Osvaldo N. Oliveira

Analyzing and modeling real-world phenomena with complex networks: a survey of applications

The success of new scientific areas can be assessed by their potential in contributing to new theoretical approaches and in applications to real-world problems. Complex networks have fared extremely well in both of these aspects, with their sound theoretical basis being developed over the years and with a variety of applications. In this survey, we analyze the applications of complex networks to real-world problems and data, with emphasis in representation, analysis and modeling. A diversity of phenomena are surveyed, which may be classified into no less than 11 areas, providing a clear indication of the impact of the field of complex networks.

Recent advances in electronic tongues

This minireview describes the main developments of electronic tongues (e-tongues) and taste sensors in recent years, with a summary of the principles of detection and materials used in the sensing units. E-tongues are sensor arrays capable of distinguishing very similar liquids employing the concept of global selectivity, where the difference in the electrical response of different materials serves as a fingerprint for the analysed sample. They have been widely used for the analysis of wines, fruit juices, coffee, milk and beverages, in addition to the detection of trace amounts of impurities or pollutants in waters. Among the various principles of detection, electrochemical measurements and impedance spectroscopy are the most prominent. With regard to the materials for the sensing units, in most cases use is made of ultrathin films produced in a layer-by-layer fashion to yield higher sensitivity with the advantage of control of the film molecular architecture. The concept of e-tongues has been extended to biosensing by using sensing units capable of molecular recognition, as in films with immobilized antigens or enzymes with specific recognition for clinical diagnosis. Because the identification of samples is basically a classification task, there has been a trend to use artificial intelligence and information visualization methods to enhance the performance of e-tongues.

Immobilization of biomolecules on nanostructured films for biosensing

This paper brings an overview of the use of nanostructured films in several types of biosensors, with emphasis on the advantageous control of molecular architecture which is typical of the layer-by-layer (LbL) and Langmuir-Blodgett films. Following introductory sections on film fabrication and detection methods, we concentrate on the immobilization of biomolecules on these nanostructured films used in units for biosensing. Important contributions in the literature in biosensors based on electrochemical and optical measurements are highlighted. Furthermore, a discussion is presented on how the concept of electronic tongues has been extended to biosensing, which resulted in increased sensitivity and selectivity. The integration of sensing units with micro-electronics is commented upon, especially in the context of using field-effect transistors (FETs) for biosensing. Examples of LbL and LB films containing proteins, lipids, metallic nanoparticles and carbon nanotubes, which are used for detecting a variety of analytes, will be provided. The prospects for clinical diagnosis with such biosensors are also assessed. Throughout the review, emphasis is placed on the importance of control of molecular architecture, particularly with synergistic combination of organic and inorganic materials. For example, nanostructured films containing capped gold nanoparticles or carbon nanotubes exhibited enhanced performance in biosensing. It is hoped that this survey may assist researchers in choosing materials, molecular architectures, and detection principles, which may be tailored for specific applications.

Enzyme immobilization on Ag nanoparticles/polyaniline nanocomposites

We show a simple strategy to obtain an efficient enzymatic bioelectrochemical device, in which urease was immobilized on electroactive nanostructured membranes (ENMs) made with polyaniline and silver nanoparticles (AgNP) stabilized in polyvinyl alcohol (PAni/PVA-AgNP). Fabrication of the modified electrodes comprised the chemical deposition of polyaniline followed by drop-coating of PVA-AgNP and urease, resulting in a final ITO/PAni/PVA-AgNP/urease electrode configuration. For comparison, the electrochemical performance of ITO/PAni/urease electrodes (without Ag nanoparticles) was also studied. The performance of the modified electrodes toward urea hydrolysis was investigated via amperometric measurements, revealing a fast increase in cathodic current with a well-defined peak upon addition of urea to the electrolytic solution. The cathodic currents for the ITO/PAni/PVA-AgNP/urease electrodes were significantly higher than for the ITO/PAni/urease electrodes. The friendly environment provided by the ITO/PAni/PVA-AgNP electrode to the immobilized enzyme promoted efficient catalytic conversion of urea into ammonium and bicarbonate ions. Using the Michaelis-Menten kinetics equation, a K(M)(app) of 2.7 mmol L(-1) was obtained, indicating that the electrode architecture employed may be advantageous for fabrication of enzymatic devices with improved biocatalytic properties.

Immbolization of uricase enzyme in Langmuir and Langmuir-Blodgett films of fatty acids: possible use as a uric acid sensor.

Preserving the enzyme structure in solid films is key for producing various bioelectronic devices, including biosensors, which has normally been performed with nanostructured films that allow for control of molecular architectures. In this paper, we investigate the adsorption of uricase onto Langmuir monolayers of stearic acid (SA), and their transfer to solid supports as Langmuir-Blodgett (LB) films. Structuring of the enzyme in β-sheets was preserved in the form of 1-layer LB film, which was corroborated with a higher catalytic activity than for other uricase-containing LB film architectures where the β-sheets structuring was not preserved. The optimized architecture was also used to detect uric acid within a range covering typical concentrations in the human blood. The approach presented here not only allows for an optimized catalytic activity toward uric acid but also permits one to explain why some film architectures exhibit a superior performance.

Interaction of chitosan and mucin in a biomembrane model environment.

