Finite-size scaling analysis of the avalanches in the three-dimensional Gaussian random-field Ising model with metastable dynamics

A numerical study is presented of the third-dimensional Gaussian random-field Ising model at T=0 driven by an external field. Standard synchronous relaxation dynamics is employed to obtain the magnetization versus field hysteresis loops. The focus is on the analysis of the number and size distribution of the magnetization avalanches. They are classified as being nonspanning, one-dimensional-spanning, two-dimensional-spanning, or three-dimensional-spanning depending on whether or not they span the whole lattice in different space directions. Moreover, finite-size scaling analysis enables identification of two different types of nonspanning avalanches (critical and noncritical) and two different types of three-dimensional-spanning avalanches (critical and subcritical), whose numbers increase with L as a power law with different exponents. We conclude by giving a scenario for avalanche behavior in the thermodynamic limit.

Hysteresis and avalanches in the T=0 random field ising model with 2-spin flip dynamics

We study the nonequilibrium behavior of the three-dimensional Gaussian random-field Ising model at T=0 in the presence of a uniform external field using a two-spin-flip dynamics. The deterministic, history-dependent evolution of the system is compared with the one obtained with the standard one-spin-flip dynamics used in previous studies of the model. The change in the dynamics yields a significant suppression of coercivity, but the distribution of avalanches (in number and size) stays remarkably similar, except for the largest ones that are responsible for the jump in the saturation magnetization curve at low disorder in the thermodynamic limit. By performing a finite-size scaling study, we find strong evidence that the change in the dynamics does not modify the universality class of the disorder-induced phase transition.

Diluted three-dimensional random field Ising model at zero temperature with metastable dynamics.

The influence of vacancy concentration on the behavior of the three-dimensional random field Ising model with metastable dynamics is studied. We have focused our analysis on the number of spanning avalanches which allows us a clear determination of the critical line where the hysteresis loops change from continuous to discontinuous. By a detailed finite-size scaling analysis we determine the phase diagram and numerically estimate the critical exponents along the whole critical line. Finally, we discuss the origin of the curvature of the critical line at high vacancy concentration.

Studies on some nonlinear optical phenomena-optical phase conjugation and continuous wave second harmonic generation

Nonlinear optics has emerged as a new area of physics , following the development of various types of lasers. A number of advancements , both theoretical and experimental . have been made in the past two decades . by scientists al1 over the world. However , onl y few scientists have attempted to study the experimental aspects of nonlinear optical phenomena i n I ndian laboratories. This thesis is the report of an attempt made in this direction. The thesis contains the details of the several investigations which the author has carried out in the past few years, on optical phase conjugation (OPC) and continuous wave CCVD second harmonic generation CSHG). OPC is a new branch of nonlinear optics, developed only in the past decade. The author has done a few experiments on low power OPC in dye molecules held in solid matrices, by making use of a degenerate four wave mixing CDFWND scheme. These samples have been characterised by studies on their absorption-spectra. fluorescence spectra. triplet lifetimes and saturation intensities. Phase conjugation efficiencies with r espect to the various parameters have been i nvesti gated . DFWM scheme was also employed i n achievi ng phase conjugation of a br oadband laser C Nd: G1ass 3 using a dye solution as the nonlinear medium.

Testing Isotropy and a related Random Walk problem

One comes across directions as the observations in a number of situations. The first inferential question that one should answer when dealing with such data is, “Are they isotropic or uniformly distributed?” The answer to this question goes back in history which we shall retrace a bit and provide an exact and approximate solution to this so-called “Pearson’s Random Walk” problem.

Structural characterization and distribution of zebrafish germ plasm during interphase and mitosis

