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.     

Comparison between an event-by-event Monte Carlo code,NOREC, and ETRAN for electron scaled point kernels between 20 keV and 1 MeV

An event-by-event Monte Carlo code called NOREC, a substantially improved version of the Oak Ridge electron transport code (OREC), was released in 2003, after a number of modifications to OREC. In spite of some earlier work, the characteristics of the code have not been clearly shown so far, especially for a wide range of electron energies. Therefore, NOREC was used in this study to generate one of the popular dosimetric quantities, the scaled point kernel, for a number of electron energies between 0.02 and 1.0 MeV. Calculated kernels were compared with the most well-known published kernels based on a condensed history Monte Carlo code, ETRAN, to show not only general agreement between the codes for the electron energy range considered but also possible differences between an event-by-event code and a condensed history code. There was general agreement between the kernels within about 5% up to 0.7 r/r ₀ for 100 keV and 1 MeV electrons. Note that r/r ₀ denotes the scaled distance, where r is the radial distance from the source to the dose point and r ₀ is the continuous slowing down approximation (CSDA) range of a mono-energetic electron. For the same range of scaled distances, the discrepancies for 20 and 500 keV electrons were up to 6 and 12%, respectively. Especially, there was more pronounced disagreement for 500 keV electrons than for 20 keV electrons. The degree of disagreement for 500 keV electrons decreased when NOREC results were compared with published EGS4/PRESTA results, producing similar agreement to other electron energies.     

Evaluation of PENFAST – A fast Monte Carlo code for dose calculations in photon and electron radiotherapy treatment planning

The aim of the present study is to demonstrate the potential of accelerated dose calculations, using the fast Monte Carlo (MC) code referred to as PENFAST, rather than the conventional MC code PENELOPE, without losing accuracy in the computed dose. For this purpose, experimental measurements of dose distributions in homogeneous and inhomogeneous phantoms were compared with simulated results using both PENELOPE and PENFAST. The simulations and experiments were performed using a Saturne 43 linac operated at 12 MV (photons), and at 18 MeV (electrons). Pre-calculated phase space files (PSFs) were used as input data to both the PENELOPE and PENFAST dose simulations. Since depth–dose and dose profile comparisons between simulations and measurements in water were found to be in good agreement (within ±1% to 1 mm), the PSF calculation is considered to have been validated. In addition, measured dose distributions were compared to simulated results in a set of clinically relevant, inhomogeneous phantoms, consisting of lung and bone heterogeneities in a water tank. In general, the PENFAST results agree to within a 1% to 1 mm difference with those produced by PENELOPE, and to within a 2% to 2 mm difference with measured values. Our study thus provides a pre-clinical validation of the PENFAST code. It also demonstrates that PENFAST provides accurate results for both photon and electron beams, equivalent to those obtained with PENELOPE. CPU time comparisons between both MC codes show that PENFAST is generally about 9–21 times faster than PENELOPE.     

Refinement of the protein backbone angle ψ in NMR structure calculations

Cross-correlated relaxation rates involving the C-H dipolar interaction and the carbonyl (C) chemical shift anisotropy (CSA) have been measured using two complementary 3D experiments. We show that the protein backbone angle can be directly refined against such cross-correlated relaxation rates (^{H C,C}) and the three-bond H/D isotope effect on the C chemical shifts (³C _(ND)). By simultaneously using both experimental parameters as restraints during NMR structure calculations, a unique value for the backbone angle is defined. We have applied the new refinement method to the -Spectrin SH3 domain (a -sheet protein) and to the Sgs1p HRDC domain (an -helical protein) and show that the quality of the NMR structures is substantially improved, judging from the atomic coordinate precision and the Ramachandran map. In addition, the -refined NMR structures of the SH3 domain deviate less from the 1.8 Å crystal structure, suggesting an improved accuracy. The proposed refinement method can be used to significantly improve the quality of NMR structures and will be applicable to larger proteins.     

