MMonCa: An Object Kinetic Monte Carlo simulator for damage irradiation evolution and defect diffusion

In this work, we introduce the Object Kinetic Monte Carlo (OKMC) simulator MMonCa and simulate the defect evolution in three different materials. We start by explaining the theory of OKMC and showing some details of how such theory is implemented by creating generic structures and algorithms in the objects that we want to simulate. Then we successfully reproduce simulated results for defect evolution in iron, silicon and tungsten using our simulator and compare with available experimental data and similar simulations. The comparisons validate MMonCa showing that it is powerful and flexible enough to be customized and used to study the damage evolution of defects in a wide range of solid materials.

Red Cell Volume Expansion at Altitude: A Meta-analysis and Monte Carlo Simulation

Meta-análisis del volumen de eritrocitos en altitud

FocusDET, a new toolbox for SISCOM analysis. Evaluation of the registration accuracy using monte carlo simulation

Subtraction of Ictal SPECT Co-registered to MRI (SISCOM) is an imaging technique used to localize the epileptogenic focus in patients with intractable partial epilepsy. The aim of this study was to determine the accuracy of registration algorithms involved in SISCOM analysis using FocusDET, a new user-friendly application. To this end, Monte Carlo simulation was employed to generate realistic SPECT studies. Simulated sinograms were reconstructed by using the Filtered BackProjection (FBP) algorithm and an Ordered Subsets Expectation Maximization (OSEM) reconstruction method that included compensation for all degradations. Registration errors in SPECT-SPECT and SPECT-MRI registration were evaluated by comparing the theoretical and actual transforms. Patient studies with well-localized epilepsy were also included in the registration assessment. Global registration errors including SPECT-SPECT and SPECT-MRI registration errors were less than 1.2 mm on average, exceeding the voxel size (3.32 mm) of SPECT studies in no case. Although images reconstructed using OSEM led to lower registration errors than images reconstructed with FBP, differences after using OSEM or FBP in reconstruction were less than 0.2 mm on average. This indicates that correction for degradations does not play a major role in the SISCOM process, thereby facilitating the application of the methodology in centers where OSEM is not implemented with correction of all degradations. These findings together with those obtained by clinicians from patients via MRI, interictal and ictal SPECT and video-EEG, show that FocusDET is a robust application for performing SISCOM analysis in clinical practice.

Massively parallelizable list-mode reconstruction using a Monte Carlo-based elliptical Gaussian model

Purpose: A fully three-dimensional (3D) massively parallelizable list-mode ordered-subsets expectation-maximization (LM-OSEM) reconstruction algorithm has been developed for high-resolution PET cameras. System response probabilities are calculated online from a set of parameters derived from Monte Carlo simulations. The shape of a system response for a given line of response (LOR) has been shown to be asymmetrical around the LOR. This work has been focused on the development of efficient region-search techniques to sample the system response probabilities, which are suitable for asymmetric kernel models, including elliptical Gaussian models that allow for high accuracy and high parallelization efficiency. The novel region-search scheme using variable kernel models is applied in the proposed PET reconstruction algorithm. Methods: A novel region-search technique has been used to sample the probability density function in correspondence with a small dynamic subset of the field of view that constitutes the region of response (ROR). The ROR is identified around the LOR by searching for any voxel within a dynamically calculated contour. The contour condition is currently defined as a fixed threshold over the posterior probability, and arbitrary kernel models can be applied using a numerical approach. The processing of the LORs is distributed in batches among the available computing devices, then, individual LORs are processed within different processing units. In this way, both multicore and multiple many-core processing units can be efficiently exploited. Tests have been conducted with probability models that take into account the noncolinearity, positron range, and crystal penetration effects, that produced tubes of response with varying elliptical sections whose axes were a function of the crystal's thickness and angle of incidence of the given LOR. The algorithm treats the probability model as a 3D scalar field defined within a reference system aligned with the ideal LOR. Results: This new technique provides superior image quality in terms of signal-to-noise ratio as compared with the histogram-mode method based on precomputed system matrices available for a commercial small animal scanner. Reconstruction times can be kept low with the use of multicore, many-core architectures, including multiple graphic processing units. Conclusions: A highly parallelizable LM reconstruction method has been proposed based on Monte Carlo simulations and new parallelization techniques aimed at improving the reconstruction speed and the image signal-to-noise of a given OSEM algorithm. The method has been validated using simulated and real phantoms. A special advantage of the new method is the possibility of defining dynamically the cut-off threshold over the calculated probabilities thus allowing for a direct control on the trade-off between speed and quality during the reconstruction.

