Papers by Ubiraci da Costa Neves
Utilizando uma técnica de matriz de transferência, expandimos em série a probabilidade de percola... more Utilizando uma técnica de matriz de transferência, expandimos em série a probabilidade de percolação P(q) para o problema da percolação por sítio na rede quadrada direcionada. Nosso método revela uma inesperada conexão entre este problema e o da enumeração dos modos de se dissecar uma bola. Mostramos que o método pode também ser usado para se expandir em série o tamanho médio do cluster S (p) . Uma análise baseada nos aproximantes de Padé fornece estimativas do valor crítico pc, e também do expoente crítico β.Using a transfer matrix technique we obtain an extended series expansion of the percolation probability P(q) for the directed site percolation problem on the square lattice. Our method reveals an up to now unsuspected connection between this problem and the enumeration of the ways of dissecting a ball. We show that the method can also be used to determine a series expansion for the mean cluster size S(p). An analysis based on Padé approximants gives estimates of the critica...
EPL (Europhysics Letters), 2016
Axelrod's model of social dynamics has been studied under the effect of external media. Here ... more Axelrod's model of social dynamics has been studied under the effect of external media. Here we study the formation of cultural domains in the model by introducing persistent agents. These are agents whose cultural traits are not allowed to change but may be spread through local neighborhood. In the absence of persistent agents, the system is known to present a transition from a monocultural to a multicultural regime at some critical Q (number of traits). Our results reveal a dependence of critical Q on the occupation probability p of persistent agents and we obtain the phase diagram of the model in the -plane. The critical locus is explained by the competition of two opposite forces named here barrier and bonding effects. Such forces are verified to be caused by non-persistent agents which adhere (adherent agents) to the set of traits of persistent ones. The adherence (concentration of adherent agents) as a function of p is found to decay for constant Q. Furthermore, adherence as a function of Q is found to decay as a power law with constant p.
Physica A: Statistical Mechanics and its Applications, 2015
ABSTRACT Axelrod’s model was proposed to study interactions between agents and the formation of c... more ABSTRACT Axelrod’s model was proposed to study interactions between agents and the formation of cultural domains. It presents a transition from a monocultural to a multicultural steady state which has been studied in the literature by evaluation of the relative size of the largest cluster. In this article, we propose new measurements based on the concept of activity per agent to study the Axelrod’s model on the square lattice. We show that the variance of system activity can be used to indicate the critical points of the transition. Furthermore the frequency distribution of the system activity is able to show a coexistence of phases typical of a first order phase transition. Finally, we verify a power law dependence between cluster activity and cluster size for multicultural steady state configurations at the critical point.
Physica A: Statistical Mechanics and its Applications, 2005
To analyze functional magnetic resonance imaging (fMRI) data sets, the physiologically induced si... more To analyze functional magnetic resonance imaging (fMRI) data sets, the physiologically induced signals have to be separated from noise or from artifacts as a result of involuntary patient motion or MRI detection techniques. In the past years various methods of analysis of fMRI data were proposed, however one of the unsolved problems is related to dependence of the results with the threshold applied within each analysis. An alternative fMRI time series analysis method based on information theory and Tsallis entropy is proposed to decrease this dependency. The method applies the generalized mutual information (GMI) concept. Within the fMRI framework the GMI between the hemodynamic response function of a given voxel and the paradigm slope is evaluated as a measure of the amount of information that the paradigm could be encoded by a given brain region or voxel. This value represented the activation of the voxels. However, the analysis relies heavily on the Tsallis q parameter, allowing for a broad spectrum of results. As a test of applicability of the method real fMRI data were obtained in a simple motor paradigm and subsequently analyzed with GMI for several values of a q as well as with classical methods (cross-correlation and Student's t-test). The simulated data were used to compare quantitatively the presented method with the classical ones by means of the construction of receiver operating characteristic (ROC) curve.
Using a transfer matrix technique we obtain an extended series expansion of the percolation proba... more Using a transfer matrix technique we obtain an extended series expansion of the percolation probability P(q) for the directed site percolation problem on the square lattice. Our method reveals an up to now unsuspected connection between this problem and the enumeration of the ways of dissecting a balI. We show that the method can also be used to determine a series expansion for the mean cluster size S(p). An analysis based on Padé approximants gives estimates of the critical threshold Pc and also of the critical exponent j3. v Capítulo 1 INTRODUÇAO A teoria de percolação forma um importante ramo na área de fenômenos críticos e transições de fase. A maior diferença entre percolação e outros modelos de transição de fase é a ausência de uma Hamiltoniana. Ao invés disto, a teoria é baseada inteiramente em argumentos probabilísticos clássicos. O início da teoria da percolação está associado a uma publicação de Broadbent e Hammersley, em 1957, na versão" por ligação" (bond percolation). Em 1959, Domb propôs a " percolação por sítio" (site percolation) .
