Combined Monte Carlo and quantum mechanics study of the solvatochromism of phenol in water. The origin of the blue shift of the lowest pi-pi* transition

A combined and sequential use of Monte Carlo simulations and quantum mechanical calculations is made to analyze the spectral shift of the lowest pi-pi* transition of phenol in water. The solute polarization is included using electrostatic embedded calculations at the MP2/aug-cc-pVDZ level giving a dipole moment of 2.25 D, corresponding to an increase of 76% compared to the calculated gas-phase value. Using statistically uncorrelated configurations sampled from the MC simulation,first-principle size-extensive calculations are performed to obtain the solvatochromic shift. Analysis is then made of the origin of the blue shift. Results both at the optimized geometry and in room-temperature liquid water show that hydrogen bonds of water with phenol promote a red shift when phenol is the proton-donor and a blue shift when phenol is the proton-acceptor. In the case of the optimized clusters the calculated shifts are in very good agreement with results obtained from mass-selected free jet expansion experiments. In the liquid case the contribution of the solute-solvent hydrogen bonds partially cancels and the total shift obtained is dominated by the contribution of the outer solvent water molecules. Our best result, including both inner and outer water molecules, is 570 +/- 35 cm(-1), in very good agreement with the small experimental shift of 460 cm(-1) for the absorption maximum.

The isotropic nuclear magnetic shielding constants of acetone in supercritical water: A sequential Monte Carlo/quantum mechanics study including solute polarization

The nuclear isotropic shielding constants sigma((17)O) and sigma((13)C) of the carbonyl bond of acetone in water at supercritical (P=340.2 atm and T=673 K) and normal water conditions have been studied theoretically using Monte Carlo simulation and quantum mechanics calculations based on the B3LYP/6-311++G(2d,2p) method. Statistically uncorrelated configurations have been obtained from Monte Carlo simulations with unpolarized and in-solution polarized solute. The results show that solvent effects on the shielding constants have a significant contribution of the electrostatic interactions and that quantitative estimates for solvent shifts of shielding constants can be obtained modeling the water molecules by point charges (electrostatic embedding). In supercritical water, there is a decrease in the magnitude of sigma((13)C) but a sizable increase in the magnitude of sigma((17)O) when compared with the results obtained in normal water. It is found that the influence of the solute polarization is mild in the supercritical regime but it is particularly important for sigma((17)O) in normal water and its shielding effect reflects the increase in the average number of hydrogen bonds between acetone and water. Changing the solvent environment from normal to supercritical water condition, the B3LYP/6-311++G(2d,2p) calculations on the statistically uncorrelated configurations sampled from the Monte Carlo simulation give a (13)C chemical shift of 11.7 +/- 0.6 ppm for polarized acetone in good agreement with the experimentally inferred result of 9-11 ppm. (C) 2008 American Institute of Physics.

Monte Carlo investigation of the critical behavior of Stavskaya's probabilistic cellular automaton

Stavskaya's model is a one-dimensional probabilistic cellular automaton (PCA) introduced in the end of the 1960s as an example of a model displaying a nonequilibrium phase transition. Although its absorbing state phase transition is well understood nowadays, the model never received a full numerical treatment to investigate its critical behavior. In this Brief Report we characterize the critical behavior of Stavskaya's PCA by means of Monte Carlo simulations and finite-size scaling analysis. The critical exponents of the model are calculated and indicate that its phase transition belongs to the directed percolation universality class of critical behavior, as would be expected on the basis of the directed percolation conjecture. We also explicitly establish the relationship of the model with the Domany-Kinzel PCA on its directed site percolation line, a connection that seems to have gone unnoticed in the literature so far.

