Two-step validation of a Monte Carlo dosimetry framework for general radiology

The Monte Carlo technique is considered gold standard when it comes to patient-specific dosimetry. Any newly developed Monte Carlo simulation framework, however, has to be carefully calibrated and validated prior to its use. For many researchers this is a tedious work. We propose a two-step validation procedure for our newly built Monte Carlo framework and provide all input data to make it feasible for future related application by the wider community. The validation was at first performed by benchmarking against simulation data available in literature. The American Association of Physicists in Medicine (AAPM) report of task group 195 (case 2) was considered most appropriate for our application. Secondly, the framework was calibrated and validated against experimental measurements for trunk X-ray imaging protocols using a water phantom. The dose results obtained from all simulations and measurements were compared. Our Monte Carlo framework proved to agree with literature data, by showing a maximal difference below 4% to the AAPM report. The mean difference with the water phantom measurements was around 7%. The statistical uncertainty for clinical applications of the dosimetry model is expected to be within 10%. This makes it reliable for clinical dose calculations in general radiology. Input data and the described procedure allow for the validation of other Monte Carlo frameworks.     

Monte Carlo calculations of radiotherapy dose in “homogeneous” anatomy

Given the substantial literature on the use of Monte Carlo (MC) simulations to verify treatment planning system (TPS) calculations of radiotherapy dose in heterogeneous regions, such as head and neck and lung, this study investigated the potential value of running MC simulations of radiotherapy treatments of nominally homogeneous pelvic anatomy. A pre-existing in-house MC job submission and analysis system, built around BEAMnrc and DOSXYZnrc, was used to evaluate the dosimetric accuracy of a sample of 12 pelvic volumetric arc therapy (VMAT) treatments, planned using the Varian Eclipse TPS, where dose was calculated with both the Analytical Anisotropic Algorithm (AAA) and the Acuros (AXB) algorithm. In-house TADA (Treatment And Dose Assessor) software was used to evaluate treatment plan complexity, in terms of the small aperture score (SAS), modulation index (MI) and a novel exposed leaf score (ELS/ELA). Results showed that the TPS generally achieved closer agreement with the MC dose distribution when treatments were planned for smaller (single-organ) targets rather than larger targets that included nodes or metastases. Analysis of these MC results with reference to the complexity metrics indicated that while AXB was useful for reducing dosimetric uncertainties associated with density heterogeneity, the residual TPS dose calculation uncertainties resulted from treatment plan complexity and TPS model simplicity. The results of this study demonstrate the value of using MC methods to recalculate and check the dose calculations provided by commercial radiotherapy TPSs, even when the treated anatomy is assumed to be comparatively homogeneous, such as in the pelvic region.     

Monte Carlo Comparison of Multiple Comparison Procedures

Seven procedures of multiple comparisons: Tukey, Scheffé, Bonferroni, Studentized Maximum Modulus, Duncan, Newman-Keuls and F are compared with respect to the probability of the correct decision. Monte Carlo simulation shows that there is no the best procedure. AMS 1985 Subject Classification: 62 J 15.     

Monte Carlo simulation for Neptun 10 PC medical linear accelerator and calculations of output factor for electron beam

AimExact knowledge of dosimetric parameters is an essential pre-requisite of an effective treatment in radiotherapy. In order to fulfill this consideration, different techniques have been used, one of which is Monte Carlo simulation.Materials and methodsThis study used the MCNP-4C^b to simulate electron beams from Neptun 10 PC medical linear accelerator. Output factors for 6, 8 and 10 MeV electrons applied to eleven different conventional fields were both measured and calculated.ResultsThe measurements were carried out by a Wellhofler-Scanditronix dose scanning system. Our findings revealed that output factors acquired by MCNP-4C simulation and the corresponding values obtained by direct measurements are in a very good agreement.ConclusionIn general, very good consistency of simulated and measured results is a good proof that the goal of this work has been accomplished.     