Open Journal of Applied Sciences, 2013
Several mathematical models have been proposed to describe the dynamics of irradiated cancer cell... more Several mathematical models have been proposed to describe the dynamics of irradiated cancer cells and to evaluate the tumour control probability (TCP). In this article, we propose a TCP model-based statistical test for predicting the outcome of a radiation treatment. We determine the foresight capability of prostate tumour erradication (cure) from Monte Carlo simulations of the Dawson-Hillen TCP model. We construct the receiver operating characteristic (ROC) curves of the test from the probability distributions of the fraction of remaining tumour cells for simulated experiments that evolve either to cure or non-cure. Simulations show that a similar procedure may be applicable to clinical data. Results suggest that the evaluation of tumour sizes after the treatment has started may be used for short-term prognosis.
Genetics and molecular biology, Jan 6, 2017
The molecular basis of anhydrobiosis, the state of suspended animation entered by some species du... more The molecular basis of anhydrobiosis, the state of suspended animation entered by some species during extreme desiccation, is still poorly understood despite a number of transcriptome and proteome studies. We therefore conducted functional screening by RNA interference (RNAi) for genes involved in anhydrobiosis in the holo-anhydrobiotic nematode Panagrolaimus superbus. A new method of survival analysis, based on staining, and proof-of-principle RNAi experiments confirmed a role for genes involved in oxidative stress tolerance, while a novel medium-scale RNAi workflow identified a further 40 anhydrobiosis-associated genes, including several involved in proteostasis, DNA repair and signal transduction pathways. This suggests that multiple genes contribute to anhydrobiosis in P. superbus.
Physica A: Statistical Mechanics and its Applications, 2015
ABSTRACT Abstract Physiologic complexity is an important concept to characterize time series from... more ABSTRACT Abstract Physiologic complexity is an important concept to characterize time series from biological systems, which associated to multiscale analysis can contribute to comprehension of many complex phenomena. Although multiscale entropy has been applied to physiological time series, it measures irregularity as function of scale. In this study we purpose and evaluate a set of three complexity metrics as function of time scales. Complexity metrics are derived from nonadditive entropy supported by generation of surrogate data, i.e. SDiff q max , q max and q zero . In order to access accuracy of proposed complexity metrics, receiver operating characteristic (ROC) curves were built and area under the curves was computed for three physiological situations. Heart rate variability (HRV) time series in normal sinus rhythm, atrial fibrillation, and congestive heart failure data set were analyzed. Results show that proposed metric for complexity is accurate and robust when compared to classic entropic irregularity metrics. Furthermore, SDiff q max is the most accurate for lower scales, whereas q max and q zero are the most accurate when higher time scales are considered. Multiscale complexity analysis described here showed potential to assess complex physiological time series and deserves further investigation in wide context.
J Phys a Math Gen, 1996
We simulate a kinetic growth model on the square lattice using a Monte Carlo approach in order to... more We simulate a kinetic growth model on the square lattice using a Monte Carlo approach in order to study ramified polymerization with short-distance attractive interactions between monomers. The phase boundary separating finite from infinite growth regimes is obtained in the (T,b) space, where T is the reduced temperature and b is the branching probability. In the thermodynamic limit, we extrapolate the temperature 0305-4470/29/20/005/img1 below which the phase is found to be always infinite. We also observe the occurrence of a roughening transition at the polymer surface.
Physica A: Statistical Mechanics and its Applications, 1995
Ramified polymerization is studied through computational simulations on the square lattice of a k... more Ramified polymerization is studied through computational simulations on the square lattice of a kinetic growth model generalized to incorporate branching and impurities. The polymer configuration is identified with a bond tree in order to examine its topology. The fractal dimensions of clusters are obtained at criticality. Simulations also allow the study of time evolution of clusters as well as the determination of time autocorrelations and dynamical critical exponents. In regard to finite size effects, a fourth-order cumulant technique is employed to estimate the critical branching probability bc and the critical exponents ~, and ft. Finally, for the case when impurities are not present, the surface roughness is described in terms of the Hurst exponents.
Physics in Medicine and Biology, 2009
Functional magnetic resonance imaging (fMRI) data analysis has been carried out recently in the f... more Functional magnetic resonance imaging (fMRI) data analysis has been carried out recently in the framework of information theory, by means of the Shannon entropy. As a natural extension, a method based on the generalized Tsallis entropy was developed to the analysis event-related (ER-fMRI), where a brief stimulus is presented, followed by a long period of rest. The new technique aims for spatial localization neuronal activity due to a specific task. This method does not require a priori hypothesis of the hemodynamic response function (HRF) shape and the linear relation between BOLD responses with the presented task. Numerical simulations were performed so as to determine the optimal values of the Tsallis q parameter and the number of levels, L. In order to avoid undesirable divergences of the Tsallis entropy, only positive q values were studied. Results from simulated data (with L = 3) indicated that, for q = 0.8, the active brain areas are detected with the highest performance. Moreover, the method was tested for an in vivo experiment and demonstrated the ability to discriminate active brain regions that selectively responded to a bilateral motor task.
