Probability currents and entropy production in nonequilibrium lattice systems

The structure of probability currents is studied for the dynamical network after consecutive contraction on two-state, nonequilibrium lattice systems. This procedure allows us to investigate the transition rates between configurations on small clusters and highlights some relevant effects of lattice symmetries on the elementary transitions that are responsible for entropy production. A method is suggested to estimate the entropy production for different levels of approximations (cluster sizes) as demonstrated in the two-dimensional contact process with mutation.

Transport in disordered two-dimensional topological insulators

The transport properties of the ""inverted"" semiconductor HgTe-based quantum well, recently shown to be a two-dimensional topological insulator, are studied experimentally in the diffusive regime. Nonlocal transport measurements are performed in the absence of magnetic field, and a large signal due to the edge states is observed. This shows that the edge states can propagate over a long distance, similar to 1 mm, and therefore, there is no difference between local and nonlocal electrical measurements in a topological insulator. In the presence of an in-plane magnetic field a strong decrease of the local resistance and complete suppression of the nonlocal resistance is observed. We attribute this behavior to an in-plane magnetic-field-induced transition from the topological insulator state to a conventional bulk metal state.

Renyi entropy and parity oscillations of anisotropic spin-s Heisenberg chains in a magnetic field

Using the density matrix renormalization group, we investigate the Renyi entropy of the anisotropic spin-s Heisenberg chains in a z-magnetic field. We considered the half-odd-integer spin-s chains, with s = 1/2, 3/2, and 5/2, and periodic and open boundary conditions. In the case of the spin-1/2 chain we were able to obtain accurate estimates of the new parity exponents p(alpha)((p)) and p(alpha)((o)) that gives the power-law decay of the oscillations of the alpha-Renyi entropy for periodic and open boundary conditions, respectively. We confirm the relations of these exponents with the Luttinger parameter K, as proposed by Calabrese et al. [Phys. Rev. Lett. 104, 095701 (2010)]. Moreover, the predicted periodicity of the oscillating term was also observed for some nonzero values of the magnetization m. We show that for s > 1/2 the amplitudes of the oscillations are quite small and get accurate estimates of p(alpha)((p)) and p(alpha)((o)) become a challenge. Although our estimates of the new universal exponents p(alpha)((p)) and p(alpha)((o)) for the spin-3/2 chain are not so accurate, they are consistent with the theoretical predictions.

Inference of gene regulatory networks from time series by Tsallis entropy

Background: The inference of gene regulatory networks (GRNs) from large-scale expression profiles is one of the most challenging problems of Systems Biology nowadays. Many techniques and models have been proposed for this task. However, it is not generally possible to recover the original topology with great accuracy, mainly due to the short time series data in face of the high complexity of the networks and the intrinsic noise of the expression measurements. In order to improve the accuracy of GRNs inference methods based on entropy (mutual information), a new criterion function is here proposed. Results: In this paper we introduce the use of generalized entropy proposed by Tsallis, for the inference of GRNs from time series expression profiles. The inference process is based on a feature selection approach and the conditional entropy is applied as criterion function. In order to assess the proposed methodology, the algorithm is applied to recover the network topology from temporal expressions generated by an artificial gene network (AGN) model as well as from the DREAM challenge. The adopted AGN is based on theoretical models of complex networks and its gene transference function is obtained from random drawing on the set of possible Boolean functions, thus creating its dynamics. On the other hand, DREAM time series data presents variation of network size and its topologies are based on real networks. The dynamics are generated by continuous differential equations with noise and perturbation. By adopting both data sources, it is possible to estimate the average quality of the inference with respect to different network topologies, transfer functions and network sizes. Conclusions: A remarkable improvement of accuracy was observed in the experimental results by reducing the number of false connections in the inferred topology by the non-Shannon entropy. The obtained best free parameter of the Tsallis entropy was on average in the range 2.5 <= q <= 3.5 (hence, subextensive entropy), which opens new perspectives for GRNs inference methods based on information theory and for investigation of the nonextensivity of such networks. The inference algorithm and criterion function proposed here were implemented and included in the DimReduction software, which is freely available at http://sourceforge.net/projects/dimreduction and http://code.google.com/p/dimreduction/.

