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PubMed2006

A practical Monte Carlo MU verification tool for IMRT quality assurance.

Quality assurance (QA) for intensity-modulated radiation therapy (IMRT) treatment planning and beam delivery, using ionization chamber measurements and film dosimetry in a phantom, is time consuming. The Monte Carlo method is the most accurate method for radiotherapy dose calculation. However, a major drawback of Monte Carlo dose calculation as currently implemented is its slow speed. The goal of this work is to bring the efficiency of Monte Carlo into a practical range by developing a fast Monte Carlo monitor unit (MU) verification tool for IMRT. A special estimator for dose at a point called the point detector has been used in this research. The point detector uses the next event estimation (NEE) method to calculate the photon energy fluence at a point of interest and then converts it to collision kerma by the mass energy absorption coefficient assuming the presence of transient charged particle equilibrium. The MU verification tool has been validated by comparing the calculation results with measurements. It can be used for both patient dose verification and phantom QA calculation. The dynamic leaf-sequence log file is used to rebuild the actual MLC leaf sequence in order to predict the dose actually received by the patient. Dose calculations for 20 patient plans have been performed using the point detector method. Results were compared with direct Monte Carlo simulations using EGS4/MCSIM, which is a well-benchmarked Monte Carlo code. The results between the point detector and MCSIM agreed to within 2%. A factor of 20 speedup can be achieved with the point detector method compared with direct Monte Carlo simulations.

Body Burden↗
PubMed2005

Beyond the Tonks-Girardeau gas: strongly correlated regime in quasi-one-dimensional Bose gases.

We consider a homogeneous 1D Bose gas with contact interactions and a large attractive coupling constant. This system can be realized in tight waveguides by exploiting a confinement induced resonance of the effective 1D scattering amplitude. By using the diffusion Monte Carlo method we show that, for small densities, the gaslike state is well described by a gas of hard rods. The critical density for cluster formation is estimated using the variational Monte Carlo method. The behavior of the correlation functions and of the frequency of the lowest breathing mode for harmonically trapped systems shows that the gas is more strongly correlated than in the Tonks-Girardeau regime.

Journal Article↗
PubMed2004

Coupled electron-ion monte carlo calculations of dense metallic hydrogen.

We present an efficient new Monte Carlo method which couples path integrals for finite temperature protons with quantum Monte Carlo calculations for ground state electrons, and we apply it to metallic hydrogen for pressures beyond molecular dissociation. We report data for the equation of state for temperatures across the melting of the proton crystal. Our data exhibit more structure and higher melting temperatures of the proton crystal than do Car-Parrinello molecular dynamics results. This method fills the gap between high temperature electron-proton path integral and ground state diffusion Monte Carlo methods and should have wide applicability.

Journal Article↗
PubMed2005

Phase coexistence in heterogeneous porous media: a new extension to Gibbs ensemble Monte Carlo simulation method.

The effect of confinement on phase behavior of simple fluids is still an area of intensive research. In between experiment and theory, molecular simulation is a powerful tool to study the effect of confinement in realistic porous materials, containing some disorder. Previous simulation works aiming at establishing the phase diagram of a confined Lennard-Jones-type fluid, concentrated on simple pore geometries (slits or cylinders). The development of the Gibbs ensemble Monte Carlo technique by Panagiotopoulos [Mol. Phys. 61, 813 (1987)], greatly favored the study of such simple geometries for two reasons. First, the technique is very efficient to calculate the phase diagram, since each run (at a given temperature) converges directly to an equilibrium between a gaslike and a liquidlike phase. Second, due to volume exchange procedure between the two phases, at least one invariant direction of space is required for applicability of this method, which is the case for slits or cylinders. Generally, the introduction of some disorder in such simple pores breaks the initial invariance in one of the space directions and prevents to work in the Gibbs ensemble. The simulation techniques for such disordered systems are numerous (grand canonical Monte Carlo, molecular dynamics, histogram reweighting, N-P-T+test method, Gibbs-Duhem integration procedure, etc.). However, the Gibbs ensemble technique, which gives directly the coexistence between phases, was never generalized to such systems. In this work, we focus on two weakly disordered pores for which a modified Gibbs ensemble Monte Carlo technique can be applied. One of the pores is geometrically undulated, whereas the second is cylindrical but presents a chemical variation which gives rise to a modulation of the wall potential. In the first case almost no change in the phase diagram is observed, whereas in the second strong modifications are reported.

