Real-time bilateral control of a nonlinear teleoperation system

In this work, we study the bilateral control of a nonlinear teleoperator system with constant delay, proposes a control strategy by state convergence, which directly connect the local and remote manipulator through feedback signals of position and speed. The control signal allows the remote manipulator follow the local manipulator through the state convergence even if it has a delay in the communication channel. The bilateral control of the teleoperator system considers the case when the human operator applies a constant force on the local manipulator and when the interaction of the remote manipulator with the environment is considered passive. The stability analysis is performed using functional of Lyapunov-Krasovskii, it showed that using a control algorithm by state convergence for the case with constant delay, the nonlinear local and remote teleoperation system is asymptotically stable, also speeds converge to zero and position tracking is achieved.

Advances in Control of Teleoperation System by State Convergence

In this work, we proposes a control strategy by state convergence applied to bilateral control of a nonlinear teleoperator system with constant delay. The bilateral control of the teleoperator system considers the case when the human operator applies a constant force on the local manipulator and when the interaction of the remote manipulator with the environment is considered passive. The stability analysis is performed using Lyapunov-Krasovskii functional, it showed that using an control algorithm by state convergence for the case with constant delay, the nonlinear local and remote teleoperation system is asymptotically stable, also speeds converge to zero and position tracking is achieved. This work also presents the implementation of an experimental platform. The mechanical structure of the arm that is located in the remote side has been built and the electric servomechanism has been mounted to control their movement.

CompactRIO: advanced data acquisition systems integration in CODAC Core System

Las herramientas de configuración basadas en lenguajes de alto nivel como LabVIEW permiten el desarrollo de sistemas de adquisición de datos basados en hardware reconfigurable FPGA muy complejos en un breve periodo de tiempo. La estandarización del ciclo de diseño hardware/software y la utilización de herramientas como EPICS facilita su integración con la plataforma de adquisición y control ITER CODAC CORE SYSTEM (CCS) basada en Linux. En este proyecto se propondrá una metodología que simplificará el ciclo completo de integración de plataformas novedosas, como cRIO, en las que el funcionamiento del hardware de adquisición puede ser modificado por el usuario para que éste se amolde a sus requisitos específicos. El objetivo principal de este proyecto fin de master es realizar la integración de un sistema cRIO NI9159 y diferentes módulos de E/S analógica y digital en EPICS y en CODAC CORE SYSTEM (CCS). Este último consiste en un conjunto de herramientas software que simplifican la integración de los sistemas de instrumentación y control del experimento ITER. Para cumplir el objetivo se realizarán las siguientes tareas: • Desarrollo de un sistema de adquisición de datos basado en FPGA con la plataforma hardware CompactRIO. En esta tarea se realizará la configuración del sistema y la implementación en LabVIEW para FPGA del hardware necesario para comunicarse con los módulos: NI9205, NI9264, NI9401.NI9477, NI9426, NI9425 y NI9476 • Implementación de un driver software utilizando la metodología de AsynDriver para integración del cRIO con EPICS. Esta tarea requiere definir todos los records necesarios que exige EPICS y crear las interfaces adecuadas que permitirán comunicarse con el hardware. • Implementar la descripción del sistema cRIO y del driver EPICS en el sistema de descripción de plantas de ITER llamado SDD. Esto automatiza la creación de las aplicaciones de EPICS que se denominan IOCs. SUMMARY The configuration tools based in high-level programing languages like LabVIEW allows the development of high complex data acquisition systems based on reconfigurable hardware FPGA in a short time period. The standardization of the hardware/software design cycle and the use of tools like EPICS ease the integration with the data acquisition and control platform of ITER, the CODAC Core System based on Linux. In this project a methodology is proposed in order to simplify the full integration cycle of new platforms like CompactRIO (cRIO), in which the data acquisition functionality can be reconfigured by the user to fits its concrete requirements. The main objective of this MSc final project is to develop the integration of a cRIO NI-9159 and its different analog and digital Input/Output modules with EPICS in a CCS. The CCS consists of a set of software tools that simplifies the integration of instrumentation and control systems in the International Thermonuclear Reactor (ITER) experiment. To achieve such goal the following tasks are carried out: • Development of a DAQ system based on FPGA using the cRIO hardware platform. This task comprehends the configuration of the system and the implementation of the mandatory hardware to communicate to the I/O adapter modules NI9205, NI9264, NI9401, NI9477, NI9426, NI9425 y NI9476 using LabVIEW for FPGA. • Implementation of a software driver using the asynDriver methodology to integrate such cRIO system with EPICS. This task requires the definition of the necessary EPICS records and the creation of the appropriate interfaces that allow the communication with the hardware. • Develop the cRIO system’s description and the EPICS driver in the ITER plant description tool named SDD. This development will automate the creation of EPICS applications, called IOCs.

