



INSERT INTO `researchers_article` VALUES (8, 'Effectiveness of Journal Ranking Schemes as a Tool for Locating Information', 0, '', 'Stringer, MJ, Sales-Pardo, M, Amaral, LAN', 'Background: The rise of electronic publishing [1], preprint archives, blogs, and wikis is raising concerns among publishers, editors, and scientists about the present day relevance of academic journals and traditional peer review [2]. These concerns are especially fuelled by the ability of search engines to automatically identify and sort information [1]. It appears that academic journals can only remain relevant if acceptance of research for publication within a journal allows readers to infer immediate, reliable information on the value of that research. Methodology/Principal Findings: Here, we systematically evaluate the effectiveness of journals, through the work of editors and reviewers, at evaluating unpublished research. We find that the distribution of the number of citations to a paper published in a given journal in a specific year converges to a steady state after a journal-specific transient time, and demonstrate that in the steady state the logarithm of the number of citations has a journal-specific typical value. We then develop a model for the asymptotic number of citations accrued by papers published in a journal that closely matches the data. Conclusions/Significance: Our model enables us to quantify both the typical impact and the range of impacts of papers published in a journal. Finally, we propose a journal-ranking scheme that maximizes the efficiency of locating high impact research.', 'PLoS One', '2008-02-27', '3', 'art. no. e1683', '', '10.1371/journal.pone.0001683', 'publication_pdfs/Stringer-2008-PLoSOne-3-e1683.pdf', 'WOS:000260586500027', 19, 'effectiveness-of-journal-ranking-schemes-as-a-tool-for-locating-information');
INSERT INTO `researchers_article` VALUES (5, 'Missing and spurious interactions and the reconstruction of complex networks', 0, 'article_images/reliability.png', 'Guimera, R, Sales-Pardo, M', 'Network analysis is currently used in a myriad of contexts, from identifying potential drug targets to predicting the spread of epidemics and designing vaccination strategies and from finding friends to uncovering criminal activity. Despite the promise of the network approach, the reliability of network data is a source of great concern in all fields where complex networks are studied. Here, we present a general mathematical and computational framework to deal with the problem of data reliability in complex networks. In particular, we are able to reliably identify both missing and spurious interactions in noisy network observations. Remarkably, our approach also enables us to obtain, from those noisy observations, network reconstructions that yield estimates of the true network properties that are more accurate than those provided by the observations themselves. Our approach has the potential to guide experiments, to better characterize network data sets, and to drive new discoveries.', 'Proc. Natl. Acad. Sci. U. S. A.', '2009-12-29', '106', '22073', '22078', '10.1073/pnas.0908366106', 'publication_pdfs/Guimera-2009-Proc.Natl.Acad.Sci.U.S.A.-106-22073.pdf', 'WOS:000273178700009', 12, 'missing-and-spurious-interactions-and-the-reconstruction-of-complex-networks');
INSERT INTO `researchers_article` VALUES (12, 'Comparison of methods for the detection of node group membership in bipartite networks', 0, '', 'Sawardecker, EN, Amundsen, CA, Sales-Pardo, M, Amaral, LAN', 'Most real-world networks considered in the literature have a modular structure. Analysis of these real-world networks often are performed under the assumption that there is only one type of node. However, social and biochemical systems are often bipartite networks, meaning that there are two exclusive sets of nodes, and that edges run exclusively between nodes belonging to different sets. Here we address the issue of module detection in bipartite networks by comparing the performance of two classes of group identification methods - modularity maximization and clique percolation - on an ensemble of modular random bipartite networks. We find that the modularity maximization methods are able to reliably detect the modular bipartite structure, and that, under some conditions, the simulated annealing method outperforms the spectral decomposition method. We also find that the clique percolation methods are not capable of reliably detecting the modular bipartite structure of the bipartite model networks considered.', 'Eur. Phys. J. B', '2009-12-01', '72', '671', '677', '10.1140/epjb/e2009-00397-6', 'publication_pdfs/Sawardecker-2009-Eur.Phys.J.B-72-671.pdf', 'WOS:000272803300022', 1, 'comparison-of-methods-for-the-detection-of-node-group-membership-in-bipartite-networks');
INSERT INTO `researchers_article` VALUES (13, 'Detection of node group membership in networks with group overlap', 0, '', 'Sawardecker, EN, Sales-Pardo, M, Amaral, LAN', 'Most networks found in social and biochemical systems have modular structures. An important question prompted by the modularity of these networks is whether nodes can be said to belong to a single group. If they cannot, we would need to consider the role of "overlapping communities." Despite some efforts in this direction, the problem of detecting overlapping groups remains unsolved because there is neither a formal definition of overlapping community, nor an ensemble of networks with which to test the performance of group detection algorithms when nodes can belong to more than one group. Here, we introduce an ensemble of networks with overlapping groups. We then apply three group identification methods - modularity maximization, k-clique percolation, and modularity-landscape surveying - to these networks. We find that the modularity-landscape surveying method is the only one able to detect heterogeneities in node memberships, and that those heterogeneities are only detectable when the overlap is small. Surprisingly, we find that the k-clique percolation method is unable to detect node membership for the overlapping case.', 'Eur. Phys. J. B', '2009-02-01', '67', '277', '284', '10.1140/epjb/e2008-00418-0', 'publication_pdfs/Sawardecker-2009-Eur.Phys.J.B-67-277.pdf', 'WOS:000263525900003', 13, 'detection-of-node-group-membership-in-networks-with-group-overlap');
INSERT INTO `researchers_article` VALUES (14, 'Micro-bias and macro-performance', 0, '', 'Seaver, SMD, Moreira, AA, Sales-Pardo, M, Malmgren, RD, Diermeier, D, Amaral, LAN', 'We use agent-based modeling to investigate the effect of conservatism and partisanship on the efficiency with which large populations solve the density classification task - a paradigmatic problem for information aggregation and consensus building. We find that conservative agents enhance the populations\' ability to efficiently solve the density classification task despite large levels of noise in the system. In contrast, we find that the presence of even a small fraction of partisans holding the minority position will result in deadlock or a consensus on an incorrect answer. Our results provide a possible explanation for the emergence of conservatism and suggest that even low levels of partisanship can lead to significant social costs.', 'Eur. Phys. J. B', '2009-02-01', '67', '369', '375', '10.1140/epjb/e2008-00406-4', 'publication_pdfs/Seaver-2009-Eur.Phys.J.B-67-369.pdf', 'WOS:000263525900012', 1, 'micro-bias-and-macro-performance');
INSERT INTO `researchers_article` VALUES (15, 'From Clean Dishes to Clean Hands Novel Perspectives in the Fight Against Infections', 0, '', 'Kho, A, Sales-Pardo, M, Wilson, J', '', 'IEEE Eng. Med. Biol. Mag.', '2008-01-01', '27', '26', '28', '10.1109/MEMB.2008.929889', 'publication_pdfs/Kho-2008-IEEEEng.Med.Biol.Mag.-27-26.pdf', 'WOS:000261077100006', 0, 'from-clean-dishes-to-clean-hands-novel-perspectives-in-the-fight-against-infections');
INSERT INTO `researchers_article` VALUES (16, 'Evolution of protein families: Is it possible to distinguish between domains of life?', 0, '', 'Sales-Pardo, M, Chan, AOB, Amaral, LAN, Guimera, R', 'Understanding evolutionary relationships between species can shed new light into the rooting of the tree of life and the origin of eukaryotes, thus, resulting in a long standing interest in accurately assessing evolutionary parameters at time scales on the order of a billion of years. Prior work suggests large variability in molecular substitution rates, however, we still do not know whether such variability is due to species-specific trends at a genomic scale, or whether it can be attributed to the fluctuations inherent in any stochastic process. Here, we study the statistical properties of gene and protein-family sizes in order to quantify the long time scale evolutionary differences and similarities across species. We first determine the protein families of 209 species of bacteria and 20 species of archaea. We find that we are unable to reject the null hypothesis that the protein-family sizes of these species are drawn from the same distribution. In addition, we find that for species classified in the same phylogenetic branch or in the same lifestyle group, family size distributions are not significantly more similar than for species in different branches. These two findings can be accounted for in terms of a dynamical birth, death, and innovation model that assumes identical protein-family evolutionary rates for all species. Our theoretical and empirical results thus strongly suggest that the variability empirically observed in protein-family size distributions is compatible with the expected stochastic fluctuations for an evolutionary process with identical genomic evolutionary rates. Our findings hold special importance for the plausibility of some theories of the origin of eukaryotes which require drastic changes in evolutionary rates for some period during the last 2 billion years. (C) 2007 Elsevier B.V. All rights reserved.', 'Gene', '2007-11-01', '402', '81', '93', '10.1016/j.gene.2007.07.029', 'publication_pdfs/Sales-Pardo-2007-Gene-402-81.pdf', 'WOS:000250195900010', 1, 'evolution-of-protein-families-is-it-possible-to-distinguish-between-domains-of-life');