Avaliação da dose absorvida na tiróide, em cintigrafias com 123I e Na99mTcO4 utilizando modelos biocinéticos e métodos de Monte Carlo

Mestrado em Radiações Aplicadas às Tecnologias da Saúde. Área de especialização: Protecção contra Radiações

The use of non-standard CT conversion ramps for Monte Carlo verification of 6 MV prostate IMRT plans

Monte Carlo (MC) dose calculation algorithms have been widely used to verify the accuracy of intensity-modulated radiotherapy (IMRT) dose distributions computed by conventional algorithms due to the ability to precisely account for the effects of tissue inhomogeneities and multileaf collimator characteristics. Both algorithms present, however, a particular difference in terms of dose calculation and report. Whereas dose from conventional methods is traditionally computed and reported as the water-equivalent dose (Dw), MC dose algorithms calculate and report dose to medium (Dm). In order to compare consistently both methods, the conversion of MC Dm into Dw is therefore necessary. This study aims to assess the effect of applying the conversion of MC-based Dm distributions to Dw for prostate IMRT plans generated for 6 MV photon beams. MC phantoms were created from the patient CT images using three different ramps to convert CT numbers into material and mass density: a conventional four material ramp (CTCREATE) and two simplified CT conversion ramps: (1) air and water with variable densities and (2) air and water with unit density. MC simulations were performed using the BEAMnrc code for the treatment head simulation and the DOSXYZnrc code for the patient dose calculation. The conversion of Dm to Dw by scaling with the stopping power ratios of water to medium was also performed in a post-MC calculation process. The comparison of MC dose distributions calculated in conventional and simplified (water with variable densities) phantoms showed that the effect of material composition on dose-volume histograms (DVH) was less than 1% for soft tissue and about 2.5% near and inside bone structures. The effect of material density on DVH was less than 1% for all tissues through the comparison of MC distributions performed in the two simplified phantoms considering water. Additionally, MC dose distributions were compared with the predictions from an Eclipse treatment planning system (TPS), which employed a pencil beam convolution (PBC) algorithm with Modified Batho Power Law heterogeneity correction. Eclipse PBC and MC calculations (conventional and simplified phantoms) agreed well (<1%) for soft tissues. For femoral heads, differences up to 3% were observed between the DVH for Eclipse PBC and MC calculated in conventional phantoms. The use of the CT conversion ramp of water with variable densities for MC simulations showed no dose discrepancies (0.5%) with the PBC algorithm. Moreover, converting Dm to Dw using mass stopping power ratios resulted in a significant shift (up to 6%) in the DVH for the femoral heads compared to the Eclipse PBC one. Our results show that, for prostate IMRT plans delivered with 6 MV photon beams, no conversion of MC dose from medium to water using stopping power ratio is needed. In contrast, MC dose calculations using water with variable density may be a simple way to solve the problem found using the dose conversion method based on the stopping power ratio.

Properties of patchy colloidal particles close to a surface: a Monte Carlo and density functional study

We investigate the behavior of a patchy particle model close to a hard-wall via Monte Carlo simulation and density functional theory (DFT). Two DFT approaches, based on the homogeneous and inhomogeneous versions of Wertheim's first order perturbation theory for the association free energy are used. We evaluate, by simulation and theory, the equilibrium bulk phase diagram of the fluid and analyze the surface properties for two isochores, one of which is close to the liquid side of the gas-liquid coexistence curve. We find that the density profile near the wall crosses over from a typical high-temperature adsorption profile to a low-temperature desorption one, for the isochore close to coexistence. We relate this behavior to the properties of the bulk network liquid and find that the theoretical descriptions are reasonably accurate in this regime. At very low temperatures, however, an almost fully bonded network is formed, and the simulations reveal a second adsorption regime which is not captured by DFT. We trace this failure to the neglect of orientational correlations of the particles, which are found to exhibit surface induced orientational order in this regime.

Parallelization of kinetic Monte Carlo algorithm to simulate AL3Sc precipitation

The present paper reports the precipitation process of Al3Sc structures in an aluminum scandium alloy, which has been simulated with a synchronous parallel kinetic Monte Carlo (spkMC) algorithm. The spkMC implementation is based on the vacancy diffusion mechanism. To filter the raw data generated by the spkMC simulations, the density-based clustering with noise (DBSCAN) method has been employed. spkMC and DBSCAN algorithms were implemented in the C language and using MPI library. The simulations were conducted in the SeARCH cluster located at the University of Minho. The Al3Sc precipitation was successfully simulated at the atomistic scale with the spkMC. DBSCAN proved to be a valuable aid to identify the precipitates by performing a cluster analysis of the simulation results. The achieved simulations results are in good agreement with those reported in the literature under sequential kinetic Monte Carlo simulations (kMC). The parallel implementation of kMC has provided a 4x speedup over the sequential version.