Output Impedance Correction Circuit (OICC): A New Concept to Improve the Dynamic Response of DC/DC Converters with Additional Energy Path

El desarrollo da las nuevas tecnologías permite a los ingenieros llevar al límite el funcionamiento de los circuitos integrados (Integrated Circuits, IC). Las nuevas generaciones de procesadores, DSPs o FPGAs son capaces de procesar la información a una alta velocidad, con un alto consumo de energía, o esperar en modo de baja potencia con el mínimo consumo posible. Esta gran variación en el consumo de potencia y el corto tiempo necesario para cambiar de un nivel al otro, afecta a las especificaciones del Módulo de Regulador de Tensión (Voltage Regulated Module, VRM) que alimenta al IC. Además, las características adicionales obligatorias, tales como adaptación del nivel de tensión (Adaptive Voltage Positioning, AVP) y escalado dinámico de la tensión (Dynamic Voltage Scaling, DVS), imponen requisitos opuestas en el diseño de la etapa de potencia del VRM. Para poder soportar las altas variaciones de los escalones de carga, el condensador de filtro de salida del VRM se ha de sobredimensionar, penalizando la densidad de energía y el rendimiento durante la operación de DVS. Por tanto, las actuales tendencias de investigación se centran en mejorar la respuesta dinámica del VRM, mientras se reduce el tamaño del condensador de salida. La reducción del condensador de salida lleva a menor coste y una prolongación de la vida del sistema ya que se podría evitar el uso de condensadores voluminosos, normalmente implementados con condensadores OSCON. Una ventaja adicional es que reduciendo el condensador de salida, el DVS se puede realizar más rápido y con menor estrés de la etapa de potencia, ya que la cantidad de carga necesaria para cambiar la tensión de salida es menor. El comportamiento dinámico del sistema con un control lineal (Control Modo Tensión, VMC, o Control Corriente de Pico, Peak Current Mode Control, PCMC,…) está limitado por la frecuencia de conmutación del convertidor y por el tamaño del filtro de salida. La reducción del condensador de salida se puede lograr incrementando la frecuencia de conmutación, así como incrementando el ancho de banda del sistema, y/o aplicando controles avanzados no-lineales. Usando esos controles, las variables del estado se saturan para conseguir el nuevo régimen permanente en un tiempo mínimo, así como el filtro de salida, más específicamente la pendiente de la corriente de la bobina, define la respuesta de la tensión de salida. Por tanto, reduciendo la inductancia de la bobina de salida, la corriente de bobina llega más rápido al nuevo régimen permanente, por lo que una menor cantidad de carga es tomada del condensador de salida durante el tránsito. El inconveniente de esa propuesta es que el rendimiento del sistema es penalizado debido al incremento de pérdidas de conmutación y las corrientes RMS. Para conseguir tanto la reducción del condensador de salida como el alto rendimiento del sistema, mientras se satisfacen las estrictas especificaciones dinámicas, un convertidor multifase es adoptado como estándar para aplicaciones VRM. Para asegurar el reparto de las corrientes entre fases, el convertidor multifase se suele implementar con control de modo de corriente. Para superar la limitación impuesta por el filtro de salida, la segunda posibilidad para reducir el condensador de salida es aplicar alguna modificación topológica (Topologic modifications) de la etapa básica de potencia para incrementar la pendiente de la corriente de bobina y así reducir la duración de tránsito. Como el transitorio se ha reducido, una menor cantidad de carga es tomada del condensador de salida bajo el mismo escalón de la corriente de salida, con lo cual, el condensador de salida se puede reducir para lograr la misma desviación de la tensión de salida. La tercera posibilidad para reducir el condensador de salida del convertidor es introducir un camino auxiliar de energía (additional energy path, AEP) para compensar el desequilibrio de la carga del condensador de salida reduciendo consecuentemente la duración del transitorio y la desviación de la tensión de salida. De esta manera, durante el régimen permanente, el sistema tiene un alto rendimiento debido a que el convertidor principal con bajo ancho de banda es diseñado para trabajar con una frecuencia de conmutación moderada para conseguir requisitos estáticos. Por otro lado, el comportamiento dinámico durante los transitorios es determinado por el AEP con un alto ancho de banda. El AEP puede ser implementado como un camino resistivo, como regulador lineal (Linear regulator, LR) o como un convertidor conmutado. Las dos primeras implementaciones proveen un mayor ancho de banda, acosta del incremento de pérdidas durante el transitorio. Por otro lado, la implementación del convertidor computado presenta menor ancho de banda, limitado por la frecuencia de conmutación, aunque produce menores pérdidas comparado