INSERT INTO `researchers_article` VALUES (69, 'Complex Systems View of Educational Policy Research', 0, '', 'Maroulis, S, Guimera, R, Petry, H, Stringer, MJ, Gomez, LM, Amaral, LAN, Wilensky, U', 'Agent-based modeling and network analysis can help integrate knowledge on "micro-level" mechanisms and "macro-level" effects.', 'Science', '2010-10-01', '330', '38', '39', '10.1126/science.1195153', 'publication_pdfs/Maroulis-2010-Science-330-38.pdf', 'WOS:000282334500021', 1, 'complex-systems-view-of-educational-policy-research');
INSERT INTO `researchers_article` VALUES (71, 'Statistical Validation of a Global Model for the Distribution of the Ultimate Number of Citations Accrued by Papers Published in a Scientific Journal', 0, '', 'Stringer, MJ, Sales-Pardo, M, Amaral, LAN', 'A central issue in evaluative bibliometrics is the characterization of the citation distribution of papers in the scientific literature. Here, we perform a large-scale empirical analysis of journals from every field in Thomson Reuters\' Web of Science database. We find that only 30 of the 2,184 journals have citation distributions that are inconsistent with a discrete lognormal distribution at the rejection threshold that controls the false discovery rate at 0.05. We find that large, multidisciplinary journals are over-represented in this set of 30 journals, leading us to conclude that, within a discipline, citation distributions are lognormal. Our results strongly suggest that the discrete lognormal distribution is a globally accurate model for the distribution of "eventual impact" of scientific papers published in single-discipline journal in a single year that is removed sufficiently from the present date.', 'J. Am. Soc. Inf. Sci. Technol.', '2010-07-01', '61', '1377', '1385', '10.1002/asi.21335', 'publication_pdfs/Stringer-2010-J.Am.Soc.InformationSci.Technol.-61-1377.pdf', 'WOS:000279151600006', 6, 'statistical-validation-of-a-global-model-for-the-distribution-of-the-ultimate-number-of-citations-accrued-by-papers-published-in-a-scientific-journal');
INSERT INTO `researchers_article` VALUES (19, 'A network-based method for target selection in metabolic networks', 0, '', 'Guimera, R, Sales-Pardo, M, Amaral, LAN', 'Motivation: The lack of new antimicrobials, combined with increasing microbial resistance to old ones, poses a serious threat to public health. With hundreds of genomes sequenced, systems biology promises to help in solving this problem by uncovering new drug targets. Results: Here, we propose an approach that is based on the mapping of the interactions between biochemical agents, such as proteins and metabolites, onto complex networks. We report that nodes and links in complex biochemical networks can be grouped into a small number of classes, based on their role in connecting different functional modules. Specifically, for metabolic networks, in which nodes represent metabolites and links represent enzymes, we demonstrate that some enzyme classes are more likely to be essential, some are more likely to be species-specific and some are likely to be both essential and specific. Our network-based enzyme classification scheme is thus a promising tool for the identification of drug targets.', 'Bioinformatics', '2007-07-01', '23', '1616', '1622', '10.1093/bioinformatics/btm150', 'publication_pdfs/Guimera-2007-Bioinformatics-23-1616.pdf', 'WOS:000248620400006', 24, 'a-network-based-method-for-target-selection-in-metabolic-networks');
INSERT INTO `researchers_article` VALUES (72, 'Extracting the hierarchical organization of complex systems', 0, '', 'Sales-Pardo, M, Guimera, R, Moreira, AA, Amaral, LAN', 'Extracting understanding from the growing "sea" of biological and socioeconomic data is one of the most pressing scientific challenges facing us. Here, we introduce and validate an unsupervised method for extracting the hierarchical organization of complex biological, social, and technological networks. We define an ensemble of hierarchically nested random graphs, which we use to validate the method. We then apply our method to real-world networks, including the air-transportation network, an electronic circuit, an e-mail exchange network, and metabolic networks. Our analysis of model and real networks demonstrates that our method extracts an accurate multiscale representation of a complex system.', 'Proc. Natl. Acad. Sci. U. S. A.', '2007-09-25', '104', '15224', '15229', '10.1073/pnas.0703740104', 'publication_pdfs/Sales-Pardo-2007-Proc.Natl.Acad.Sci.U.S.A.-104-15224_.pdf', 'WOS:000249806900012', 94, 'extracting-the-hierarchical-organization-of-complex-systems');
INSERT INTO `researchers_article` VALUES (21, 'Form follows function: the architecture of complex networks', 0, '', 'Guimera, R, Sales-Pardo, M', '', 'Mol. Syst. Biol.', '2006-01-01', '2', 'art. no. 42', '', '10.1038/msb4100082', 'publication_pdfs/Guimera-2006-Mol.Syst.Biol.-2-42.pdf', 'WOS:000243245400042', 5, 'form-follows-function-the-architecture-of-complex-networks');
INSERT INTO `researchers_article` VALUES (22, 'Mesoscopic modeling for nucleic acid chain dynamics', 0, '', 'Sales-Pardo, M, Guimera, R, Moreira, AA, Widom, J, Amaral, LAN', 'To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a mesoscopic-level computational model that provides a new window into nucleic acid dynamics. We model a single-stranded nucleic as a polymer chain whose monomers are the nucleosides. Each monomer comprises a bead representing the sugar molecule and a pin representing the base. The bead-pin complex can rotate about the backbone of the chain. We consider pairwise stacking and hydrogen-bonding interactions. We use a modified Monte Carlo dynamics that splits the dynamics into translational bead motion and rotational pin motion. By performing a number of tests, we first show that our model is physically sound. We then focus on a study of the kinetics of a DNA hairpin-a single-stranded molecule comprising two complementary segments joined by a noncomplementary loop-studied experimentally. We find that results from our simulations agree with experimental observations, demonstrating that our model is a suitable tool for the investigation of the hybridization of single strands.', 'Phys. Rev. E', '2005-05-01', '71', 'art. no. 051902', '', '10.1103/PhysRevE.71.051902', 'publication_pdfs/Sales-Pardo-2005-Phys.Rev.E-71-051902.pdf', 'WOS:000231687700058', 24, 'mesoscopic-modeling-for-nucleic-acid-chain-dynamics');
INSERT INTO `researchers_article` VALUES (24, 'Order-parameter fluctuations in Ising spin glasses at low temperatures', 0, '', 'Palassini, M, Sales, M, Ritort, F', 'We present a numerical study of the order-parameter fluctuations for Ising spin glasses in three and four dimensions at very low temperatures and without an external field. Accurate measurements of two previously introduced parameters A and G show that the order parameter is not self-averaging, consistent with a zero-temperature thermal exponent value theta\'similar or equal to0, and confirms the validity of the relation G=1/3 in the thermodynamic limit in the whole low-temperature phase, as predicted by stochastic stability arguments.', 'Phys. Rev. B', '2003-12-01', '68', 'art. no. 224430', '', '10.1103/PhysRevB.68.224430', 'publication_pdfs/Palassini-2003-Phys.Rev.B-68-224430.pdf', 'WOS:000188081900075', 4, 'order-parameter-fluctuations-in-ising-spin-glasses-at-low-temperatures');
INSERT INTO `researchers_article` VALUES (25, 'Temperature shifts in the Sinai model: static and dynamical effects', 0, '', 'Sales, M, Bouchaud, JP, Ritort, F', 'We study analytically and numerically the role of temperature shifts in the simplest model where the energy landscape is explicitly hierarchical, namely the Sinai model. This model has both attractive features (there are valleys within valleys in a strict self-similar sense), but also one important drawback: there is no phase transition so that the model is, in the large-size limit, effectively at zero temperature. We compute various static chaos indicators, that are found to be trivial in the large-size limit, but exhibit interesting features for finite sizes. Correspondingly, for finite times, some interesting rejuvenation effects, related to the self-similar nature of the potential, are observed. Still, the separation of time scales/length scales with temperature in this model is much weaker than in experimental spin glasses.', 'J. Phys. A-Math. Gen.', '2003-01-24', '36', '665', '684', '10.1088/0305-4470/36/3/306', 'publication_pdfs/Sales-2003-J.Phys.A-Math.Gen.-36-665.pdf', 'WOS:000185020200009', 4, 'temperature-shifts-in-the-sinai-model-static-and-dynamical-effects');
INSERT INTO `researchers_article` VALUES (26, 'Statistics of lowest droplets in two-dimensional Gaussian Ising spin glasses', 0, '', 'Picco, M, Ritort, F, Sales, M', 'An approach to determine the value of the zero-temperature thermal exponent theta in spin glasses is presented. It consists in describing the energy level spectrum in spin glasses only in terms of the properties of the lowest energy droplets and the lowest droplet exponents (LDE\'s) lambda(l),theta(l) that describe the statistics of their sizes and gaps. We show how these LDE\'s yield the standard thermal exponent of droplet theory theta through the relation theta = theta(l) + dlambda(l). The present approach provides a new way to measure the thermal exponent theta without any assumption about the correct procedure to generate typical low-lying excitations as is commonly done in many perturbation methods including domain wall calculations. To illustrate the usefulness of the method we present a detailed investigation of the properties of the lowest energy droplets in two-dimensional Gaussian Ising spin glasses. By independent measurements of both LDE\'s and an aspect-ratio analysis, we find theta(2d)similar or equal to -0.46(1)<&theta;(DW)(2d)&SIME; -0.287 where &theta;(DW) is the thermal exponent obtained in domain-wall theory. We also discuss the origin of finite-volume corrections in the behavior of the LDE &theta;(l) and relate them to the finite-volume corrections in the statistics of extreme values. Finally, we analyze some geometrical properties of the lowest energy droplets, finding results in agreement with those recently reported by Kawashima and Aoki [J. Phys. Soc. Jpn. 69, 169 (2000)]. All in all, we show that typical large-scale droplets are not probed by most of the present perturbation methods, since they probably do not have a compact structure as has been recently suggested. We speculate that a multifractal scenario could be at the roots of the reported discrepancies on the value of the thermal exponent &theta; in the two-dimensional Gaussian Ising spin glass.', 'Phys. Rev. B', '2003-05-01', '67', 'art. no. 184421', '', '10.1103/PhysRevD.67.184421', 'publication_pdfs/Picco-2003-Phys.Rev.B-67-184421.pdf', 'WOS:000183378800059', 7, 'statistics-of-lowest-droplets-in-two-dimensional-gaussian-ising-spin-glasses');
