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.

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

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

A simulation tool for transient stability analysis on vector computers

This paper deals with transient stability analysis based on time domain simulation on vector processing. This approach requires the solution of a set of differential equations in conjunction of another set of algebraic equations. The solution of the algebraic equations has presented a scalar as sequential set of tasks, and the solution of these equations, on vector computers, has required much more investigations to speedup the simulations. Therefore, the main objective of this paper has been to present methods to solve the algebraic equations using vector processing. The results, using a GRAY computer, have shown that on-line transient stability assessment is feasible.

Effect of target bias on magnetic field enhanced plasma immersion ion implantation

Recent studies have demonstrated that sheath dynamics in plasma immersion ion implantation (PIII) is significantly affected by an external magnetic field, especially in the case when the magnetic field is parallel to the workpiece surface or intersects it at small angles. In this work we report the results from two-dimensional, particle-in-cell (PIC) computer simulations of magnetic field enhanced plasma immersion implantation system at different bias voltages. The simulations begin with initial low-density nitrogen plasma, which extends with uniform density through a grounded cylindrical chamber. Negative bias voltage is applied to a cylindrical target located on the axis of the vacuum chamber. An axial magnetic field is created by a solenoid installed inside the target holder. A set of simulations at a fixed magnetic field of 0.0025 T at the target surface is performed. Secondary electron emission from the target subjected to ion bombardment is also included. It is found that the plasma density around the cylindrical target increases because of intense background gas ionization by the electrons drifting in the crossed E x B fields. Suppression of the sheath expansion and increase of the implantation current density in front of the high-density plasma region are observed. The effect of target bias on the sheath dynamics and implantation current of the magnetic field enhanced PIII is discussed. (C) 2007 Elsevier B.V. All rights reserved.

Numerical simulation of magnetic field enhanced plasma immersion ion implantation

The behavior of plasma and sheath characteristics under the action of an applied magnetic field is important in many applications including plasma probes and material processing. Plasma immersion ion implantation (PIII) has been developed as a fast and efficient surface modification technique of complex shaped three-dimensional objects. The PIII process relies on the acceleration of ions across a high-voltage plasma sheath that develops around the target. Recent studies have shown that the sheath dynamics is significantly affected by an external magnetic field. In this work we describe a two-dimensional computer simulation of magnetic field enhanced plasma immersion implantation system. Negative bias voltage is applied to a cylindrical target located on the axis of a grounded cylindrical vacuum chamber filled with uniform nitrogen plasma. An axial magnetic field is created by a solenoid installed inside the cylindrical target. The computer code employs the Monte Carlo method for collision of electrons and neutrals in the plasma and a particle-in-cell (PIC) algorithm for simulating the movement of charged particles in the electromagnetic field. Secondary electron emission from the target subjected to ion bombardment is also included. It is found that a high-density plasma region is formed around the cylindrical target due to the intense background gas ionization by the magnetized electrons drifting in the crossed ExB fields. An increase of implantation current density in front of high density plasma region is observed. (C) 2007 Elsevier B.V. All rights reserved.

Numerical simulation of magnetic-field-enhanced plasma immersion ion implantation in cylindrical geometry

Recent studies have demonstrated that the sheath dynamics in plasma immersion ion implantation (PIII) is significantly affected by an external magnetic field. In this paper, a two-dimensional computer simulation of a magnetic-field-enhanced PHI system is described. Negative bias voltage is applied to a cylindrical target located on the axis of a grounded vacuum chamber filled with uniform molecular nitrogen plasma. A static magnetic field is created by a small coil installed inside the target holder. The vacuum chamber is filled with background nitrogen gas to form a plasma in which collisions of electrons and neutrals are simulated by the Monte Carlo algorithm. It is found that a high-density plasma is formed around the target due to the intense background gas ionization by the magnetized electrons drifting in the crossed E x B fields. The effect of the magnetic field intensity, the target bias, and the gas pressure on the sheath dynamics and implantation current of the PHI system is investigated.

Dynamic modeling and simulation of a flexible robotic manipulator

This work focuses on the dynamic modeling of a flexible robotic manipulator with two flexible links and two revolute joints, which rotates in the horizontal plane. The dynamic equations are derived using the Newton-Euler formulation and the finite element method, based on elementary beam theory. Computer simulation results are presented to illustrate this study. The dynamic model becomes necessary for use in future design and control applications.