con las dos anteriores implementaciones. Dependiendo de la aplicación, la implementación y la estrategia de control del sistema, hay una variedad de soluciones propuestas en el Estado del Arte (State-of-the-Art, SoA), teniendo diferentes propiedades donde una solución ofrece más ventajas que las otras, pero también unas desventajas. En general, un sistema con AEP ideal debería tener las siguientes propiedades: 1. El impacto del AEP a las pérdidas del sistema debería ser mínimo. A lo largo de la operación, el AEP genera pérdidas adicionales, con lo cual, en el caso ideal, el AEP debería trabajar por un pequeño intervalo de tiempo, solo durante los tránsitos; la otra opción es tener el AEP constantemente activo pero, por la compensación del rizado de la corriente de bobina, se generan pérdidas innecesarias. 2. El AEP debería ser activado inmediatamente para minimizar la desviación de la tensión de salida. Para conseguir una activación casi instantánea, el sistema puede ser informado por la carga antes del escalón o el sistema puede observar la corriente del condensador de salida, debido a que es la primera variable del estado que actúa a la perturbación de la corriente de salida. De esa manera, el AEP es activado con casi cero error de la tensión de salida, logrando una menor desviación de la tensión de salida. 3. El AEP debería ser desactivado una vez que el nuevo régimen permanente es detectado para evitar los transitorios adicionales de establecimiento. La mayoría de las soluciones de SoA estiman la duración del transitorio, que puede provocar un transitorio adicional si la estimación no se ha hecho correctamente (por ejemplo, si la corriente de bobina del convertidor principal tiene un nivel superior o inferior al necesitado, el regulador lento del convertidor principal tiene que compensar esa diferencia una vez que el AEP es desactivado). Otras soluciones de SoA observan las variables de estado, asegurando que el sistema llegue al nuevo régimen permanente, o pueden ser informadas por la carga. 4. Durante el transitorio, como mínimo un subsistema, o bien el convertidor principal o el AEP, debería operar en el lazo cerrado. Implementando un sistema en el lazo cerrado, preferiblemente el subsistema AEP por su ancho de banda elevado, se incrementa la robustez del sistema a los parásitos. Además, el AEP puede operar con cualquier tipo de corriente de carga. Las soluciones que funcionan en el lazo abierto suelen preformar el control de balance de carga con mínimo tiempo, así reducen la duración del transitorio y tienen un impacto menor a las pérdidas del sistema. Por otro lado, esas soluciones demuestran una alta sensibilidad a las tolerancias y parásitos de los componentes. 5. El AEP debería inyectar la corriente a la salida en una manera controlada, así se reduce el riesgo de unas corrientes elevadas y potencialmente peligrosas y se incrementa la robustez del sistema bajo las perturbaciones de la tensión de entrada. Ese problema suele ser relacionado con los sistemas donde el AEP es implementado como un convertidor auxiliar. El convertidor auxiliar es diseñado para una potencia baja, con lo cual, los dispositivos elegidos son de baja corriente/potencia. Si la corriente no es controlada, bajo un pico de tensión de entrada provocada por otro parte del sistema (por ejemplo, otro convertidor conectado al mismo bus), se puede llegar a un pico en la corriente auxiliar que puede causar la perturbación de tensión de salida e incluso el fallo de los dispositivos del convertidor auxiliar. Sin embargo, cuando la corriente es controlada, usando control del pico de corriente o control con histéresis, la corriente auxiliar tiene el control con prealimentación (feed-forward) de tensión de entrada y la corriente es definida y limitada. Por otro lado, si la solución utiliza el control de balance de carga, el sistema puede actuar de forma deficiente si la tensión de entrada tiene un valor diferente del nominal, provocando que el AEP inyecta/toma más/menos carga que necesitada. 6. Escalabilidad del sistema a convertidores multifase. Como ya ha sido comentado anteriormente, para las aplicaciones VRM por la corriente de carga elevada, el convertidor principal suele ser implementado como multifase para distribuir las perdidas entre las fases y bajar el estrés térmico de los dispositivos. Para asegurar el reparto de las corrientes, normalmente un control de modo corriente es usado. Las soluciones de SoA que usan VMC son limitadas a la implementación con solo una fase. Esta tesis propone un nuevo método de control del flujo de energía por el AEP y el convertidor principal. El concepto propuesto se basa en la inyección controlada de la corriente auxiliar al nodo de salida donde la amplitud de la corriente es n-1 veces mayor que la corriente del condensador de salida con las direcciones apropiadas. De esta manera, el AEP genera un condensador virtual cuya capacidad es n veces mayor que el condensador físico y reduce la