INSERT INTO `researchers_article` VALUES (27, 'Fragility of the free-energy landscape of a directed polymer in random media', 0, '', 'Sales, M, Yoshino, H', 'We examine the sensitiveness of the free-energy landscape of a directed polymer in random media with respect to various kinds of infinitesimally weak perturbation including the intriguing case of temperature chaos. To this end, we combine the replica Bethe Ansatz approach outlined by Sales and Yoshino (e-print cond-mat/0112384), the mapping to a modified Sinai model, and numerically exact calculations by the transfer-matrix method. Our results imply that for all the perturbations under study there is a slow crossover from a weakly perturbed regime, where rare events take place, to a strongly perturbed regime at larger length scales beyond the so-called overlap length, where typical events take place leading to chaos, i.e., a complete reshuffling of the free-energy landscape. Within the replica space, the evidence for chaos is found in the factorization of the replicated partition function induced by infinitesimal perturbations. This is the reflex of explicit replica-symmetry breaking.', 'Phys. Rev. E', '2002-06-01', '65', 'art. no. 066131', '', '10.1103/PhysRevE.65.066131', 'publication_pdfs/Sales-2002-Phys.Rev.E-65-066131.pdf', 'WOS:000176762900038', 29, 'fragility-of-the-free-energy-landscape-of-a-directed-polymer-in-random-media');
INSERT INTO `researchers_article` VALUES (87, 'Exploration of cyclopropyl radical ring opening to allyl radical by Newton trajectories: importance of valley-ridge inflection points to understand the topography', 0, '', 'Quapp, W, Bofill, JM, Aguilar-Mogas, A', 'Valley-ridge inflection points (VRI) on the potential energy surface for the ring opening of the cyclopropyl radical to allyl radical are determined using the tool of Newton trajectories (Quapp and Schmidt in Theor Chem Acc 128: 47, 2011). VRIs play a role in the understanding of bifurcating reactions. The region where the bifurcation takes place is usually governed by a VRI point. For this important ring opening, the knowledge of the VRI point after the transition state was demanded some years ago (Mann and Hase in J Am Chem Soc 124: 3208, 2002). Because the transition state is not symmetric, also the steepest descent from the transition state is not along a symmetry axis, and in such cases the steepest descent can fail the VRI point. That is the case here, indeed, though the pathway of the steepest descent goes near to a VRI point downhill. However, an electronic intersection seam disturbs the relations. The exploration of the notorious curvilinear potential energy surface of this ring opening has delivered some further VRI points, which are reported. They give a frame for possible ring-opening channels including the conrotatory case.', 'Theor. Chem. Acc.', '2011-08-01', '129', '803', '821', '10.1007/s00214-011-0938-4', '', 'WOS:000294054700007', 0, 'exploration-of-cyclopropyl-radical-ring-opening-to-allyl-radical-by-newton-trajectories-importance-of-valley-ridge-inflection-points-to-understand-the-topography');
INSERT INTO `researchers_article` VALUES (29, 'Scaling approach to order parameter fluctuations in disordered frustrated systems', 0, '', 'Ritort, F, Sales, M', 'We present a constructive approach to obtain information about the compactness and shape of large-scale lowest excitations in disordered systems by studying order parameter fluctuations (OPF) at low temperatures. We show that the parameter G that measures OFF is 1/3 at T = 0 provided the ground state is unique and the probability distribution for the lowest excitations is gapless and with finite weight at zero excitation energy We then apply zero temperature scaling to describe the energy and volume spectra of the lowest large-scale excitations that scale with the system size and have a weight at zero energy (P) over cap (0) similar to l(-theta \') with nu = l(d). A low-temperature expansion reveals that, OFF vanish like L-theta, if theta > 0 and remain finite for space-filling lowest excitations with theta = 0. The method can be extended to extract information about the shape and fractal surface of the large-scale lowest excitations.', 'J. Phys. A-Math. Gen.', '2001-06-08', '34', 'L333', 'L339', '10.1088/0305-4470/34/22/103', 'publication_pdfs/Ritort-2001-J.Phys.A-Math.Gen.-34-L333.pdf', 'WOS:000169462100003', 3, 'scaling-approach-to-order-parameter-fluctuations-in-disordered-frustrated-systems');
INSERT INTO `researchers_article` VALUES (30, 'Order-parameter fluctuations (OPF) in spin glasses: Monte Carlo simulations and exact results for small sizes', 0, '', 'Picco, M, Ritort, F, Sales, M', 'The rise of parameters measuring order-parameter fluctuations: (OPF) has been encouraged by the recent results reported in reference [2,3] which show that two of these parameters, G and G,, take universal values in the lim(T -->0). In this paper we present a detailed study of parameters measuring OPF for two mean-field models with and without time-reversal symmetry which exhibit different patterns of replica symmetry breaking below the transition: the Sherrington-Kirkpatrick model with and without a field and tire Ising p-spin glass (p = 3). We give numerical results and analyze the consequences which replica equivalence imposes on these models in the infinite volume limit. We give evidence for the transition in each system and discuss tire character of finite-size effects. Furthermore, a comparative study between this new family of parameters and tire usual Binder cumulant analysis shows what kind of new information can be extracted from the finite T behavior of these quantities. Tire two main outcomes of this work are: 1) Parameters measuring OPF give better estimates than the Binder cumulant for T-c and even for very small systems they give evidence for the transition. 2) For systems with no time-reversal symmetry, parameters defined in terms of connected quantities are the proper ones to look at.', 'Eur. Phys. J. B', '2001-02-01', '19', '565', '582', '10.1007/s100510170302', 'publication_pdfs/Picco-2001-Eur.Phys.J.B-19-565.pdf', 'WOS:000168069200010', 16, 'order-parameter-fluctuations-opf-in-spin-glasses-monte-carlo-simulations-and-exact-results-for-small-sizes');
INSERT INTO `researchers_article` VALUES (31, 'A conjectured scenario for order-parameter fluctuations in spin glasses', 0, '', 'Ritort, F, Sales, M', 'We study order-parameter fluctuations (OPF) in disordered systems by considering the behaviour of some recently introduced parameters G, G(c) which have proven very useful in locating phase transitions. We prove that both parameters G (for disconnected overlap disorder averages) and G(c) (for connected disorder averages) take the respective universal values 1/3 and 13/31 in the T --> 0 limit for any finite volume provided the ground state is unique and there is no gap in the ground-state local-field distributions, conditions which are met in generic spin-glass models with continuous couplings and no gap at zero coupling. This makes G, G(c) ideal parameters to locate phase transitions in disordered systems much like the Binder cumulant for ordered systems. We check our results by exactly computing OPF in a simple example of uncoupled spins in the presence of random fields and the one-dimensional Ising spin glass. At finite temperatures, we discuss under which conditions the value 1/3 for G may be recovered by conjecturing different scenarios depending on whether OPF are finite or vanish in the infinite-volume limit. In particular, we discuss replica equivalence and its natural consequence lim(v-->infinity) G(V, T) = 1/3 when OPF are finite. As an example of a model where OPF vanish and replica equivalence does not give information about G we study the Sherrington-Kirkpatrick spherical spin-glass model by performing numerical simulations for small sizes. Again we find results compatible with G = 1/3 in the spin-glass phase.', 'J. Phys. A-Math. Gen.', '2000-09-22', '33', '6505', '6526', '10.1088/0305-4470/33/37/304', 'publication_pdfs/Ritort-2000-J.Phys.A-Math.Gen.-33-6505.pdf', 'WOS:000089706000005', 6, 'a-conjectured-scenario-for-order-parameter-fluctuations-in-spin-glasses');
INSERT INTO `researchers_article` VALUES (33, 'Spin-phonon avalanches in Mn-12 acetate', 0, '', 'del Barco, E, Hernandez, JM, Sales, M, Tejada, J, Rakoto, H, Broto, JM, Chudnovsky, EM', 'We report experimental studies and suggest a quantitative model of spin relaxation in Mn-12 acetate in a pulsed magnetic field in the temperature range 1.9-5.0 K. When the field applied along the anisotropy axis is swept at 140 T/s through a nonmagnetized Mn-12 acetate sample, the sample\'s magnetization switches, within a few milliseconds, from zero to saturation at a well-defined field whose value depends on temperature but is quantized in units of 0.46 T. A quantitative explanation of the effect is given in terms of a spin-phonon avalanche combined with thermally assisted resonant spin tunneling. [S0163-1829(99)11529-7].', 'Phys. Rev. B', '1999-11-01', '60', '11898', '11901', '10.1103/PhysRevB.60.11898', 'publication_pdfs/del_Barco-1999-Phys.Rev.B-60-11898.pdf', 'WOS:000083808700016', 37, 'spin-phonon-avalanches-in-mn-12-acetate');