Selection of new glass-forming compositions in Al-La system using a combination of topological instability and thermodynamic criteria

A combination of an extension of the topological instability ""lambda criterion"" and a thermodynamic criterion were applied to the Al-La system, indicating the best range of compositions for glass formation. Alloy compositions in this range were prepared by melt-spinning and casting in an arc-melting furnace with a wedge-section copper mold. The GFA of these samples was evaluated by X-ray diffraction, differential scanning calorimetry and scanning electron microscopy. The results indicated that the gamma* parameter of compositions with high GFA is higher, corresponding to a range in which the lambda parameter is greater than 0.1, which are compositions far from Al solid solution. A new alloy was identified with the best GFA reported so far for this system, showing a maximum thickness of 286 mu m in a wedge-section copper mold. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.

Crystallisation behaviours of Al-based metallic glasses: Compositional and topological aspects

The different types of thermal crystallisation behaviours observed during continuous heating of M-based metallic glasses have been successfully associated with the topological instability. criterion, which is simply calculated from the alloy composition and metallic radii of the alloying elements and aluminium. In the present work, we report on new results evidencing the correlation between the values of X and the crystallisation behaviours in Al-based alloys of the Al-Ni-Ce system and we compare the glass-forming abilities of alloys designed with compositions corresponding to the same topological instability condition. The results are discussed in terms of compositional and topological aspects emphasizing the relevance of the different types of clusters in the amorphous phase in defining the stability of the glass and the types of thermal crystallisation. (C) 2008 Elsevier B.V. All rights reserved.

Topological instability, average electronegativity difference and glass forming ability of amorphous alloys

In this paper, we report the remarkable agreement of the glass forming ability of binary alloys with a new criterion that combines the topological instability parameter (lambda) and the average electronegativity difference among the elements of an alloy, assuming both exert a synergetic effect. The best glass forming compositions for Zr-Cu and Ti-Ni systems are well predicted by this new approach. Although the new criterion needs further refinement, it is concluded that the proposed approach is a promising and simple tool to guide and reduce the tedious and labour intensive work to find good glass former compositions in metallic systems. (C) 2008 Elsevier Ltd. All rights reserved.

Thermodynamic and topological instability approaches for forecasting glass-forming ability in the ternary Al-Ni-Y system

A thermodynamic approach to predict bulk glass-forming compositions in binary metallic systems was recently proposed. In this approach. the parameter gamma* = Delta H-amor/(Delta H-inter - Delta H-amor) indicates the glass-forming ability (GFA) from the standpoint of the driving force to form different competing phases, and Delta H-amor and Delta H-inter are the enthalpies for-lass and intermetallic formation, respectively. Good glass-forming compositions should have a large negative enthalpy for glass formation and a very small difference for intermetallic formation, thus making the glassy phase easily reachable even under low cooling rates. The gamma* parameter showed a good correlation with GFA experimental data in the Ni-Nb binary system. In this work, a simple extension of the gamma* parameter is applied in the ternary Al-Ni-Y system. The calculated gamma* isocontours in the ternary diagram are compared with experimental results of glass formation in that system. Despite sonic misfitting, the best glass formers are found quite close to the highest gamma* values, leading to the conclusion that this thermodynamic approach can lie extended to ternary systems, serving as a useful tool for the development of new glass-forming compositions. Finally the thermodynamic approach is compared with the topological instability criteria used to predict the thermal behavior of glassy Al alloys. (C) 2007 Elsevier B. V. All rights reserved.

Topological instability and electronegativity effects on the glass-forming ability of metallic alloys

The glass-forming ability (GFA) of metallic alloys is associated with a topological instability criterion combined with a new parameter based on the average electronegativity difference of an element and its surrounding neighbours. In this model, we assume that during solidification the glassy phase competes directly with the supersaturated solid solution having the lowest topological instability factor for a given composition. This criterion is combined with the average electronegativity difference among the elements in the alloy, which reflects the strength of the liquid. The GFA is successfully correlated with this combined criterion in several binary glass-forming systems.