Journal Article↗
PubMed1996

Reconstruction of radionuclide releases from the Hanford Site, 1944-1972.

Historic releases of key radionuclides were estimated as a first step in determining the radiation doses that resulted from Hanford Site operations. The Hanford Site was built in southcentral Washington State during World War II to provide plutonium for the U.S. nuclear weapons program. As part of the Hanford Environmental Dose Reconstruction (HEDR) Project, releases to the Columbia River of 24Na, 32P, 46Sc, 51Cr, 56Mn, 65Zn, 72Ga, 76As, 90Y, 131I, 239Np, and nonvolatile gross beta activity from operation of eight Hanford single-pass production reactors were estimated. Releases of 90Sr, 103Ru, 106Ru, 131I, 144Ce, and 239Pu to the atmosphere from operation of chemical separation facilities were also estimated. These radionuclides and the atmospheric and Columbia River pathways were selected for study because scoping studies showed them to be the largest contributors to dose from Hanford operations. The highest doses resulted from releases to the atmosphere of 131I from chemical separations plants in the pre-1950 period. Prior to 1950, the technology for limiting iodine releases had not been developed. Hence, a very detailed reconstruction of the hourly 131I release history was achieved for 1944-1949 using Monte Carlo methods. Atmospheric releases of the other radionuclides were estimated on a monthly basis for 1944-1972 using deterministic calculations. Monthly releases to the Columbia River for 1944-1971 were based on Monte Carlo methods.

Air Pollutants, Radioactive↗
PubMed2005

Hybrid Monte Carlo implementation of the Fourier path integral algorithm.

This paper formulates a hybrid Monte Carlo implementation of the Fourier path integral (FPI-HMC) approach with partial averaging. Such a hybrid Monte Carlo approach allows one to generate collective moves through configuration space using molecular dynamics while retaining the computational advantages associated with the Fourier path integral Monte Carlo method. In comparison with the earlier Metropolis Monte Carlo implementations of the FPI algorithm, the present HMC method is shown to be significantly more efficient for quantum Lennard-Jones solids and suggests that such algorithms may prove useful for efficient simulations of a range of atomic and molecular systems.

Journal Article↗
PubMed2001

Application of hard sphere perturbation theory for thermodynamics of model liquid metals.

Hard sphere perturbation theory (HSPT) has contributed toward the fundamental understanding of dense fluids for over 30 years. In recent decades, other techniques have been more popular. In this paper, we argue for the revival of hard sphere perturbation theory for the study of thermodynamics of dense liquid in general, and in liquid metal in particular. The weakness of HSPT is now well understood, and can be easily overcome by using a simple convenient Monte Carlo method to calculate the intrinsic error of HSPT free energy density. To demonstrate this approach, we consider models of liquid aluminum and sodium. We obtain the intrinsic error of HSPT with the Monte Carlo method. HSPT is shown to provide a lower free energy upper bound than one-component plasma (OCP) for alkali metals and polyvalent metals. We are thus able to provide insight into the long standing observation that a OCP is a better reference system than a HS for alkali metals.

Journal Article↗
PubMed2000

Electron beam modeling and commissioning for Monte Carlo treatment planning.

A hybrid approach for commissioning electron beam Monte Carlo treatment planning systems has been studied. The approach is based on the assumption that accelerators of the same type have very similar electron beam characteristics and the major difference comes from the on-site tuning of the electron incident energy at the exit window. For one type of accelerator, a reference machine can be selected and simulated with the Monte Carlo method. A multiple source model can be built on the full Monte Carlo simulation of the reference beam. When commissioning electron beams from other accelerators of the same type, the energy spectra in the source model are tuned to match the measured dose distributions. A Varian Clinac 2100C accelerator was chosen as the reference machine and a four-source beam model was established based on the Monte Carlo simulations. This simplified beam model can be used to generate Monte Carlo dose distributions accurately (within 2%/2 mm compared to those calculated with full phase space data) for electron beams from the reference machine with various nominal energies, applicator sizes, and SSDs. Three electron beams were commissioned by adjusting the energy spectra in the source model. The dose distributions calculated with the adjusted source model were compared with the dose distributions calculated using the phase space data for these beams. The agreement is within 1% in most of cases and 2% in all situations. This preliminary study has shown the capability of the commissioning approach for handling large variation in the electron incident energy. The possibility of making the approach more versatile is also discussed.

