker data, we have developed a general methodology for estimating genetic relationships between a set of individuals. The purpose of this paper is to illustrate the practical utility of these methods as applied to the problem of paternity testing. Bayesian methods are used to compute the posterior probability distribution of the genetic relationship parameters. Use of an interval-estimation approach rather than a hypothesis-testing one avoids the problem of the specification of an appropriate null hypothesis in calculating the probability of paternity. Monte Carlo methods are used to evaluate the utility of two sets of genetic markers in obtaining suitably precise estimates of genetic relationship as well as the effect of the prior distribution chosen. Results indicate that with currently available markers a "true" father may be reliably distinguished from any other genetic relationship to the child and that with a reasonable number of markers one can often discriminate between an unrelated individual and one with a second-degree relationship to the child.

Bayes Theorem↗

PubMed1975

Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions.

A lattice model of proteins is introduced. "A protein molecule" is a chain of nown-intersecting units of a given length on the two-dimensional square lattice. The copolymeric character of protein molecules is incorporated into the model in the form of specificities of inter-unit interactions. This model proved most effective for studying the statistical mechanical characteristics of protein folding, unfolding and fluctuations. The specificities of inter-unit interactions are shown to be the primary factors responsible for the all-or-none type transition from native to denatured states of globular proteins. The model has been studied by the Monte Carlo method of Metropolis et al., which is now shown applied to approximately simulating a kinetic process. In the strong limit of the specificity of the inter-unit interaction the native conformation was reached in this method by starting from an extended conformation. The possible generalization and application of this method for finding the native conformation of proteins form their amino sequence are discussed.

Amino Acid Sequence↗

PubMed2005

Fast flat-histogram method for generalized spin models.

We present a Monte Carlo method that efficiently computes the density of states for spin models having any number of interaction per spin. By combining a random walk in the energy space with collective updates controlled by the microcanonical temperature, our method yields dynamic exponents close to their ideal random-walk values, reduced equilibrium times, and very low statistical error in the density of states. The method can host any density of states estimation scheme, including the Wang-Landau algorithm and the transition matrix method. Our approach proves remarkably powerful in the numerical study of models governed by long-range interactions, where it is shown to reduce the algorithm complexity to that of a short-range model with the same number of spins. We apply the method to the -state Potts chains with power-law decaying interactions in their first-order regime; we find that conventional local-update algorithms are outperformed already for sizes above a few hundred spins. By considering chains containing up to spins, which we simulated in fairly reasonable time, we obtain estimates of transition temperatures correct to five-figure accuracy. Finally, we propose several efficient schemes aimed at estimating the microcanonical temperature.

Journal Article↗

PubMed2003

Reverse Monte Carlo analysis of extended energy-loss fine structure for disordered structures of tetrahedrally coordinated materials: its applicability.

Capabilities of the reverse Monte Carlo method for characterizing the short-range structural correlations of solids were examined in the analysis of extended energy-loss fine structure (EXELFS). Since this method gives a three-dimensional atomic configuration consistent with the experimental EXELFS spectra, one can extract the statistical distributions of bond lengths, coordination numbers and bond angles of atom species of interest, which have been hard to achieve by conventional EXELFS analysis. The method was applied for the determination of amorphous Si structures and the damaged structure of an electron-irradiated SiC crystal. Advantages and disadvantages of the present method over the precise diffraction intensity measurement are discussed.

Carbon↗

PubMed2000

Ligand-induced conformational changes in tissue transglutaminase: Monte Carlo analysis of small-angle scattering data.

Small-angle neutron and x-ray scattering experiments have been performed on type 2 tissular transglutaminase to characterize the conformational changes that bring about Ca(2+) activation and guanosine triphosphate (GTP) inhibition. The native and a proteolyzed form of the enzyme, in the presence and in the absence of the two effectors, were considered. To describe the shape of transglutaminase in the different conformations, a Monte Carlo method for calculating small-angle neutron scattering profiles was developed by taking into account the computer-designed structure of the native transglutaminase, the results of the Guinier analysis, and the essential role played by the solvent-exposed peptide loop for the conformational changes of the protein after activation. Although the range of the neutron scattering data is rather limited, by using the Monte Carlo analysis, and because the structure of the native protein is available, the distribution of the protein conformations after ligand interaction was obtained. Calcium activation promotes a rotation of the C-terminal with respect to the N-terminal domain around the solvent-exposed peptide loop that connects the two regions. The psi angle between the longest axes of the two pairs of domains is found to be above 50 degrees, larger than the psi value of 35 degrees calculated for the native transglutaminase. On the other hand, the addition of GTP makes possible conformations characterized by psi angles lower than 34 degrees. These results are in good agreement with the proposed enzyme activity regulation: in the presence of GTP, the catalytic site is shielded by the more compact protein structure, while the conformational changes induced by Ca(2+) make the active site accessible to the substrate.

Calcium↗

PubMed2005

Dosimetric verification of IMRT treatment planning using Monte Carlo simulations for prostate cancer.

The purpose of this work is to investigate the accuracy of dose calculation of a commercial treatment planning system (Corvus, Normos Corp., Sewickley, PA). In this study, 30 prostate intensity-modulated radiotherapy (IMRT) treatment plans from the commercial treatment planning system were recalculated using the Monte Carlo method. Dose-volume histograms and isodose distributions were compared. Other quantities such as minimum dose to the target (D(min)), the dose received by 98% of the target volume (D98), dose at the isocentre (D(iso)), mean target dose (D(mean)) and the maximum critical structure dose (D(max)) were also evaluated based on our clinical criteria. For coplanar plans, the dose differences between Monte Carlo and the commercial treatment planning system with and without heterogeneity correction were not significant. The differences in the isocentre dose between the commercial treatment planning system and Monte Carlo simulations were less than 3% for all coplanar cases. The differences on D98 were less than 2% on average. The differences in the mean dose to the target between the commercial system and Monte Carlo results were within 3%. The differences in the maximum bladder dose were within 3% for most cases. The maximum dose differences for the rectum were less than 4% for all the cases. For non-coplanar plans, the difference in the minimum target dose between the treatment planning system and Monte Carlo calculations was up to 9% if the heterogeneity correction was not applied in Corvus. This was caused by the excessive attenuation of the non-coplanar beams by the femurs. When the heterogeneity correction was applied in Corvus, the differences were reduced significantly. These results suggest that heterogeneity correction should be used in dose calculation for prostate cancer with non-coplanar beam arrangements.

Computer Simulation↗