In zebrafish, germ cells are responsible for transmitting the genetic information from one generation to the next. During the first cleavages of zebrafish embryonic development, a specialized part of the cytoplasm known as germ plasm, is responsible of committing four blastomeres to become the progenitors of all germ cells in the forming embryo. Much is known about how the germ plasm is spatially distributed in early stages of primordial germ cell development, a process described to be dependant on microtubules and actin. However, little is known about how the material is inherited after it reorganizes into a perinuclear location, or how is the symmetrical distribution regulated in order to ensure proper inheritance of the material by both daughter cells. It is also not clear whether there is a controlled mechanism that regulates the number of granules inherited by the daughter cells, or whether it is a random process. We describe the distribution of germ plasm material from 4hpf to 24hpf in zebrafish primordial germ cells using Vasa protein as marker. Vasa positive material appears to be conglomerate into 3 to 4 big spherical structures at 4hpf. While development progresses, these big structures become smaller perinuclear granules that reach a total number of approximately 30 at 24hpf. We investigated how this transformation occurs and how the minus-end microtubule dependent motor protein Dynein plays a role in this process. Additionally, we describe specific colocalization of microtubules and perinuclear granules during interphase and more interestingly, during all different stages of cell division. We show that distribution of granules follow what seems to be a regulated distribution: during cells division, daughter cells inherit an equal number of granules. We propose that due to the permanent colocalization of microtubular structures with germinal granules during interphase and cell division, a coordinated mechanism between these structures may ensure proper distribution of the material among daughter cells. Furthermore, we show that exposure to the microtubule-depolymerizing drug nocodazole leads to disassembly of the germ cell nuclear lamin matrix, chromatin condensation, and fusion of granules to a big conglomerate, revealing dependence of granular distribution on microtubules and proper nuclear structure.

Medical image registration based on random line sampling

One of the key aspects in 3D-image registration is the computation of the joint intensity histogram. We propose a new approach to compute this histogram using uniformly distributed random lines to sample stochastically the overlapping volume between two 3D-images. The intensity values are captured from the lines at evenly spaced positions, taking an initial random offset different for each line. This method provides us with an accurate, robust and fast mutual information-based registration. The interpolation effects are drastically reduced, due to the stochastic nature of the line generation, and the alignment process is also accelerated. The results obtained show a better performance of the introduced method than the classic computation of the joint histogram

Image classification for a large number of object categories

L'increment de bases de dades que cada vegada contenen imatges més difícils i amb un nombre més elevat de categories, està forçant el desenvolupament de tècniques de representació d'imatges que siguin discriminatives quan es vol treballar amb múltiples classes i d'algorismes que siguin eficients en l'aprenentatge i classificació. Aquesta tesi explora el problema de classificar les imatges segons l'objecte que contenen quan es disposa d'un gran nombre de categories. Primerament s'investiga com un sistema híbrid format per un model generatiu i un model discriminatiu pot beneficiar la tasca de classificació d'imatges on el nivell d'anotació humà sigui mínim. Per aquesta tasca introduïm un nou vocabulari utilitzant una representació densa de descriptors color-SIFT, i desprès s'investiga com els diferents paràmetres afecten la classificació final. Tot seguit es proposa un mètode par tal d'incorporar informació espacial amb el sistema híbrid, mostrant que la informació de context es de gran ajuda per la classificació d'imatges. Desprès introduïm un nou descriptor de forma que representa la imatge segons la seva forma local i la seva forma espacial, tot junt amb un kernel que incorpora aquesta informació espacial en forma piramidal. La forma es representada per un vector compacte obtenint un descriptor molt adequat per ésser utilitzat amb algorismes d'aprenentatge amb kernels. Els experiments realitzats postren que aquesta informació de forma te uns resultats semblants (i a vegades millors) als descriptors basats en aparença. També s'investiga com diferents característiques es poden combinar per ésser utilitzades en la classificació d'imatges i es mostra com el descriptor de forma proposat juntament amb un descriptor d'aparença millora substancialment la classificació. Finalment es descriu un algoritme que detecta les regions d'interès automàticament durant l'entrenament i la classificació. Això proporciona un mètode per inhibir el fons de la imatge i afegeix invariança a la posició dels objectes dins les imatges. S'ensenya que la forma i l'aparença sobre aquesta regió d'interès i utilitzant els classificadors random forests millora la classificació i el temps computacional. Es comparen els postres resultats amb resultats de la literatura utilitzant les mateixes bases de dades que els autors Aixa com els mateixos protocols d'aprenentatge i classificació. Es veu com totes les innovacions introduïdes incrementen la classificació final de les imatges.

