A Monte Carlo model of DNA double-strand break clustering and rejoining kinetics for the analysis of pulsed-field gel electrophoresis data

In studies of radiation-induced DNA fragmentation and repair, analytical models may provide rapid and easy-to-use methods to test simple hypotheses regarding the breakage and rejoining mechanisms involved. The random breakage model, according to which lesions are distributed uniformly and independently of each other along the DNA, has been the model most used to describe spatial distribution of radiation-induced DNA damage. Recently several mechanistic approaches have been proposed that model clustered damage to DNA. In general, such approaches focus on the study of initial radiation-induced DNA damage and repair, without considering the effects of additional (unwanted and unavoidable) fragmentation that may take place during the experimental procedures. While most approaches, including measurement of total DNA mass below a specified value, allow for the occurrence of background experimental damage by means of simple subtractive procedures, a more detailed analysis of DNA fragmentation necessitates a more accurate treatment. We have developed a new, relatively simple model of DNA breakage and the resulting rejoining kinetics of broken fragments. Initial radiation-induced DNA damage is simulated using a clustered breakage approach, with three free parameters: the number of independently located clusters, each containing several DNA double-strand breaks (DSBs), the average number of DSBs within a cluster (multiplicity of the cluster), and the maximum allowed radius within which DSBs belonging to the same cluster are distributed. Random breakage is simulated as a special case of the DSB clustering procedure. When the model is applied to the analysis of DNA fragmentation as measured with pulsed-field gel electrophoresis (PFGE), the hypothesis that DSBs in proximity rejoin at a different rate from that of sparse isolated breaks can be tested, since the kinetics of rejoining of fragments of varying size may be followed by means of computer simulations. The problem of how to account for background damage from experimental handling is also carefully considered. We have shown that the conventional procedure of subtracting the background damage from the experimental data may lead to erroneous conclusions during the analysis of both initial fragmentation and DSB rejoining. Despite its relative simplicity, the method presented allows both the quantitative and qualitative description of radiation-induced DNA fragmentation and subsequent rejoining of double-stranded DNA fragments. (C) 2004 by Radiation Research Society.

Two-dimensional Monte Carlo simulations of H i line formation in massive young stellar object disc winds

Massive young stellar objects (YSOs) are powerful infrared Hi line emitters. It has been suggested that these lines form in an outflow from a disc surrounding the YSO. Here, new two-dimensional Monte Carlo radiative transfer calculations are described which test this hypothesis. Infrared spectra are synthesized for a YSO disc wind model based on earlier hydrodynamical calculations. The model spectra are in qualitative agreement with the observed spectra from massive YSOs, and therefore provide support for a disc wind explanation for the Hi lines. However, there are some significant differences: the models tend to overpredict the Bra/Br? ratio of equivalent widths and produce line profiles which are slightly too broad and, in contrast to typical observations, are double-peaked. The interpretation of these differences within the context of the disc wind picture and suggestions for their resolution via modifications to the assumed disc and outflow structure are discussed. © 2005 RAS.

Monte Carlo radiation hydrodynamics:Methods, tests and application to Type Ia supernova ejecta

In astrophysical systems, radiation-matter interactions are important in transferring energy and momentum between the radiation field and the surrounding material. This coupling often makes it necessary to consider the role of radiation when modelling the dynamics of astrophysical fluids. During the last few years, there have been rapid developments in the use of Monte Carlo methods for numerical radiative transfer simulations. Here, we present an approach to radiation hydrodynamics that is based on coupling Monte Carlo radiative transfer techniques with finite-volume hydrodynamical methods in an operator-split manner. In particular, we adopt an indivisible packet formalism to discretize the radiation field into an ensemble of Monte Carlo packets and employ volume-based estimators to reconstruct the radiation field characteristics. In this paper the numerical tools of this method are presented and their accuracy is verified in a series of test calculations. Finally, as a practical example, we use our approach to study the influence of the radiation-matter coupling on the homologous expansion phase and the bolometric light curve of Type Ia supernova explosions. © 2012 The Authors Monthly Notices of the Royal Astronomical Society © 2012 RAS.

Hybrid fuzzy Monte Carlo technique for reliability assessment in transmission power systems

This paper proposes a new methodology to reduce the probability of occurring states that cause load curtailment, while minimizing the involved costs to achieve that reduction. The methodology is supported by a hybrid method based on Fuzzy Set and Monte Carlo Simulation to catch both randomness and fuzziness of component outage parameters of transmission power system. The novelty of this research work consists in proposing two fundamentals approaches: 1) a global steady approach which deals with building the model of a faulted transmission power system aiming at minimizing the unavailability corresponding to each faulted component in transmission power system. This, results in the minimal global cost investment for the faulted components in a system states sample of the transmission network; 2) a dynamic iterative approach that checks individually the investment’s effect on the transmission network. A case study using the Reliability Test System (RTS) 1996 IEEE 24 Buses is presented to illustrate in detail the application of the proposed methodology.