Mobile shielding evaluation on the fetal dose during a breast radiotherapy using Monte Carlo simulation

PurposeEvaluation of the out-of-field dose is an important aspect in radiotherapy. Due to the fetus radiosensitivity, this evaluation becomes even more conclusive when the patient is pregnant. In this work, a linear accelerator Varian Clinac 2100c operating at 6 MV, a pregnant anthropomorphic phantom (Maria), and different shields added above the abdominal region of the phantom were used for the analysis based on MCNPX. Methods: The simulations were performed for the medial and lateral projections, using either an open field collimation (10×16 cm²) or a multileaf collimator. The added shields (M1 and M2) were designed based on models proposed by Stovall et al. [1], intending to reduce the deposited dose on the fetus and related structures. Results: The presence of the shields showed to be effective in reducing the doses on the fetus, amniotic sac, and placenta, for example. A reduction of about 43% was found in the dose on the fetus when M2 was added, using the open field collimation, in comparison with the situation with no shield, being the lateral projection the main responsible for the dose. The use of MLC significatively reduced the doses in different structures, including on the fetus and amniotic sac, for example, in comparison to the open field situation. A slight increment on the dose in organs such as the eyes, thyroid and brain was found in both collimation systems, due to the presence of the shields. The contribution of the leakage radiation from the tube head of the linear accelerator was found to be in the order of µGy, being reduced by the presence of the M2 shield. Conclusion: Using the shields showed to be an essential feature in order to reduce the dose not only on the fetus, but also in important structures responsible to its development.     

Monte Carlo Simulation of Polyampholyte Chains

Abstract

Polyampholyte copolymers containing both positive and negative monomers regularly dispersed along the chain were studied. The Monte Carlo method was used to simulate chains with charged monomers interacting by screened Coulomb potential. The neutral polyampholyte chains collapse due to the attractive electrostatic interactions. The nonneutral chains are in extended conformations due to the repulsive polyelectrolyte effects that dominate the attractive polyampholyte interactions. The results are in good agreement with experiment.     

Fast Monte Carlo codes for occupational dosimetry in interventional radiology

PurposeInterventional radiology techniques cause radiation exposure both to patient and personnel. The radiation dose to the operator is usually measured with dosimeters located at specific points above or below the lead aprons. The aim of this study is to develop and validate two fast Monte Carlo (MC) codes for radiation transport in order to improve the assessment of individual doses in interventional radiology. The proposed methodology reduces the number of required dosemeters and provides immediate dose results.MethodsTwo fast MC simulation codes, PENELOPE/penEasyIR and MCGPU-IR, have been developed. Both codes have been validated by comparing fast MC calculations with the multipurpose PENELOPE MC code and with measurements during a realistic interventional procedure.ResultsThe new codes were tested with a computation time of about 120 s to estimate operator doses while a standard simulation needs several days to obtain similar uncertainties. When compared with the standard calculation in simple set-ups, MCGPU-IR tends to underestimate doses (up to 5%), while PENELOPE/penEasyIR overestimates them (up to 18%). When comparing both fast MC codes with experimental values in realistic set-ups, differences are within 25%. These differences are within accepted uncertainties in individual monitoring.ConclusionThe study highlights the fact that computational dosimetry based on the use of fast MC codes can provide good estimates of the personal dose equivalent and overcome some of the limitations of occupational monitoring in interventional radiology. Notably, MCGPU-IR calculates both organ doses and effective dose, providing a better estimate of radiation risk.     

Conformational free energy of alkylsilanes by nonequilibrium-pulling Monte Carlo simulation