A new PET prototype for proton therapy: comparison of data and Monte Carlo simulations

Ion beam therapy is a valuable method for the treatment of deep-seated and radio-resistant tumors thanks to the favorable depth-dose distribution characterized by the Bragg peak. Hadrontherapy facilities take advantage of the specific ion range, resulting in a highly conformal dose in the target volume, while the dose in critical organs is reduced as compared to photon therapy. The necessity to monitor the delivery precision, i.e. the ion range, is unquestionable, thus different approaches have been investigated, such as the detection of prompt photons or annihilation photons of positron emitter nuclei created during the therapeutic treatment. Based on the measurement of the induced β+ activity, our group has developed various in-beam PET prototypes: the one under test is composed by two planar detector heads, each one consisting of four modules with a total active area of 10 × 10 cm2. A single detector module is made of a LYSO crystal matrix coupled to a position sensitive photomultiplier and is read-out by dedicated frontend electronics. A preliminary data taking was performed at the Italian National Centre for Oncological Hadron Therapy (CNAO, Pavia), using proton beams in the energy range of 93–112 MeV impinging on a plastic phantom. The measured activity profiles are presented and compared with the simulated ones based on the Monte Carlo FLUKA package.

On-road visual vehicle tracking using Markov chain Monte Carlo with metropolis sampling

In this study, a method for vehicle tracking through video analysis based on Markov chain Monte Carlo (MCMC) particle filtering with metropolis sampling is proposed. The method handles multiple targets with low computational requirements and is, therefore, ideally suited for advanced-driver assistance systems that involve real-time operation. The method exploits the removed perspective domain given by inverse perspective mapping (IPM) to define a fast and efficient likelihood model. Additionally, the method encompasses an interaction model using Markov Random Fields (MRF) that allows treatment of dependencies between the motions of targets. The proposed method is tested in highway sequences and compared to state-of-the-art methods for vehicle tracking, i.e., independent target tracking with Kalman filtering (KF) and joint tracking with particle filtering. The results showed fewer tracking failures using the proposed method.

Review and comparison of effective delayed neutron fraction calculation methods with Monte Carlo codes

The calculation of the effective delayed neutron fraction, beff , with Monte Carlo codes is a complex task due to the requirement of properly considering the adjoint weighting of delayed neutrons. Nevertheless, several techniques have been proposed to circumvent this difficulty and obtain accurate Monte Carlo results for beff without the need of explicitly determining the adjoint flux. In this paper, we make a review of some of these techniques; namely we have analyzed two variants of what we call the k-eigenvalue technique and other techniques based on different interpretations of the physical meaning of the adjoint weighting. To test the validity of all these techniques we have implemented them with the MCNPX code and we have benchmarked them against a range of critical and subcritical systems for which either experimental or deterministic values of beff are available. Furthermore, several nuclear data libraries have been used in order to assess the impact of the uncertainty in nuclear data in the calculated value of beff .

Efficient Monte Carlo optimization for multi-label classifier chains

Multi-label classification (MLC) is the supervised learning problem where an instance may be associated with multiple labels. Modeling dependencies between labels allows MLC methods to improve their performance at the expense of an increased computational cost. In this paper we focus on the classifier chains (CC) approach for modeling dependencies. On the one hand, the original CC algorithm makes a greedy approximation, and is fast but tends to propagate errors down the chain. On the other hand, a recent Bayes-optimal method improves the performance, but is computationally intractable in practice. Here we present a novel double-Monte Carlo scheme (M2CC), both for finding a good chain sequence and performing efficient inference. The M2CC algorithm remains tractable for high-dimensional data sets and obtains the best overall accuracy, as shown on several real data sets with input dimension as high as 1449 and up to 103 labels.

Feasibility assessment of the interactive use of a Monte Carlo algorithm in treatment planning for intraoperative electron radiation therapy

This work analysed the feasibility of using a fast, customized Monte Carlo (MC) method to perform accurate computation of dose distributions during pre- and intraplanning of intraoperative electron radiation therapy (IOERT) procedures. The MC method that was implemented, which has been integrated into a specific innovative simulation and planning tool, is able to simulate the fate of thousands of particles per second, and it was the aim of this work to determine the level of interactivity that could be achieved. The planning workflow enabled calibration of the imaging and treatment equipment, as well as manipulation of the surgical frame and insertion of the protection shields around the organs at risk and other beam modifiers. In this way, the multidisciplinary team involved in IOERT has all the tools necessary to perform complex MC dosage simulations adapted to their equipment in an efficient and transparent way. To assess the accuracy and reliability of this MC technique, dose distributions for a monoenergetic source were compared with those obtained using a general-purpose software package used widely in medical physics applications. Once accuracy of the underlying simulator was confirmed, a clinical accelerator was modelled and experimental measurements in water were conducted. A comparison was made with the output from the simulator to identify the conditions under which accurate dose estimations could be obtained in less than 3 min, which is the threshold imposed to allow for interactive use of the tool in treatment planning. Finally, a clinically relevant scenario, namely early-stage breast cancer treatment, was simulated with pre- and intraoperative volumes to verify that it was feasible to use the MC tool intraoperatively and to adjust dose delivery based on the simulation output, without compromising accuracy. The workflow provided a satisfactory model of the treatment head and the imaging system, enabling proper configuration of the treatment planning system and providing good accuracy in the dosage simulation.

