A survey of the parallel performance and accuracy of Poisson solvers for electronic structure calculations.

We present an analysis of different methods to calculate the classical electrostatic Hartree potential created by charge distributions. Our goal is to provide the reader with an estimation on the performance-in terms of both numerical complexity and accuracy-of popular Poisson solvers, and to give an intuitive idea on the way these solvers operate. Highly parallelizable routines have been implemented in a first-principle simulation code (Octopus) to be used in our tests, so that reliable conclusions about the capability of methods to tackle large systems in cluster computing can be obtained from our work.

Evolutionary vaccination dilemma in complex networks.

In this work we analyze the evolution of voluntary vaccination in networked populations by entangling the spreading dynamics of an influenza-like disease with an evolutionary framework taking place at the end of each influenza season so that individuals take or do not take the vaccine upon their previous experience. Our framework thus puts in competition two well-known dynamical properties of scale-free networks: the fast propagation of diseases and the promotion of cooperative behaviors. Our results show that when vaccine is perfect, scale-free networks enhance the vaccination behavior with respect to random graphs with homogeneous connectivity patterns.

Unraveling the redox properties of the global regulator FurA from Anabaena sp. PCC 7120: disulfide reductase activity based on its CXXC motifs.

Unlabelled: Cyanobacterial FurA works as a global regulator linking iron homeostasis to photosynthetic metabolism and the responses to different environmental stresses. Additionally, FurA modulates several genes involved in redox homeostasis and fulfills the characteristics of a heme-sensor protein whose interaction with this cofactor negatively affects its DNA binding ability. FurA from Anabaena PCC 7120 contains five cysteine residues, four of them arranged in two redox CXXC motifs.

Theoretical shaping of femtosecond laser pulses for ultrafast molecular photo-dissociation with control techniques based on time-dependent density functional theory.

The combination of time-dependent density functional theory and quantum optimal control formalism is used to optimize the shape of ultra-short laser pulses in order to achieve the photodissociation of the hydrogen molecule. The very short pulse durations used in this work (a few femtoseconds) do not allow for significant nuclear movement during irradiation, and thus the dissociation mechanism is sequential. During pulse irradiation, a large sudden momentum is communicated which can be understood in terms of population of excited, bound or unbound, dissociative electronic states.

Emergence of network features from multiplexity.

Many biological and man-made networked systems are characterized by the simultaneous presence of different sub-networks organized in separate layers, with links and nodes of qualitatively different types. While during the past few years theoretical studies have examined a variety of structural features of complex networks, the outstanding question is whether such features are characterizing all single layers, or rather emerge as a result of coarse-graining, i.e.

Role of key residues at the flavin mononucleotide (FMN):adenylyltransferase catalytic site of the bifunctional riboflavin kinase/flavin adenine dinucleotide (FAD) Synthetase from Corynebacterium ammoniagenes.

In mammals and in yeast the conversion of Riboflavin (RF) into flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) is catalysed by the sequential action of two enzymes: an ATP:riboflavin kinase (RFK) and an ATP:FMN adenylyltransferase (FMNAT). However, most prokaryotes depend on a single bifunctional enzyme, FAD synthetase (FADS), which folds into two modules: the C-terminal associated with RFK activity and the N-terminal associated with FMNAT activity. Sequence and structural analysis suggest that the 28-HxGH-31, 123-Gx(D/N)-125 and 161-xxSSTxxR-168 motifs from FADS must be involved in ATP stabilisation for the adenylylation of FMN, as well as in FAD stabilisation for FAD phyrophosphorolysis.

Theoretical study of the mechanism of the hydride transfer between ferredoxin-NADP+ reductase and NADP+: the role of Tyr303.

During photosynthesis, ferredoxin-NADP(+) reductase (FNR) catalyzes the electron transfer from ferredoxin to NADP(+) via its FAD cofactor. The final hydride transfer event between FNR and the nucleotide is a reversible process. Two different transient charge-transfer complexes form prior to and upon hydride transfer, FNR(rd)-NADP(+) and FNR(ox)-NADPH, regardless of the hydride transfer direction.

Controlling the dynamics of many-electron systems from first principles: a combination of optimal control and time-dependent density-functional theory.