INSERT INTO `researchers_article` VALUES (34, 'Magnetocaloric effect in La0.65Ca0.35Ti1-xMnxO3 ceramic perovskites', 0, '', 'Bohigas, X, del Barco, E, Sales, M, Tejada, J', 'In this paper, we comment on experiments we have carried out on ceramic perovskites of composition La0.65Ca0.35Ti1-xMnxO3. From low- and high-field magnetic measurements recorded at different temperatures, we have discovered the existence of a large entropic change associated to the ferrimagnetic-paramagnetic transition. Our conclusion is that these materials are excellent candidates as working materials in refrigeration devices. (C) 1999 Published by Elsevier Science B.V. All rights reserved.', 'J. Magn. Magn. Mater.', '1999-05-01', '196', '455', '457', '10.1016/S0304-8853(98)00812-9', 'publication_pdfs/Bohigas-1999-J.Magn.Magn.Mater.-196-455.pdf', 'WOS:000080271900171', 17, 'magnetocaloric-effect-in-la065ca035ti1-xmnxo3-ceramic-perovskites');
INSERT INTO `researchers_article` VALUES (35, 'Tunable magnetocaloric effect in ceramic perovskites', 0, '', 'Bohigas, X, Tejada, J, del Barco, E, Zhang, XX, Sales, M', 'A large entropy variation (magnetocaloric effect) has been discovered in ceramic perovskites with the formulas La0.65Ca0.35Ti1-xMnxO3-z and La0.5+x+yLi0.5-3yTi1-3xMn3xO3-z. Both Curie temperature and entropy change were studied from 4.2 to 400 K for different stoichiometric compositions and applied magnetic fields. Our conclusion is that these materials are excellent candidates for working materials in magnetic refrigeration and liquefaction devices in a wide temperature range. (C) 1998 American Institute of Physics.', 'Appl. Phys. Lett.', '1998-07-20', '73', '390', '392', '10.1063/1.121844', 'publication_pdfs/Bohigas-1998-Appl.Phys.Lett.-73-390.pdf', 'WOS:000075275600038', 102, 'tunable-magnetocaloric-effect-in-ceramic-perovskites');
INSERT INTO `researchers_article` VALUES (36, 'The real communication network behind the formal chart: Community structure in organizations', 0, '', 'Guimera, R, Danon, L, Diaz-Guilera, A, Giralt, E, Arenas, A', 'The formal chart of an organization is intended to prescribe how employees interact. However, ties between individuals arise for personal, political, and cultural reasons. The characterization of the structure of such informal networks behind the formal chart is a key element for successful management. We surmise that the exchange of e-mails between individuals in organizations reveals how people interact and therefore provides a map of the real network structure behind the formal chart. We propose a methodology that allows extraction of relevant information about the community structure of an organization from the network of e-mail interactions between its employees. (c) 2006 Elsevier B.V. All rights reserved.', 'J. Econ. Behav. Organ.', '2006-12-01', '61', '653', '667', '10.1016/j.jebo.2004.07.021', 'publication_pdfs/Guimera-2006-J.Econ.Behav.Organ.-61-653.pdf', 'WOS:000243246000009', 12, 'the-real-communication-network-behind-the-formal-chart-community-structure-in-organizations');
INSERT INTO `researchers_article` VALUES (37, 'Lies, damned lies and statistics', 0, '', 'Amaral, LAN, Guimera, R', '', 'Nat. Phys.', '2006-02-01', '2', '75', '76', '', 'publication_pdfs/Amaral-2006-Nat.Phys.-2-75.pdf', 'WOS:000235464700013', 12, 'lies-damned-lies-and-statistics');
INSERT INTO `researchers_article` VALUES (39, 'Quantitative patterns in the structure of model and empirical food webs', 0, '', 'Stouffer, DB, Camacho, J, Guimera, R, Ng, CA, Amaral, LAN', 'Understanding the structure of food webs, and the mechanisms that give rise to this structure, is one of the most challenging problems in ecology. We analyze from a statistical physics perspective the network structure of model food webs and of 15 community food webs from a variety of environments, including freshwater, marine, estuarine, and terrestrial environments. We perform a theoretical analysis of two recently proposed models for food webs, the niche model of R. J. Williams and N. D. Martinez and the nested-hierarchy model of M.-E Cattin et al. We find that the two models generate distributions of numbers of prey, predators, and links that are described by the same analytical expressions. Our analytical treatment reveals that a model\'s capacity to reproduce empirical data is principally determined by its ability to satisfy two conditions: (1) the species\' niche values form a totally ordered set and (2) each species has a specific exponentially decaying probability of preying on a given fraction of the species with lower niche values. To test this hypothesis, we generalize the cascade model of J. E. Cohen and C. M. Newman so that it satisfies condition 2 and find that the new model is able to reproduce the properties of empirical food webs, validating our hypothesis. We use our analytical predictions as a guide to the analysis of 15 of the most complete empirical food webs available. We demonstrate that the quantitative unifying patterns that describe the properties of the food-web models considered earlier also describe the majority of the empirical webs considered. We find good agreement between the empirical data and the models for the average distance between species and the average clustering coefficient. Our results strongly support two hypotheses: first, that any model satisfying the two conditions we identify will accurately reproduce a number of the statistical properties of empirical food webs, and second, that the empirical distributions of number of prey and number of predators follow universal functional,forms that, without free parameters, match our analytical predictions.', 'Ecology', '2005-05-01', '86', '1301', '1311', '10.1890/04-0957', 'publication_pdfs/Stouffer-2005-Ecology-86-1301.pdf', 'WOS:000228960000025', 70, 'quantitative-patterns-in-the-structure-of-model-and-empirical-food-webs');
INSERT INTO `researchers_article` VALUES (41, 'Cartography of complex networks: modules and universal roles', 0, '', 'Guimera, R, Amaral, LAN', 'Integrative approaches to the study of complex systems demand that one knows the manner in which the parts comprising the system are connected. The structure of the complex network defining the interactions provides insight into the function and evolution of the components of the system. Unfortunately, the large size and intricacy of these networks implies that such insight is usually difficult to extract. Here, we propose a method that allows one to systematically extract and display information contained in complex networks. Specifically, we demonstrate that one can (i) find modules in complex networks and (ii) classify nodes into universal roles according to their pattern of within- and between-module connections. The method thus yields a \'cartographic representation\' of complex networks.', 'J. Stat. Mech.-Theory Exp.', '2005-02-01', '', 'art. no. P02001', '', '10.1088/1742-5468/2005/02/P02001', 'publication_pdfs/Guimera-2005-J.Stat.Mech.-TheoryExp.--1-P02001.pdf', 'WOS:000227304500006', 72, 'cartography-of-complex-networks-modules-and-universal-roles');
INSERT INTO `researchers_article` VALUES (43, 'Local search with congestion in complex communication networks', 0, '', 'Arenas, A, Danon, L, Diaz-Guilera, A, Guimera, R', 'We present a formalism that is able to cope with search and congestion simultaneously. This formalism avoids the problem of simulating the dynamics of the search-communication process which turns out to be impracticable, specially close to the congestion point where search costs (time) diverge.', 'LECT NOTE COMPUT SCI', '2004-01-01', '3038', '1078', '1085', '', 'publication_pdfs/Arenas-2004-LECT.NOTE.COMPUT.SCI.-3038-1078.pdf', 'WOS:000222048900139', 2, 'local-search-with-congestion-in-complex-communication-networks');
INSERT INTO `researchers_article` VALUES (44, 'Community analysis in social networks', 0, '', 'Arenas, A, Danon, L, Diaz-Guilera, A, Gleiser, PM, Guimera, R', 'We present an empirical study of different social networks obtained from digital repositories. Our analysis reveals the community structure and provides a useful visualising technique. We investigate the scaling properties of the community size distribution, and find that all the networks exhibit power law scaling in the community size distributions with exponent either -0.5 or -1. Finally we find that the networks\' community structure is topologically self-similar using the Horton-Strahler index.', 'Eur. Phys. J. B', '2004-03-01', '38', '373', '380', '10.1140/epjb/e2004-00130-1', 'publication_pdfs/Arenas-2004-Eur.Phys.J.B-38-373.pdf', 'WOS:000221447300031', 59, 'community-analysis-in-social-networks');
INSERT INTO `researchers_article` VALUES (45, 'Modeling the world-wide airport network', 0, '', 'Guimera, R, Amaral, LAN', 'Recently, we have presented the first exhaustive analysis of the world-wide airport network. Two important results of that study are that: (i) the world-wide airport network is a small-world network with power-law decaying degree and betweenness centrality distributions; (ii) the most connected cities (largest degree) are typically not the most central cities (largest betweenness centrality). This second finding is particularly significant because of results demonstrating that nodes with high betweenness tend to play a more important role in keeping networks connected than those with high degree. Here, we investigate if current network models can explain this finding and we show that they cannot. Thus, we propose a new model that explains this behavior in terms of the geo-political constraints that affect the growth of the airport network. We further hypothesize that in other infrastructures, affected by similar geo-political constraints, critical locations might not coincide with highly-connected hubs.', 'Eur. Phys. J. B', '2004-03-01', '38', '381', '385', '10.1140/epjb/e2004-00131-0', 'publication_pdfs/Guimera-2004-Eur.Phys.J.B-38-381.pdf', 'WOS:000221447300032', 103, 'modeling-the-world-wide-airport-network');