Algorithms↗
PubMed2003

A quality assurance phantom for IMRT dose verification.

This paper investigates a quality assurance (QA) phantom specially designed to verify the accuracy of dose distributions and monitor units (MU) calculated by clinical treatment planning optimization systems and by the Monte Carlo method for intensity-modulated radiotherapy (IMRT). The QA phantom is a PMMA cylinder of 30 cm diameter and 40 cm length with various bone and lung inserts. A procedure (and formalism) has been developed to measure the absolute dose to water in the PMMA phantom. Another cylindrical phantom of the same dimensions, but made of water, was used to confirm the results obtained with the PMMA phantom. The PMMA phantom was irradiated by 4, 6 and 15 MV photon beams and the dose was measured using an ionization chamber and compared to the results calculated by a commercial inverse planning system (CORVUS, NOMOS, Sewickley, PA) and by the Monte Carlo method. The results show that the dose distributions calculated by both CORVUS and Monte Carlo agreed to within 2% of dose maximum with measured results in the uniform PMMA phantom for both open and intensity-modulated fields. Similar agreement was obtained between Monte Carlo calculations and measured results with the bone and lung heterogeneity inside the PMMA phantom while the CORVUS results were 4% different. The QA phantom has been integrated as a routine QA procedure for the patient's IMRT dose verification at Stanford since 1999.

Equipment Design↗
PubMed1998

Monte Carlo/numerical treatment of alpha-particle spectra from sources buried in bone and resultant doses to surface cells.

PURPOSE: To calculate the depth distribution of radioactive decays in bone by fitting a calculated alpha-particle energy spectrum to a measured spectrum. The dose to bone surface cells is then calculated from the depth distribution. MATERIALS AND METHODS: The spectra are calculated using Monte Carlo methods and a numerical depth distribution obtained by trial and error. RESULTS: Alpha spectra for 210Po and 226Ra (plus decay products) in bone were calculated and fitted to experimental spectra. The dose to bone surface cells was calculated using the numerical technique and compared to previously published data. CONCLUSIONS: Alpha-particle spectra can be successful fitted using this method, which gives a more realistic distribution of decays with depth than simple surface and volume models.

Alpha Particles↗
PubMed2005

Protein folding by motion planning.

We investigate a novel approach for studying protein folding that has evolved from robotics motion planning techniques called probabilistic roadmap methods (PRMs). Our focus is to study issues related to the folding process, such as the formation of secondary and tertiary structures, assuming we know the native fold. A feature of our PRM-based framework is that the large sets of folding pathways in the roadmaps it produces, in just a few hours on a desktop PC, provide global information about the protein's energy landscape. This is an advantage over other simulation methods such as molecular dynamics or Monte Carlo methods which require more computation and produce only a single trajectory in each run. In our initial studies, we obtained encouraging results for several small proteins. In this paper, we investigate more sophisticated techniques for analyzing the folding pathways in our roadmaps. In addition to more formally revalidating our previous results, we present a case study showing that our technique captures known folding differences between the structurally similar proteins G and L.

Animals↗
PubMed2001

Calculated pH-dependent population and protonation of carbon-monoxy-myoglobin conformers.

