http://hdl.handle.net/2117/394 2013-06-19T12:47:16Z http://hdl.handle.net/2117/19550 Title: Second layer of H2 and D2 adsorbed on graphene Authors: Gordillo Bargueño, Maria Carmen; Boronat Medico, Jordi Abstract: We report diffusion Monte Carlo calculations on the phase diagrams of para-H2 and ortho-D2 adsorbed on top of a first layer of the same substances on graphene. We found that the ground state of the second layer is a triangular incommensurate solid for both isotopes. The densities for promotion to a second layer and for the onset of a two-dimensional solid on that second layer compare favorably with available experimental data in both cases. 2013-06-13T15:12:58Z http://hdl.handle.net/2117/19503 Title: Size effects on water adsorbed on hydrophobic probes at the nanometric scale Authors: Calero Borrallo, Carles; Gordillo, Carmen; Martí Rabassa, Jordi Abstract: Molecular dynamics simulations of liquid water at ambient conditions, adsorbed at the external walls of (n,n) single-walled armchair carbon nanotubes have been performed for n = 5, 9, 12. The comparison with the case of water adsorbed on graphene has also been included. The analysis of Helmholtz free energies reveals qualitatively different ranges of thermodynamical stability, eventually starting at a given threshold surface density. We observed that, in the framework of the force field considered here, water does not wet graphene nor (12,12) tubes, but it can coat thinner tubes such as (9,9) and (5,5), which indicates that the width of the carbon nanotube plays a role on wetting. On the other hand, density profiles, orientational distributions of water, and hydrogen-bond populations indicate significant changes of structure of water for the different surfaces. Further, we computed self-diffusion of water and spectral densities of water and carbon molecules, which again revealed different qualitative behavior of interfacial water depending on the size of the nanotube. The crossover size corresponds to tube diameters of around 1 nm. 2013-06-04T13:59:08Z http://hdl.handle.net/2117/19480 Title: Atomic data mining numerical methods, source code SQlite with Python Authors: Khwaldeh, Ali; Tahat, Amani; Martí Rabassa, Jordi; Tahat, Mofleh Abstract: This paper introduces a recently published Python data mining book (chapters, topics, samples of Python source code written by its authors) to be used in data mining via world wide web and any specific database in several disciplines (economic, physics, education, marketing. etc). The book started with an introduction to data mining by explaining some of the data mining tasks involved classification, dependence modelling, clustering and discovery of association rules. The book addressed that using Python in data mining has been gaining some interest from data miner community due to its open source, general purpose programming and web scripting language; furthermore, it is a cross platform and it can be run on a wide variety of operating systens such as Linux, Windows, FreeBSD, Macintosh, Solaris, OS/2, Amiga, AROS, AS/400, BeOS, OS/390, z/OS, Palm OS, QNX, VMS, Psion, Acorn RISC OS, VxWorks, PlayStation, Sharp Zaurus, Windows CE and even PocketPC. Finally this book can be considered as a teaching textbook for data mining in which several methods such as machine learning and statistics are used to extract high-level knowledge from real-world datasets. 2013-05-31T15:58:19Z http://hdl.handle.net/2117/19248 Title: Phase transitions with infinitely many absorbing states in complex networks Authors: Sander, Renan; Ferreira, Silvio C.; Pastor Satorras, Romualdo Abstract: We investigate the properties of the threshold contact process (TCP), a process showing an absorbing-state phase transition with infinitely many absorbing states, on random complex networks. The finite-size scaling exponents characterizing the transition are obtained in a heterogeneous mean-field (HMF) approximation and compared with extensive simulations, particularly in the case of heterogeneous scale-free networks. We observe that the TCP exhibits the same critical properties as the contact process, which undergoes an absorbing-state phase transition to a single absorbing state. The accordance among the critical exponents of different models and networks leads to conjecture that the critical behavior of the contact process in a HMF theory is a universal feature of absorbing-state phase transitions in complex networks, depending only on the locality of the interactions and independent of the number of absorbing states. The conditions for the applicability of the conjecture are discussed considering a parallel with the susceptible-infected-susceptible epidemic spreading model, which in fact belongs to a different universality class in complex networks. 