Chitosans have been widely exploited in biological applications, including drug delivery and tissue engineering, especially owing to their mucoadhesive properties, but the molecular-level mechanisms for the chitosan action are not known in detail. It is believed that chitosan could affect the mucus by interacting with the proteins mucins, in a process mediated by the cell membrane. In this study we used Langmuir monolayers of dimyristoylphosphatidic acid (DMPA) as simplified membrane models to investigate the interplay between the activity of mucins and chitosan. Surface pressure and surface potential measurements were performed with DMPA monolayers onto which chitosan and/or mucin was adsorbed. We found that the expanding effect from mucin was considerably reduced when chitosan was injected after mucin had been adsorbed on the DMPA monolayer. The results were consistent with the formation of complexes between mucin and chitosan, thus highlighting the importance of electrostatic interactions. Furthermore, chitosan could remove mucin that was co-deposited along with DMPA in Langmuir-Blodgett (LB) films, which could be ascribed to molecular-level interactions between chitosan and mucin inferred from the FTIR spectra of the LB films. In conclusion, the results with Langmuir and LB films suggest that electrostatic interactions are crucial for the mucoadhesive mechanism, which is affected by the complexation between chitosan and mucin.

Probing the interaction of oppositely charged gold nanoparticles with DPPG and DPPC Langmuir monolayers as cell membrane models

The growing use of nanoparticles in a variety of applications calls for detailed studies of their toxicology, which in turn require understanding the interactions between nanoparticles and living cells. Since simulating the interaction with real cell membranes is rather complex, Langmuir monolayers (LMs) have been used to mimic the first barrier encountered by a nanoparticle as it approaches a biological membrane to assess molecular-level interactions. In this study, we show how oppositely charged gold nanoparticles (Au-NPs) interact with monolayers of the zwitterionic dipalmitoylphosphatidyl choline (DPPC) and negatively charged dipalmitoylphosphatidyl glycerol (DPPG). The monolayers were spread on subphases containing two concentrations of either negatively charged Au-NPs coated with citrate anions or positively charged Au-NPs functionalized with the cationic polyelectrolyte poly(allylamine hydrochloride) (PAH). For DPPG, electrostatic effects dominated which depended strongly on the NPs capping agent, being obviously larger for the positive nanoparticles. The in-plane elasticity for DPPG monolayers within the surface pressure range corresponding to real cell membranes increased with adsorption of positively charged NPs, but decreased with the negative ones. For the zwitterionic DPPC, on the other hand, significant effects only occurred for negatively charged NPs, including a decrease in elasticity. Therefore, it is concluded that the nature, namely the charge of the capping agents, is crucial for the interaction of charged NPs with the cell membrane.

The interaction of an antiparasitic peptide active against African Sleeping Sickness with cell membrane models

Zwitterionic peptides with trypanocidal activity are promising lead compounds for the treatment of African Sleeping Sickness, and have motivated research into the design of compounds capable of disrupting the protozoan membrane. In this study, we use the Langmuir monolayer technique to investigate the surface properties of an antiparasitic peptide, namely S-(2,4-dinitrophenyl)glutathione di-2-propyl ester, and its interaction with a model membrane comprising a phospholipid monolayer. The drug formed stable Langmuir monolayers, whose main feature was a phase transition accompanied by a negative surface elasticity. This was attributed to aggregation upon compression due to intermolecular bond associations of the molecules, inferred from surface pressure and surface potential isotherms, Brewster angle microscopy (BAM) images, infrared spectroscopy and dynamic elasticity measurements. When co-spread with dipalmitoyl phosphatidyl choline (DPPC), the drug affected both the surface pressure and the monolayer morphology, even at high surface pressures and with low amounts of the drug. The results were interpreted by assuming a repulsive, cooperative interaction between the drug and DPPC molecules. Such repulsive interaction and the large changes in fluidity arising from drug aggregation may be related to the disruption of the membrane, which is key for the parasite killing property.

Correlations between structure and random walk dynamics in directed complex networks

In this letter the authors discuss the relationship between structure and random walk dynamics in directed complex networks, with an emphasis on identifying whether a topological hub is also a dynamical hub. They establish the necessary conditions for networks to be topologically and dynamically fully correlated (e.g., word adjacency and airport networks), and show that in this case Zipf’s law is a consequence of the match between structure and dynamics. They also show that real-world neuronal networks and the world wide web are not fully correlated, implying that their more intensely connected nodes are not necessarily highly active.

Using complex networks concepts to assess approaches for citations in scientific papers

The number of citations received by authors in scientific journals has become a major parameter to assess individual researchers and the journals themselves through the impact factor. A fair assessment therefore requires that the criteria for selecting references in a given manuscript should be unbiased with regard to the authors or journals cited. In this paper, we assess approaches for citations considering two recommendations for authors to follow while preparing a manuscript: (i) consider similarity of contents with the topics investigated, lest related work should be reproduced or ignored; (ii) perform a systematic search over the network of citations including seminal or very related papers. We use formalisms of complex networks for two datasets of papers from the arXiv and the Web of Science repositories to show that neither of these two criteria is fulfilled in practice. By representing the texts as complex networks we estimated a similarity index between pieces of texts and found that the list of references did not contain the most similar papers in the dataset. This was quantified by calculating a consistency index, whose maximum value is one if the references in a given paper are the most similar in the dataset. For the areas of “complex networks” and “graphenes”, the consistency index was only 0.11–0.23 and 0.10–0.25, respectively. To simulate a systematic search in the citation network, we employed a traditional random walk search (i.e. diffusion) and a random walk whose probabilities of transition are proportional to the number of the ingoing edges of the neighbours. The frequency of visits to the nodes (papers) in the network had a very small correlation with either the actual list of references in the papers or with the number of downloads from the arXiv repository. Therefore, apparently the authors and users of the repository did not follow the criterion related to a systematic search over the network of citations. Based on these results, we propose an approach that we believe is fairer for evaluating and complementing citations of a given author, effectively leading to a virtual scientometry.