Physica A: Statistical Mechanics and its Applications, 2003
The branched polymer growth model (BPGM) has been employed to study the kinetic growth of ramiÿed... more The branched polymer growth model (BPGM) has been employed to study the kinetic growth of ramiÿed polymers in the presence of impurities. In this article, the BPGM is revisited on the square lattice and a subtle modiÿcation in its dynamics is proposed in order to adapt it to a scenario closer to reality and experimentation. This new version of the model is denominated the adapted branched polymer growth model (ABPGM). It is shown that the ABPGM preserves the functionalities of the monomers and so recovers the branching probability b as an input parameter which e ectively controls the relative incidence of bifurcations. The critical locus separating inÿnite from ÿnite growth regimes of the ABPGM is obtained in the (b; c) space (where c is the impurity concentration). Unlike the original model, the phase diagram of the ABPGM exhibits a peculiar reentrance.
Physica A: Statistical Mechanics and its Applications, 1998
We investigate two-dimensional Ising systems with multisping interactions of three-(m = 3) and fo... more We investigate two-dimensional Ising systems with multisping interactions of three-(m = 3) and four-body terms (m = 4). The application of a new type of finite-size algorithm of de Oliveira allow us to clearly distinguish a first-order transition (in the m = 4 case) from a continuous one (in the m = 3 one). We also study the damage spreading in these systems. In this study, a dynamical phenomenon is observed to occur at a critical point separating a chaotic phase from a frozen one. However, the width of the interval where this transition happens does not yield a conclusive evidence about the order of the phase transition.
Physica A: Statistical Mechanics and its Applications, 2009
The generalized Kullback–Leibler distance Dq (q is the Tsallis parameter) is shown to be an usefu... more The generalized Kullback–Leibler distance Dq (q is the Tsallis parameter) is shown to be an useful measure for analysis of functional magnetic resonance imaging (fMRI) data series. This generalized form of entropy is used to evaluate the “distance” between the probability functions p1 and p2 of the signal levels related to periods of stimulus and non-stimulus in event-related fMRI experiments.
Neurocomputing, 2002
The collective behavior of cortical neurons during processes of reorganization after amputation o... more The collective behavior of cortical neurons during processes of reorganization after amputation of a digit in a realistic computational model of the somatosensory system is studied with Tsallis entropy measure. The presence of transient events and signiÿcant alterations into the level of entropy associated with the reorganization processes in the simulated cortical area during and after the organization of new representational areas show that the application of this kind of analysis may provide interesting insights into the analysis of reorganization processes in cortical areas by means of extracellular ÿeld potentials recordings.
Journal of Statistical Physics, 1996
The phase diagram and the tricritical point of a collapsing lattice animal are studied through an... more The phase diagram and the tricritical point of a collapsing lattice animal are studied through an extended series expansion of the isothermal compressibility Kr on a square lattice. As a function of the variables of fugacity and Boltzmann weight, K r is investigated using partial differential approximant techniques. The characteristic flow pattern of partial differential approximant trajectories is determined for a stable fixed point. We obtain satisfactory estimates for the tricritical fugacity x, = 0.024 + 0.005 and temperature T, = 0.54-I-0.04. Taking into account only linear scaling fields, we are also able to get the scaling exponent ),= 1.4_ 0.2 and the crossover ~ = 0.66 + 0.08. Our results are in reasonable agreement with previous estimates in the literature.
Journal of Physics A: Mathematical and General, 1992
AbslracL Using a transfermatrix technique we obain ertended = e r i s apnrion of the percolalion ... more AbslracL Using a transfermatrix technique we obain ertended = e r i s apnrion of the percolalion probability for Ule directed site percolation problem on the square lattice. Our approach meals a pmiously unsuspected mnnection between this problem and the enumeration of the number of ways of dissecting a ball. We show that the method can also be used 10 determine a series expansion for the mean cluster size. An analysis based on Pad6 approximants gives estimates of the critical threshold and also of the critical exponent p.
Brazilian Journal of Physics, 2008
The Kullback-Leibler distance (or relative entropy) is applied in the analysis of functional magn... more The Kullback-Leibler distance (or relative entropy) is applied in the analysis of functional magnetic resonance (fMRI) data series. Our study is designed for event-related (ER) experiments, where a brief stimulus is presented and a long period of rest is followed. In particular, this relative entropy is used as a measure of the "distance" between the probability distributions p 1 and p 2 of the signal levels related to stimulus and non-stimulus. In order to avoid undesirable divergences of the Kullback-Leibler distance, a small positive parameter δ is introduced in the definition of the probability functions in such a way that it does not bias the comparison between both distributions. Numerical simulations are performed so as to determine the probability densities of the mean Kullback-Leibler distance D (throughout the N epochs of the whole experiment). For small values of N (N < 30), such probability densities f (D) are found to be fitted very well by Gamma distributions (χ 2 < 0.0009). The sensitivity and specificity of the method are evaluated by construction of the receiver operating characteristic (ROC) curves for some values of signal-to-noise ratio (SNR). The functional maps corresponding to real data series from an asymptomatic volunteer submitted to an ER motor stimulus is obtained by using the proposed technique. The maps present activation in primary and secondary motor brain areas. Both simulated and real data analyses indicate that the relative entropy can be useful for fMRI analysis in the information measure scenario.
Uploads
Papers by Ubiraci da Costa Neves