INSERT INTO `researchers_article` VALUES (94, 'Justice Blocks and Predictability of U.S. Supreme Court Votes', 1, 'article_images/roberts8.png', 'Guimera, R, Sales-Pardo, M', 'Successful attempts to predict judges\' votes shed light into how legal decisions are made and, ultimately, into the behavior and evolution of the judiciary. Here, we investigate to what extent it is possible to make predictions of a justice\'s vote based on the other justices\' votes in the same case. For our predictions, we use models and methods that have been developed to uncover hidden associations between actors in complex social networks. We show that these methods are more accurate at predicting justice\'s votes than forecasts made by legal experts and by algorithms that take into consideration the content of the cases. We argue that, within our framework, high predictability is a quantitative proxy for stable justice (and case) blocks, which probably reflect stable a priori attitudes toward the law. We find that U.S. Supreme Court justice votes are more predictable than one would expect from an ideal court composed of perfectly independent justices. Deviations from ideal behavior are most apparent in divided 54 decisions, where justice blocks seem to be most stable. Moreover, we find evidence that justice predictability decreased during the 50-year period spanning from the Warren Court to the Rehnquist Court, and that aggregate court predictability has been significantly lower during Democratic presidencies. More broadly, our results show that it is possible to use methods developed for the analysis of complex social networks to quantitatively investigate historical questions related to political decision-making.', 'PLoS ONE', '2011-11-09', '6(11)', 'e27188', '', '10.1371/journal.pone.0027188', 'publication_pdfs/journal.pone.0027188.pdf', '', 0, 'justice-blocks-and-predictability-us-supreme-court-votes');
INSERT INTO `researchers_article` VALUES (47, 'Search and congestion in complex networks', 0, '', 'Arenas, A, Cabrales, A, Diaz-Guilera, A, Guimera, R, Vega-Redondo, F', 'A model of communication that is able to cope simultaneously with the problems of search and congestion is presented. We investigate the communication dynamics in model networks. Those networks consist in a regular lattice ordering plus some long-range short-cuts with a given probability. The destination nodes of the short-cuts are chosen according to some degree of preferentiality. We study then the interplay between short- and long-range links and preferentiality. We also introduce a general framework that enables a search of optimal structures. A relation between dynamical properties and topological properties of the network is found and exploited.', 'LECT NOTES PHYS', '2003-01-01', '625', '175', '194', '', 'publication_pdfs/Arenas-2003-Lect.Not.Phys.pdf', 'WOS:000185214000010', 7, 'search-and-congestion-in-complex-networks');
INSERT INTO `researchers_article` VALUES (48, 'Comparison of simulated annealing and mean field annealing as applied to the generation of block designs', 0, '', 'Bofill, P, Guimera, R, Torras, C', 'This paper describes an experimental comparison between a discrete stochastic optimization procedure (Simulated Annealing, SA) and a continuous deterministic one (Mean Field Annealing), as applied to the generation of Balanced Incomplete Block Designs (BIBDs). A neural cost function for BIBD generation is proposed with connections of arity four, and its continuous counterpart is derived, as required by the mean field formulation. Both strategies are optimized with regard to the critical temperature, and the expected cost to the first solution is used as a performance measure for the comparison. The results show that SA performs slightly better, but the most important observation is that the pattern of difficulty across the 25 problem instances tried is very similar for both strategies, implying that the main factor to success is the energy landscape, rather than the exploration procedure used. (C) 2003 Elsevier Ltd. All rights reserved.', 'Neural Netw.', '2003-12-01', '16', '1421', '1428', '10.1016/j.neunet.2003.07.003', 'publication_pdfs/Bofill-2003-NeuralNetw.-16-1421.pdf', 'WOS:000186862100003', 6, 'comparison-of-simulated-annealing-and-mean-field-annealing-as-applied-to-the-generation-of-block-designs');
INSERT INTO `researchers_article` VALUES (49, 'Optimal network topologies for local search with congestion', 0, '', 'Guimera, R, Diaz-Guilera, A, Vega-Redondo, F, Cabrales, A, Arenas, A', 'The problem of searchability in decentralized complex networks is of great importance in computer science, economy, and sociology. We present a formalism that is able to cope simultaneously with the problem of search and the congestion effects that arise when parallel searches are performed, and we obtain expressions for the average search cost both in the presence and the absence of congestion. This formalism is used to obtain optimal network structures for a system using a local search algorithm. It is found that only two classes of networks can be optimal: starlike configurations, when the number of parallel searches is small, and homogeneous-isotropic configurations, when it is large.', 'Phys. Rev. Lett.', '2002-12-09', '89', 'art. no. 248701', '', '10.1103/PhysRevLett.89.248701', 'publication_pdfs/Guimera-2002-Phys.Rev.Lett.-89-248701.pdf', 'WOS:000179484700058', 218, 'optimal-network-topologies-for-local-search-with-congestion');
INSERT INTO `researchers_article` VALUES (50, 'Dynamical properties of model communication networks', 0, '', 'Guimera, R, Arenas, A, Diaz-Guilera, A, Giralt, F', 'We study the dynamical properties of a collection of models for communication processes, characterized by a single parameter xi representing the relation between information load of the nodes and its ability to deliver this information. The critical transition to congestion reported so far occurs only for xi=1. This case is well analyzed for different network topologies. We focus on the properties of the order parameter, the susceptibility, and the time correlations when approaching the critical point. For xi<1, no transition to congestion is observed but it remains a crossover from a low-density to a high-density state. For xi>1, the transition to congestion is discontinuous and congestion nuclei arise.', 'Phys. Rev. E', '2002-08-01', '66', 'art. no. 026704', '', '10.1103/PhysRevE.66.026704', 'publication_pdfs/Guimera-2002-Phys.Rev.E-66-026704.pdf', 'WOS:000177971300094', 76, 'dynamical-properties-of-model-communication-networks');
INSERT INTO `researchers_article` VALUES (51, 'Robust patterns in food web structure', 0, '', 'Camacho, J, Guimera, R, Amaral, LAN', 'We analyze the properties of seven community food webs from a variety of environments, including freshwater, marine-freshwater interfaces, and terrestrial environments. We uncover quantitative unifying patterns that describe the properties of the diverse trophic webs considered and suggest that statistical physics concepts such as scaling and universality may be useful in the description of ecosystems. Specifically, we find that several quantities characterizing these diverse food webs obey functional forms that are universal across the different environments considered. The empirical results are in remarkable agreement with the analytical solution of a recently proposed model for food webs.', 'Phys. Rev. Lett.', '2002-06-03', '88', 'art. no. 228102', '', '10.1103/PhysRevLett.88.228102', 'publication_pdfs/Camacho-2002-Phys.Rev.Lett.-88-228102.pdf', 'WOS:000175709100057', 135, 'robust-patterns-in-food-web-structure');
INSERT INTO `researchers_article` VALUES (52, 'Analytical solution of a model for complex food webs', 0, '', 'Camacho, J, Guimera, R, Amaral, LAN', 'We investigate numerically and analytically a recently proposed model for food webs [Nature 404, 180 (2000)] in the limit of large web sizes and sparse interaction matrices. We obtain analytical expressions for several quantities with ecological interest, in particular, the probability distributions for the number of prey and the number of predators. We find that these distributions have fast-decaying exponential and Gaussian tails, respectively. We also find that our analytical expressions are robust to changes in the details of the model.', 'Phys. Rev. E', '2002-03-01', '65', 'art. no. 030901', '', '10.1103/PhysRevE.65.030901', 'publication_pdfs/Camacho-2002-Phys.Rev.E-65-030901.pdf', 'WOS:000174548800009', 46, 'analytical-solution-of-a-model-for-complex-food-webs');
INSERT INTO `researchers_article` VALUES (53, 'Communication and optimal hierarchical networks', 0, '', 'Guimera, R, Arenas, A, Diaz-Guilera, A', 'We study a general and simple model for communication processes. In the model, agents in a network (in particular, an organization) interchange information packets following simple rules that take into account the limited capability of the agents to deal with packets and the cost associated with the existence of open communication channels. Due to the limitation in the capability, the network collapses under certain conditions. We focus on when the collapse occurs for hierarchical networks and also on the influence of the flatness or steepness of the structure. We find that the need for hierarchy is related to the existence of costly connections. (C) 2001 Elsevier Science B.V. All rights reserved.', 'Physica A', '2001-10-01', '299', '247', '252', '10.1016/S0378-4371(01)00302-8', 'publication_pdfs/Guimera-2001-PhysicaA-299-247.pdf', 'WOS:000171675300027', 26, 'communication-and-optimal-hierarchical-networks');
