Distinct Unfolding and Refolding Pathways of Ribonuclease A Revealed by Heating and Cooling Temperature Jumps

Heating and cooling temperature jumps (T-jumps) were performed using a newly developed technique to trigger unfolding and refolding of wild-type ribonuclease A and a tryptophan-containing variant (Y115W). From the linear Arrhenius plots of the microscopic folding and unfolding rate constants, activation enthalpy (ΔH#), and activation entropy (ΔS#) were determined to characterize the kinetic transition states (TS) for the unfolding and refolding reactions. The single TS of the wild-type protein was split into three for the Y115W variant. Two of these transition states, TS1 and TS2, characterize a slow kinetic phase, and one, TS3, a fast phase. Heating T-jumps induced protein unfolding via TS2 and TS3; cooling T-jumps induced refolding via TS1 and TS3. The observed speed of the fast phase increased at lower temperature, due to a strongly negative ΔH# of the folding-rate constant. The results are consistent with a path-dependent protein folding/unfolding mechanism. TS1 and TS2 are likely to reflect X-Pro114 isomerization in the folded and unfolded protein, respectively, and TS3 the local conformational change of the β-hairpin comprising Trp115. A very fast protein folding/unfolding phase appears to precede both processes. The path dependence of the observed kinetics is suggestive of a rugged energy protein folding funne

Dynamic simulation studies of structural formation and transition in electro-magneto-rheological fluids

The computer simulation method has been used to study the structural formation and transition of electro-magneto-rheological (EMR) fluids under compatible electric and magnetic fields. When the fields are applied simultaneously and perpendicularly to each other, the particles rapidly arrange into two-dimensional close-packed layer structures parallel to both fields. The layers then combine together to form thicker sheet-like structures, which finally relax into three-dimensional close-packed structures with the help of the thermal fluctuations. On the other hand, if the electric field is applied firstly to induce the body-centered tetragonal (BCT) columns in the system, and then the magnetic field is applied in the perpendicular direction. the BCT to face-centered cubic (FCC) structure transition is observed in very short time. Following that. the structure keeps on evolving due to the demagnetization effect and finally form the three-dimensional close-packed structures.

Simulation of field-induced structural formation and transition in electromagnetorheological suspensions

A computer simulation method has been used to study the three-dimensional structural formation and transition of eleetromagnetorheological (EMR) suspensions under compatible electric and magnetic fields. When the fields are applied simultaneously and perpendicularly to each other, the particles rapidly arrange into single layer structures parallel to both fields. In each layer, there is a two-dimensional hexagonal lattice. The single layers then combine together to form thicker sheetlike structures. With the help of the thermal fluctuations, the thicker structures relax into three-dimensional close-packed structures, which may be face-centered cubic (fcc), hexagonal close-packed (hup) lattices, or, more probably, the mixture of them, depending on the initial configurations and the thermal fluctuations. On the other hand, if the electric field is applied first to induce the body-centered tetragonal (bct) columns in the system, and then the magnetic field is applied in the perpendicular direction, the bet to fee structure transition is observed in a very short time. Following that, the structure keeps on evolving due to the demagnetization effect and finally forms close-packed structures with fee and hcp lattice character. The simulation results are in agreement with the theoretical and experimental results.

On developing efficient applications using conservative distributed simulation paradigm

This paper aims to present, using a set of guidelines, how to apply the conservative distributed simulation paradigm (CMB protocol) to develop efficient applications. Using these guidelines, even a user with little experience on distributed simulation and computer architecture can have good performance on distributed simulations using conservative synchronization protocols for parallel processes.The set of guidelines is focus on a specific application domain, the performance evaluation of computer systems, considering models with coarse granularity and few logical processes and running over two platforms: parallel (high performance communication environment) and distributed (low performance communication environment).

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.

Another prefiltering algorithm for adaptive IIR filtering

An algorithm for adaptive IIR filtering that uses prefiltering structure in direct form is presented. This structure has an estimation error that is a linear function of the coefficients. This property greatly simplifies the derivation of gradient-based algorithms. Computer simulations show that the proposed structure improves convergence speed.

Uma aplicacao da celula de comutacao ZVS-PWM-GEPAE ao conversor DC-AC

This work presents the design and procedure of a DC-to-AC converter using a ZVS Commutation Cell developed by Barbi and Martins (1991) and applied to the family of DC-to-DC PWM converters. Firstly, we show the cell applied to buck converter. The stages of operation and the main current and voltage equations of the resonant devices are presented. Next, we adapt the converter to the regenerative operation mode. Hence, the full bridge converter at low frequency operation is conected on the DC-to-DC stage (at high frequency) output ends (Seixas, 1993). Commutation of zero voltage for all switches, PWM at constant frequency and neither overvoltage nor additional current stress are observed by digital simulation. The design example and experimental results obtained by prototype rated at 275 V, 1 kW and 40 kHz are also presented.

Numerical simulation of viscous three-dimensional flow over aerospace vehicles using Euler/boundary-layer zonal approach

This paper presents a viscous three-dimensional simulations coupling Euler and boundary layer codes for calculating flows over arbitrary surfaces. The governing equations are written in a general non orthogonal coordinate system. The Levy-Lees transformation generalized to three-dimensional flows is utilized. The inviscid properties are obtained from the Euler equations using the Beam and Warming implicit approximate factorization scheme. The resulting equations are discretized and approximated by a two-point fmitedifference numerical scheme. The code developed is validated and applied to the simulation of the flowfield over aerospace vehicle configurations. The results present good correlation with the available data.

On optimizing micropower MOS regulated cascode circuits on switched current techniques

Trade-off between settling time and micropower consumption in MOS regulated cascode current sources as building parts in high-accuracy, current-switching D/A converters is analyzed. The regulation-loop frequency characteristic is obtained and difficulties to impose a dominant-pole condition to the resulting 2nd-order system are discussed. Raising pole frequencies while meeting consumption requirements is basically limited by parasitic capacitances. An alternative is found by imposing a twin-pole system in which design constraints are somewhat relaxed and settling slightly faster. Relationships between pole frequencies, transistor geometry and bias are established. Simulated waveforms obtained with PSpice of designed circuits following a voltage perturbation suggest a good agreement with theory. The proposed approach applied to the design of a micropower current-mode D/A converter improves its simulated settling performance.

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.

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.

Simulation of active control using fuzzy logic applied to a pulse combustor

This work analyzes an active fuzzy logic control system in a Rijke type pulse combustor. During the system development, a study of the existing types of control for pulse combustion was carried out and a simulation model was implemented to be used with the package Matlab and Simulink. Blocks which were not available in the simulator library were developed. A fuzzy controller was developed and its membership functions and inference rules were established. The obtained simulation showed that fuzzy logic is viable in the control of combustion instabilities. The obtained results indicated that the control system responded to pulses in an efficient and desirable way. It was verified that the system needed approximately 0.2 s to increase the tube internal pressure from 30 to 90 mbar, with an assumed total delay of 2 ms. The effects of delay variation were studied. Convergence was always obtained and general performance was not affected by the delay. The controller sends a pressure signal in phase with the Rijke tube internal pressure signal, through the speakers, when an increase the oscillations pressure amplitude is desired. On the other hand, when a decrease of the tube internal pressure amplitude is desired, the controller sends a signal 180° out of phase.