Analysis of noise-induced temporal correlations in neuronal spike sequences

This is a copy of the author 's final draft version of an article published in the journal European physical journal. Special topics. The final publication is available at Springer via http://dx.doi.org/10.1140/epjst/e2016-60024-6We investigate temporal correlations in sequences of noise-induced neuronal spikes, using a symbolic method of time-series analysis. We focus on the sequence of time-intervals between consecutive spikes (inter-spike-intervals, ISIs). The analysis method, known as ordinal analysis, transforms the ISI sequence into a sequence of ordinal patterns (OPs), which are defined in terms of the relative ordering of consecutive ISIs. The ISI sequences are obtained from extensive simulations of two neuron models (FitzHugh-Nagumo, FHN, and integrate-and-fire, IF), with correlated noise. We find that, as the noise strength increases, temporal order gradually emerges, revealed by the existence of more frequent ordinal patterns in the ISI sequence. While in the FHN model the most frequent OP depends on the noise strength, in the IF model it is independent of the noise strength. In both models, the correlation time of the noise affects the OP probabilities but does not modify the most probable pattern.Peer ReviewedPostprint (author's final draft

Orbital-Free Molecular Dynamics Simulations of Melting in Na8 and Na20: Melting in Steps

The melting-like transitions of Na8 and Na20 are investigated by ab initio constant energy molecular dynamics simulations, using a variant of the Car-Parrinello method which employs an explicit electronic kinetic energy functional of the density, thus avoiding the use of one-particle orbitals. Several melting indicators are evaluated in order to determine the nature of the various transitions, and compared with other simulations. Both Na8 and Na20 melt over a wide temperature range. For Na8, a transition is observed to begin at approx. 110 K, between a rigid phase and a phase involving isomerizations between the different permutational isomers of the ground state structure. The ``liquid'' phase is completely established at approx. 220 K. For Na20, two transitions are observed: the first, at approx. 110 K, is associated with isomerization transitions between those permutational isomers of the ground state structure which are obtained by interchanging the positions of the surface-like atoms; the second, at approx. 160 K, involves a structural transition from the ground state isomer to a new set of isomers with the surface molten. The cluster is completely ``liquid'' at approx. 220 K.Comment: Revised version, accepted for publication in J. Chem. Phys. The changes include longer simulations for the Na20 microcluster, a more complete comparison to previous theoretical results, and the discussion of some technical details of the method applie

Do theoretical physicists care about the protein-folding problem?

The prediction of the biologically active native conformation of a protein is one of the fundamental challenges of structural biology. This problem remains yet unsolved mainly due to three factors: the partial knowledge of the effective free energy function that governs the folding process, the enormous size of the conformational space of a protein and, finally, the relatively small differences of energy between conformations, in particular, between the native one and the ones that make up the unfolded state. Herein, we recall the importance of taking into account, in a detailed manner, the many interactions involved in the protein folding problem (such as steric volume exclusion, Ramachandran forces, hydrogen bonds, weakly polar interactions, coulombic energy or hydrophobic attraction) and we propose a strategy to effectively construct a free energy function that, including the effects of the solvent, could be numerically tractable. It must be pointed out that, since the internal free energy function that is mainly described does not include the constraints of the native conformation, it could only help to reach the 'molten globule' state. We also discuss about the limits and the lacks from which suffer the simple models that we, physicists, love so much.Comment: 27 pages, 4 figures, LaTeX file, aipproc package. To be published in the book: "Meeting on Fundamental Physics 'Alberto Galindo'", Alvarez-Estrada R. F. et al. (Ed.), Madrid: Aula Documental, 200

Materials chemistry under high pressures - Some recent aspects

Among the thermodynamic parameters governing the preparation of novel materials, temperature (T) and pressure (p) play an important role. In Materials Chemistry, the synthesis of materials needs energy in order to enhance the diffusion of atoms to the equilibrium positions required by the specific structure and to induce the formation of chemical bonds..

Competitive dominance in plant communities: Modeling approaches and theoretical predictions

Quantitative predictions about the processes that promote species coexistence are a subject of active research in ecology. In particular, competitive interactions are known to shape and maintain ecological communities, and situations where some species out-compete or dominate over some others are key to describe natural ecosystems. Here we develop ecological theory using a stochastic, synthetic framework for plant community assembly that leads to predictions amenable to empirical testing. We propose two stochastic continuous-time Markov models that incorporate competitive dominance through a hierarchy of species heights. The first model, which is spatially implicit, predicts both the expected number of species that survive and the conditions under which heights are clustered in realized model communities. The second one allows spatially-explicit interactions of individuals and alternative mechanisms that can help shorter plants overcome height-driven competition, and it demonstrates that clustering patterns remain not only locally but also across increasing spatial scales. Moreover, although plants are actually height-clustered in the spatially-explicit model, it allows for plant species abundances not necessarily skewed to taller plants

Development of low-pH cementitious materials for HLRW repositories. Resistance against ground waters aggression

One of the most accepted engineering construction concepts of underground repositories for high radioactive waste considers the use of low-pH cementitious materials. This paper deals with the design of those based on Ordinary Portland Cements with high contents of silica fume and/or fly ashes that modify most of the concrete “standard” properties, the pore fluid composition and the microstructure of the hydrated products. Their resistance to long-term groundwater aggression is also evaluated. The results show that the use of OPC cement binders with high silica content produces low-pH pore waters and the microstructure of these cement pastes is different from the conventional OPC ones, generating C–S–H gels with lower CaO/SiO2 ratios that possibly bind alkali ions. Leaching tests show a good resistance of low-pH concretes against groundwater aggression although an altered front can be observe