INSERT INTO `researchers_article` VALUES (54, 'Communication in networks with hierarchical branching', 0, '', 'Arenas, A, Diaz-Guilera, A, Guimera, R', 'We present a simple model of communication in networks with hierarchical branching. We analyze the behavior of the model from the viewpoint of critical systems under different situations. For certain values of the parameters, a continuous phase transition between a sparse and a congested regime is observed and accurately described by an order parameter and the power spectra. At the critical point the behavior of the model is totally independent of the number of hierarchical levels. Also scaling properties are observed when the size of the system varies. The presence of noise in the communication is shown to break the transition. The analytical results are a useful guide to forecasting the main features of real networks.', 'Phys. Rev. Lett.', '2001-04-02', '86', '3196', '3199', '10.1103/PhysRevLett.86.3196', 'publication_pdfs/Arenas-2001-Phys.Rev.Lett.-86-3196.pdf', 'WOS:000167866300071', 143, 'communication-in-networks-with-hierarchical-branching');
INSERT INTO `researchers_article` VALUES (86, 'Modular coherence of protein dynamics in yeast cell polarity system', 1, 'article_images/gao2011.png', 'Gao, JT, Guimera, R, Lia, H, Mendes Pinto, I, Sales-Pardo, M, Wai, SC, Rubinstein, B, Li, R', 'In this study, we investigated on a systems level how complex protein interactions underlying cell polarity in yeast determine the dynamic association of proteins with the polar cortical domain (PCD) where they localize and perform morphogenetic functions. We constructed a network of physical interactions among >100 proteins localized to the PCD. This network was further divided into five robust modules correlating with distinct subprocesses associated with cell polarity. Based on this reconstructed network, we proposed a simple model that approximates a PCD protein\'s molecular residence time as the sum of the characteristic time constants of the functional modules with which it interacts, weighted by the number of edges forming these interactions. Regression analyses showed excellent fitting of the model with experimentally measured residence times for a large subset of the PCD proteins. The model is able to predict residence times using small training sets. Our analysis also revealed a scaffold protein that imposes a local constraint of dynamics for certain interacting proteins.', 'Proc. Natl. Acad. Sci. U. S. A.', '2011-05-03', '108', '7647', '7652', '10.1073/pnas.1017567108', 'publication_pdfs/PNAS-2011-Gao-7647-52.pdf', 'WOS:000290203100073', 0, 'modular-coherence-protein-dynamics-yeast-cell-polarity-system');
INSERT INTO `researchers_article` VALUES (98, 'On the role of conserved moieties in shaping the robustness and production capabilities of reaction networks', 0, '', 'De Martino, A, Martelli, C, Massucci, FA', 'We study a simplified, solvable model of a fully connected metabolic network with constrained quenched disorder to mimic the conservation laws imposed by stoichiometry on chemical reactions. Within a spin-glass type of approach, we show that in the presence of a conserved metabolic pool the flux state corresponding to maximal growth is stationary independently of the pool size. In addition, and at odds with the case of unconstrained networks, the volume of optimal flux configurations remains finite, indicating that the frustration imposed by stoichiometric constraints, while reducing growth capabilities, confers robustness and flexibility to the system. These results have a clear biological interpretation and provide a basic, fully analytical explanation to features recently observed in real metabolic networks. Copyright (C) EPLA, 2009', 'EPL', '2009-02-01', '85', 'art. no. 38007', '', '10.1209/0295-5075/85/38007', '', 'WOS:000263693200030', 3, 'on-the-role-of-conserved-moieties-in-shaping-the-robustness-and-production-capabilities-of-reaction-networks');
INSERT INTO `researchers_article` VALUES (70, 'Optimal information transmission in organizations: search and congestion', 0, '', 'Arenas, A, Cabrales, A, Danon, L, Diaz-Guilera, A, Guimera, R, Vega-Redondo, F', 'We propose a stylized model of a problem-solving organization whose internal communication structure is given by a fixed network. Problems arrive randomly anywhere in this network and must find their way to their respective specialized solvers by relying on local information alone. The organization handles multiple problems simultaneously. For this reason, the process may be subject to congestion. We provide a characterization of the threshold of collapse of the network and of the stock of floating problems (or average delay) that prevails below that threshold. We build upon this characterization to address a design problem: the determination of what kind of network architecture optimizes performance for any given problem arrival rate. We conclude that, for low arrival rates, the optimal network is very polarized (i.e. star-like or centralized), whereas it is largely homogenous (or decentralized) for high arrival rates. These observations are in line with a common transformation experienced by information-intensive organizations as their work flow has risen in recent years.', 'Rev. Econ. Des.', '2010-03-01', '14', '75', '93', '10.1007/s10058-008-0067-2', 'publication_pdfs/Arenas-2010-Rev.Econ.Design-14-75.pdf', 'WOS:000282989600005', 3, 'optimal-information-transmission-in-organizations-search-and-congestion');
INSERT INTO `researchers_article` VALUES (95, 'Time-dependent heat capacity of Mn(12) clusters', 0, '', 'Sales, M, Hernandez, JM, Tejada, J, Martinez, JL', 'In this paper we discuss both theoretical and experimental results on the time dependence of the heat capacity of oriented Mn(12) magnetic clusters when a magnetic field is applied along their easy axis. Our calculations are based on the existence of two contributions. The first one is associated with the thermal populations of the 21 different S(z) levels in the two potential wells of the magnetic uniaxial anisotropy and the second one is related to the transitions between the S(z) levels. We compare our theoretical predictions with experimental data on the heat capacity for different resolution times at different fields and temperatures. [S0163-1829(99)01937-2].', 'Phys. Rev. B', '1999-12-01', '60', '14557', '14560', '10.1103/PhysRevB.60.14557', '', 'WOS:000084141700023', 9, 'time-dependent-heat-capacity-of-mn12-clusters');
INSERT INTO `researchers_article` VALUES (79, 'Rejuvenation in the random energy model', 0, '', 'Sales, M, Bouchaud, JP', 'We show that the Random Energy Model has interesting rejuvenation properties in its frozen phase. Different susceptibilities to temperature changes, for the free energy and for other ( magnetic) observables, can be computed exactly. These susceptibilities diverge at the transition temperature, as (1T/T-c)(-3) for the free energy.', 'Europhys. Lett.', '2001-10-01', '56', '181', '186', '10.1209/epl/i2001-00111-0', 'publication_pdfs/Sales-2001-Europhys.Lett.-56-181.pdf', 'WOS:000171629500004', 9, 'rejuvenation-in-the-random-energy-model');
INSERT INTO `researchers_article` VALUES (61, 'Origin of compartmentalization in food webs', 0, '', 'Guimera, R, Stouffer, DB, Sales-Pardo, M, Leicht, EA, Newman, MEJ, Amaral, LAN', 'The response of an ecosystem to perturbations is mediated by both antagonistic and facilitative interactions between species. It is thought that a community\'s resilience depends crucially on the food web---the network of trophic interactions---and on the food web\'s degree of compartmentalization. Despite its ecological importance, compartmentalization and the mechanisms that give rise to it remain poorly understood. Here we investigate several definitions of compartments, propose ways to understand the ecological meaning of these definitions, and quantify the degree of compartmentalization of empirical food webs. We find that the compartmentalization observed in empirical food webs can be accounted for solely by the niche organization of species and their diets. By uncovering connections between compartmentalization and species\' diet contiguity, our findings help us understand which perturbations can result in fragmentation of the food web and which can lead to catastrophic effects. Additionally, we show that the composition of compartments can be used to address the long-standing question of what determines the ecological niche of a species.', 'Ecology', '2010-10-01', '91', '2941', '2951', '10.1890/09-1175.1', 'publication_pdfs/Guimera-2010-Ecology-91-2941__.pdf', 'WOS:000282654700013', 5, 'origin-compartmentalization-food-webs');
INSERT INTO `researchers_article` VALUES (62, 'Strange bedfellows: Communities in BitTorrent', 0, '', 'Choffnes, DR, Duch, J, Malmgren, RD, Guimera, R, Bustamante, FE, Amaral, LAN', 'While P2P systems benefit from large numbers of interconnected nodes, each of these connections provides an opportunity for eavesdropping. Using only the connection patterns gathered from 10,000 BitTorrent (BT) users during a one-month period, we determine whether randomized connection patterns give rise to communities of users. Even though connections in BT require not only shared interest in content, but also concurrent sessions, we find that strong communities naturally form -- users inside a typical community are 5 to 25 times more likely to connect to each other than with users outside. These strong communities enable guilt by association, where the behavior of an entire community of users can be inferred by monitoring one of its members.Our study shows that through a single observation point, an attacker trying to identify such communities can uncover 50% of the network within a distance of two hops. Finally, we propose and evaluate a practical solution that mitigates this threat.', 'Proc. of the 9th International Workshop on Peer-to-Peer Systems (IPTPS)', '2010-04-01', '', ' ', '', '', 'publication_pdfs/DChoffnes10IPTPS.pdf', '', 0, 'strange-bedfellows-communities-bittorrent');
