Electromagnetic form factor of the pion in the space- and time-like regions within the front-form dynamics

The pion electromagnetic form factor is calculated in the space- and time-like regions from -10 (GeV/c)2 up to 10 (GeV/c)2, within a front-form model. The dressed photon vertex where a photon decays in a quark-antiquark pair is depicted generalizing the vector meson dominance ansatz, by means of the vector meson vertex functions. An important feature of our model is the description of the on-mass-shell vertex functions in the valence sector, for the pion and the vector mesons, through the front-form wave functions obtained within a realistic quark model. The theoretical results show an excellent agreement with the data in the space-like region, while in the time-like region the description is quite encouraging. © 2003 Elsevier B.V. All rights reserved.

Cooperative RNA Polymerase Molecules Behavior on a Stochastic Sequence-Dependent Model for Transcription Elongation

The transcription process is crucial to life and the enzyme RNA polymerase (RNAP) is the major component of the transcription machinery. The development of single-molecule techniques, such as magnetic and optical tweezers, atomic-force microscopy and single-molecule fluorescence, increased our understanding of the transcription process and complements traditional biochemical studies. Based on these studies, theoretical models have been proposed to explain and predict the kinetics of the RNAP during the polymerization, highlighting the results achieved by models based on the thermodynamic stability of the transcription elongation complex. However, experiments showed that if more than one RNAP initiates from the same promoter, the transcription behavior slightly changes and new phenomenona are observed. We proposed and implemented a theoretical model that considers collisions between RNAPs and predicts their cooperative behavior during multi-round transcription generalizing the Bai et al. stochastic sequence-dependent model. In our approach, collisions between elongating enzymes modify their transcription rate values. We performed the simulations in Mathematica® and compared the results of the single and the multiple-molecule transcription with experimental results and other theoretical models. Our multi-round approach can recover several expected behaviors, showing that the transcription process for the studied sequences can be accelerated up to 48% when collisions are allowed: the dwell times on pause sites are reduced as well as the distance that the RNAPs backtracked from backtracking sites. © 2013 Costa et al.

Modelling polymers with side chains: MEH-PPV and P3HT

Modelling polymers with side chains is always a challenge once the degrees of freedom are very high. In this study, we present a successful methodology to model poly[2-methoxy-5-(2′-ethyl-hexyloxy)-p-phenylenevinylene] (MEH-PPV) and poly[3-hexylthiophene] (P3HT) in solutions, taking into account the influence of side chains on the polymer conformation. Molecular dynamics and semi-empirical quantum mechanical methods were used for structure optimisation and evaluation of optical properties. The methodology allows to describe structural and optical characteristics of the polymers in a satisfactory way, as well as to evaluate some usual simplifications adopted for modelling these systems. Effective conjugation lengths of 8-14.6 and 21 monomers were obtained for MEH-PPV and P3HT, respectively, in accordance with experimental findings. In addition, anti/syn conformations of these polymers could be predicted based on intrinsic interactions of the lateral branches. © 2013 Copyright Taylor and Francis Group, LLC.

Dynamics of DNA Methylation during Early Development of the Preimplantation Bovine Embryo

There is species divergence in control of DNA methylation during preimplantation development. The exact pattern of methylation in the bovine embryo has not been established nor has its regulation by gender or maternal signals that regulate development such as colony stimulating factor 2 (CSF2). Using immunofluorescent labeling with anti-5-methylcytosine and embryos produced with X-chromosome sorted sperm, it was demonstrated that methylation decreased from the 2-cell stage to the 6-8 cell stage and then increased thereafter up to the blastocyst stage. In a second experiment, embryos of specific genders were produced by fertilization with X- or Y-sorted sperm. The developmental pattern was similar to the first experiment, but there was stage × gender interaction. Methylation was greater for females at the 8-cell stage but greater for males at the blastocyst stage. Treatment with CSF2 had no effect on labeling for DNA methylation in blastocysts. Methylation was lower for inner cell mass cells (i.e., cells that did not label with anti-CDX2) than for trophectoderm (CDX2-positive). The possible role for DNMT3B in developmental changes in methylation was evaluated by determining gene expression and degree of methylation. Steady-state mRNA for DNMT3B decreased from the 2-cell stage to a nadir for D 5 embryos >16 cells and then increased at the blastocyst stage. High resolution melting analysis was used to assess methylation of a CpG rich region in an intronic region of DNMT3B. Methylation percent decreased between the 6-8 cell and the blastocyst stage but there was no difference in methylation between ICM and TE. Results indicate that DNA methylation undergoes dynamic changes during the preimplantation period in a manner that is dependent upon gender and cell lineage. Developmental changes in expression of DNMT3B are indicative of a possible role in changes in methylation. Moreover, DNMT3B itself appears to be under epigenetic control by methylation. © 2013 Dobbs et al.

Estruturação do Eumenine Mastroparano por dinâmica molecular em misturas de TFE-água

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Simulações por dinâmica molecular fine-e coarse-grained das interações intermoleculares entre peptídeos antimicrobianos da família Mastoparano e membranas modelo

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

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.

Aspergillus niger beta-Glucosidase Has a Cellulase-like Tadpole Molecular Shape INSIGHTS INTO GLYCOSIDE HYDROLASE FAMILY 3 (GH3) beta-GLUCOSIDASE STRUCTURE AND FUNCTION

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

Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Combining Experimental Evidence and Molecular Dynamic Simulations To Understand the Mechanism of Action of the Antimicrobial Octapeptide Jelleine-I

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

Mechanical properties and fracture dynamics of silicene membranes

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Prospecção de novos peptídeos com ação leishmanicida por dinâmica molecular

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estudo das interações de peptídeos antimicrobianos e sistemas miméticos de membrana por dinâmica molecular

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Interaction of cyclic and linear labaditin peptides with anionic and zwitterionic micelles

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