Free energy calculations on the stability of the 14-3-3ζ protein

Mutations of cysteine are often introduced to e.g. avoid formation of non-physiological inter-molecular disulfide bridges in in-vitro experiments, or to maintain specificity in labeling experiments. Alanine or serine is typically preferred, which usually do not alter the overall protein stability, when the original cysteine was surface exposed. However, selecting the optimal mutation for cysteines in the hydrophobic core of the protein is more challenging. In this work, the stability of selected Cys mutants of 14-3-3ζ was predicted by free-energy calculations and the obtained data were compared with experimentally determined stabilities. Both the computational predictions as well as the experimental validation point at a significant destabilization of mutants C94A and C94S. This destabilization could be attributed to the formation of hydrophobic cavities and a polar solvation of a hydrophilic side chain. A L12E, M78K double mutant was further studied in terms of its reduced dimerization propensity. In contrast to naïve expectations, this double mutant did not lead to the formation of strong salt bridges, which was rationalized in terms of a preferred solvation of the ionic species. Again, experiments agreed with the calculations by confirming the monomerization of the double mutants. Overall, the simulation data is in good agreement with experiments and offers additional insight into the stability and dimerization of this important family of regulatory proteins.     

Electron stopping power and inelastic mean free path in amino acids and protein over the energy range of 20–20,000 eV

Systematic calculations of stopping power (SPs) and inelastic mean free path (IMFP) values for 20–20,000 eV electrons in a group of 15 amino acids and a simple protein have been performed. The calculations are based on the dielectric response model and take into account the exchange effect between the incident electron and target electrons. The optical energy-loss functions for the 15 investigated amino acids and the protein are evaluated by using an empirical approach, because of the lack of experimental optical data. For all the considered materials, the calculated mean ionization potentials are in good agreement with those given by Bragg’s rule, and the evaluated SP values at 20 keV converge well to the Bethe–Bloch predictions. The data shown represent the first results of SP and IMFP, for these 15 amino acids and the protein in the energy range below 20 keV, and might be useful for studies of various radiation effects in these materials. In addition, the average energy deposited by inelastic scattering of the electrons on this group of 15 amino acids, on the protein, on Formvar and on DNA, respectively, has been estimated for energies below 20 keV. The dependences of the average energy deposition on the electron energy are given. These results are important for any detailed studies of radiation-induced inactivation of proteins and the DNA.     

Monte Carlo calculation of photo-neutron dose produced by circular cones at 18 MV photon beams

Aim

The aim of this study is to calculate neutron contamination at the presence of circular cones irradiating by 18 MV photons using Monte Carlo code.

Dicentric chromosomes in monolayers of human lymphocytes produced by monochromatized synchrotron radiation with photon energies from 1.83 keV to 17.4 keV

A systematic approach was used to examine the induction of dicentric chromosomes in human lymphocytes irradiated in vitro with monochromatized synchrotron radiation produced with photon energies in the range from 1.83 keV to 17.4 keV. To avoid potential confounding factors that could influence the outcome of the experiments, only blood from one individual was used. Since for the irradiation experiments with these low photon energies the local dose variations would become unacceptable, monolayers of lymphocytes attached within 3 h PHA stimulation have been used. The culture conditions ensured that the chromosome analysis could be performed exclusively in metaphases of the first cell cycle in vitro. There is a strong indication for a systematic change of the coefficient of the linear quadratic dose-response relationship from 1.83 keV (=1.26±0.28) with increasing energy up to 6.9 keV (=8.24±0.41) and a decrease with further increase of energy up to 17.4 keV (=3.83±1.72). A tendency for a systematic change of the coefficient seems to be present at energies of 6.9 keV (=8.04±0.40) and 4.8 keV (=9.48±1.57) as well as at energies of 3.10 keV (=2.99±0.51) and 1.83 keV (=0.40±0.25). These results agree in essence with the previously published large data set from Sasakis laboratory.     

Alteration in virulence characteristics of biofilm cells of Pseudomonas aeruginosa in presence of Tamm-Horsfall protein

Summary Tamm-Horsfall glycoprotein is the most abundant protein in human urine. The present investigation was planned to study the effect of Tamm-Horsfall protein (THP) on elaboration of virulence factors by biofilm cells of Pseudomonas aeruginosa. It was observed that with increase in concentration of THP from 10 to 50 μg/ml there was significant enhancement in elaboration of all the virulence factors by biofilm cells of P. aeruginosa. However, with further increase in concentration of THP from 50 to 70 μg/ml, significant decrease in elaboration of all the virulence traits was observed. Implications of these findings in relation to urinary tract infections caused by P. aeruginosa have been discussed.     

Continuous fractional component Monte Carlo simulations of high-density adsorption in metal–organic frameworks

The continuous fractional component Monte Carlo method, which was designed to overcome difficulties with insertions and deletions of molecules, is modified to include configurational bias Monte Carlo methods and is further extended to binary systems. The modified method is shown to correctly predict adsorption of Ar in silicalite, Xe and Kr in HKUST-1, and enantiomers in a homochiral metal–organic framework. The modified method is also found to be approximately an order of magnitude more efficient in inserting and deleting molecules than traditional configurational bias grand canonical Monte Carlo simulations in dense systems.     

