Prediction of 3D structure and ligand-binding properties : ABC transporters and flavodiiron proteins from Synechocystis sp. strain PCC 6803

Cyanobacteria are unicellular, non-nitrogen-fixing prokaryotes, which perform photosynthesis similarly as higher plants. The cyanobacterium Synechocystis sp. strain PCC 6803 is used as a model organism in photosynthesis research. My research described herein aims at understanding the function of the photosynthetic machinery and how it responds to changes in the environment. Detailed knowledge of the regulation of photosynthesis in cyanobacteria can be utilized for biotechnological purposes, for example in the harnessing of solar energy for biofuel production. In photosynthesis, iron participates in electron transfer. Here, we focused on iron transport in Synechocystis sp. strain PCC 6803 and particularly on the environmental regulation of the genes encoding the FutA2BC ferric iron transporter, which belongs to the ABC transporter family. A homology model built for the ATP-binding subunit FutC indicates that it has a functional ATPbinding site as well as conserved interactions with the channel-forming subunit FutB in the transporter complex. Polyamines are important for the cell proliferation, differentiation and apoptosis in prokaryotic and eukaryotic cells. In plants, polyamines have special roles in stress response and in plant survival. The polyamine metabolism in cyanobacteria in response to environmental stress is of interest in research on stress tolerance of higher plants. In this thesis, the potd gene encoding an polyamine transporter subunit from Synechocystis sp. strain PCC 6803 was characterized for the first time. A homology model built for PotD protein indicated that it has capability of binding polyamines, with the preference for spermidine. Furthermore, in order to investigate the structural features of the substrate specificity, polyamines were docked into the binding site. Spermidine was positioned very similarly in Synechocystis PotD as in the template structure and had most favorable interactions of the docked polyamines. Based on the homology model, experimental work was conducted, which confirmed the binding preference. Flavodiiron proteins (Flv) are enzymes, which protect the cell against toxicity of oxygen and/or nitric oxide by reduction. In this thesis, we present a novel type of photoprotection mechanism in cyanobacteria by the heterodimer of Flv2/Flv4. The constructed homology model of Flv2/Flv4 suggests a functional heterodimer capable of rapid electron transfer. The unknown protein sll0218, encoded by the flv2-flv4 operon, is assumed to facilitate the interaction of the Flv2/Flv4 heterodimer and energy transfer between the phycobilisome and PSII. Flv2/Flv4 provides an alternative electron transfer pathway and functions as an electron sink in PSII electron transfer.

A temperature predicting model for manufacturing processes requiring coiling

A model for predicting temperature evolution for automatic controling systems in manufacturing processes requiring the coiling of bars in the transfer table is presented. Although the method is of a general nature, the presentation in this work refers to the manufacturing of steel plates in hot rolling mills. The predicting strategy is based on a mathematical model of the evolution of temperature in a coiling and uncoiling bar and is presented in the form of a parabolic partial differential equation for a shape changing domain. The mathematical model is solved numerically by a space discretization via geometrically adaptive finite elements which accomodate the change in shape of the domain, using a computationally novel treatment of the resulting thermal contact problem due to coiling. Time is discretized according to a Crank-Nicolson scheme. Since the actual physical process takes less time than the time required by the process controlling computer to solve the full mathematical model, a special predictive device was developed, in the form of a set of least squares polynomials, based on the off-line numerical solution of the mathematical model.

Dynamics of coherent vortices in mixing layers using direct numerical and large-eddy simulations

Coherent vortices in turbulent mixing layers are investigated by means of Direct Numerical Simulation (DNS) and Large-Eddy Simulation (LES). Subgrid-scale models defined in spectral and physical spaces are reviewed. The new "spectral-dynamic viscosity model", that allows to account for non-developed turbulence in the subgrid-scales, is discussed. Pseudo-spectral methods, combined with sixth-order compact finite differences schemes (when periodic boundary conditions cannot be established), are used to solve the Navier- Stokes equations. Simulations in temporal and spatial mixing layers show two types of pairing of primary Kelvin-Helmholtz (KH) vortices depending on initial conditions (or upstream conditions): quasi-2D and helical pairings. In both cases, secondary streamwise vortices are stretched in between the KH vortices at an angle of 45° with the horizontal plane. These streamwise vortices are not only identified in the early transitional stage of the mixing layer but also in self-similar turbulence conditions. The Re dependence of the "diameter" of these vortices is analyzed. Results obtained in spatial growing mixing layers show some evidences of pairing of secondary vortices; after a pairing of the primary Kelvin-Helmholtz (KH) vortices, the streamwise vortices are less numerous and their diameter has increased than before the pairing of KH vortices.