2013-05-15T12:52:57Z http://hdl.handle.net/2117/18430 Title: Evolution in a changing environment Authors: Baronchelli, Andrea; Chater, Nick; Christiansen, M.H.; Pastor Satorras, Romualdo Abstract: We propose a simple model for genetic adaptation to a changing environment, describing a fitness landscape characterized by two maxima. One is associated with “specialist” individuals that are adapted to the environment; this maximum moves over time as the environment changes. The other maximum is static, and represents “generalist” individuals not affected by environmental changes. The rest of the landscape is occupied by “maladapted” individuals. Our analysis considers the evolution of these three subpopulations. Our main result is that, in presence of a sufficiently stable environmental feature, as in the case of an unchanging aspect of a physical habitat, specialists can dominate the population. By contrast, rapidly changing environmental features, such as language or cultural habits, are a moving target for the genes; here, generalists dominate, because the best evolutionary strategy is to adopt neutral alleles not specialized for any specific environment. The model we propose is based on simple assumptions about evolutionary dynamics and describes all possible scenarios in a non-trivial phase diagram. The approach provides a general framework to address such fundamental issues as the Baldwin effect, the biological basis for language, or the ecological consequences of a rapid climate change. 2013-03-19T19:45:52Z http://hdl.handle.net/2117/16982 Title: Excess protons in mesoscopic water-acetone nanoclusters Authors: Semino, Rocío; Martí Rabassa, Jordi; Guàrdia Manuel, Elvira; Laria, Daniel Abstract: We carried out molecular dynamics simulation experiments to examine equilibrium and dynamical characteristics of the solvation of excess protons in mesoscopic, [m:n] binary polar clusters comprising m = 50 water molecules and n = 6, 25, and 100 acetone molecules. Contrasting from what is found in conventional macroscopic phases, the characteristics of the proton solvation are dictated, to a large extent, by the nature of the concentration fluctuations prevailing within the clusters. At low acetone contents, the overall cluster morphology corresponds to a segregated aqueous nucleus coated by an external aprotic phase. Under these circumstances, the proton remains localized at the surface of the water core, in a region locally deprived from acetone molecules. At higher acetone concentrations, we found clear evidence of the onset of the mixing process. The cluster structures present aqueous domains with irregular shape, fully embedded within the acetone phase. Still, the proton remains coordinated to the aqueous phase, with its closest solvation shell composed exclusively by three water molecules. As the relative concentration of acetone increases, the time scales characterizing proton transfer events between neighboring water molecules show considerable retardations, stretching into the nanosecond time domain already for n ∼ 25. In water-rich aggregates, and similarly to what is found in the bulk, proton transfers are controlled by acetone/water exchange processes taking place at the second solvation shell of the proton. As a distinctive feature of the transfer mechanism, translocation pathways also include diffusive motions of the proton from the surface down into inner regions of the underlying water domain. 2012-11-20T18:12:21Z http://hdl.handle.net/2117/16829 Title: Software refactoring: solving the time-dependent Schrodinger equation via fast Fourier transforms and parallel programming Authors: Khwaldeh, Ali; Tahat, Amani; Martí Rabassa, Jordi Abstract: In this study a multiprocessor C++ message passing interface implementation of a new bit-reversal algorithm to numerically solve the time dependent Schrodinger equation using a spectral method based on Fourier transform was presented. The major issues of parallel computer performance were discussed in terms of efficiency; speed up, cost and fraction of the execution time that could be parallelized. The scalable performance to a very high number of processors was addressed as well as compared with ideal values of Amdahl’s Law when presenting the parallel performance of the new developed algorithms. The results showed that message passing interface was an optimal method of implementing a parallelized bit-reversal algorithm. 2012-11-02T14:27:57Z http://hdl.handle.net/2117/16719 Title: Slow dynamics and rare-region effects in the contact process on weighted tree networks Authors: Odor, G.; Pastor Satorras, Romualdo Abstract: We show that generic, slow dynamics can occur in the contact process on complex networks with a tree-like structure and a superimposed weight pattern, in the absence of additional (nontopological) sources of quenched disorder. The slow dynamics is induced by rare-region effects occurring on correlated subspaces of vertices connected by large weight edges and manifests in the form of a smeared phase transition. We conjecture that more sophisticated network motifs could be able to induce Griffiths phases, as a consequence of purely topological disorder. 