The stationary phase in supercritical fluid chromatography includes alkylsilanes, bearing typically 18-carbon alkane chains, bonded to silica. The silanes are in contact with supercritical carbon dioxide. Interaction of the stationary phase with analytes from the mobile phase depends on conformation of the silanes, whether they form a collapsed layer between the silica and the carbon dioxide or are extended into the carbon dioxide. Although equilibrium conformation of alkylsilanes can be determined by equilibrium Monte Carlo (MC) simulation, that is hampered by slow relaxation of the chains. An alternative is to pull alkylsilanes from collapsed to extended conformations, then calculate free energy change from the Jarzynski equality. This work compares conformational results from equilibrium MC simulation to free energies from nonequilibrium pulling simulations. Because both equilibrium and nonequilibrium simulations are faster for shorter silanes, this work also compares results from 8-carbon and 18-carbon silanes. Free energies from nonequilibrium pulling predict that alkylsilanes tend to bend over and form a layer between silica and carbon dioxide. Results from equilibrium simulations are qualitatively consistent with results from nonequilibrium pulling. Longer-chain silanes have greater tendency to extend slightly into the carbon dioxide.     

A Monte Carlo method for the simulation of kinetie models

The purpose of this note is to illustrate the feasibility of simulating kinetic systems, such as commonly encountered in photosynthesis research, using the Monte Carlo (MC) method. In this approach, chemical events are considered at the molecular level where they occur randomly and the macroscopic kinetic evolution results from averaging a large number of such events. Their repeated simulation is easily accomplished using digital computing. It is shown that the MC approach is well suited to the capabilities and resources of modern microcomputers. A software package is briefly described and discussed, allowing a simple programming of any kinetic model system and its resolution. The execution is reasonably fast and accurate; it is not subject to such instabilities as found with the conventional analytical approach.Abbreviations MC Monte Carlo - RN random number - PSU photosynthetic unit Dedicated to Prof. L.N.M. Duysens on the occasion of his retirement.     

Grand Canonical Ensemble Monte Carlo Simulation on a Transputer Array

Five methods are described for the distribution over a 3D Transputer array of the calculation of the pair interaction component of particle energy. The most efficient method, expressed in terms of the time to complete a simulation, depends on the size of the simulation and the Transputer array. This dependence is quantified, with emphasis on Grand Canonical Ensemble Monte Carlo simulation, and yields criteria for the optimum strategy for parallel implementation of GCEMC algorithms. The equations derived are generally applicable, and have implications for the programming of Molecular Dynamics simulations.     

Test of the Inverse Monte Carlo Method for the Calculation of Interatomic Potential Energies in Atomic Liquids

Abstract

The principle purpose of this paper is to demonstrate the use of the Inverse Monte Carlo technique for calculating pair interaction energies in monoatomic liquids from a given equilibrium property. This method is based on the mathematical relation between transition probability and pair potential given by the fundamental equation of the “importance sampling” Monte Carlo method. In order to have well defined conditions for the test of the Inverse Monte Carlo method a Metropolis Monte Carlo simulation of a Lennard Jones liquid is carried out to give the equilibrium pair correlation function determined by the assumed potential. Because an equilibrium configuration is prerequisite for an Inverse Monte Carlo simulation a model system is generated reproducing the pair correlation function, which has been calculated by the Metropolis Monte Carlo simulation and therefore representing the system in thermal equilibrium. This configuration is used to simulate virtual atom displacements. The resulting changes in atom distribution for each single simulation step are inserted in a set of non-linear equations defining the transition probability for the virtual change of configuration. The solution of the set of equations for pair interaction energies yields the Lennard Jones potential by which the equilibrium configuration has been determined.     

All-Atom Monte Carlo Approach to Protein-Peptide Binding

We develop a procedure for exploring the free energy landscape of protein-peptide binding at atomic detail and apply it to PDZ domain-peptide interactions. The procedure involves soft constraints on receptor proteins providing limited chain flexibility, including backbone motions. Peptide chains are left fully flexible and kept in spatial proximity of the protein through periodic boundary conditions. By extensive Monte Carlo simulations, full representative conformational ensembles at temperatures where bound and unbound states coexist are obtained. To make this approach computationally feasible, we develop an effective all-atom energy function centering on hydrophobicity, hydrogen bonding, and electrostatic interactions. Our initial focus is a set of 11 PDZ domain-peptide pairs with experimentally determined complex structures. Minimum-energy conformations are found to be highly similar to the respective native structures in eight of the cases (all-atom peptide RMSDs < 6 Å). Having achieved that, we turn to a more complete characterization of the bound peptide state through a clustering scheme applied on the full ensembles of peptide structures. We find a significant diversity among bound peptide conformations for several PDZ domains, in particular involving the N terminal side of the peptide chains. Our computational model is then tested further on a set of nine PDZ domain-peptide pairs where the peptides are not originally present in the experimentally determined structures. We find a similar success rate in terms of the nativeness of minimum-energy conformations. Finally, we investigate the ability of our approach to capture variations in binding affinities for different peptide sequences. This is done in particular for a set of related sequences binding to the third PDZ domain of PSD-95 with encouraging results.     