impedancia de salida. Como el concepto propuesto reduce la impedancia de salida usando el AEP, el concepto es llamado Output Impedance Correction Circuit (OICC) concept. El concepto se desarrolla para un convertidor tipo reductor síncrono multifase con control modo de corriente CMC (incluyendo e implementación con una fase) y puede operar con la tensión de salida constante o con AVP. Además, el concepto es extendido a un convertidor de una fase con control modo de tensión VMC. Durante la operación, el control de tensión de salida de convertidor principal y control de corriente del subsistema OICC están siempre cerrados, incrementando la robustez a las tolerancias de componentes y a los parásitos del cirquito y permitiendo que el sistema se pueda enfrentar a cualquier tipo de la corriente de carga. Según el método de control propuesto, el sistema se puede encontrar en dos estados: durante el régimen permanente, el sistema se encuentra en el estado Idle y el subsistema OICC esta desactivado. Por otro lado, durante el transitorio, el sistema se encuentra en estado Activo y el subsistema OICC está activado para reducir la impedancia de salida. El cambio entre los estados se hace de forma autónoma: el sistema entra en el estado Activo observando la corriente de condensador de salida y vuelve al estado Idle cunado el nuevo régimen permanente es detectado, observando las variables del estado. La validación del concepto OICC es hecha aplicándolo a un convertidor tipo reductor síncrono con dos fases y de 30W cuyo condensador de salida tiene capacidad de 140μF, mientras el factor de multiplicación n es 15, generando en el estado Activo el condensador virtual de 2.1mF. El subsistema OICC es implementado como un convertidor tipo reductor síncrono con PCMC. Comparando el funcionamiento del convertidor con y sin el OICC, los resultados demuestran que se ha logrado una reducción de la desviación de tensión de salida con factor 12, tanto con funcionamiento básico como con funcionamiento AVP. Además, los resultados son comparados con un prototipo de referencia que tiene la misma etapa de potencia y un condensador de salida físico de 2.1mF. Los resultados demuestran que los dos sistemas tienen el mismo comportamiento dinámico. Más aun, se ha cuantificado el impacto en las pérdidas del sistema operando bajo una corriente de carga pulsante y bajo DVS. Se demuestra que el sistema con OICC mejora el rendimiento del sistema, considerando las pérdidas cuando el sistema trabaja con la carga pulsante y con DVS. Por lo último, el condensador de salida de sistema con OICC es mucho más pequeño que el condensador de salida del convertidor de referencia, con lo cual, por usar el concepto OICC, la densidad de energía se incrementa. En resumen, las contribuciones principales de la tesis son: • El concepto propuesto de Output Impedance Correction Circuit (OICC), • El control a nivel de sistema basado en el método usado para cambiar los estados de operación, • La implementación del subsistema OICC en lazo cerrado conjunto con la implementación del convertidor principal, • La cuantificación de las perdidas dinámicas bajo la carga pulsante y bajo la operación DVS, y • La robustez del sistema bajo la variación del condensador de salida y bajo los escalones de carga consecutiva. ABSTRACT Development of new technologies allows engineers to push the performance of the integrated circuits to its limits. New generations of processors, DSPs or FPGAs are able to process information with high speed and high consumption or to wait in low power mode with minimum possible consumption. This huge variation in power consumption and the short time needed to change from one level to another, affect the specifications of the Voltage Regulated Module (VRM) that supplies the IC. Furthermore, additional mandatory features, such as Adaptive Voltage Positioning (AVP) and Dynamic Voltage Scaling (DVS), impose opposite trends on the design of the VRM power stage. In order to cope with high load-step amplitudes, the output capacitor of the VRM power stage output filter is drastically oversized, penalizing power density and the efficiency during the DVS operation. Therefore, the ongoing research trend is directed to improve the dynamic response of the VRM while reducing the size of the output capacitor. The output capacitor reduction leads to a smaller cost and longer life-time of the system since the big bulk capacitors, usually implemented with OSCON capacitors, may not be needed to achieve the desired dynamic behavior. An additional advantage is that, by reducing the output capacitance, dynamic voltage scaling (DVS) can be performed faster and with smaller stress on the power stage, since the needed amount of charge to change the output voltage is smaller. The dynamic behavior of the system with a linear control (Voltage mode control, VMC, Peak Current Mode Control, PCMC,…) is limited by the converter switching frequency and filter size. The reduction of the