Using a FRET Library with Multiple Probe Pairs To Drive Monte Carlo Simulations of α-Synuclein

We describe a strategy for experimentally-constraining computational simulations of intrinsically disordered proteins (IDPs), using α-synuclein, an IDP with a central role in Parkinson’s disease pathology, as an example. Previously, data from single-molecule Förster Resonance Energy Transfer (FRET) experiments have been effectively utilized to generate experimentally constrained computational models of IDPs. However, the fluorophores required for single-molecule FRET experiments are not amenable to the study of short-range (<30 Å) interactions. Using ensemble FRET measurements allows one to acquire data from probes with multiple distance ranges, which can be used to constrain Monte Carlo simulations in PyRosetta. To appropriately employ ensemble FRET data as constraints, we optimized the shape and weight of constraining potentials to afford ensembles of structures that are consistent with experimental data. We also used this approach to examine the structure of α-synuclein in the presence of the compacting osmolyte trimethylamine-N-oxide. Despite significant compaction imparted by 2 M trimethylamine-N-oxide, the underlying ensemble of α-synuclein remains largely disordered and capable of aggregation, also in agreement with experimental data. These proof-of-concept experiments demonstrate that our modeling protocol enables one to efficiently generate experimentally constrained models of IDPs that incorporate atomic-scale detail, allowing one to study an IDP under a variety of conditions.     

The Extrapolation of Vapour–liquid Equilibrium Curves of Pure Fluids in Alternative Gibbs Ensemble Monte Carlo Implementations

Extrapolation schemes based on Taylor series expansion to determine the vapour–liquid equilibrium (VLE) curves of pure molecular fluids are presented for the NpH and μVL versions of the Gibbs ensemble Monte Carlo (GEMC) simulations. The coexistence curves of the various configurational quantities can be expressed as Taylor series around the simulated equilibrium point as a function of pressure in the NpH version and chemical potential in the μVL version. The coefficients of the Taylor series are calculated from single GEMC simulations using Clapeyron-like equations and fluctuation formulas. A Padè approximant is used to widen the range where the extrapolation is accurate. These methods are demonstrated on atomic Lennard-Jones fluid. The procedure is found to be an accurate and useful tool to calculate wide sections of the VLE curves. With this procedure the saturation heat capacity can be directly determined using the calculated derivatives.     

Effects of the dietary protein content and the feeding level on protein and energy metabolism in Iberian pigs growing from 50 to 100 kg body weight

Nutritional requirements of the Iberian pig, a slow-growing, obese porcine breed, are not well defined and seem to differ from those of conventional or high-performing pigs. The effects of the dietary protein content and the feeding level on the utilisation of metabolisable energy (ME) and the rates of gain, protein, and fat deposition were studied with 81 Iberian castrates growing from 50 to 100 kg body weight (BW) by using the comparative slaughter technique. The animals were fed 4 diets providing 145, 120, 95, and 70 g ideal crude protein (CP) per kg dry matter (DM), and containing 13.94, 14.29, 14.56, and 14.83 MJ ME per kg DM, respectively. Three levels of feeding were evaluated: 0.60, 0.80, and 0.95 × ad libitum intake. Growth rate increased (linear and quadratic, P < 0.001) as the dietary ideal CP content decreased. It also increased with the feeding level (linear, P < 0.001; quadratic, P < 0.05). Gain:feed and gain:ME intake improved by decreasing the ideal CP content in the diet (linear, P < 0.001 and P < 0.05, respectively; quadratic P < 0.001 for both variables). Increasing the feeding level improved linearly gain:feed and gain:ME intake ( P < 0.001). Protein deposition (PD):ME intake ranged between 1.23 and 1.44 g/MJ, and it showed a tendency to reach the maximum value when the diet providing 95 g ideal CP per kg DM was fed (quadratic, P = 0.078). When this diet was offered at 0.95 × ad libitum, PD reached a maximum value of 71 g/day. This dietary treatment resulted in average values for average daily gain and retained energy (RE) of 854 g/day and 21.4 MJ/day, respectively. The average rate of gain was 19.93 g/MJ increase in ME intake, equivalent to an energy cost of 50.2 kJ ME per g gain, irrespective of the dietary ideal CP content. Also, the overall marginal efficiency of protein deposition (ΔPD:ΔME; g/MJ) was 1.34. Increasing the feeding level led to increases in PD (linear, P <  0.001) and RE (linear, P <  0.001; quadratic, P <  0.01) irrespective of the dietary ideal CP concentrations. Between 50 and 100 kg BW, the chemical composition of 1 kg gain averaged 78, 592, 28.7, and 284 g for CP, fat, ash, and water respectively. The net efficiency of use of ME for growth ( k_g) and the maintenance energy requirements were 0.606 and 396 kJ/kg BW ^0.75 per day, respectively. The results support earlier findings that the genotype has marked effects on protein and energy metabolism of growing pigs and underline important compositional differences of the Iberian pig compared with conventional or modern porcine genotypes.     

