Developing descriptors to predict mechanical properties of nanotubes

Descriptors and quantitative structure property relationships (QSPR) were investigated for mechanical property prediction of carbon nanotubes (CNTs). 78 molecular dynamics (MD) simulations were carried out, and 20 descriptors were calculated to build quantitative structure property relationships (QSPRs) for Young's modulus and Poisson's ratio in two separate analyses: vacancy only and vacancy plus methyl functionalization. In the first analysis, C N2/CT (number of non-sp2 hybridized carbons per the total carbons) and chiral angle were identified as critical descriptors for both Young's modulus and Poisson's ratio. Further analysis and literature findings indicate the effect of chiral angle is negligible at larger CNT radii for both properties. Raman spectroscopy can be used to measure CN2/C T, providing a direct link between experimental and computational results. Poisson's ratio approaches two different limiting values as CNT radii increases: 0.23-0.25 for chiral and armchair CNTs and 0.10 for zigzag CNTs (surface defects <3%). In the second analysis, the critical descriptors were CN2/CT, chiral angle, and MN/CT (number of methyl groups per total carbons). These results imply new types of defects can be represented as a new descriptor in QSPR models. Finally, results are qualified and quantified against experimental data. © 2013 American Chemical Society.

Intermolecular interactions of the malate synthase of Paracoccidioides spp

Background: The fungus Paracoccidioides spp is the agent of paracoccidioidomycosis (PCM), a pulmonary mycosis acquired by the inhalation of fungal propagules. Paracoccidioides malate synthase (PbMLS) is important in the infectious process of Paracoccidioides spp because the transcript is up-regulated during the transition from mycelium to yeast and in yeast cells during phagocytosis by murine macrophages. In addition, PbMLS acts as an adhesin in Paracoccidioides spp. The evidence for the multifunctionality of PbMLS indicates that it could interact with other proteins from the fungus and host. The objective of this study was to identify and analyze proteins that possibly bind to PbMLS (PbMLS-interacting proteins) because protein interactions are intrinsic to cell processes, and it might be possible to infer the function of a protein through the identification of its ligands. Results: The search for interactions was performed using an in vivo assay with a two-hybrid library constructed in S. cerevisiae; the transcripts were sequenced and identified. In addition, an in vitro assay using pull-down GST methodology with different protein extracts (yeast, mycelium, yeast-secreted proteins and macrophage) was performed, and the resulting interactions were identified by mass spectrometry (MS). Some of the protein interactions were confirmed by Far-Western blotting using specific antibodies, and the interaction of PbMLS with macrophages was validated by indirect immunofluorescence and confocal microscopy. In silico analysis using molecular modeling, dynamics and docking identified the amino acids that were involved in the interactions between PbMLS and PbMLS-interacting proteins. Finally, the interactions were visualized graphically using Osprey software. Conclusion: These observations indicate that PbMLS interacts with proteins that are in different functional categories, such as cellular transport, protein biosynthesis, modification and degradation of proteins and signal transduction. These data suggest that PbMLS could play different roles in the fungal cell. © 2013 de Oliveira et al.; licensee BioMed Central Ltd.

Fetal-Maternal Interactions in the Synepitheliochorial Placenta Using the eGFP Cloned Cattle Model

Background: To investigate mechanisms of fetal-maternal cell interactions in the bovine placenta, we developed a model of transgenic enhanced Green Fluorescent Protein (t-eGFP) expressing bovine embryos produced by nuclear transfer (NT) to assess the distribution of fetal-derived products in the bovine placenta. In addition, we searched for male specific DNA in the blood of females carrying in vitro produced male embryos. Our hypothesis is that the bovine placenta is more permeable to fetal-derived products than described elsewhere. Methodology/Principal Findings: Samples of placentomes, chorion, endometrium, maternal peripheral blood leukocytes and blood plasma were collected during early gestation and processed for nested-PCR for eGFP and testis-specific Y-encoded protein (TSPY), western blotting and immunohistochemistry for eGFP detection, as well as transmission electron microscopy to verify the level of interaction between maternal and fetal cells. TSPY and eGFP DNA were present in the blood of cows carrying male pregnancies at day 60 of pregnancy. Protein and mRNA of eGFP were observed in the trophoblast and uterine tissues. In the placentomes, the protein expression was weak in the syncytial regions, but intense in neighboring cells on both sides of the fetal-maternal interface. Ultrastructurally, our samples from t-eGFP expressing NT pregnancies showed to be normal, such as the presence of interdigitating structures between fetal and maternal cells. In addition, channels-like structures were present in the trophoblast cells. Conclusions/Significance: Data suggested that there is a delivery of fetal contents to the maternal system on both systemic and local levels that involved nuclear acids and proteins. It not clear the mechanisms involved in the transfer of fetal-derived molecules to the maternal system. This delivery may occur through nonclassical protein secretion; throughout transtrophoblastic-like channels and/or by apoptotic processes previously described. In conclusion, the bovine synepitheliochorial placenta displays an intimate fetal-maternal interaction, similar to other placental types for instance human and mouse. © 2013 Pereira et al.

The effects of pinning on critical currents of superconducting films

Using molecular dynamics simulations, we analyze the effects of artificial periodic arrays of pinning sites on the critical current of superconducting thin films as a function of vortex density. We analyze two types of periodic pinning array: hexagonal and Kagomé. For the Kagome pinning network we make calculations using two directions of transport current: along and perpendicular to the main axis of the lattice. Our results show that the hexagonal pinning array presents higher critical currents than the Kagomé and random pinning configuration for all vortex densities. In addition, the Kagomé networks show anisotropy in their transport properties. © 2012 Springer Science+Business Media, LLC.