INSERT INTO `researchers_article` VALUES (64, 'Module identification in bipartite and directed networks', 0, '', 'Guimera, R, Sales-Pardo, M, Amaral, LAN', 'Modularity is one of the most prominent properties of real-world complex networks. Here, we address the issue of module identification in two important classes of networks: bipartite networks and directed unipartite networks. Nodes in bipartite networks are divided into two nonoverlapping sets, and the links must have one end node from each set. Directed unipartite networks only have one type of node, but links have an origin and an end. We show that directed unipartite networks can be conveniently represented as bipartite networks for module identification purposes. We report on an approach especially suited for module detection in bipartite networks, and we define a set of random networks that enable us to validate the approach.', 'Phys. Rev. E', '2007-09-01', '76', 'art. no. 036102', '', '10.1103/PhysRevE.76.036102', 'publication_pdfs/Guimera-2007-Phys.Rev.E-76-036102.pdf', 'WOS:000249785900009', 46, 'module-identification-in-bipartite-and-directed-networks');
INSERT INTO `researchers_article` VALUES (97, 'The luminosity evolution over the equitemporal surfaces in the prompt emission of gamma-ray bursts', 0, '', 'Bianco, CL, Massucci, FA, Ruffini, R', 'Due to the ultrarelativistic velocity of the expanding "fireshell" (Lorentz gamma factor gamma similar to 10(2) -10(3)), photons emitted at the same time from the fireshell surface do not reach the observer at the same arrival time. In interpreting Gamma-Ray Bursts (GRBs) it is crucial to determine the properties of the EQuiTemporal Surfaces (EQTSs): the locus of points which are source of radiation reaching the observer at the same arrival time. In the current literature this analysis is performed only in the latest phases of the afterglow. Here we study the distribution of the GRB bolometric luminosity over the EQTSs, with special attention to the prompt emission phase. We analyze as well the temporal evolution of the EQTS apparent size in the sky. We use the analytic solutions of the equations of motion of the fireshell and the corresponding analytic expressions of the EQTSs which have been presented in recent works and which are valid for both the fully radiative and the adiabatic dynamics. We find the novel result that at the beginning of the prompt emission the most luminous regions of the EQTSs are the ones closest to the line of sight. On the contrary, in the late prompt emission and in the early afterglow phases the most luminous EQTS regions are the ones closest to the boundary of the visible region. This transition in the emitting region may lead to specific observational signatures, i.e. an anomalous spectral evolution, in the rising part or at the peak of the prompt emission. We find as well an expression for the apparent radius of the EQTS in the sky, valid in both the fully radiative and the adiabatic regimes. Such considerations are essential for the theoretical interpretation of the prompt emission phase of GRBs.', 'Int. J. Mod. Phys. D', '2011-09-01', '20', '1919', '1929', '10.1142/S0218271811019943', '', 'WOS:000295277300016', 0, 'the-luminosity-evolution-over-the-equitemporal-surfaces-in-the-prompt-emission-of-gamma-ray-bursts');
INSERT INTO `researchers_article` VALUES (73, 'Classes of complex networks defined by role-to-role connectivity profiles', 0, '', 'Guimera, R, Sales-Pardo, M, Amaral, LAN', 'In physical, biological, technological and social systems, interactions between units give rise to intricate networks. These-typically non-trivial-structures, in turn, critically affect the dynamics and properties of the system. The focus of most current research on complex networks is, still, on global network properties. A caveat of this approach is that the relevance of global properties hinges on the premise that networks are homogeneous, whereas most real-world networks have a markedly modular structure. Here, we report that networks with different functions, including the Internet, metabolic, air transportation and protein interaction networks, have distinct patterns of connections among nodes with different roles, and that, as a consequence, complex networks can be classified into two distinct functional classes on the basis of their link type frequency. Importantly, we demonstrate that these structural features cannot be captured by means of often studied global properties.', 'Nat. Phys.', '2007-01-01', '3', '63', '69', '10.1038/nphys489', 'publication_pdfs/Guimera-2007-Nat.Phys.-3-63.pdf', 'WOS:000243729900020', 79, 'classes-of-complex-networks-defined-by-role-to-role-connectivity-profiles');
INSERT INTO `researchers_article` VALUES (74, 'Modularity from fluctuations in random graphs and complex networks', 0, '', 'Guimera, R, Sales-Pardo, M, Amaral, LAN', 'The mechanisms by which modularity emerges in complex networks are not well understood but recent reports have suggested that modularity may arise from evolutionary selection. We show that finding the modularity of a network is analogous to finding the ground-state energy of a spin system. Moreover, we demonstrate that, due to fluctuations, stochastic network models give rise to modular networks. Specifically, we show both numerically and analytically that random graphs and scale-free networks have modularity. We argue that this fact must be taken into consideration to define statistically significant modularity in complex networks.', 'Phys. Rev. E', '2004-08-01', '70', 'art. no. 025101', '', '10.1103/PhysRevE.70.025101', 'publication_pdfs/Guimera-2004-Phys.Rev.E-70-025101.pdf', 'WOS:000223784600001', 156, 'modularity-from-fluctuations-in-random-graphs-and-complex-networks');
INSERT INTO `researchers_article` VALUES (75, 'The worldwide air transportation network: Anomalous centrality, community structure, and cities\' global roles', 0, '', 'Guimera, R, Mossa, S, Turtschi, A, Amaral, LAN', 'We analyze the global structure of the worldwide air transportation network, a critical infrastructure with an enormous impact on local, national, and international economies. We find that the worldwide air transportation network is a scale-free small-world network. In contrast to the prediction of scale-free network models, however, we find that the most connected cities are not necessarily the most central, resulting in anomalous values of the centrality. We demonstrate that these anomalies arise because of the multicommunity structure of the network. We identify the communities in the air transportation network and show that the community structure cannot be explained solely based on geographical constraints and that geopolitical considerations have to be taken into account. We identify each city\'s global role based on its pattern of intercommunity and intracommunity connections, which enables us to obtain scale-specific representations of the network.', 'Proc. Natl. Acad. Sci. U. S. A.', '2005-05-31', '102', '7794', '7799', '10.1073/pnas.0407994102', 'publication_pdfs/Guimera-2005-Proc.Natl.Acad.Sci.U.S.A.-102-7794.pdf', 'WOS:000229531000005', 267, 'the-worldwide-air-transportation-network-anomalous-centrality-community-structure-and-cities-global-roles');
INSERT INTO `researchers_article` VALUES (76, 'Team assembly mechanisms determine collaboration network structure and team performance', 0, '', 'Guimera, R, Uzzi, B, Spiro, J, Amaral, LAN', 'Agents in creative enterprises are embedded in networks that inspire, support, and evaluate their work. Here, we investigate how the mechanisms by which creative teams self-assemble determine the structure of these collaboration networks. We propose a model for the self-assembly of creative teams that has its basis in three parameters: team size, the fraction of newcomers in new productions, and the tendency of incumbents to repeat previous collaborations. The model suggests that the emergence of a large connected community of practitioners can be described as a phase transition. We find that team assembly mechanisms determine both the structure of the collaboration network and team performance for teams derived from both artistic and scientific fields.', 'Science', '2005-04-29', '308', '697', '702', '10.1126/science.1106340', 'publication_pdfs/Guimera-2005-Science-308-697.pdf', 'WOS:000228810900051', 137, 'team-assembly-mechanisms-determine-collaboration-network-structure-and-team-performance');
INSERT INTO `researchers_article` VALUES (77, 'Functional cartography of complex metabolic networks', 0, '', 'Guimera, R, Amaral, LAN', 'High-throughput techniques are leading to an explosive growth in the size of biological databases and creating the opportunity to revolutionize our understanding of life and disease. Interpretation of these data remains, however, a major scientific challenge. Here, we propose a methodology that enables us to extract and display information contained in complex networks(1-3). Specifically, we demonstrate that we can find functional modules(4,5) in complex networks, and classify nodes into universal roles according to their pattern of intra- and inter-module connections. The method thus yields a \'cartographic representation\' of complex networks. Metabolic networks(6-8) are among the most challenging biological networks and, arguably, the ones with most potential for immediate applicability(9). We use our method to analyse the metabolic networks of twelve organisms from three different superkingdoms. We find that, typically, 80% of the nodes are only connected to other nodes within their respective modules, and that nodes with different roles are affected by different evolutionary constraints and pressures. Remarkably, we find that metabolites that participate in only a few reactions but that connect different modules are more conserved than hubs whose links are mostly within a single module.', 'Nature', '2005-02-24', '433', '895', '900', '10.1038/nature03288', 'publication_pdfs/Guimera-2005-Nature-433-895.pdf', 'WOS:000227174600050', 478, 'functional-cartography-of-complex-metabolic-networks');