On the generation mechanisms of short-scale unbalanced modes in rotating two-layer flows with vertical shear

We report on the results of a laboratory investigation using a rotating two-layer annulus experiment, which exhibits both large-scale vortical modes and short-scale divergent modes. A sophisticated visualization method allows us to observe the flow at very high spatial and temporal resolution. The balanced long-wavelength modes appear only when the Froude number is supercritical (i.e. $F\,{>}\,F_\mathrm{critical}\,{\equiv}\, \upi^2/2$), and are therefore consistent with generation by a baroclinic instability. The unbalanced short-wavelength modes appear locally in every single baroclinically unstable flow, providing perhaps the first direct experimental evidence that all evolving vortical flows will tend to emit freely propagating inertia–gravity waves. The short-wavelength modes also appear in certain baroclinically stable flows. We infer the generation mechanisms of the short-scale waves, both for the baro-clinically unstable case in which they co-exist with a large-scale wave, and for the baroclinically stable case in which they exist alone. The two possible mechanisms considered are spontaneous adjustment of the large-scale flow, and Kelvin–Helmholtz shear instability. Short modes in the baroclinically stable regime are generated only when the Richardson number is subcritical (i.e. $\hbox{\it Ri}\,{<}\,\hbox{\it Ri}_\mathrm{critical}\,{\equiv}\, 1$), and are therefore consistent with generation by a Kelvin–Helmholtz instability. We calculate five indicators of short-wave generation in the baroclinically unstable regime, using data from a quasi-geostrophic numerical model of the annulus. There is excellent agreement between the spatial locations of short-wave emission observed in the laboratory, and regions in which the model Lighthill/Ford inertia–gravity wave source term is large. We infer that the short waves in the baroclinically unstable fluid are freely propagating inertia–gravity waves generated by spontaneous adjustment of the large-scale flow.

Developing the next-generation climate system models: challenges and achievements

Although climate models have been improving in accuracy and efficiency over the past few decades, it now seems that these incremental improvements may be slowing. As tera/petascale computing becomes massively parallel, our legacy codes are less suitable, and even with the increased resolution that we are now beginning to use, these models cannot represent the multiscale nature of the climate system. This paper argues that it may be time to reconsider the use of adaptive mesh refinement for weather and climate forecasting in order to achieve good scaling and representation of the wide range of spatial scales in the atmosphere and ocean. Furthermore, the challenge of introducing living organisms and human responses into climate system models is only just beginning to be tackled. We do not yet have a clear framework in which to approach the problem, but it is likely to cover such a huge number of different scales and processes that radically different methods may have to be considered. The challenges of multiscale modelling and petascale computing provide an opportunity to consider a fresh approach to numerical modelling of the climate (or Earth) system, which takes advantage of the computational fluid dynamics developments in other fields and brings new perspectives on how to incorporate Earth system processes. This paper reviews some of the current issues in climate (and, by implication, Earth) system modelling, and asks the question whether a new generation of models is needed to tackle these problems.

Algorithm for generating defective graphene sheets

An algorithm is presented for the generation of molecular models of defective graphene fragments, containing a majority of 6-membered rings with a small number of 5- and 7-membered rings as defects. The structures are generated from an initial random array of points in 2D space, which are then subject to Delaunay triangulation. The dual of the triangulation forms a Voronoi tessellation of polygons with a range of ring sizes. An iterative cycle of refinement, involving deletion and addition of points followed by further triangulation, is performed until the user-defined criteria for the number of defects are met. The array of points and connectivities are then converted to a molecular structure and subject to geometry optimization using a standard molecular modeling package to generate final atomic coordinates. On the basis of molecular mechanics with minimization, this automated method can generate structures, which conform to user-supplied criteria and avoid the potential bias associated with the manual building of structures. One application of the algorithm is the generation of structures for the evaluation of the reactivity of different defect sites. Ab initio electronic structure calculations on a representative structure indicate preferential fluorination close to 5-ring defects.

What do patients want to know? An empirical approach to explanation generation and validation

This article describes an empirical, user-centred approach to explanation design. It reports three studies that investigate what patients want to know when they have been prescribed medication. The question is asked in the context of the development of a drug prescription system called OPADE. The system is aimed primarily at improving the prescribing behaviour of physicians, but will also produce written explanations for indirect users such as patients. In the first study, a large number of people were presented with a scenario about a visit to the doctor, and were asked to list the questions that they would like to ask the doctor about the prescription. On the basis of the results of the study, a categorization of question types was developed in terms of how frequently particular questions were asked. In the second and third studies a number of different explanations were generated in accordance with this categorization, and a new sample of people were presented with another scenario and were asked to rate the explanations on a number of dimensions. The results showed significant differences between the different explanations. People preferred explanations that included items corresponding to frequently asked questions in study 1. For an explanation to be considered useful, it had to include information about side effects, what the medication does, and any lifestyle changes involved. The implications of the results of the three studies are discussed in terms of the development of OPADE's explanation facility.