Modelling of the influence of the layer pollution thickness in high voltage polluted insulators

An experimental model and a mathematical model with the introduction of a ramp in the channel of Obenaus model are presented. The aim is to present a better reproduction of the real layer pollution deposited on the HV insulators. This better reproduction is obtained from two types of thickness variation: the introduction of a ramp (soft variation) and the introduction of a step (sudden variation). The computational simulations and the experimental data suggest that the introduction of the ramp is the better reproduction of the layer pollution. The ramp approximates to the real layer pollution more than the step.

Neural networks training using the constructivism paradigms

The Backpropagation Algorithm (BA) is the standard method for training multilayer Artificial Neural Networks (ANN), although it converges very slowly and can stop in a local minimum. We present a new method for neural network training using the BA inspired on constructivism, an alphabetization method proposed by Emilia Ferreiro based on Piaget philosophy. Simulation results show that the proposed configuration usually obtains a lower final mean square error, when compared with the standard BA and with the BA with momentum factor.

Electric power systems transient stability analysis by neural networks

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Absorption and fluorescence of Er3+-doped LiYF4: Measurements and simulation

Er3+:LiYF4 single crystal has been studied by absorption and fluorescence spectroscopy in the IR-visible-UV (0-44000 cm-1) region from 4.2 K to room temperature. Polarized spectra were recorded in order to assign numerous Stark levels of electronic transitions mentioned but not attributed before in the related literature and to discuss the irreducible representations (irreps) of the 4I15/2 sublevels. A parametric hamiltonian, including free ion (Eν, α, β, γ, Tλ, ζ, Mk and Pi) and crystal field parameters (B2 0, B4 0, B4 4, B6 0 and B6 4) in an approximate D2d symmetry for the rare earth site in this scheelite type structure, was used to simulate 109 energy positions of the Er ion with a r.m.s. standard deviation of 14.6 cm-1. A comparison with previously published results for Nd3+ in the same matrix is done. © 1998 Elsevier Science S.A.

Inverter-fed linear asynchronous machine

The behaviors of an arc-shaped stator induction machine (the sector-motor) and a disc-secondary linear induction motor are analyzed in this work for different values of the frequency. Variable frequency is produced by a voltage source controlled-current inverter which keeps constant the r.m.s. value of the phase current, also assuring a sinusoidal waveform. For the simulations of the machine developed thrust, an equivalent circuit is used. It is obtained through the application of the one-dimensional theory to the modeling. The circuit parameters take into account the end effects, always present is these kind of machines. The phase current waveforms are analyzed for their harmonic contents. Experimental measurements were carried out in laboratory and are presented with the simulations, for comparison.

Economic viability and selection of irrigation systems using simulation and stochastic dominance

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

Novos resultados sobre a estabilidade e controle de sistemas nao-lineares utilizando modelos fuzzy e LMI

Relaxed conditions for the stability study of nonlinear, continuous and discrete-time systems given by fuzzy models are presented. A theoretical analysis shows that the proposed method provides better or at least the same results of the methods presented in the literature. Digital simulations exemplify this fact. These results are also used for the fuzzy regulators design. The nonlinear systems are represented by the fuzzy models proposed by Takagi and Sugeno. The stability analysis and the design of controllers are described by LMIs (Linear Matrix Inequalities), that can be solved efficiently by convex programming techniques. The specification of the decay rate, constraints on control input and output are also described by LMIs. Finally, the proposed design method is applied in the control of an inverted pendulum.

An accurate low-voltage analog memory-cell with built-in multiplication

A CMOS memory-cell for dynamic storage of analog data and suitable for LVLP applications is proposed. Information is memorized as the gate-voltage of input-transistor of a gain-boosting triode-transconductor. The enhanced output-resistance improves accuracy on reading out the sampled currents. Additionally, a four-quadrant multiplication between the input to regulation-amplifier of the transconductor and the stored voltage is provided. Designing complies with a low-voltage 1.2μm N-well CMOS fabrication process. For a 1.3V-supply, CCELL=3.6pF and sampling interval is 0.25μA≤ ISAMPLE ≤ 0.75μA. The specified retention time is 1.28ms and corresponds to a charge-variation of 1% due to junction leakage @75°C. A range of MR simulations confirm circuit performance. Absolute read-out error is below O.40% while the four-quadrant multiplier nonlinearity, at full-scale is 8.2%. Maximum stand-by consumption is 3.6μW/cell.