Fuzzy Monte Carlo mathematical model for load curtailment minimization in transmission power systems

This paper presents a methodology which is based on statistical failure and repair data of the transmission power system components and uses fuzzyprobabilistic modeling for system component outage parameters. Using statistical records allows developing the fuzzy membership functions of system component outage parameters. The proposed hybrid method of fuzzy set and Monte Carlo simulation based on the fuzzy-probabilistic models allows catching both randomness and fuzziness of component outage parameters. A network contingency analysis to identify any overloading or voltage violation in the network is performed once obtained the system states by Monte Carlo simulation. This is followed by a remedial action algorithm, based on optimal power flow, to reschedule generations and alleviate constraint violations and, at the same time, to avoid any load curtailment, if possible, or, otherwise, to minimize the total load curtailment, for the states identified by the contingency analysis. In order to illustrate the application of the proposed methodology to a practical case, the paper will include a case study for the Reliability Test System (RTS) 1996 IEEE 24 BUS.

Le progiciel PoweR : un outil de recherche reproductible pour faciliter les calculs de puissance de certains tests d'hypothèses au moyen de simulations de Monte Carlo

Notre progiciel PoweR vise à faciliter l'obtention ou la vérification des études empiriques de puissance pour les tests d'ajustement. En tant que tel, il peut être considéré comme un outil de calcul de recherche reproductible, car il devient très facile à reproduire (ou détecter les erreurs) des résultats de simulation déjà publiés dans la littérature. En utilisant notre progiciel, il devient facile de concevoir de nouvelles études de simulation. Les valeurs critiques et puissances de nombreuses statistiques de tests sous une grande variété de distributions alternatives sont obtenues très rapidement et avec précision en utilisant un C/C++ et R environnement. On peut même compter sur le progiciel snow de R pour le calcul parallèle, en utilisant un processeur multicœur. Les résultats peuvent être affichés en utilisant des tables latex ou des graphiques spécialisés, qui peuvent être incorporés directement dans vos publications. Ce document donne un aperçu des principaux objectifs et les principes de conception ainsi que les stratégies d'adaptation et d'extension.

Modelo de gestión de la red de distribución tercerizada segmento tiendas región central, en productos de consumo masivo, mediante datos de panel y simulación de Monte Carlo.

El proyecto de investigación parte de la dinámica del modelo de distribución tercerizada para una compañía de consumo masivo en Colombia, especializada en lácteos, que para este estudio se ha denominado “Lactosa”. Mediante datos de panel con estudio de caso, se construyen dos modelos de demanda por categoría de producto y distribuidor y mediante simulación estocástica, se identifican las variables relevantes que inciden sus estructuras de costos. El problema se modela a partir del estado de resultados por cada uno de los cuatro distribuidores analizados en la región central del país. Se analiza la estructura de costos y el comportamiento de ventas dado un margen (%) de distribución logístico, en función de las variables independientes relevantes, y referidas al negocio, al mercado y al entorno macroeconómico, descritas en el objeto de estudio. Entre otros hallazgos, se destacan brechas notorias en los costos de distribución y costos en la fuerza de ventas, pese a la homogeneidad de segmentos. Identifica generadores de valor y costos de mayor dispersión individual y sugiere uniones estratégicas de algunos grupos de distribuidores. La modelación con datos de panel, identifica las variables relevantes de gestión que inciden sobre el volumen de ventas por categoría y distribuidor, que focaliza los esfuerzos de la dirección. Se recomienda disminuir brechas y promover desde el productor estrategias focalizadas a la estandarización de procesos internos de los distribuidores; promover y replicar los modelos de análisis, sin pretender remplazar conocimiento de expertos. La construcción de escenarios fortalece de manera conjunta y segura la posición competitiva de la compañía y sus distribuidores.

Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo

We describe a Bayesian method for investigating correlated evolution of discrete binary traits on phylogenetic trees. The method fits a continuous-time Markov model to a pair of traits, seeking the best fitting models that describe their joint evolution on a phylogeny. We employ the methodology of reversible-jump ( RJ) Markov chain Monte Carlo to search among the large number of possible models, some of which conform to independent evolution of the two traits, others to correlated evolution. The RJ Markov chain visits these models in proportion to their posterior probabilities, thereby directly estimating the support for the hypothesis of correlated evolution. In addition, the RJ Markov chain simultaneously estimates the posterior distributions of the rate parameters of the model of trait evolution. These posterior distributions can be used to test among alternative evolutionary scenarios to explain the observed data. All results are integrated over a sample of phylogenetic trees to account for phylogenetic uncertainty. We implement the method in a program called RJ Discrete and illustrate it by analyzing the question of whether mating system and advertisement of estrus by females have coevolved in the Old World monkeys and great apes.

Finding the smallest eigenvalue by the inverse Monte Carlo method with refinement

Finding the smallest eigenvalue of a given square matrix A of order n is computationally very intensive problem. The most popular method for this problem is the Inverse Power Method which uses LU-decomposition and forward and backward solving of the factored system at every iteration step. An alternative to this method is the Resolvent Monte Carlo method which uses representation of the resolvent matrix [I -qA](-m) as a series and then performs Monte Carlo iterations (random walks) on the elements of the matrix. This leads to great savings in computations, but the method has many restrictions and a very slow convergence. In this paper we propose a method that includes fast Monte Carlo procedure for finding the inverse matrix, refinement procedure to improve approximation of the inverse if necessary, and Monte Carlo power iterations to compute the smallest eigenvalue. We provide not only theoretical estimations about accuracy and convergence but also results from numerical tests performed on a number of test matrices.

