Vortex-Antivortex annihilation dynamics in a square mesoscopic superconducting cylinder

The dynamics of the annihilation of a vortex-antivortex pair is investigated. The pair is activated magnetically during the run of a simulated hysteresis loop on a square mesoscopic superconducting cylinder with an antidot inserted at its center. We study the nucleation of vortices and antivortices by first increasing the magnetic field, applied parallel to the axis of the sample, from zero until the first vortex is created. A further increase of the field pulls the vortex in, until it reaches the antidot. As the polarity of the field is reversed, an antivortex enters the scene, travels toward the center of the sample and eventually the pair is annihilated. Depending on the sample size, its temperature, and Ginzburg-Landau parameter, the vortex-antivortex encounter takes place at the antidot or at the superconducting sea around it. The position and velocity of the vortex and antivortex singularities were evaluated as a function of time. The current density, magnetization and order parameter topology were also calculated.Comment: One REVTeX file and 5 EPS figure

SPATIAL AND TEMPORALVARIATION OF DISSOLVED INORGANIC NUTRIENTS, AND CHLOROPHYLL-α IN A TROPICAL ESTUARY IN NORTHEASTERN BRAZIL: DYNAMICS OF NUTRIENT REMOVAL

Monthly sampling campaigns were carried out between February 2010 and January 2011 to evaluate the spatial and temporal distribution of nutrients (ammonium, nitrite, nitrate, dissolved organic nitrogen, phosphate, dissolved organic phosphorus and silicate) and chlorophyll-α along a salinity gradient in the tropical Cachoeira River estuary, subject to the untreated effluents of a sewage treatment plant (STP). During the study period the lowest and highest river discharge occurred in February and April 2010, respectively. High river outflow promoted increased concentrations of inorganic nitrogen and silicate but did not affect the concentration of phosphate. Based on the chlorophyll-α concentration the estuary may be classified as eutrophic / hypereutrophic in its inner portion and mesotrophic in the lower region. The inner portion is more affected by the nutrient load carried out by the river and STP, while dilution by seawater contributed to the reduction of the nutrient concentrations in the lower reaches of the estuary. The results indicate that nutrient uptake by the phytoplankton is the most effective dissolved inorganic nutrient removal processes, especially for phosphate. Mixing diagrams suggest that the coupling of nitrification and denitrification processes is also responsible for the elimination of nitrogen from this ecosystem.Campanhas de amostragens mensais foram realizadas entre fevereiro de 2010 e janeiro de 2011 para avaliar a distribuição espacial e temporal de nutrientes (amônia, nitrito, nitrato, nitrogênio orgânico dissolvido, fosfato, fósforo orgânico dissolvido e silicato) e clorofila-α, ao longo do gradiente de salinidade no estuário tropical do Rio Cachoeira. Este estuário é sujeito aos efluentes de esgotos não tratados de uma estação de tratamento de esgoto (ETE). No período estudado a maior e menor vazão do rio ocorreram em fevereiro e abril de 2010, respectivamente. A alta vazão do rio promoveu aumento das concentrações de nitrogênio inorgânico e silicato, mas não afetou as concentrações de fosfato. Baseado nas concentrações de clorofila-α, o estuário pode ser classificado como eutrófico/hipereutrófico na porção interna e mesotrófico na região externa. A porção interna é mais afetada pela carga de nutrientes do rio e da ETE, enquanto a diluição pela água marinha contribuiu para diminuir as concentrações de nutrientes na porção externa. Os resultados indicam que a absorção de nutrientes pelo fitoplâncton é o processo mais eficiente na remoção desses nutrientes, especialmente do fosfato. No entanto, os diagramas de mistura sugerem que a nitrificação e denitrificação acopladas no rio também são responsáveis pela eliminação do nitrogênio do ecossistema

(L, U): bounded priority queues and the codification of Rényi k-Trees

We introduce in this paper a data structure named (L, U)- bounded priority queue, which particularizes priority queues in two aspects: the priorities associated to the elements must be integer numbers constrained to a predefined interval and, in a sequence of operations, no more than one Insert can immediatly follow a DeleteMin. This data structure is used in the development of efficient algorithms for coding and decoding Rényi k-trees

Loss compensation in microring-based Si photonics devices via Er3+doped claddings

FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOWe propose and demonstrate a method to compensate insertion losses in Si photonics devices based on ring resonators fabricated in SOI foundries, with no additional chip area used. It consists in the employment of Er:Al2O3 as the upper cladding layer on standard Si/SiO2 rings, requiring only one simple post-processing step. The method is modeled in detail, and simulation results for single-ring configurations and photonic molecules are discussed, where the potential for loss reduction is predicted for different design choices based on the quality factor. We experimentally verify the viability of the method, obtaining an output power increase of 1 dB when a single-ring resonator is pumped. This value is increased when the method is applied to devices based on photonic molecules, where a value of 2.6 dB has been measured. This is equivalent to a loss reduction potential higher than 3 dB for a photonic molecule designed to achieve a quality factor of 50000.104113FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO08/57857-22014/04748-2574017/2008-