Adaptive Approach for a Maximum Entropy Algorithm in Ecological Niche Modeling

This paper presents an Adaptive Maximum Entropy (AME) approach for modeling biological species. The Maximum Entropy algorithm (MaxEnt) is one of the most used methods in modeling biological species geographical distribution. The approach presented here is an alternative to the classical algorithm. Instead of using the same set features in the training, the AME approach tries to insert or to remove a single feature at each iteration. The aim is to reach the convergence faster without affect the performance of the generated models. The preliminary experiments were well performed. They showed an increasing on performance both in accuracy and in execution time. Comparisons with other algorithms are beyond the scope of this paper. Some important researches are proposed as future works.

On the basic reproduction number and the topological properties of the contact network: An epidemiological study in mainly locally connected cellular automata

We study the spreading of contagious diseases in a population of constant size using susceptible-infective-recovered (SIR) models described in terms of ordinary differential equations (ODEs) and probabilistic cellular automata (PCA). In the PCA model, each individual (represented by a cell in the lattice) is mainly locally connected to others. We investigate how the topological properties of the random network representing contacts among individuals influence the transient behavior and the permanent regime of the epidemiological system described by ODE and PCA. Our main conclusions are: (1) the basic reproduction number (commonly called R(0)) related to a disease propagation in a population cannot be uniquely determined from some features of transient behavior of the infective group; (2) R(0) cannot be associated to a unique combination of clustering coefficient and average shortest path length characterizing the contact network. We discuss how these results can embarrass the specification of control strategies for combating disease propagations. (C) 2009 Elsevier B.V. All rights reserved.

Effects of temperature-dependent viscosity variation on entropy generation, heat and fluid flow through a porous-saturated duct of rectangular cross-section

Effect of temperature-dependent viscosity on fully developed forced convection in a duct of rectangular cross-section occupied by a fluid-saturated porous medium is investigated analytically. The Darcy flow model is applied and the viscosity-temperature relation is assumed to be an inverse-linear one. The case of uniform heat flux on the walls, i.e. the H boundary condition in the terminology of Kays and Crawford, is treated. For the case of a fluid whose viscosity decreases with temperature, it is found that the effect of the variation is to increase the Nusselt number for heated walls. Having found the velocity and the temperature distribution, the second law of thermodynamics is invoked to find the local and average entropy generation rate. Expressions for the entropy generation rate, the Bejan number, the heat transfer irreversibility, and the fluid flow irreversibility are presented in terms of the Brinkman number, the Péclet number, the viscosity variation number, the dimensionless wall heat flux, and the aspect ratio (width to height ratio). These expressions let a parametric study of the problem based on which it is observed that the entropy generated due to flow in a duct of square cross-section is more than those of rectangular counterparts while increasing the aspect ratio decreases the entropy generation rate similar to what previously reported for the clear flow case.

Heat transfer and entropy generation optimization of forced convection in a porous-saturated duct of rectangular cross-section

We investigate analytically the first and the second law characteristics of fully developed forced convection inside a porous-saturated duct of rectangular cross-section. The Darcy-Brinkman flow model is employed. Three different types of thermal boundary conditions are examined. Expressions for the Nusselt number, the Bejan number, and the dimensionless entropy generation rate are presented in terms of the system parameters. The conclusions of this analytical study will make it possible to compare, evaluate, and optimize alternative rectangular duct design options in terms of heat transfer, pressure drop, and entropy generation. (c) 2006 Elsevier Ltd. All rights reserved.

Entropy generation for forced convection in a porous saturated circular tube with uniform wall temperature

A numerical study is reported to investigate both the First and the Second Law of Thermodynamics for thermally developing forced convection in a circular tube filled by a saturated porous medium, with uniform wall temperature, and with the effects of viscous dissipation included. A theoretical analysis is also presented to study the problem for the asymptotic region applying the perturbation solution of the Brinkman momentum equation reported by Hooman and Kani [1]. Expressions are reported for the temperature profile, the Nusselt number, the Bejan number, and the dimensionless entropy generation rate in the asymptotic region. Numerical results are found to be in good agreement with theoretical counterparts.