X-ray structures of carbonmonoxymyoglobin (MbCO) are available for different pH values. We used conventional electrostatic continuum methods to calculate the titration behavior of MbCO in the pH range from 3 to 7. For our calculations, we considered five different x-ray structures determined at pH values of 4, 5, and 6. We developed a Monte Carlo method to sample protonation states and conformations at the same time so that we could calculate the population of the considered MbCO structures at different pH values and the titration behavior of MbCO for an ensemble of conformers. To increase the sampling efficiency, we introduced parallel tempering in our Monte Carlo method. The calculated population probabilities show, as expected, that the x-ray structures determined at pH 4 are most populated at low pH, whereas the x-ray structure determined at pH 6 is most populated at high pH, and the population of the x-ray structures determined at pH 5 possesses a maximum at intermediate pH. The calculated titration behavior is in better agreement with experimental results compared to calculations using only a single conformation. The most striking feature of pH-dependent conformational changes in MbCO-the rotation of His-64 out of the CO binding pocket-is reproduced by our calculations and is correlated with a protonation of His-64, as proposed earlier.

Animals↗
PubMed2003

A path planning-based study of protein folding with a case study of hairpin formation in protein G and L.

We investigate a novel approach for studying protein folding that has evolved from robotics motion planning techniques called probabilistic roadmap methods (PRMS). Our focus is to study issues related to the folding process, such as the formation of secondary and tertiary structure, assuming we know the native fold. A feature of our PRM-based framework is that the large sets of folding pathways in the roadmaps it produces, in a few hours on a desktop PC, provide global information about the protein's energy landscape. This is an advantage over other simulation methods such as molecular dynamics or Monte Carlo methods which require more computation and produce only a single trajectory in each run. In our initial studies, we obtained encouraging results for several small proteins. In this paper, we investigate more sophisticated techniques for analyzing the folding pathways in our roadmaps. In addition to more formally revalidating our previous results, we present a case study showing our technique captures known folding differences between the structurally similar proteins G and L.

Bacterial Proteins↗
PubMed1976

Three tests for randomness of attack of social groups during an epidemic.

It is suggested that investigation of the attack of social units can be more illuminating of an epidemic process than the usual study of secondary attack rates of individuals. Three tests for detecting non-random differences in the occurrence of a disease between two groups of social units are presented. In each method the number of units attacked (X) in one of two groups of units is considered, rather than the number of individuals attacked. The tests are: (a) to use the Monte Carlo method, computer simulation of the epidemic process, to obtain an empirical distribution to which the observed value of X is compared; (b) to obtain the exact distribution of X; (c) to standardize X and compare it to the standard normal distribution. The three approaches are compared using data obtained from an epidemic of variola minor in two schools and the differences between the results are trivial. However, for large samples the only feasible approach is the Monte Carlo method.

Brazil↗
PubMedDate not supplied

The effect of scattered radiation in 60Co beams on wall correction factors for ionization chambers.

The Awall correction factors used in dosimetry protocols are obtained by Monte Carlo methods that assume 60Co beams equivalent to 1.25-MeV radiation. Real 60Co beams contain lower energy components; in addition, Awall is defined differently by different authors. In the present work, Awall as defined by Rogers, Bielajew, and Nahum (1985) has been calculated by Monte Carlo methods at several energies, for a graphite cavity chamber, using the revised stopping-power data of Seltzer and Berger (1982). It is concluded that the true value of Awall for chambers designed for use in 60Co beams will not move more than 0.1% below the value calculated for 1.25-MeV photons.

Cobalt Radioisotopes↗
PubMed2005

Method for computing protein binding affinity.

A Monte Carlo method is given to compute the binding affinity of a ligand to a protein. The method involves extending configuration space by a discrete variable indicating whether the ligand is bound to the protein and a special Monte Carlo move, which allows transitions between the unbound and bound states. Provided that an accurate protein structure is given, that the protein-ligand binding site is known, and that an accurate chemical force field together with a continuum solvation model is used, this method provides a quantitative estimate of the free energy of binding.

Binding Sites↗
PubMed1995

Statistical basis for the determination of optical pathlength in tissue.

In this paper we show how to derive the mean and variance of the transilluminated signal obtained in models of light propagation in tissue, based both on a stochastic Monte Carlo method and on a deterministic diffusion approximation. The theoretical treatment of the Monte Carlo model applies only to integrated intensity measurements, whereas the diffusion approximation gives an estimator for the time-dependent case as well. We present results that show the accurate prediction of Monte Carlo statistics, and propose that the diffusion approximation is therefore a suitable mechanism for incorporating noise into modelling procedures.

Animals↗