The Analysis of interval censoring and double censoring via Markov chain Monte Carlo methods

L'Anàlisi de la supervivència s'utilitza en diferents camps per analitzar el temps transcorregut entre dos esdeveniments. El que distingeix l'anàlisi de la supervivència d'altres àrees de l'estadística és que les dades normalment estan censurades. La censura en un interval apareix quan l'esdeveniment final d'interès no és directament observable i només se sap que el temps de fallada està en un interval concret. Un esquema de censura més complex encara apareix quan tant el temps inicial com el temps final estan censurats en un interval. Aquesta situació s'anomena doble censura. En aquest article donem una descripció formal d'un mètode bayesà paramètric per a l'anàlisi de dades censurades en un interval i dades doblement censurades així com unes indicacions clares de la seva utilització o pràctica. La metodologia proposada s'ilustra amb dades d'una cohort de pacients hemofílics que es varen infectar amb el virus VIH a principis dels anys 1980's.

Evaluation of organ-specific peripheral doses after 2-dimensional, 3-dimensional and hybrid intensity modulated radiation therapy for breast cancer based on Monte Carlo and convolution/superposition algorithms: implications for secondary cancer risk assessment.

To make a comprehensive evaluation of organ-specific out-of-field doses using Monte Carlo (MC) simulations for different breast cancer irradiation techniques and to compare results with a commercial treatment planning system (TPS). Three breast radiotherapy techniques using 6MV tangential photon beams were compared: (a) 2DRT (open rectangular fields), (b) 3DCRT (conformal wedged fields), and (c) hybrid IMRT (open conformal+modulated fields). Over 35 organs were contoured in a whole-body CT scan and organ-specific dose distributions were determined with MC and the TPS. Large differences in out-of-field doses were observed between MC and TPS calculations, even for organs close to the target volume such as the heart, the lungs and the contralateral breast (up to 70% difference). MC simulations showed that a large fraction of the out-of-field dose comes from the out-of-field head scatter fluence (>40%) which is not adequately modeled by the TPS. Based on MC simulations, the 3DCRT technique using external wedges yielded significantly higher doses (up to a factor 4-5 in the pelvis) than the 2DRT and the hybrid IMRT techniques which yielded similar out-of-field doses. In sharp contrast to popular belief, the IMRT technique investigated here does not increase the out-of-field dose compared to conventional techniques and may offer the most optimal plan. The 3DCRT technique with external wedges yields the largest out-of-field doses. For accurate out-of-field dose assessment, a commercial TPS should not be used, even for organs near the target volume (contralateral breast, lungs, heart).

Biblioteca de l'heurística constructiva Clarke and Wright combinada amb simulació Monte Carlo per resoldre el problema d'adreçament de vehicles

En aquesta recerca es presenta una biblioteca de programari lliure basada en l'heurística constructiva de Clarke & Wright combinada amb simulació Monte Carlo que permet, de manera simple, generar solucions al problema d'adreçament de vehicles. Aquesta metodologia construeix solucions competents en poc temps i sense necessitat d'ajustar o configurar paràmetres previs. La biblioteca pot integrar-se fàcilment en projectes que resolguin variants del VRP amb canvis mínims sobre el codi. Aquest es troba ben documentat i accessible de manera lliure a través de la xarxa. Els resultats computacionals indiquen que es resolen instàncies VRP en temps i costos significativament inferiors a altres propostes de la mateixa família.