output capacitor can be achieved by increasing the switching frequency of the converter, thus increasing the bandwidth of the system, and/or by applying advanced non-linear controls. Applying nonlinear control, the system variables get saturated in order to reach the new steady-state in a minimum time, thus the output filter, more specifically the output inductor current slew-rate, determines the output voltage response. Therefore, by reducing the output inductor value, the inductor current reaches faster the new steady state, so a smaller amount of charge is taken from the output capacitor during the transient. The drawback of this approach is that the system efficiency is penalized due to increased switching losses and RMS currents. In order to achieve both the output capacitor reduction and high system efficiency, while satisfying strict dynamic specifications, a Multiphase converter system is adopted as a standard for VRM applications. In order to ensure the current sharing among the phases, the multiphase converter is usually implemented with current mode control. In order to overcome the limitation imposed by the output filter, the second possibility to reduce the output capacitor is to apply Topologic modifications of the basic power stage topology in order to increase the slew-rate of the inductor current and, therefore, reduce the transient duration. Since the transient is reduced, smaller amount of charge is taken from the output capacitor under the same load current, thus, the output capacitor can be reduced to achieve the same output voltage deviation. The third possibility to reduce the output capacitor of the converter is to introduce an additional energy path (AEP) to compensate the charge unbalance of the output capacitor, consequently reducing the transient time and output voltage deviation. Doing so, during the steady-state operation the system has high efficiency because the main low-bandwidth converter is designed to operate at moderate switching frequency, to meet the static requirements, whereas the dynamic behavior during the transients is determined by the high-bandwidth auxiliary energy path. The auxiliary energy path can be implemented as a resistive path, as a Linear regulator, LR, or as a switching converter. The first two implementations provide higher bandwidth, at the expense of increasing losses during the transient. On the other hand, the switching converter implementation presents lower bandwidth, limited by the auxiliary converter switching frequency, though it produces smaller losses compared to the two previous implementations. Depending on the application, the implementation and the control strategy of the system, there is a variety of proposed solutions in the State-of-the-Art (SoA), having different features where one solution offers some advantages over the others, but also some disadvantages. In general, an ideal additional energy path system should have the following features: 1. The impact on the system losses should be minimal. During its operation, the AEP generates additional losses, thus ideally, the AEP should operate for a short period of time, only when the transient is occurring; the other option is to have the AEP constantly on, but due to the inductor current ripple compensation at the output, unnecessary losses are generated. 2. The AEP should be activated nearly instantaneously to prevent bigger output voltage deviation. To achieve near instantaneous activation, the converter system can be informed by the load prior to the load-step or the system can observe the output capacitor current, which is the first system state variable that reacts on the load current perturbation. In this manner, the AEP is turned on with near zero output voltage error, providing smaller output voltage deviation. 3. The AEP should be deactivated once the new steady state is reached to avoid additional settling transients. Most of the SoA solutions estimate duration of the transient which may cause additional transient if the estimation is not performed correctly (e.g. if the main converter inductor current has higher or lower value than needed, the slow regulator of the main converter needs to compensate the difference after the AEP is deactivated). Other SoA solutions are observing state variables, ensuring that the system reaches the new steady state or they are informed by the load. 4. During the transient, at least one subsystem, either the main converter or the AEP, should be in closed-loop. Implementing a closed loop system, preferably the AEP subsystem, due its higher bandwidth, increases the robustness under system tolerances and circuit parasitic. In addition, the AEP can operate with any type of load. The solutions that operate in open loop usually perform minimum time charge balance control, thus reducing the transient length and minimizing the impact on the losses, however they are very sensitive to tolerances and parasitics. 