2012-10-11T13:21:51Z http://hdl.handle.net/2117/16713 Title: Activity driven modeling of time varying networks Authors: Perra, N.; Gonçalves, B.; Pastor Satorras, Romualdo; Vespignani, Alessandro Abstract: Network modeling plays a critical role in identifying statistical regularities and structural principles common to many systems. The large majority of recent modeling approaches are connectivity driven. The structural patterns of the network are at the basis of the mechanisms ruling the network formation. Connectivity driven models necessarily provide a time-aggregated representation that may fail to describe the instantaneous and fluctuating dynamics of many networks. We address this challenge by defining the activity potential, a time invariant function characterizing the agents' interactions and constructing an activity driven model capable of encoding the instantaneous time description of the network dynamics. The model provides an explanation of structural features such as the presence of hubs, which simply originate from the heterogeneous activity of agents. Within this framework, highly dynamical networks can be described analytically, allowing a quantitative discussion of the biases induced by the time-aggregated representations in the analysis of dynamical processes. 2012-10-10T18:10:01Z http://hdl.handle.net/2117/16707 Title: Water absorbed by polyaniline emeraldine tends to organize, forming nanodrops Authors: Casanovas, Jordi; Canales Gabriel, Manel; Fabregat Jové, Georgina; Meneguzzi, Álvaro; Alemán Llansó, Carlos Abstract: Interactions, in terms of both binding energies and microscopic organization, of water molecules absorbed by hydrophilic polyaniline emeraldine base have been investigated using quantum mechanical calculations, molecular dynamics simulation, FTIR spectroscopy, and 1H NMR. From an enthalpic point of view, water molecules interact more favorably with imine nitrogen atoms than with amine ones, even though the latter are entropically favored with respect to the former because of their two binding sites. Quantum mechanical results show that interaction energies of water molecules reversibly absorbed but organized individually around a binding site range from 3.0 to 6.3 kcal/mol, which is in good agreement with activation energies of 3–5 kcal/mol previously determined by thermodynamic measurements. The irreversible absorption of water to produce C–OH groups in rings of diimine units has been examined considering a three steps process in which water molecules act as both acidic and nucleophilic reagent. Although calculations predict that the whole process is disfavored by 5–8 kcal/mol only, FTIR and 1H NMR detected the existence of reversibly absorbed water but not of C–OH groups. Both the binding energies and the structural information provided by molecular dynamics simulations have been used to interpret the existence of two types of physisorbed water molecules: (i) those that interact individually with polymer chains and (ii) those immersed in nanodrops that are contained within the polymeric matrix. The binding energies calculated for these two types of water molecules are fully consistent with the thermodynamic activation energies previously reported. 2012-10-10T13:38:30Z http://hdl.handle.net/2117/16697 Title: Zero-temperature phase diagram of the second layer of 4He adsorbed on graphene Authors: Gordillo Bargueño, Maria Carmen; Boronat Medico, Jordi Abstract: The phase diagram at zero temperature of 4He adsorbed on a helium incommensurate triangular solid on top of a single graphene sheet has been obtained using the diffusion Monte Carlo method. We have found that, in accordance with previous experimental and simulation results for graphite, the ground state of 4He on this setup is a liquid that, upon compression, transforms into a triangular solid. To define the stability limits of both liquid and solid phases, we considered not only the adsorption energies of the atoms located on the second layer but the average energy of the atoms in both layers. Our results show that the lower density limit for a stable liquid in the second layer is 0.163±0.005 Å−2 and that the lower limit for the existence of an incommensurate solid on the second layer is 0.186±0.003 Å−2. Both values are in overall agreement with the results of torsional oscillator experiments and heat capacity measurements on graphite. The 4/7 and 7/12 registered solids are found to be metastable with respect to triangular incommensurate arrangements of the same density. 