Main results of the Monte Carlo studies carried out for nuclear medicine practices within the ORAMED project

The aim of ORAMED work package 4 was the optimization of the medical practices in nuclear medicine during the preparation of radiopharmaceuticals and their administration to the patient. During the project a wide campaign of measurements was performed in the nuclear medicine departments of the collaborating hospitals. Such data were intrinsically characterized by a large variability that depended on the procedure, the employed techniques and the operator's habits. That variability could easily hide some important parameter, for example, the effectiveness of the adopted shielding (for syringe and vial) or the effect of the distances from the source. This information is necessary for a valuable optimization purpose of radiation protection. To this end a sensitivity analysis was carried out through Monte Carlo simulations employing voxel models, representing operator's hand during the considered practices. Such analysis allowed understanding at what extent the range of personal dose equivalent evaluated during measurements can be considered intrinsically related to the procedures. Furthermore, with the Monte Carlo simulations it was possible to study the appropriateness of the shielding usually utilized in these practices.

On the robustness of least-squares Monte Carlo (LSM) for pricing American derivatives

This paper analyses the robustness of Least-Squares Monte Carlo, a techniquerecently proposed by Longstaff and Schwartz (2001) for pricing Americanoptions. This method is based on least-squares regressions in which theexplanatory variables are certain polynomial functions. We analyze theimpact of different basis functions on option prices. Numerical resultsfor American put options provide evidence that a) this approach is veryrobust to the choice of different alternative polynomials and b) few basisfunctions are required. However, these conclusions are not reached whenanalyzing more complex derivatives.

PENELOPE-2008: A Code System for Monte Carlo Simulation of Electron and Photon Transport

The computer code system PENELOPE (version 2008) performs Monte Carlo simulation of coupledelectron-photon transport in arbitrary materials for a wide energy range, from a few hundred eV toabout 1 GeV. Photon transport is simulated by means of the standard, detailed simulation scheme.Electron and positron histories are generated on the basis of a mixed procedure, which combinesdetailed simulation of hard events with condensed simulation of soft interactions. A geometry packagecalled PENGEOM permits the generation of random electron-photon showers in material systemsconsisting of homogeneous bodies limited by quadric surfaces, i.e., planes, spheres, cylinders, etc. Thisreport is intended not only to serve as a manual of the PENELOPE code system, but also to provide theuser with the necessary information to understand the details of the Monte Carlo algorithm.

Monte Carlo Study of the Growth of L12 ordered domains in fcc A3B binary alloys

A Monte Carlo study of the late time growth of L12-ordered domains in a fcc A3B binary alloy is presented. The energy of the alloy has been modeled by a nearest-neighbor interaction Ising Hamiltonian. The system exhibits a fourfold degenerated ground state and two kinds of interfaces separating ordered domains: flat and curved antiphase boundaries. Two different dynamics are used in the simulations: the standard atom-atom exchange mechanism and the more realistic vacancy-atom exchange mechanism. The results obtained by both methods are compared. In particular we study the time evolution of the excess energy, the structure factor and the mean distance between walls. In the case of atom-atom exchange mechanism anisotropic growth has been found: two characteristic lengths are needed in order to describe the evolution. Contrarily, with the vacancyatom exchange mechanism scaling with a single length holds. Results are contrasted with existing experiments in Cu3Au and theories for anisotropic growth.

Magnetic microstructures from magnetic force microscopy and Monte Carlo simulation in CoFe-Ag-Cu granular films

CoFe-Ag-Cu granular films, prepared by rf sputtering, displayed magnetic domain microstructures for ferromagnetic concentrations above about 32% at, and below the percolation threshold. All samples have a fcc structure with an (111) texture perpendicular to the film plane. Magnetic force microscopy (MFM) showed a variety of magnetic domain microstructures, extremely sensitive to the magnetic history of the sample, which arise from the balance of the ferromagnetic exchange, the dipolar interactions and perpendicular magnetocrystalline anisotropy, MFM images indicate that in virgin samples, magnetic bubble domains with an out-of-plane component of the magnetization are surrounded by a quasicontinuous background of opposite magnetization domains. The application of a magnetic field in different geometries drastically modifies the microstructure of the system in the remanent state: i) for an in-plane field, the MFM images show that most of the magnetic moments are aligned along the film plane, ii) for an out-of-plane field, the MFM signal increases about one order of magnitude, and out-of-plane striped domains with alternating up and down magnetization are stabilized. Numerical simulations show that a variety of metastable domain structures (similar to those observed experimentally) can be reached, depending on magnetic history, in systems with competing perpendicular anisotropy, exchange and dipolar interactions.