5. The AEP should inject current at the output in a controlled manner, thus reducing the risk of high and potentially damaging currents and increasing robustness on the input voltage deviation. This issue is mainly related to the systems where AEP is implemented as auxiliary converter. The auxiliary converter is designed for small power and, as such, the MOSFETs are rated for small power/currents. If the current is not controlled, due to the some unpredicted spike in input voltage caused by some other part of the system (e.g. different converter), it may lead to a current spike in auxiliary current which will cause the perturbation of the output voltage and even failure of the switching components of auxiliary converter. In the case when the current is controlled, using peak CMC or Hysteretic Window CMC, the auxiliary converter has inherent feed-forwarding of the input voltage in current control and the current is defined and limited. Furthermore, if the solution employs charge balance control, the system may perform poorly if the input voltage has different value than the nominal, causing that AEP injects/extracts more/less charge than needed. 6. Scalability of the system to multiphase converters. As commented previously, in VRM applications, due to the high load currents, the main converters are implemented as multiphase to redistribute losses among the modules, lowering temperature stress of the components. To ensure the current sharing, usually a Current Mode Control (CMC) is employed. The SoA solutions that are implemented with VMC are limited to a single stage implementation. This thesis proposes a novel control method of the energy flow through the AEP and the main converter system. The proposed concept relays on a controlled injection of the auxiliary current at the output node where the instantaneous current value is n-1 times bigger than the output capacitor current with appropriate directions. Doing so, the AEP creates an equivalent n times bigger virtual capacitor at the output, thus reducing the output impedance. Due to the fact that the proposed concept reduces the output impedance using the AEP, it has been named the Output Impedance Correction Circuit (OICC) concept. The concept is developed for a multiphase CMC synchronous buck converter (including a single phase implementation), operating with a constant output voltage and with AVP feature. Further, it is extended to a single phase VMC synchronous buck converter. During the operation, the main converter voltage loop and the OICC subsystem capacitor current loop is constantly closed, increasing the robustness under system tolerances and circuit parasitic and allowing the system to operate with any load-current shape or pattern. According to the proposed control method, the system operates in two states: during the steady-state the system is in the Idle state and the OICC subsystem is deactivated, while during the load-step transient the system is in the Active state and the OICC subsystem is activated in order to reduce the output impedance. The state changes are performed autonomously: the system enters in the Active state by observing the output capacitor current and it returns back to the Idle state when the steady-state operation is detected by observing the state variables. The validation of the OICC concept has been done by applying it to a 30W two phase synchronous buck converter with 140μF output capacitor and with the multiplication factor n equal to 15, generating during the Active state equivalent output capacitor of 2.1mF. The OICC subsystem is implemented as single phase PCMC synchronous buck converter. Comparing the converter operation with and without the OICC the results demonstrate that the 12 times reduction of the output voltage deviation is achieved, for both basic operation and for the AVP operation. Furthermore, the results have been compared to a reference prototype which has the same power stage and a fiscal output capacitor of 2.1mF. The results show that the two systems have the same dynamic behavior. Moreover, an impact on the system losses under the pulsating load and DVS operation has been quantified and it has been demonstrated that the OICC system has improved the system efficiency, considering the losses when the system operates with the pulsating load and the DVS operation. Lastly, the output capacitor of the OICC system is much smaller than the reference design output capacitor, therefore, by applying the OICC concept the power density can be increased. In summary, the main contributions of the thesis are: • The proposed Output Impedance Correction Circuit (OICC) concept, • The system level control based on the used approach to change the states of operation, • The OICC subsystem closed-loop implementation, together with the main converter implementation, • The dynamic losses under the pulsating load and the DVS operation quantification, and • The system robustness on the capacitor impedance variation and consecutive load-steps.

