Modelagem molecular na caracterização eletrônica de oligopeptídeos e na descrição quântica da interação fármaco-receptor

In this dissertation, the theoretical principles governing the molecular modeling were applied for electronic characterization of oligopeptide α3 and its variants (5Q, 7Q)-α3, as well as in the quantum description of the interaction of the aminoglycoside hygromycin B and the 30S subunit of bacterial ribosome. In the first study, the linear and neutral dipeptides which make up the mentioned oligopeptides were modeled and then optimized for a structure of lower potential energy and appropriate dihedral angles. In this case, three subsequent geometric optimization processes, based on classical Newtonian theory, the semi-empirical and density functional theory (DFT), explore the energy landscape of each dipeptide during the search of ideal minimum energy structures. Finally, great conformers were described about its electrostatic potential, ionization energy (amino acids), and frontier molecular orbitals and hopping term. From the hopping terms described in this study, it was possible in subsequent studies to characterize the charge transport propertie of these peptides models. It envisioned a new biosensor technology capable of diagnosing amyloid diseases, related to an accumulation of misshapen proteins, based on the conductivity displayed by proteins of the patient. In a second step of this dissertation, a study carried out by quantum molecular modeling of the interaction energy of an antibiotic ribosomal aminoglicosídico on your receiver. It is known that the hygromycin B (hygB) is an aminoglycoside antibiotic that affects ribosomal translocation by direct interaction with the small subunit of the bacterial ribosome (30S), specifically with nucleotides in helix 44 of the 16S ribosomal RNA (16S rRNA). Due to strong electrostatic character of this connection, it was proposed an energetic investigation of the binding mechanism of this complex using different values of dielectric constants (ε = 0, 4, 10, 20 and 40), which have been widely used to study the electrostatic properties of biomolecules. For this, increasing radii centered on the hygB centroid were measured from the 30S-hygB crystal structure (1HNZ.pdb), and only the individual interaction energy of each enclosed nucleotide was determined for quantum calculations using molecular fractionation with conjugate caps (MFCC) strategy. It was noticed that the dielectric constants underestimated the energies of individual interactions, allowing the convergence state is achieved quickly. But only for ε = 40, the total binding energy of drug-receptor interaction is stabilized at r = 18A, which provided an appropriate binding pocket because it encompassed the main residues that interact more strongly with the hygB - C1403, C1404, G1405, A1493, G1494, U1495, U1498 and C1496. Thus, the dielectric constant ≈ 40 is ideal for the treatment of systems with many electrical charges. By comparing the individual binding energies of 16S rRNA nucleotides with the experimental tests that determine the minimum inhibitory concentration (MIC) of hygB, it is believed that those residues with high binding values generated bacterial resistance to the drug when mutated. With the same reasoning, since those with low interaction energy do not influence effectively the affinity of the hygB in its binding site, there is no loss of effectiveness if they were replaced.

Desenvolvimento de uma ferramenta computacional para aplicação em métodos de elevação por bombeio centrífugo submerso

The Electrical Submersible Pump (ESP) has been one of the most appropriate solutions for lifting method in onshore and offshore applications. The typical features for this application are adverse temperature, viscosity fluids and gas environments. The difficulties in equipments maintenance and setup contributing to increasing costs of oil production in deep water, therefore, the optimization through automation can be a excellent approach for decrease costs and failures in subsurface equipment. This work describe a computer simulation related with the artificial lifting method ESP. This tool support the dynamic behavior of ESP approach, considering the source and electric energy transmission model for the motor, the electric motor model (including the thermal calculation), flow tubbing simulation, centrifugal pump behavior simulation with liquid nature effects and reservoir requirements. In addition, there are tri-dimensional animation for each ESP subsytem (transformer, motor, pump, seal, gas separator, command unit). This computer simulation propose a improvement for monitoring oil wells for maximization of well production. Currenty, the proprietaries simulators are based on specific equipments manufactures. Therefore, it is not possible simulation equipments of another manufactures. In the propose approach there are support for diverse kinds of manufactures equipments

Análise da formulação em Monte Carlo dos pacotes de energia multiespectrais aplicada a meios constituídos por vapor d'água

The Monte Carlo method is accurate and is relatively simple to implement for the solution of problems involving complex geometries and anisotropic scattering of radiation as compared with other numerical techniques. In addition, differently of what happens for most of numerical techniques, for which the associated simulations computational time tends to increase exponentially with the complexity of the problems, in the Monte Carlo the increase of the computational time tends to be linear. Nevertheless, the Monte Carlo solution is highly computer time consuming for most of the interest problems. The Multispectral Energy Bundle model allows the reduction of the computational time associated to the Monte Carlo solution. The referred model is here analyzed for applications in media constituted for nonparticipating species and water vapor, which is an important emitting species formed during the combustion of hydrocarbon fuels. Aspects related to computer time optimization are investigated the model solutions are compared with benchmark line-by-line solutions