Dual-energy contrast-enhanced digital mammography: Glandular dose estimation using a Monte Carlo code and voxel phantom

PurposeTo estimate the mean glandular dose of contrast enhanced digital mammography, using the EGSnrc Monte Carlo code and female adult voxel phantom.MethodsAutomatic exposure control of full field digital mammography system was used for the selection of the X-ray spectrum and the exposure settings for dual energy imaging. Measurements of the air-kerma and of the half value layers were performed and a Monte Carlo simulation of the digital mammography system was used to compute the mean glandular dose, for breast phantoms of various thicknesses, glandularities and for different X-ray spectra (low and high energy).ResultsFor breast phantoms of 2.0–8.0 cm thick and 0.1–100% glandular fraction, CC view acquisition, from AEC settings, can result in a mean glandular dose of 0.450 ± 0.022 mGy −2.575 ± 0.033 mGy for low energy images and 0.061 ± 0.021 mGy – 0.232 ± 0.033 mGy for high energy images. In MLO view acquisition mean glandular dose values ranged between 0.488 ± 0.007 mGy – 2.080 ± 0.021 mGy for low energy images and 0.065 ± 0.012 mGy – 0.215 ± 0.010 mGy for high energy images.ConclusionThe low kV part of contrast enhanced digital mammography is the main contributor to total mean glandular breast dose. The results of this study can be used to provide an estimated mean glandular dose for individual cases.     

Monte Carlo simulation of damascene electroplating: effects of additives

The influence of additives on the filling process of via holes in damascene electroplating is investigated with use of a kinetic Monte Carlo method. The basic system is the solid-by-solid model for crystal growth which includes the vacancy formation during the growth of thin film. Three kinds of additives are included in the model to control the local surface growth rate. Inhibitors and levelers have the effect of preventing the deposition, while accelerators increase the local growth rate. Levelers are modeled to stick to the tips of the surface. We performed a series of simulations by changing the parameters which characterize the additives to see their influence on the filling mechanism. It is shown that void-free filling is possible by the combination of the effects of the additives.     

Monte Carlo docking with ubiquitin.

The development of general strategies for the performance of docking simulations is prerequisite to the exploitation of this powerful computational method. Comprehensive strategies can only be derived from docking experiences with a diverse array of biological systems, and we have chosen the ubiquitin/diubiquitin system as a learning tool for this process. Using our multiple-start Monte Carlo docking method, we have reconstructed the known structure of diubiquitin from its two halves as well as from two copies of the uncomplexed monomer. For both of these cases, our relatively simple potential function ranked the correct solution among the lowest energy configurations. In the experiments involving the ubiquitin monomer, various structural modifications were made to compensate for the lack of flexibility and for the lack of a covalent bond in the modeled interaction. Potentially flexible regions could be identified using available biochemical and structural information. A systematic conformational search ruled out the possibility that the required covalent bond could be formed in one family of low-energy configurations, which was distant from the observed dimer configuration. A variety of analyses was performed on the low-energy dockings obtained in the experiment involving structurally modified ubiquitin. Characterization of the size and chemical nature of the interface surfaces was a powerful adjunct to our potential function, enabling us to distinguish more accurately between correct and incorrect dockings. Calculations with the structure of tetraubiquitin indicated that the dimer configuration in this molecule is much less favorable than that observed in the diubiquitin structure, for a simple monomer-monomer pair. Based on the analysis of our results, we draw conclusions regarding some of the approximations involved in our simulations, the use of diverse chemical and biochemical information in experimental design and the analysis of docking results, as well as possible modifications to our docking protocol.     