Hybrid Monte Carlo dose algorithm for low energy X-rays intraoperative radiation therapy

Low energy X-rays Intra-Operative Radiation Therapy (XIORT) treatment delivered during surgery (ex: INTRABEAM, Carl Zeiss, and Axxent, Xoft) can benefit from accurate and fast dose prediction in a patient 3D volume.

Efficient Monte Carlo methods for multi-dimensional learning with classifier chains

Multi-dimensional classification (MDC) is the supervised learning problem where an instance is associated with multiple classes, rather than with a single class, as in traditional classification problems. Since these classes are often strongly correlated, modeling the dependencies between them allows MDC methods to improve their performance – at the expense of an increased computational cost. In this paper we focus on the classifier chains (CC) approach for modeling dependencies, one of the most popular and highest-performing methods for multi-label classification (MLC), a particular case of MDC which involves only binary classes (i.e., labels). The original CC algorithm makes a greedy approximation, and is fast but tends to propagate errors along the chain. Here we present novel Monte Carlo schemes, both for finding a good chain sequence and performing efficient inference. Our algorithms remain tractable for high-dimensional data sets and obtain the best predictive performance across several real data sets.

Student academic performance stochastic simulator based on the Monte Carlo method

In this paper, a computer-based tool is developed to analyze student performance along a given curriculum. The proposed software makes use of historical data to compute passing/failing probabilities and simulates future student academic performance based on stochastic programming methods (MonteCarlo) according to the specific university regulations. This allows to compute the academic performance rates for the specific subjects of the curriculum for each semester, as well as the overall rates (the set of subjects in the semester), which are the efficiency rate and the success rate. Additionally, we compute the rates for the Bachelors degree, which are the graduation rate measured as the percentage of students who finish as scheduled or taking an extra year and the efficiency rate (measured as the percentage of credits of the curriculum with respect to the credits really taken). In Spain, these metrics have been defined by the National Quality Evaluation and Accreditation Agency (ANECA). Moreover, the sensitivity of the performance metrics to some of the parameters of the simulator is analyzed using statistical tools (Design of Experiments). The simulator has been adapted to the curriculum characteristics of the Bachelor in Engineering Technologies at the Technical University of Madrid(UPM).

Monte Carlo limit cycle characterization

The fixed point implementation of IIR digital filters usually leads to the appearance of zero-input limit cycles, which degrade the performance of the system. In this paper, we develop an efficient Monte Carlo algorithm to detect and characterize limit cycles in fixed-point IIR digital filters. The proposed approach considers filters formulated in the state space and is valid for any fixed point representation and quantization function. Numerical simulations on several high-order filters, where an exhaustive search is unfeasible, show the effectiveness of the proposed approach.

Modelo de gestión de un embalse en tiempo real durante avenidas basado en redes bayesianas entrenadas con el método de optimización PLEM