2012-10-09T17:55:08Z http://hdl.handle.net/2117/16693 Title: Competing activation mechanisms in epidemics on networks Authors: Castellano, Claudio; Pastor Satorras, Romualdo Abstract: In contrast to previous common wisdom that epidemic activity in heterogeneous networks is dominated by the hubs with the largest number of connections, recent research has pointed out the role that the innermost, dense core of the network plays in sustaining epidemic processes. Here we show that the mechanism responsible of spreading depends on the nature of the process. Epidemics with a transient state are boosted by the innermost core. Contrarily, epidemics allowing a steady state present a dual scenario, where either the hub independently sustains activity and propagates it to the rest of the system, or, alternatively, the innermost network core collectively turns into the active state, maintaining it globally. In uncorrelated networks the former mechanism dominates if the degree distribution decays with an exponent larger than 5/2, and the latter otherwise. Topological correlations, rife in real networks, may perturb this picture, mixing the role of both mechanisms. 2012-10-09T13:42:34Z http://hdl.handle.net/2117/16681 Title: Maintenance and reengineering of software: creating a Visual C++ graphical user interface to perform specific tasks related to soil structure interaction in poroelastic soil Authors: Khwaldeh, Ali; Tahat, Amani; Martí Rabassa, Jordi; Tahat, Mohammad Abstract: In this study, an interactive Graphical User Interface (GUI) application was introduced and tested. It worked as a utility program to facilitate and maximize the re-use of existing FORTRAN software. The GUI had been designed to generate tabulated seismic data (e.g., coefficient of reflection and propagation wave velocities: P-wave and SV-wave), in order to perform investigating the wave propagation in fluid saturated poroelastic medium, through using a simple two-dimensional soil-structure interaction model. Additionally, the theoretical background was also involved. The output data was of interest for understanding the effects of water saturation on the response of the ground and building structures to some degree earthquake excitation. Furthermore, the GUI application provided several utilities (e.g., viewing and plotting capabilities, file manipulation, editing as well as cloning the input parameters). Operating systems for which program had been designed were Windows XP, Windows Vista, Windows 7 and any (32) bits windows. The compilers were: Microsoft VC++ VS 6.0, Digital Visual FORTRAN 6.0 and Borland C++ Builder 6.0. The produced source code could be considered as successful case study for software engineers GUI developers, who were interested in creating (C++ /GUI), for FORTRAN by using the experience of such open source codes. 2012-10-08T18:25:30Z http://hdl.handle.net/2117/16428 Title: Tracking energy transfer from excited to accepting modes : application to water bend vibrational relaxation Authors: Rey Oriol, Rosendo; Hynes, James T. Abstract: We extend, via a reformulation in terms of Poisson brackets, the method developed previously (Rey et al., J. Phys. Chem. A, 2009, 113, 8949) allowing analysis of the pathways of an excited molecule's ultrafast vibrational relaxation in terms of intramolecular and intermolecular contributions. In particular we show how to ascertain, through the computation of power and work, which portion of an initial excess molecular energy (e.g. vibrational) is transferred to various degrees of freedom (e.g. rotational, translational) of the excited molecule itself and its neighbors. The particular case of bend excess energy relaxation in pure water is treated in detail, completing the picture reported in the work cited above. It is shown explicitly, within a classical description, that almost all of the initial water bend excitation energy is transferred—either indirectly, via Fermi resonance centrifugal coupling to the bend-excited water's rotation, or directly via intermolecular coupling— to local water librations, only involving molecules in the first two hydration shells of the vibrationally excited water molecule. Finally, it is pointed out that the Poisson bracket formulation can also be applied to elucidate the microscopic character of solvation and rotational dynamics, and should prove useful in developing a quantum treatment for energy flow in condensed phases. 2012-09-04T17:44:05Z http://hdl.handle.net/2117/16422 Title: Ferromagnetic transition of a two-component Fermi gas of hard spheres Authors: Arias de Saavedra, F.; Mazzanti Castrillejo, Fernando Pablo; Boronat Medico, Jordi; Polls, A. Abstract: We use microscopic many-body theory to analyze the problem of itinerant ferromagnetism in a repulsive atomic Fermi gas of hard spheres. Using simple arguments we show that the available theoretical predictions for the onset of the ferromagnetic transition predict a transition point at a density (kF a ∼ 1) that is too large to be compatible with the universal low-density expansion of the energy. We present variational calculations for the hard-sphere Fermi gas, in the framework of Fermi hypernetted chain theory, that shift the transition to higher densities (kF a ∼ 1.8). Backflow correlations, which are mainly active in the unpolarized system, are essential for this shift. 2012-09-04T15:03:23Z