Nonlinear normal modes in mechanical systems: concept and computation with numerical continuation

The purpose of this Project is, first and foremost, to disclose the topic of nonlinear vibrations and oscillations in mechanical systems and, namely, nonlinear normal modes NNMs to a greater audience of researchers and technicians. To do so, first of all, the dynamical behavior and properties of nonlinear mechanical systems is outlined from the analysis of a pair of exemplary models with the harmonic balanced method. The conclusions drawn are contrasted with the Linear Vibration Theory. Then, it is argued how the nonlinear normal modes could, in spite of their limitations, predict the frequency response of a mechanical system. After discussing those introductory concepts, I present a Matlab package called 'NNMcont' developed by a group of researchers from the University of Liege. This package allows the analysis of nonlinear normal modes of vibration in a range of mechanical systems as extensions of the linear modes. This package relies on numerical methods and a 'continuation algorithm' for the computation of the nonlinear normal modes of a conservative mechanical system. In order to prove its functionality, a two degrees of freedom mechanical system with elastic nonlinearities is analized. This model comprises a mass suspended on a foundation by means of a spring-viscous damper mechanism -analogous to a very simplified model of most suspended structures and machines- that has attached a mass damper as a passive vibration control system. The results of the computation are displayed on frequency energy plots showing the NNMs branches along with modal curves and time-series plots for each normal mode. Finally, a critical analysis of the results obtained is carried out with an eye on devising what they can tell the researcher about the dynamical properties of the system.