An Allosteric Pathway in Copper, Zinc Superoxide Dismutase Unravels the Molecular Mechanism of the G93A Amyotrophic Lateral Sclerosis-Linked Mutation

Several different mutations of the protein copper, zinc superoxide dismutase (SOD1) produce the neurodegenerative disorder amyotrophic lateral sclerosis (ALS). The molecular mechanism by which the diverse mutations converge to a similar pathology is currently unknown. The electrostatic loop (EL) of SOD1 is known to be affected in all of the studied ALS-linked mutations of SOD1. In this work, we employ a multiscale simulation approach to show that this perturbation corresponds to an increased probability of the EL detaching from its native position, exposing the metal site of the protein to water. From extensive atomistic and coarse-grained molecular dynamics (MD) simulations, we identify an allosteric pathway that explains the action of the distant G93A mutation on the EL. Finally, we employ quantum mechanics/molecular mechanics MD simulations to show that the opening of the EL decreases the Zn(II) affinity of the protein. As the loss of Zn(II) is at the center of several proposed pathogenic mechanisms in SOD1-linked ALS, the structural effect identified here not only is in agreement with the experimental data but also places the opening of the electrostatic loop as the possible main pathogenic effect for a significant number of ALS-linked SOD1 mutations

Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations

Molecular docking is central to rational drug design. Current docking techniques suffer, however, from limitations in protein flexibility and solvation models and by the use of simplified scoring functions. All-atom molecular dynamics simulations, on the other hand, feature a realistic representation of protein flexibility and solvent, but require knowledge of the binding site. Recently we showed that coarse-grained molecular dynamics simulations, based on the most recent version of the Martini force field, can be used to predict protein/ligand binding sites and pathways, without requiring any a priori information, and offer a level of accuracy approaching all-atom simulations. Given the excellent computational efficiency of Martini, this opens the way to high-throughput drug screening based on dynamic docking pipelines. In this opinion article, we sketch the roadmap to achieve this goal

Polyply:A python suite for facilitating simulations of macromolecules and nanomaterials

Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is a major bottleneck, especially for high throughput protocols and for complex multi-component systems. To eliminate this bottleneck, we present the polyply software suite that provides 1) a multi-scale graph matching algorithm designed to generate parameters quickly and for arbitrarily complex polymeric topologies, and 2) a generic multi-scale random walk protocol capable of setting up complex systems efficiently and independent of the target force-field or model resolution. We benchmark quality and performance of the approach by creating realistic coordinates for polymer melt simulations, single-stranded as well as circular single-stranded DNA. We further demonstrate the power of our approach by setting up a microphase-separated block copolymer system, and by generating a liquid-liquid phase separated system inside a lipid vesicle

An alternative conformation of ERβ bound to estradiol reveals H12 in a stable antagonist position

FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOThe natural ligand 17β-estradiol (E2) is so far believed to induce a unique agonist-bound active conformation in the ligand binding domain (LBD) of the estrogen receptors (ERs). Both subtypes, ERα and ERβ, are transcriptionally activated in the presence o7FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO2014/22007-02013/08293-72012/24750-6301981/2011-6This work was supported by the São Paulo Research Foundation FAPESP (grants 2014/22007-0, 2013/08293-7, 2012/24750-6) and by CNPq (grant 301981/2011-6

A new and concise strategy to the enantioselective synthesis of (S)-2-amino-4-oxo-4-(pyridine-2-yl) butanoic acid from aspartic acid

The a-amino acid (S)-5 was synthesized using in the key step a chemoselective nucleophilic substitution between a diester derived from L-aspartic acid and 2-lithium pyridine. The overall yield (13%, 5 steps) was similar to those previously described by our group for the R isomer (the first exogen full agonist of the NMDA receptors) from D-mannitol (12%, 10 steps) and by Lovey and Copper for the racemic synthesis (17%, 5 steps)

Revisiting RFID Mifare Classic security in the context of investigations that account millionaire losses a case study based on the ticketing system implemented in Brazil/ Revisitando a segurança do RFID Mifare Classic no contexto de investigações que contabilizam perdas milionárias um estudo de caso baseado no sistema de bilhética implementado no Brasil

Electronic systems in the infrastructure of public and private transport services are increasing. This growth comes from the various benefits for its implementation. In the capital of Brazil, the Federal District, as well as other federative entities, an electronic ticketing system based on smart cards was adopted. The card adopted in the capital belongs to the Mifare Classic series whose internal characteristics are widely known. Although several vulnerabilities are known, this card is still widely used in Brazil and worldwide. The focus of this study is on the security of this card as a credit storage medium within the ticketing system adopted locally. The most relevant and known vulnerabilities were enumerated. These vulnerabilities were confronted with the real possibility of building a cloned card. As an expected result, it was possible to build a cloned and accepted card within the system. Finally, significant storage areas were revealed: serial number location, registration number, credit total, credit batches and a 64 bits signature. This reinforces the need to withdraw Mifare Classic cards urgently