Testing isotherm models and recovering empirical relationships for adsorption in microporous carbons using virtual carbon models and grand canonical Monte Carlo simulations

Using the plausible model of activated carbon proposed by Harris and co-workers and grand canonical Monte Carlo simulations, we study the applicability of standard methods for describing adsorption data on microporous carbons widely used in adsorption science. Two carbon structures are studied, one with a small distribution of micropores in the range up to 1 nm, and the other with micropores covering a wide range of porosity. For both structures, adsorption isotherms of noble gases (from Ne to Xe), carbon tetrachloride and benzene are simulated. The data obtained are considered in terms of Dubinin-Radushkevich plots. Moreover, for benzene and carbon tetrachloride the temperature invariance of the characteristic curve is also studied. We show that using simulated data some empirical relationships obtained from experiment can be successfully recovered. Next we test the applicability of Dubinin's related models including the Dubinin-Izotova, Dubinin-Radushkevich-Stoeckli, and Jaroniec-Choma equations. The results obtained demonstrate the limits and applications of the models studied in the field of carbon porosity characterization.

Portmanteau model diagnostics and tests for nonlinearity: a comparative Monte Carlo study of two alternative methods

This paper employs an extensive Monte Carlo study to test the size and power of the BDS and close return methods of testing for departures from independent and identical distribution. It is found that the finite sample properties of the BDS test are far superior and that the close return method cannot be recommended as a model diagnostic. Neither test can be reliably used for very small samples, while the close return test has low power even at large sample sizes

Reducing noise associated with the Monte Carlo Independent Column Approximation for weather forecasting models

The Monte Carlo Independent Column Approximation (McICA) is a flexible method for representing subgrid-scale cloud inhomogeneity in radiative transfer schemes. It does, however, introduce conditional random errors but these have been shown to have little effect on climate simulations, where spatial and temporal scales of interest are large enough for effects of noise to be averaged out. This article considers the effect of McICA noise on a numerical weather prediction (NWP) model, where the time and spatial scales of interest are much closer to those at which the errors manifest themselves; this, as we show, means that noise is more significant. We suggest methods for efficiently reducing the magnitude of McICA noise and test these methods in a global NWP version of the UK Met Office Unified Model (MetUM). The resultant errors are put into context by comparison with errors due to the widely used assumption of maximum-random-overlap of plane-parallel homogeneous cloud. For a simple implementation of the McICA scheme, forecasts of near-surface temperature are found to be worse than those obtained using the plane-parallel, maximum-random-overlap representation of clouds. However, by applying the methods suggested in this article, we can reduce noise enough to give forecasts of near-surface temperature that are an improvement on the plane-parallel maximum-random-overlap forecasts. We conclude that the McICA scheme can be used to improve the representation of clouds in NWP models, with the provision that the associated noise is sufficiently small.

Estimation of DSGE Models: A Monte Carlo Analysis

Neste trabalho investigamos as propriedades em pequena amostra e a robustez das estimativas dos parâmetros de modelos DSGE. Tomamos o modelo de Smets and Wouters (2007) como base e avaliamos a performance de dois procedimentos de estimação: Método dos Momentos Simulados (MMS) e Máxima Verossimilhança (MV). Examinamos a distribuição empírica das estimativas dos parâmetros e sua implicação para as análises de impulso-resposta e decomposição de variância nos casos de especificação correta e má especificação. Nossos resultados apontam para um desempenho ruim de MMS e alguns padrões de viés nas análises de impulso-resposta e decomposição de variância com estimativas de MV nos casos de má especificação considerados.

A new algorithm for Reverse Monte Carlo simulations

We present a new algorithm for Reverse Monte Carlo (RMC) simulations of liquids. During the simulations, we calculate energy, excess chemical potentials, bond-angle distributions and three-body correlations. This allows us to test the quality and physical meaning of RMC-generated results and its limitations. It also indicates the possibility to explore orientational correlations from simple scattering experiments. The new technique has been applied to bulk hard-sphere and Lennard-Jones systems and compared to standard Metropolis Monte Carlo results. (C) 1998 American Institute of Physics.

Aplicação da Simulação de Monte Carlo no estudo de testes de fadiga em rodas agrícolas

Due to the increasing demand from clients and the search for better performances in the heavy vehicles industry, a progressive evolution in technology in a general way was needed. This paper uses a scientific method to validate, prior to its manufacture, the project of an agricultural wheel for sugar cane harvesters. Monte Carlo Simulation is used in conjunction with Finite Elements Method, in order to simulate the wheel's behavior in a cornering test, identify possible failure regions and get an estimate for its life under fatigue. To this end, test conditions according to EUWA Standards were simulated and obeyed, relevant to fatigue. Simulation results were interesting, according to industry experts involved in the project and manufacture of the product in question, and have provided important elements for the decision making regarding improvements that could be made on the product project before its execution