Monte Carlo simulation of gas free molecular flow in turbo molecular pump’s inlet tube

Due to the beaming effect of inlet tube and reflection effect of turbine cover in the turbo molecular pump, the positional and angular distribution of incident gas molecules (IGM) on the turbine blades would no longer be uniformly distributed. Based on the test particle Monte Caro method, a new self-defining procedure is proposed and it can be more accurate to describe the status of IGM into turbine blades. The results show that the influence of rotor speed on the transmission probability is indistinctive. Meanwhile, the incident density between the tip and root of the blades is distinct. The positional beaming effect and the angular beaming effect are enhanced with the lengthening of the tube and less molecule diverge towards the tube wall. The positive transmission probability of first-stage turbine blades using our new method is different from those obeying the cosine distribution under the same number of incident molecules. The calculation results of new method verified by another procedure are reasonable and accurate.     

Celebrating 20 years of historical papers in Photosynthesis Research

This Editorial has four goals: (1) to inform the readers of ‘Photosynthesis Research‘ about the past of the ‘Historical corner’; which began 20 years ago; (2) to encourage photosynthesis researchers and historians of science to contact me for publishing papers of historical interest; these include: (a) Obituaries and Tributes; (b) historical papers on current and past discoveries and controversies; (c) history of research in specific laboratories, or in specific countries, or at specific conferences; (d) Personal perspectives (not discussed any further); (3) to encourage researchers not to discard, but to save correspondence and data of their discoveries for the future historians by donating them to their Archives, when appropriate (not discussed any further); and (4) to reinforce to the readers that the concept of two-light reaction and two-pigment system was already there in 1959. I mention here three key papers presented at the IX^th International Botanical Congress, held at Montreal Canada (in August, 1959) prior to the famous April 9, 1960 paper by Robert Hill and Fay Bendall on the ‘Z-scheme’ of photosynthesis, that was based on thermodynamic and energetic considerations. ^★ This Historical corner Editorial is dedicated to Bessel Kok (1918–1978).     

Monte Carlo characterizations mapping of the (γ,n) and (n,γ) photonuclear reactions in the high energy X-ray radiation therapy

Aim

The aim of this work was to map the characteristics of (n,γ) and (γ,n) reactions in a high energy photon radiation therapy.

Background

Photoneutrons produced in the high energy X-Ray radiation therapy may damage patients and staff. It is due to high RBE of the produced neutrons according to their energy and isotropic emission. Characterization of the photoneutrons can help us in appropriate shielding.

Materials and methods

This study focused on the photoneutron and capture gamma ray phenomena. Characteristics such as dose value, fluence and spectra of both the neutrons and the by produced prompt gamma ray were described.

Results and discussion

Neutron and prompt gamma spectra in different points showed the neutrons to be thermalized when increasing the distance from the linac. Energy of the neutrons changed from about 0.6 MeV at the isocentre to around 10⁻⁰⁸ MeV at the outer door position. Although the neutrons were found as fast neutrons, their spectra showed they were thermal neutrons at the outer door position. Additionally, it was seen that the energy of the gamma rays is higher than the scattered X-ray energy. The energy of gamma rays was seen to be up to 10 MeV while the linac photons had energy lower than 1 MeV. Neutron source strength obtained in this work was in good agreement with the published data, which may be a confirmation of our simulation accuracy.

Conclusion

The study showed that the Monte Carlo simulation can be applied in the radiotherapy and industrial radiation works as a useful and precise estimator. We also concluded that the dose from the prompt gamma ray at the outer door location is higher than the scattered radiation from the linac and should be considered in the shielding.