Navegando por Autor "Fulco, Umberto Laico"
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Artigo Current–voltage characteristics of double-strand DNA sequences(Elsevier, 2009-09-07) Moreira, Darlan Araújo; Bezerril, Leonardo Mafra; Albuquerque, Eudenilson Lins de; Fulco, Umberto Laico; Oliveira, E. L. de; Sousa, J. S. deWe use a tight-binding formulation to investigate the transmissivity and the current–voltage (I–V) characteristics of sequences of double-strand DNA molecules. In order to reveal the relevance of the underlying correlations in the nucleotides distribution, we compare the results for the genomic DNA sequence with those of artificial sequences (the long-range correlated Fibonacci and Rudin–Shapiro one) and a random sequence, which is a kind of prototype of a short-range correlated system. The random sequence is presented here with the same first neighbors pair correlations of the human DNA sequence. We found that the long-range character of the correlations is important to the transmissivity spectra, although the I–V curves seem to be mostly influenced by the short-range correlationsArtigo Electronic specific heat of an a3-helical polypeptide and its biochemical variants(Elsevier, 2012-07-23) Bezerril, Leonardo Mafra; Mendes, G. A.; Albuquerque, Eudenilson Lins de; Fulco, Umberto Laico; Caetano, E. W. S.; Freire, V. N.We perform a theoretical study of the temperature dependent electronic specific heat at constant volume CV ðTÞ for a fibrous a3-helical polypeptide, which has the amino acid sequence (Leu-Glu-Thr-Leu-Ala-Lys- Ala)3, considering only its primary structure. We focus also on two different variants of the a3-helical polypeptide, namely those with (5Qa3 variant, mutation Ala5Gln) and without (7Qa3 variant, mutation Ala7Gln) fibrous assemblies. The energy spectra are calculated using a two-dimensional Schrödinger equation within a tight-binding approximation in which the isolated amino acid vertical ionization energy and the hopping terms are found using density functional theory computationsArtigo Molecular modelling and quantum biochemistry computations of a naturally occurring bioremediation enzyme: Alkane hydroxylase from Pseudomonas putida P1(Elsevier, 2017-10) Sousa, Bruno Gomes de; Oliveira, Jonas Ivan Nobre; Albuquerque, Eudenilson Lins de; Fulco, Umberto Laico; Amaro, Venerando Eustáquio; Blaha, Carlos Alfredo GalindoMany species of bacteria involved in degradation of n-alkanes have an important constitutional metabolic enzyme, the alkane hydroxylase called AlkB, specialized in the conversion of hydrocarbons molecules that can be used as carbon and/or energy source. This enzyme plays an important role in the microbial degradation of oil, chlorinated hydrocarbons, fuel additives, and many other compounds. A number of these enzymes has been biochemically characterized in detail because the potential of alkane hydroxylases to catalyse high added-value reactions is widely recognized. Nevertheless, the industrial and process bioremediation application of them is restricted, owing to their complex biochemistry, challenging process requirements, and the limited number of their three-dimensional structures. Furthermore, AlkB has great potential as biocatalysts for selective transformation of a wide range of chemically inert unreactive alkanes into reactive chemical precursors that can be used as tools for bioremediation and bioprocesses. Aiming to understand the possible ways the AlkB enzyme Pseudomonas putida P1 interacts with octane, octanol and 1-octyne, we consider its suitable biochemical structure taking into account a 3-D homology modelling. Besides, by using a quantum chemistry computational model based on the density functional theory (DFT), we determine possible protein-substrate interaction regions measured by means of its binding energy simulated throughout the Molecular Fractionation with Conjugated Caps (MFCC) approachArtigo Photonic band gap spectra in Octonacci metamaterial quasicrystals(Elsevier, 2017) Brandão, E. R.; Vasconcelos, Manoel Silva de; Albuquerque, Eudenilson Lins de; Fulco, Umberto LaicoIn this work we study theoretically the photonic band gap spectra for a one-dimensional quasicrystal made up of SiO2 (layer A) and a metamaterial (layer B) organized following the Octonacci sequence, where its nth-stage Sn is given by the inflation rule Sn ¼ Sn1Sn2Sn1 for n 3, with initial conditions S1 ¼ A and S2 ¼ B. The metamaterial is characterized by a frequency dependent electric permittivity εðuÞ and magnetic permeability mðuÞ. The polariton dispersion relation is obtained analytically by employing a theoretical calculation based on a transfer-matrix approach. A quantitative analysis of the spectra is then discussed, stressing the distribution of the allowed photonic band widths for high generations of the Octonacci structure, which depict a self-similar scaling property behavior, with a power law depending on the common in-plane wavevector kxArtigo A quantum chemistry investigation of a potential inhibitory drug against the dengue virus(Royal Society of Chemistry, 2016) Ourique, G. S.; Vianna, Jéssica de Fátima; Lima Neto, José Xavier de; Oliveira, J. I. N.; Mauriz, Paulo Wilson; Vasconcelos, Manoel Silva de; Caetano, E. W. S.; Freire, V. N.; Albuquerque, Eudenilson Lins de; Fulco, Umberto LaicoWe present an in silico study of the interaction energy between NS2B–NS3, a serine protease of the dengue virus (DENV), and the inhibitor benzoyl-norleucine-Lys-Arg-Arg-aldehyde (Bz-nKRR-H), a crucial step in the design and development of dengue's antiviral drugs, using quantum chemistry calculations based on the density functional theory (DFT) at the generalized gradient approximation (GGA). The interaction energies between the inhibitor Bz-nKRR-H and each amino acid belonging to the binding site was calculated through the molecular fragmentation with conjugate caps (MFCC) approach employing a dispersion corrected exchange-correlation functional. Besides the interaction energy, we also calculated the distances, types of molecular interactions, and the atomic groups involved in the process. Our results show that the interaction energy of the system reached convergence at 15.0 Å, with the central residues identified in this interaction radius, as well as their attraction/repulsion energies, all of them being important inputs to improve the effectiveness of antiviral drugs to avoid the dissemination of the dengue virusArtigo The DNA electronic specific heat at low temperature: the role of aperiodicity(Elsevier, 2012) Sarmento, R.G.; Mendes, G.A.; Albuquerque, Eudenilson Lins de; Fulco, Umberto Laico; Vasconcelos, Manoel Silva de; Ujsághy, O.; Freire, V.N.; Caetano, E.W.S.The electronic specific heat spectra at constant volume (CV ) of a long-range correlated extended ladder model, mimicking a DNA molecule, is theoretically analyzed for a stacked array of a double-stranded structure made up from the nucleotides guanine G, adenine A, cytosine C and thymine T . The role of the aperiodicity on CV is discussed, considering two different nucleotide arrangements with increasing disorder, namely the Fibonacci and the Rudin–Shapiro quasiperiodic structures. Comparisons are made for different values of the band fillings, considering also a finite segment of natural DNA, as part of the human chromosome Ch22.