En la actualidad, la gestión de embalses para el control de avenidas se realiza, comúnmente, utilizando modelos de simulación. Esto se debe, principalmente, a su facilidad de uso en tiempo real por parte del operador de la presa. Se han desarrollado modelos de optimización de la gestión del embalse que, aunque mejoran los resultados de los modelos de simulación, su aplicación en tiempo real se hace muy difícil o simplemente inviable, pues está limitada al conocimiento de la avenida futura que entra al embalse antes de tomar la decisión de vertido. Por esta razón, se ha planteado el objetivo de desarrollar un modelo de gestión de embalses en avenidas que incorpore las ventajas de un modelo de optimización y que sea de fácil uso en tiempo real por parte del gestor de la presa. Para ello, se construyó un modelo de red Bayesiana que representa los procesos de la cuenca vertiente y del embalse y, que aprende de casos generados sintéticamente mediante un modelo hidrológico agregado y un modelo de optimización de la gestión del embalse. En una primera etapa, se generó un gran número de episodios sintéticos de avenida utilizando el método de Monte Carlo, para obtener las lluvias, y un modelo agregado compuesto de transformación lluvia- escorrentía, para obtener los hidrogramas de avenida. Posteriormente, se utilizaron las series obtenidas como señales de entrada al modelo de gestión de embalses PLEM, que optimiza una función objetivo de costes mediante programación lineal entera mixta, generando igual número de eventos óptimos de caudal vertido y de evolución de niveles en el embalse. Los episodios simulados fueron usados para entrenar y evaluar dos modelos de red Bayesiana, uno que pronostica el caudal de entrada al embalse, y otro que predice el caudal vertido, ambos en un horizonte de tiempo que va desde una a cinco horas, en intervalos de una hora. En el caso de la red Bayesiana hidrológica, el caudal de entrada que se elige es el promedio de la distribución de probabilidad de pronóstico. En el caso de la red Bayesiana hidráulica, debido al comportamiento marcadamente no lineal de este proceso y a que la red Bayesiana devuelve un rango de posibles valores de caudal vertido, se ha desarrollado una metodología para seleccionar un único valor, que facilite el trabajo del operador de la presa. Esta metodología consiste en probar diversas estrategias propuestas, que incluyen zonificaciones y alternativas de selección de un único valor de caudal vertido en cada zonificación, a un conjunto suficiente de episodios sintéticos. Los resultados de cada estrategia se compararon con el método MEV, seleccionándose las estrategias que mejoran los resultados del MEV, en cuanto al caudal máximo vertido y el nivel máximo alcanzado por el embalse, cualquiera de las cuales puede usarse por el operador de la presa en tiempo real para el embalse de estudio (Talave). La metodología propuesta podría aplicarse a cualquier embalse aislado y, de esta manera, obtener, para ese embalse particular, diversas estrategias que mejoran los resultados del MEV. Finalmente, a modo de ejemplo, se ha aplicado la metodología a una avenida sintética, obteniendo el caudal vertido y el nivel del embalse en cada intervalo de tiempo, y se ha aplicado el modelo MIGEL para obtener en cada instante la configuración de apertura de los órganos de desagüe que evacuarán el caudal. Currently, the dam operator for the management of dams uses simulation models during flood events, mainly due to its ease of use in real time. Some models have been developed to optimize the management of the reservoir to improve the results of simulation models. However, real-time application becomes very difficult or simply unworkable, because the decision to discharge depends on the unknown future avenue entering the reservoir. For this reason, the main goal is to develop a model of reservoir management at avenues that incorporates the advantages of an optimization model. At the same time, it should be easy to use in real-time by the dam manager. For this purpose, a Bayesian network model has been developed to represent the processes of the watershed and reservoir. This model learns from cases generated synthetically by a hydrological model and an optimization model for managing the reservoir. In a first stage, a large number of synthetic flood events was generated using the Monte Carlo method, for rain, and rain-added processing model composed of runoff for the flood hydrographs. Subsequently, the series obtained were used as input signals to the reservoir management model PLEM that optimizes a target cost function using mixed integer linear programming. As a result, many optimal discharge rate events and water levels in the reservoir levels were generated. The simulated events were used to train and test two models of Bayesian network. The first one predicts the flow into the reservoir, and the second predicts the discharge flow. They work in a time horizon ranging from one to five hours, in intervals of an hour. In the case of hydrological Bayesian network, the chosen inflow is the average of the probability distribution forecast. In the case of hydraulic Bayesian network the highly non-linear behavior of this process results on a range of possible values of discharge flow. A methodology to select a single value has been developed to facilitate the dam operator work. This methodology tests various strategies proposed. They include zoning and alternative selection of a single value in each discharge rate zoning from a sufficient set of synthetic episodes. The results of each strategy are compared with the MEV method. The strategies that improve the outcomes of MEV are selected and can be used by the dam operator in real time applied to the reservoir study case (Talave). The methodology could be applied to any single reservoir and, thus, obtain, for the particular reservoir, various strategies that improve results from MEV. Finally, the methodology has been applied to a synthetic flood, obtaining the discharge flow and the reservoir level in each time interval. The open configuration floodgates to evacuate the flow at each interval have been obtained applying the MIGEL model.

Monte Carlo simulations of densely-packed athermal polymers in the bulk and under confinement

We review the main results from extensive Monte Carlo (MC) simulations on athermal polymer packings in the bulk and under confinement. By employing the simplest possible model of excluded volume, macromolecules are represented as freely-jointed chains of hard spheres of uniform size. Simulations are carried out in a wide concentration range: from very dilute up to very high volume fractions, reaching the maximally random jammed (MRJ) state. We study how factors like chain length, volume fraction and flexibility of bond lengths affect the structure, shape and size of polymers, their packing efficiency and their phase behaviour (disorder–order transition). In addition, we observe how these properties are affected by confinement realized by flat, impenetrable walls in one dimension. Finally, by mapping the parent polymer chains to primitive paths through direct geometrical algorithms, we analyse the characteristics of the entanglement network as a function of packing density.