INSERT INTO `researchers_article` VALUES (78, 'Self-similar community structure in a network of human interactions', 0, '', 'Guimera, R, Danon, L, Diaz-Guilera, A, Giralt, F, Arenas, A', 'We propose a procedure for analyzing and characterizing complex networks. We apply this to the social network as constructed from email communications within a medium sized university with about 1700 employees. Email networks provide an accurate and nonintrusive description of the flow of information within human organizations. Our results reveal the self-organization of the network into a state where the distribution of community sizes is self-similar. This suggests that a universal mechanism, responsible for emergence of scaling in other self-organized complex systems, as, for instance, river networks, could also be the underlying driving force in the formation and evolution of social networks.', 'Phys. Rev. E', '2003-12-01', '68', 'art. no. 065103', '', '10.1103/PhysRevE.68.065103', 'publication_pdfs/Guimera-2003-Phys.Rev.E-68-065103.pdf', 'WOS:000188316700003', 164, 'self-similar-community-structure-in-a-network-of-human-interactions');
INSERT INTO `researchers_article` VALUES (96, 'The reaction between HO and (H(2)O) (n) (n=1, 3) clusters: reaction mechanisms and tunneling effects', 0, '', 'Gonzalez, J, Caballero, M, Aguilar-Mogas, A, Torrent-Sucarrat, M, Crehuet, R, Sole, A, Gimenez, X, Olivella, S, Bofill, JM, Anglada, JM', 'The reaction between the HO radical and (H(2)O)n (n = 1, 3) clusters has been investigated employing high-level quantum mechanical calculations using DFT-BH&HLYP, QCISD, and CCSD(T) theoretical approaches in connection with the 6-311 + G(2df,2p), aug-cc-pVTZ, and aug-cc-pVQZ basis sets. The rate constants have also been calculated and the tunneling effects have been studied by means of time-dependent wavepacket calculations, performed using the Quantum-Reaction Path Hamiltonian method. According to the findings of previously reported theoretical works, the reaction between HO and H(2)O begins with the formation of a pre-reactive complex that is formed before the transition state, the formation of a post-reactive complex, and the release of the products. The reaction between HO and (H(2)O)(2) also begins with the formation of a pre-reactive complex, which dissociates into H(2)OaEuro broken vertical bar HO + H(2)O. The reaction between HO and (H(2)O)(3) is much more complex. The hydroxyl radical adds to the water trimer, and then it occurs a geometrical rearrangement in the pre-reactive hydrogen-bonded complex region, before the transition state. The reaction between hydroxyl radical and water trimer is computed to be much faster than the reaction between hydroxyl radical and a single water molecule, and, in both cases, the tunneling effects are very important mainly at low temperatures. A prediction of the atmospheric concentration of the hydrogen-bonded complexes studied in this work is also reported.', 'Theor. Chem. Acc.', '2011-03-01', '128', '579', '592', '10.1007/s00214-010-0824-5', '', 'WOS:000287748900020', 2, 'the-reaction-between-ho-and-h2o-n-n1-3-clusters-reaction-mechanisms-and-tunneling-effects');
INSERT INTO `researchers_article` VALUES (89, 'Implementation of an Algorithm Based on the Runge-Kutta-Fehlberg Technique and the Potential Energy as a Reaction Coordinate to Locate Intrinsic Reaction Paths', 0, '', 'Aguilar-Mogas, A, Gimenez, X, Bofill, JM', 'The intrinsic reaction coordinate (IRC) curve is used widely as a representation of the Reaction Path and can be parameterized taking the potential energy as a reaction coordinate (Aguilar-Mogas et al., J Chem Phys 2008, 128, 104102). Taking this parameterization and its variational nature, an algorithm is proposed that permits to locate this type of curve joining two points from an arbitrary curve that joints the same initial and final points. The initial and final points are minima of the potential energy surface associated with the geometry of reactants and products of the reaction whose mechanism is under study. The arbitrary curves are moved toward the IRC curve by a Runge-Kutta-Fehlberg technique. This technique integrates a set of differential equations resulting from the minimization until value zero of the line integral over the Weierstrass E-function. The Weierstrass E-function is related with the second variation in the theory of calculus of variations. The algorithm has been proved in real chemical systems. (C) 2010 Wiley Periodicals, Inc. J Comput Chem 31: 2510-2525, 2010', 'J. Comput. Chem.', '2010-10-01', '31', '2510', '2525', '10.1002/jcc.21539', '', 'WOS:000280890700014', 4, 'implementation-of-an-algorithm-based-on-the-runge-kutta-fehlberg-technique-and-the-potential-energy-as-a-reaction-coordinate-to-locate-intrinsic-reaction-paths');
INSERT INTO `researchers_article` VALUES (90, 'A Bohmian total potential view to quantum effects. II: decay of temporarily trapped states', 0, '', 'Gonzalez, MF, Aguilar-Mogas, A, Gonzalez, J, Crehuet, R, Anglada, JM, Bofill, JM, Gimenez, X', 'Formation, persistence and decay of temporarily trapped states, the time-dependent generalization of resonances, are analysed within the framework of Bohmian Mechanics. More specifically, the so-called Bohm\'s total potential, the sum of classical plus Bohm\'s quantum potential, is used. It is found that both formation and decay are triggered by the frequency in the oscillations of the total potential. These oscillations have been studied at the specific locations where the classical potential displays maxima, i.e. the \'walls\' temporarily capturing the system\'s density. Our main result is that the total potential oscillation frequency is solely dependent on the steepness of the classical potential ramp and, surprisingly, independent of the classical barrier height and width, well depth and width, collision energy or wavepacket width.', 'Theor. Chem. Acc.', '2009-05-01', '123', '51', '58', '10.1007/s00214-009-0548-6', '', 'WOS:000265566100007', 1, 'a-bohmian-total-potential-view-to-quantum-effects-ii-decay-of-temporarily-trapped-states');
INSERT INTO `researchers_article` VALUES (91, 'Finding reaction paths using the potential energy as reaction coordinate', 0, '', 'Aguilar-Mogas, A, Gimenez, X, Bofill, JM', 'The intrinsic reaction coordinate curve (IRC), normally proposed as a representation of a reaction path, is parametrized as a function of the potential energy rather than the arc-length. This change in the parametrization of the curve implies that the values of the energy of the potential energy surface points, where the IRC curve is located, play the role of reaction coordinate. We use Caratheodory\'s relation to derive in a rigorous manner the proposed parametrization of the IRC path. Since this Caratheodory\'s relation is the basis of the theory of calculus of variations, then this fact permits to reformulate the IRC model from this mathematical theory. In this mathematical theory, the character of the variational solution (either maximum or minimum) is given through the Weierstrass E-function. As proposed by Crehuet and Bofill [J. Chem. Phys. 122, 234105 (2005)], we use the minimization of the Weierstrass E-function, as a function of the potential energy, to locate an IRC path between two minima from an arbitrary curve on the potential energy surface, and then join these two minima. We also prove, from the analysis of the Weierstrass E-function, the mathematical bases for the algorithms proposed to locate the IRC path. The proposed algorithm is applied to a set of examples. Finally, the algorithm is used to locate a discontinuous, or broken, IRC path, namely, when the path connects two first order saddle points through a valley-ridged inflection point. (c) 2008 American Institute of Physics.', 'J. Chem. Phys.', '2008-03-14', '128', 'art. no. 104102', '', '10.1063/1.2834930', '', 'WOS:000254025300004', 8, 'finding-reaction-paths-using-the-potential-energy-as-reaction-coordinate');
INSERT INTO `researchers_article` VALUES (92, 'Applications of analytic and geometry concepts of the theory of calculus of variations to the Intrinsic Reaction Coordinate model', 0, '', 'Aguilar-Mogas, A, Crehuet, R, Gimenez, X, Bofill, JM', 'A mathematical analysis of several algorithms, for the integration of the differential equation associated to the Intrinsic Reaction Coordinate path, is performed. This analysis first shows that the Intrinsic Reaction Coordinate path can be derived from a variational problem, so that it has the properties of an extremal curve. Then, one may borrow the mathematical methods for the integration of extremal curves, to formulate new algorithms for the integration of the Intrinsic Reaction Coordinate path. One may use also this theoretical framework, to recast recently formulated algorithms based on direct minimization of an arbitrary curve, such as the Nudged Elastic Band Method or String Method. In this view a new algorithm is proposed. Finally, the theory of broken extremals is used to analyse an Intrinsic Reaction Coordinate path possessing a valley ridge inflection point.', 'Mol. Phys.', '2007-01-01', '105', '2475', '2492', '10.1080/00268970701519762', '', 'WOS:000251751200004', 5, 'applications-of-analytic-and-geometry-concepts-of-the-theory-of-calculus-of-variations-to-the-intrinsic-reaction-coordinate-model');
INSERT INTO `researchers_article` VALUES (93, 'On the implementation of the Runge-Kutta-Fehlberg algorithm to integrate intrinsic reaction coordinate paths', 0, '', 'Aguilar-Mogas, A, Gimenez, X, Bofill, J', 'A new algorithm for the integration of the intrinsic reaction coordinate path on a potential energy surface is proposed, based in solving the set of differential equations associated to the corresponding characteristic curve, rather than the differential equation of the curve itself. The integration of this set of differential equations is carried out by employing a Runge-Kutta-Fehlberg with tau-stage and p-algebraic order technique. In addition, an update Hessian matrix formula is reported for this specific algorithm. The examples show that the proposed algorithm is numerically stable, with no extra computational effort with respect to the standard algorithms. (c) 2006 Elsevier B.V. All rights reserved.', 'Chem. Phys. Lett.', '2006-12-04', '432', '375', '382', '10.1016/j.cplett.2006.10.061', '', 'WOS:000242520100071', 5, 'on-the-implementation-of-the-runge-kutta-fehlberg-algorithm-to-integrate-intrinsic-reaction-coordinate-paths');