An experimental/numerical study of the turbulent boundary layer development along a surface with a sudden change in roughness

A theory for the description of turbulent boundary layer flows over surfaces with a sudden change in roughness is considered. The theory resorts to the concept of displacement in origin to specify a wall function boundary condition for a kappa-epsilon model. An approximate algebraic expression for the displacement in origin is obtained from the experimental data by using the chart method of Perry and Joubert(J.F.M., vol. 17, pp. 193-122, 1963). This expression is subsequently included in the near wall logarithmic velocity profile, which is then adopted as a boundary condition for a kappa-epsilon modelling of the external flow. The results are compared with the lower atmospheric observations made by Bradley(Q. J. Roy. Meteo. Soc., vol. 94, pp. 361-379, 1968) as well as with velocity profiles extracted from a set of wind tunnel experiments carried out by Avelino et al.( 7th ENCIT, 1998). The measurements are found to be in good agreement with the theoretical computations. The skin-friction coefficient was calculated according to the chart method of Perry and Joubert(J.F.M., vol. 17, pp. 193-122, 1963) and to a balance of the integral momentum equation. In particular, the growth of the internal boundary layer thickness obtained from the numerical simulation is compared with predictions of the experimental data calculated by two methods, the "knee" point method and the "merge" point method.

On the numerical simulation of machining processes

Numerical simulation of machining processes can be traced back to the early seventies when finite element models for continuous chip formation were proposed. The advent of fast computers and development of new techniques to model large plastic deformations have favoured machining simulation. Relevant aspects of finite element simulation of machining processes are discussed in this paper, such as solution methods, material models, thermo-mechanical coupling, friction models, chip separation and breakage strategies and meshing/re-meshing strategies.

Application of the finite element method in cold forging processes

The demand for more efficient manufacturing processes has been increasing in the last few years. The cold forging process is presented as a possible solution, because it allows the production of parts with a good surface finish and with good mechanical properties. Nevertheless, the cold forming sequence design is very empirical and it is based on the designer experience. The computational modeling of each forming process stage by the finite element method can make the sequence design faster and more efficient, decreasing the use of conventional "trial and error" methods. In this study, the application of a commercial general finite element software - ANSYS - has been applied to model a forming operation. Models have been developed to simulate the ring compression test and to simulate a basic forming operation (upsetting) that is applied in most of the cold forging parts sequences. The simulated upsetting operation is one stage of the automotive starter parts manufacturing process. Experiments have been done to obtain the stress-strain material curve, the material flow during the simulated stage, and the required forming force. These experiments provided results used as numerical model input data and as validation of model results. The comparison between experiments and numerical results confirms the developed methodology potential on die filling prediction.

Numerical study of Petrov-Galerkin formulations for the shallow water wave equations

The behavior of Petrov-Galerkin formulations for shallow water wave equations is evaluated numerically considering typical one-dimensional propagation problems. The formulations considered here use stabilizing operators to improve classical Galerkin approaches. Their advantages and disadvantages are pointed out according to the intrinsic time scale (free parameter) which has a particular importance in this kind of problem. The influence of the Courant number and the performance of the formulation in dealing with spurious oscillations are adressed.

Prediction of transients and control reactions in a transonic wind tunnel

This work describes a lumped parameter mathematical model for the prediction of transients in an aerodynamic circuit of a transonic wind tunnel. Control actions to properly handle those perturbations are also assessed. The tunnel circuit technology is up to date and incorporates a novel feature: high-enthalpy air injection to extend the tunnel’s Reynolds number capability. The model solves the equations of continuity, energy and momentum and defines density, internal energy and mass flow as the basic parameters in the aerodynamic study as well as Mach number, stagnation pressure and stagnation temperature, all referred to test section conditions, as the main control variables. The tunnel circuit response to control actions and the stability of the flow are numerically investigated. Initially, for validation purposes, the code was applied to the AWT ("Altitude Wind Tunnel" of NASA-Lewis). In the sequel, the Brazilian transonic wind tunnel was investigated, with all the main control systems modeled, including injection.

Numerical study on mixed convection in a horizontal flow past a square porous cavity using UNIFAES scheme

Mixed convection on the flow past a heated length and past a porous cavity located in a horizontal wall bounding a saturated porous medium is numerically simulated. The cavity is heated from below. The steady-state regime is studied for several intensities of the buoyancy effects due to temperature variations. The influences of Péclet and Rayleigh numbers on the flow pattern and the temperature distributions are examined. Local and global Nusselt numbers are reported for the heated surface. The convective-diffusive fluxes at the volume boundaries are represented using the UNIFAES, Unified Finite Approach Exponential-type Scheme, with the Power-Law approximation to reduce the computing time. The conditions established by Rivas for the quadratic order of accuracy of the central differencing to be maintained in irregular grids are shown to be extensible to other quadratic schemes, including UNIFAES, so that accuracy estimates could be obtained.