Quantum optimal control theory (QOCT) provides the necessary tools to theoretically design driving fields capable of controlling a quantum system towards a given state or along a prescribed path in Hilbert space. This theory must be complemented with a suitable model for describing the dynamics of the quantum system. Here, we are concerned with many electron systems (atoms, molecules, quantum dots, etc.

Stability of Boolean multilevel networks.

The study of the interplay between the structure and dynamics of complex multilevel systems is a pressing challenge nowadays. In this paper, we use a semiannealed approximation to study the stability properties of random Boolean networks in multiplex (multilayered) graphs. Our main finding is that the multilevel structure provides a mechanism for the stabilization of the dynamics of the whole system even when individual layers work on the chaotic regime, therefore identifying new ways of feedback between the structure and the dynamics of these systems.

Spreading of persistent infections in heterogeneous populations.

Up to now, the effects of having heterogeneous networks of contacts have been studied mostly for diseases which are not persistent in time, i.e., for diseases where the infectious period can be considered very small compared to the lifetime of an individual.

Mutants of Anabaena sp. PCC 7120 lacking alr1690 and alpha-furA antisense RNA show a pleiotropic phenotype and altered photosynthetic machinery.

Fur proteins are global regulators present in all prokaryotes. In Anabaena sp. PCC 7120 FurA controls iron uptake and modulates an important set of genes related primarily to photosynthesis, nitrogen metabolism and oxidative stress defense.

Social network reciprocity as a phase transition in evolutionary cooperation.

In evolutionary dynamics the understanding of cooperative phenomena in natural and social systems has been the subject of intense research during decades. We focus attention here on the so-called "lattice reciprocity" mechanisms that enhance evolutionary survival of the cooperative phenotype in the prisoner's dilemma game when the population of Darwinian replicators interact through a fixed network of social contacts. Exact results on a "dipole model" are presented, along with a mean-field analysis as well as results from extensive numerical Monte Carlo simulations.

Complex cooperative networks from evolutionary preferential attachment.

In spite of its relevance to the origin of complex networks, the interplay between form and function and its role during network formation remains largely unexplored. While recent studies introduce dynamics by considering rewiring processes of a pre-existent network, we study network growth and formation by proposing an evolutionary preferential attachment model, its main feature being that the capacity of a node to attract new links depends on a dynamical variable governed in turn by the node interactions. As a specific example, we focus on the problem of the emergence of cooperation by analyzing the formation of a social network with interactions given by the Prisoner's Dilemma.

Natural selection of cooperation and degree hierarchy in heterogeneous populations.

One of the current theoretical challenges to the explanatory powers of Evolutionary Theory is the understanding of the observed evolutionary survival of cooperative behavior when selfish actions provide higher fitness (reproductive success). In unstructured populations natural selection drives cooperation to extinction. However, when individuals are allowed to interact only with their neighbors, specified by a graph of social contacts, cooperation-promoting mechanisms (known as lattice reciprocity) offer to cooperation the opportunity of evolutionary survival.

Synchronizability determined by coupling strengths and topology on complex networks.

We investigate in depth the synchronization of coupled oscillators on top of complex networks with different degrees of heterogeneity within the context of the Kuramoto model. In a previous paper [Phys. Rev.

Paths to synchronization on complex networks.

The understanding of emergent collective phenomena in natural and social systems has driven the interest of scientists from different disciplines during decades. Among these phenomena, the synchronization of a set of interacting individuals or units has been intensively studied because of its ubiquity in the natural world. In this Letter, we show how for fixed coupling strengths local patterns of synchronization emerge differently in homogeneous and heterogeneous complex networks, driving the process towards a certain global synchronization degree following different paths.

Dynamical organization of cooperation in complex topologies.

In this Letter, we study how cooperation is organized in complex topologies by analyzing the evolutionary (replicator) dynamics of the prisoner's dilemma, a two-player game with two available strategies, defection and cooperation, whose payoff matrix favors defection. We show that, asymptotically, the population is partitioned into three subsets: individuals that always cooperate (pure cooperators), always defect (pure defectors), and those that intermittently change their strategy. In fact, the size of the later set is the biggest for a wide range of the "stimulus to defect" parameter.