Molecular Dynamics simulations of track formation at different ensembles

A series of Molecular Dynamics simulations of thermal spikes has been run in zircon. For two different ensembles: microcanonical one and a combination of microcanonical one acting on the simulation core with Langevin one on the side walls of simulation. Depending on the used ensemble, different track-formation threshold energies were found. When the combined ensemble is carried out, the total energy of the simulations varies with the temperature which can influence how annealing fission-track models should deal with the lattice recovery. A fission-track annealing model is tested with the simulation results. © 2012 Elsevier Ltd. 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.

Artificial neural network model of discharge lamps in the power quality context

This paper presents a methodology for modeling high intensity discharge lamps based on artificial neural networks. The methodology provides a model which is able to represent the device operating in the frequency of distribution systems, facing events related to power quality. With the aid of a data acquisition system to monitor the laboratory experiment, and using $$\text{ MATLAB }^{\textregistered }$$ software, data was obtained for the training of two neural networks. These neural networks, working together, were able to represent with high fidelity the behavior of a discharge lamp. The excellent performance obtained by these models allowed the simulation of a group of lamps in a distribution system with shorter simulation time when compared to mathematical models. This fact justified the application of this family of loads in electric power systems. The representation of the device facing power quality disturbances also proved to be a useful tool for more complex studies in distribution systems. © 2013 Brazilian Society for Automatics - SBA.

Regular and switching platform: Bone stress analysis with varying implant diameter

The aim of this study was to evaluate stress distribution of the peri-implant bone by simulating the biomechanical influence of implants with different diameters of regular or platform switched connections by means of 3-dimensional finite element analysis. Five mathematical models of an implant-supported central incisor were created by varying the diameter (5.5 and 4.5 mm, internal hexagon) and abutment platform (regular and platform switched). For the cortical bone, the highest stress values (rmax and rvm) were observed in situation R1, followed by situations S1, R2, S3, and S2. For the trabecular bone, the highest stress values (rmax) were observed in situation S3, followed by situations R1, S1, R2, and S2. The influence of platform switching was more evident for cortical bone than for trabecular bone and was mainly seen in large platform diameter reduction.

Dynamics characterization of modified Gross-Pitaevskii equation

The dynamics of dissipative and coherent N-body systems, such as a Bose-Einstein condensate, which can be described by an extended Gross-Pitaevskii formalism, is investigated. In order to analyze chaotic and unstable regimes, two approaches are considered: a metric one, based on calculations of Lyapunov exponents, and an algorithmic one, based on the Lempel-Ziv criterion. The consistency of both approaches is established, with the Lempel-Ziv algorithmic found as an efficient complementary approach to the metric one for the fast characterization of dynamical behaviors obtained from finite sequences. © 2013 Elsevier B.V. All rights reserved.

Performance analysis of smart grid communication protocol DNP3 over TCP/IP in a heterogeneous traffic environment

This paper presents simulation results of the DNP3 communication protocol over a TCP/IP network, for Smart Grid applications. The simulation was performed using the NS-2 network simulator. This study aimed to use the simulation to verify the performance of the DNP3 protocol in a heterogeneous LAN. Analyzing the results it was possible to verify that the DNP3 over a heterogeneous traffic network, with communication channel capacity between 60 and 85 percent, it works well with low packet loss and low delay, however, with traffic values upper 85 percent, the DNP3 usage becomes unfeasible because the information lost, re-transmissions and latency are significantly increased. © 2013 IEEE.

Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations

Multifunctional enzyme engineering can improve enzyme cocktails for emerging biofuel technology. Molecular dynamics through structure-based models (SB) is an effective tool for assessing the tridimensional arrangement of chimeric enzymes as well as for inferring the functional practicability before experimental validation. This study describes the computational design of a bifunctional xylanase-lichenase chimera (XylLich) using the xynA and bglS genes from Bacillus subtilis. In silico analysis of the average solvent accessible surface area (SAS) and the root mean square fluctuation (RMSF) predicted a fully functional chimera, with minor fluctuations and variations along the polypeptide chains. Afterwards, the chimeric enzyme was built by fusing the xynA and bglS genes. XylLich was evaluated through small-angle X-ray scattering (SAXS) experiments, resulting in scattering curves with a very accurate fit to the theoretical protein model. The chimera preserved the biochemical characteristics of the parental enzymes, with the exception of a slight variation in the temperature of operation and the catalytic efficiency (k cat/Km). The absence of substantial shifts in the catalytic mode of operation was also verified. Furthermore, the production of chimeric enzymes could be more profitable than producing a single enzyme separately, based on comparing the recombinant protein production yield and the hydrolytic activity achieved for XylLich with that of the parental enzymes. © 2013 Elsevier B.V. All rights reserved.

Docking e análise do modo de ligação de três moléculas pequenas, um benzimidazol e dois compostos de crômio, nos sulcos do DNA 5'-CGCGAATTCGCG-3

Pós-graduação em Ciência e Tecnologia de Materiais - FC

Simulação numérica de escoamentos incompressíveis pelo método de elementos finitos com esquema de Separação Baseado na Característica (CBS)

Pós-graduação em Engenharia Mecânica - FEIS

Avaliação energética da secagem combinada de milho na região de Pedrinhas Paulista, SP

Pós-graduação em Agronomia (Energia na Agricultura) - FCA

Conforto térmico em habitações de interesse social: um estudo de caso

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Propriedades e aspectos geométricos de estimadores tipo James-Stein e do estimador de Hartigan

The James-Stein estimator is a biased shrinkage estimator with uniformly smaller risk than the risk of the sample mean estimator for the mean of multivariate normal distribution, except in the one-dimensional or two-dimensional cases. In this work we have used more heuristic arguments and intensified the geometric treatment of the theory of James-Stein estimator. New type James-Stein shrinking estimators are proposed and the Mahalanobis metric used to address the James-Stein estimator. . To evaluate the performance of the estimator proposed, in relation to the sample mean estimator, we used the computer simulation by the Monte Carlo method by calculating the mean square error. The result indicates that the new estimator has better performance relative to the sample mean estimator.

Ecologia populacional de Lucilia cuprina (Wiedemann, 1830) (Diptera, Calliphoridae): aspecto do desenvolvimento em diferentes densidades larvais e seus efeitos sobre os adultos resultantes

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Simulação computacional do enovelamento de proteínas utilizando o Modelo HP

Pós-graduação em Ciência e Tecnologia de Materiais - FC

Efeito de vacâncias de nitrogênio, gálio e outros parâmetros da célula unitária nas propriedades eletrônicas do GaN

Pós-graduação em Ciência e Tecnologia de Materiais - FC