Sampling uncertainty properties of cloud fraction estimates from random transect observations

[1] Cloud cover is conventionally estimated from satellite images as the observed fraction of cloudy pixels. Active instruments such as radar and Lidar observe in narrow transects that sample only a small percentage of the area over which the cloud fraction is estimated. As a consequence, the fraction estimate has an associated sampling uncertainty, which usually remains unspecified. This paper extends a Bayesian method of cloud fraction estimation, which also provides an analytical estimate of the sampling error. This method is applied to test the sensitivity of this error to sampling characteristics, such as the number of observed transects and the variability of the underlying cloud field. The dependence of the uncertainty on these characteristics is investigated using synthetic data simulated to have properties closely resembling observations of the spaceborne Lidar NASA-LITE mission. Results suggest that the variance of the cloud fraction is greatest for medium cloud cover and least when conditions are mostly cloudy or clear. However, there is a bias in the estimation, which is greatest around 25% and 75% cloud cover. The sampling uncertainty is also affected by the mean lengths of clouds and of clear intervals; shorter lengths decrease uncertainty, primarily because there are more cloud observations in a transect of a given length. Uncertainty also falls with increasing number of transects. Therefore a sampling strategy aimed at minimizing the uncertainty in transect derived cloud fraction will have to take into account both the cloud and clear sky length distributions as well as the cloud fraction of the observed field. These conclusions have implications for the design of future satellite missions. This paper describes the first integrated methodology for the analytical assessment of sampling uncertainty in cloud fraction observations from forthcoming spaceborne radar and Lidar missions such as NASA's Calipso and CloudSat.

Lack of myostatin results in excessive muscle growth but impaired force generation

The lack of myostatin promotes growth of skeletal muscle, and blockade of its activity has been proposed as a treatment for various muscle-wasting disorders. Here, we have examined two independent mouse lines that harbor mutations in the myostatin gene, constitutive null (Mstn(-/-)) and compact (Berlin High Line, BEH(c/c)). We report that, despite a larger muscle mass relative to age-matched wild types, there was no increase in maximum tetanic force generation, but that when expressed as a function of muscle size (specific force), muscles of myostatin-deficient mice were weaker than wild-type muscles. In addition, Mstn(-/-) muscle contracted and relaxed faster during a single twitch and had a marked increase in the number of type IIb fibers relative to wild-type controls. This change was also accompanied by a significant increase in type IIB fibers containing tubular aggregates. Moreover, the ratio of mitochondrial DNA to nuclear DNA and mitochondria number were decreased in myostatin-deficient muscle, suggesting a mitochondrial depletion. Overall, our results suggest that lack of myostatin compromises force production in association with loss of oxidative characteristics of skeletal muscle.

The automation and evaluation of nested clade phylogeographic analysis

Nested clade phylogeographic analysis (NCPA) is a popular method for reconstructing the demographic history of spatially distributed populations from genetic data. Although some parts of the analysis are automated, there is no unique and widely followed algorithm for doing this in its entirety, beginning with the data, and ending with the inferences drawn from the data. This article describes a method that automates NCPA, thereby providing a framework for replicating analyses in an objective way. To do so, a number of decisions need to be made so that the automated implementation is representative of previous analyses. We review how the NCPA procedure has evolved since its inception and conclude that there is scope for some variability in the manual application of NCPA. We apply the automated software to three published datasets previously analyzed manually and replicate many details of the manual analyses, suggesting that the current algorithm is representative of how a typical user will perform NCPA. We simulate a large number of replicate datasets for geographically distributed, but entirely random-mating, populations. These are then analyzed using the automated NCPA algorithm. Results indicate that NCPA tends to give a high frequency of false positives. In our simulations we observe that 14% of the clades give a conclusive inference that a demographic event has occurred, and that 75% of the datasets have at least one clade that gives such an inference. This is mainly due to the generation of multiple statistics per clade, of which only one is required to be significant to apply the inference key. We survey the inferences that have been made in recent publications and show that the most commonly inferred processes (restricted gene flow with isolation by distance and contiguous range expansion) are those that are commonly inferred in our simulations. However, published datasets typically yield a richer set of inferences with NCPA than obtained in our random-mating simulations, and further testing of NCPA with models of structured populations is necessary to examine its accuracy.