Fetal radiation dose in three common CT examinations during pregnancy – Monte Carlo study

PurposeTo determine fetal doses in different stages of pregnancy in three common computed tomography (CT) examinations: pulmonary CT angiography, abdomino-pelvic and trauma scan with Monte Carlo (MC) simulations.MethodsAn adult female anthropomorphic phantom was scanned with a 64-slice CT using pulmonary angiography, abdomino-pelvic and trauma CT scan protocols. Three different sized gelatin boluses placed on the phantom’s abdomen simulated different stages of pregnancy. Intrauterine dose was used as a surrogate to a dose absorbed to the fetus. MC simulations were performed to estimate uterine doses. The simulation dose levels were calibrated with volumetric CT dose index (CTDI_vol) measurements and MC simulations in a cylindrical CTDI body phantom and compared with ten point doses measured with metal-oxide-semiconductor field-effect-transistor dosimeters. Intrauterine volumes and uterine walls were segmented and the respective dose volume histograms were calculated.ResultsThe mean intrauterine doses in different stages of pregnancy varied from 0.04 to 1.04 mGy, from 4.8 to 5.8 mGy, and from 9.8 to 12.6 mGy in the CT scans for pulmonary angiography, abdomino-pelvic and trauma CT scans, respectively. MC simulations showed good correlation with the MOSFET measurement at the measured locations.ConclusionsThe three studied examinations provided highly varying fetal doses increasing from sub-mGy level in pulmonary CT angiography to notably higher levels in abdomino-pelvic and trauma scans where the fetus is in the primary exposure range. Volumetric dose distribution offered by MC simulations in an appropriate anthropomorphic phantom provides a comprehensive dose assessment when applied in adjunct to point-dose measurements.     

Monte Carlo Study of Structural and Thermodynamic Properties of Liquid Chloroform Using a Five Site Model

A five site potential model combining Lennard–Jones plus Coulomb potential functions has been developed for chloroform molecule. The partial charges needed for Coulombic interactions were derived using the chelpg procedure implemented in the gaussian 92 program. These calculations were performed at the MP2 level with MC-311G* basis set for Cl and 6-311G** for C and H atoms. The parameters for the Lennard–Jones potentials were optimized to reproduce experimental values for the density and enthalpy of vaporization of the pure liquid at 298 K and 1 atm. The statistical mechanics calculations were performed with the Monte Carlo method in the isothermic and isobaric (NpT) ensemble. Besides the values obtained for density, ρ, and molar enthalpy of vaporization at constant pressure, Δ H_V, for liquid chloroform, results for molar volume, V_m, molar heat capacity, C_p, isobaric thermal expansivity, α_p, and isothermal compressibility, κ_T, for this pure liquid are also in very good agreement with experimental observations. Size effects on the values of thermodynamic properties were investigated. The potential model was also tested by computing the free energy for solvating one chloroform molecule into its own liquid at 298 K using a statistical perturbation approach. The result obtained compares well with the experimental value. Site–site pair correlation functions were calculated and are in good accordance with theoretical results available in the literature. Dipole–dipole correlation functions for the present five site model were also calculated at different carbon–carbon distances. These correlations were compared to those obtained using the four site model reported in the literature. An investigation of the solvent dependence of the relative free energy for cis/trans conversion of a hypothetical solute in TIP4P water and chloroform was accomplished. The results show strong interaction of water and chloroform molecules with the gauche conformer. The value obtained for the free energy barrier for cis/trans rotation in TIP4P water is higher than that for chloroform. This result is in agreement with the continuous theory for solvation as the conformer with higher dipole moment is more favoured by the solvent with higher dieletric constant. The results also show an increase in entropy as the solute goes from the cis to the trans geometry and this result is more appreciable in the aqueous solution. This revised version was published online in June 2006 with corrections to the Cover Date.