Critical currents and melting temperature of a two-dimensional vortex lattice with periodic pinning

The critical current and melting temperature of a vortex system are analyzed. Calculations are made for a two-dimensional film at finite temperature with two kinds of periodic pinning: hexagonal and Kagomé. A transport current parallel and perpendicular to the main axis of the pinning arrays is applied and molecular dynamics simulations are used to calculate the vortex velocities to obtain the critical currents. The structure factor and displacements of vortices at zero transport current are used to obtain the melting temperature for both pinning arrays. The critical currents are higher for the hexagonal pinning lattice and anisotropic for both pinning arrays. This anisotropy is stronger with temperature for the hexagonal array. For the Kagomé pinning lattice, our analysis shows a multi stage phase melting; that is, as we increase the temperature, each different dynamic phase melts before reaching the melting temperature. Both the melting temperature and critical currents are larger for the hexagonal lattice, indicating the role for the interstitial vortices in decreasing the pinning strength. © 2012 Springer Science+Business Media New York.

Analyzing the effect of homogeneous frustration in protein folding

The energy landscape theory has been an invaluable theoretical framework in the understanding of biological processes such as protein folding, oligomerization, and functional transitions. According to the theory, the energy landscape of protein folding is funneled toward the native state, a conformational state that is consistent with the principle of minimal frustration. It has been accepted that real proteins are selected through natural evolution, satisfying the minimum frustration criterion. However, there is evidence that a low degree of frustration accelerates folding. We examined the interplay between topological and energetic protein frustration. We employed a Cα structure-based model for simulations with a controlled nonspecific energetic frustration added to the potential energy function. Thermodynamics and kinetics of a group of 19 proteins are completely characterized as a function of increasing level of energetic frustration. We observed two well-separated groups of proteins: one group where a little frustration enhances folding rates to an optimal value and another where any energetic frustration slows down folding. Protein energetic frustration regimes and their mechanisms are explained by the role of non-native contact interactions in different folding scenarios. These findings strongly correlate with the protein free-energy folding barrier and the absolute contact order parameters. These computational results are corroborated by principal component analysis and partial least square techniques. One simple theoretical model is proposed as a useful tool for experimentalists to predict the limits of improvements in real proteins. © 2013 Wiley Periodicals, Inc.

Análise vibracional do α-tocoferol

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Estudo do efeito da adição de frustração no enovelamento de proteínas utilizando modelos baseados em estruturas

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Análise conformacional dos petídeos protonectina e protonectina (1-6), isolados e em associação, em mistura TFE-água

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Regimes de frustração ótima em enovelamento de proteínas com modelos baseado em estrutura

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Efeitos do pinning nos regimes dinâmicos de vórtices em supercondutores do tipo II

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estudos conformocionais de diversas proteínas em solução utilizando a técnica de espalhamento de raios-X à baixo ângulo-saxs

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Estrutura e função de mastoparanos dos venenos de vespas

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estudo de nanofios de Au e dendrímeros

A primeira parte deste trabalho aborda a simulação computacional de dinâmica molecular clássica da interação de sistemas matriciais constituídos de nanofios paralelos de Au simuladas em função do tempo. Como resultados foram encontrados os tempos de colisões entre os fios da matriz. A segunda parte deste trabalho utiliza dinâmica molecular clássica para simular cinco gerações de dendrímeros PAMAM, cada qual interagindo individualmente com um nanotubo de carbono em função do tempo resultando num motor molecular. Além disso, foram calculados os espectros de absorção deste sistema e foi verificado que eles são nanomotores controlados pela luz. Para todos estes sistemas foram calculadas energias cinética, potencial, total, velocidade, propriedades termodinâmicas como variação de entropia molar, capacidade molar térmica e temperatura in situ. Estas grandezas nos forneceram valiosas informações sobre o comportamento destes sistemas.

Simulação computacional da adsorção dos poluentes benzeno, tolueno e p-xileno sobre carvão ativado

Os maiores problemas de contaminação de aquíferos e solos são atribuídos aos hidrocarbonetos monoaromáticos, que são os constituintes mais solúveis e mais móveis da fração de algumas substâncias, como por exemplo, da gasolina. Para a remoção destes contaminantes, a adsorção por carvão ativado é o método mais utilizado, pois o carvão apresenta uma habilidade significativa para adsorver componentes orgânicos de baixo peso molecular, como o benzeno, o tolueno e o p-xileno. Neste trabalho, verificou-se a adsorção dos mesmos sobre carvão ativado via simulação computacional. Como base, utilizou-se o modelo postulado de carvão preparado por Bourke et al. (2007). Várias etapas foram concluídas desde os modelos das estruturas do carvão e dos poluentes até as simulações de dinâmica molecular. Para a análise conformacional da estrutura do carvão, foi utilizado o método semi-empírico PM3 e para o processo de dinâmica, o campo de força AMBER FF99SB. A estrutura passou por um aquecimento, à pressão constante, até alcançar uma temperatura final de 298K (25ºC), sendo suas informações coletadas a cada 50ps. Posteriormente, a estrutura foi submetida a equilíbrio de sistema, à temperatura constante de 298K (25ºC), por 500ps para então suas informações serem analisadas. Por fim, o sistema foi então submetido à dinâmica molecular durante 15 ns. Após análise dos resultados, constatou-se que os grupos éter, lactona e carbonila (cetona) presentes na estrutura de carvão ativado conferem caráter ácido à mesma e devido a isto e à sua consequente carga superficial negativa, a adsorção tornou-se viável uma vez que os poluentes apresentavam carga superficial positiva, o que corrobora o entendimento que já se tem a respeito desse tipo de fenômeno.