On the numerical integration of rigid body nonlinear dynamics in presence of parameters singularities

One of the main complexities in the simulation of the nonlinear dynamics of rigid bodies consists in describing properly the finite rotations that they may undergo. It is well known that, to avoid singularities in the representation of the SO(3) rotation group, at least four parameters must be used. However, it is computationally expensive to use a four-parameters representation since, as only three of the parameters are independent, one needs to introduce constraint equations in the model, leading to differential-algebraic equations instead of ordinary differential ones. Three-parameter representations are numerically more efficient. Therefore, the objective of this paper is to evaluate numerically the influence of the parametrization and its singularities on the simulation of the dynamics of a rigid body. This is done through the analysis of a heavy top with a fixed point, using two three-parameter systems, Euler's angles and rotation vector. Theoretical results were used to guide the numerical simulation and to assure that all possible cases were analyzed. The two parametrizations were compared using several integrators. The results show that Euler's angles lead to faster integration compared to the rotation vector. An Euler's angles singular case, where representation approaches a theoretical singular point, was analyzed in detail. It is shown that on the contrary of what may be expected, 1) the numerical integration is very efficient, even more than for any other case, and 2) in spite of the uncertainty on the Euler's angles themselves, the body motion is well represented.

Fluid dynamic modelling and simulation of circulating fluidized bed reactors: importance of the interface turbulence transfer

The main objective of this work is to analyze the importance of the gas-solid interface transfer of the kinetic energy of the turbulent motion on the accuracy of prediction of the fluid dynamic of Circulating Fluidized Bed (CFB) reactors. CFB reactors are used in a variety of industrial applications related to combustion, incineration and catalytic cracking. In this work a two-dimensional fluid dynamic model for gas-particle flow has been used to compute the porosity, the pressure, and the velocity fields of both phases in 2-D axisymmetrical cylindrical co-ordinates. The fluid dynamic model is based on the two fluid model approach in which both phases are considered to be continuous and fully interpenetrating. CFB processes are essentially turbulent. The model of effective stress on each phase is that of a Newtonian fluid, where the effective gas viscosity was calculated from the standard k-epsilon turbulence model and the transport coefficients of the particulate phase were calculated from the kinetic theory of granular flow (KTGF). This work shows that the turbulence transfer between the phases is very important for a better representation of the fluid dynamics of CFB reactors, especially for systems with internal recirculation and high gradients of particle concentration. Two systems with different characteristics were analyzed. The results were compared with experimental data available in the literature. The results were obtained by using a computer code developed by the authors. The finite volume method with collocated grid, the hybrid interpolation scheme, the false time step strategy and SIMPLEC (Semi-Implicit Method for Pressure Linked Equations - Consistent) algorithm were used to obtain the numerical solution.

Numerical and experimental investigation of thermal louvers for space applications

Thermal louvers, using movable or rotating shutters over a radiating surface, have gained a wide acceptance as highly efficient devices for controlling the temperature of a spacecraft. This paper presents a detailed analysis of the performance of a rectangular thermal louver with movable blades. The radiative capacity of the louver, determined by its effective emittance, is calculated for different values of the blades opening angle. Experimental results obtained with a prototype of a spacecraft thermal louver show good agreement with the theoretical values.

Gas-solid two-phase flow in the riser of circulating fluidized beds: mathematical modelling and numerical simulation

A mathematical model is developed for gas-solids flows in circulating fluidized beds. An Eulerian formulation is followed based on the two-fluids model approach where both the fluid and the particulate phases are treated as a continuum. The physical modelling is discussed, including the formulation of boundary conditions and the description of the numerical methodology. Results of numerical simulation are presented and discussed. The model is validated through comparison to experiment, and simulation is performed to investigate the effects on the flow hydrodynamics of the solids viscosity.

Numerical Simulation of the Cavitation in the Hydrodynamic Lubrication of Journal Bearings: a Parallel Algorithm

In this paper we present an algorithm for the numerical simulation of the cavitation in the hydrodynamic lubrication of journal bearings. Despite the fact that this physical process is usually modelled as a free boundary problem, we adopted the equivalent variational inequality formulation. We propose a two-level iterative algorithm, where the outer iteration is associated to the penalty method, used to transform the variational inequality into a variational equation, and the inner iteration is associated to the conjugate gradient method, used to solve the linear system generated by applying the finite element method to the variational equation. This inner part was implemented using the element by element strategy, which is easily parallelized. We analyse the behavior of two physical parameters and discuss some numerical results. Also, we analyse some results related to the performance of a parallel implementation of the algorithm.

Modeling of the Fluid-Structure Interaction in Inelastic Piping Systems

In many engineering applications, compliant piping systems conveying liquids are subjected to inelastic deformations due to severe pressure surges such as plastic tubes in modern water supply transmission lines and metallic pipings in nuclear power plants. In these cases the design of such systems may require an adequate modeling of the interactions between the fluid dynamics and the inelastic structural pipe motions. The reliability of the prediction of fluid-pipe behavior depends mainly on the adequacy of the constitutive equations employed in the analysis. In this paper it is proposed a systematic and general approach to consistently incorporate different kinds of inelastic behaviors of the pipe material in a fluid-structure interaction analysis. The main feature of the constitutive equations considered in this work is that a very simple numerical technique can be used for solving the coupled equations describing the dynamics of the fluid and pipe wall. Numerical examples concerning the analysis of polyethylene and stainless steel pipe networks are presented to illustrate the versatility of the proposed approach.