Dual roles for DNA sequence identity and the mismatch repair system in the regulation of mitotic crossing-over in yeast

Sequence divergence acts as a potent barrier to homologous recombination; much of this barrier derives from an antirecombination activity exerted by mismatch repair proteins. An inverted repeat assay system with recombination substrates ranging in identity from 74% to 100% has been used to define the relationship between sequence divergence and the rate of mitotic crossing-over in yeast. To elucidate the role of the mismatch repair machinery in regulating recombination between mismatched substrates, we performed experiments in both wild-type and mismatch repair defective strains. We find that a single mismatch is sufficient to inhibit recombination between otherwise identical sequences, and that this inhibition is dependent on the mismatch repair system. Additional mismatches have a cumulative negative effect on the recombination rate. With sequence divergence of up to approximately 10%, the inhibitory effect of mismatches results mainly from antirecombination activity of the mismatch repair system. With greater levels of divergence, recombination is inefficient even in the absence of mismatch repair activity. In both wild-type and mismatch repair defective strains, an approximate log-linear relationship is observed between the recombination rate and the level of sequence divergence.

A three-hybrid system for detecting small ligand–protein receptor interactions

Small ligand–receptor interactions underlie many fundamental processes in biology and form the basis for pharmacological intervention of human diseases in medicine. We report herein a genetic system, named the yeast three-hybrid system, for detecting ligand–receptor interactions in vivo. This system is adapted from the yeast two-hybrid system with which a third synthetic hybrid ligand is combined. The feasibility of this system was demonstrated using as the hybrid ligand a heterodimer of covalently linked dexamethasone and FK506. Yeast expressing fusion proteins of the hormone binding domain of the rat glucocorticoid receptor fused to the LexA DNA-binding domain and of FKBP12 fused to a transcriptional activation domain activated reporter genes when plated on medium containing the dexamethasone–FK506 heterodimer. The reporter gene activation is completely abrogated in a competitive manner by the presence of excess FK506. Using this system, we screened a Jurkat cDNA library fused to the transcriptional activation domain in yeast expressing the hormone binding domain of rat glucocorticoid receptor–LexA DNA binding domain fusion protein in the presence of dexamethasone–FK506 heterodimer. We isolated overlapping clones of human FKBP12. These results demonstrate that the three-hybrid system can be used to discover receptors for small ligands and to screen for new ligands to known receptors.

Genetic footprinting with mariner-based transposition in Pseudomonas aeruginosa

The complete DNA sequence of Pseudomonas aeruginosa provides an opportunity to apply functional genomics to a major human pathogen. A comparative genomics approach combined with genetic footprinting was used as a strategy to identify genes required for viability in P. aeruginosa. Use of a highly efficient in vivo mariner transposition system in P. aeruginosa facilitated the analysis of candidate genes of this class. We have developed a rapid and efficient allelic exchange system by using the I-SceI homing endonuclease in conjunction with in vitro mariner mutagenesis to generate mutants within targeted regions of the P. aeruginosa chromosome for genetic footprinting analyses. This technique for generating transposon insertion mutants should be widely applicable to other organisms that are not naturally transformable or may lack well developed in vivo transposition systems. We tested this system with three genes in P. aeruginosa that have putative essential homologs in Haemophilus influenzae. We show that one of three H. influenzae essential gene homologs is needed for growth in P. aeruginosa, validating the practicality of this comparative genomics strategy to identify essential genes in P. aeruginosa.

A novel tetracycline-dependent transactivator with E2F4 transcriptional activation domain

A tetracycline-controlled gene expression system provides a powerful tool to dissect the functions of gene products. However, it often appears difficult to establish cell lines or transgenic animals stably expressing tetracycline-dependent transactivators, possibly as a result of toxicity of the transactivator domains used. In order to overcome this problem, we developed a novel tetracycline-dependent transactivator that works efficiently in mammalian cells. This transactivator is a fusion of the tet reverse repressor mutant and the transcriptional activating domain of human E2F4, which is ubiquitously expressed in vivo. We demonstrate here that this tetracycline-regulated gene expression system provides a two log transcriptional activation in mammalian cells as assessed by northern blot and luciferase analyses. Combining this system with green fluorescent protein reporter systems or microarray gene expression profiling will facilitate the study of gene function.

Identification of GIT1/Cat-1 as a substrate molecule of protein tyrosine phosphatase ζ/β by the yeast substrate-trapping system

We used a genetic method, the yeast substrate-trapping system, to identify substrates for protein tyrosine phosphatases ζ (PTPζ/RPTPβ). This method is based on the yeast two-hybrid system, with two essential modifications: conditional expression of protein tyrosine kinase v-src (active src) to tyrosine-phosphorylate the prey proteins and screening by using a substrate-trap mutant of PTPζ (PTPζ-D1902A) as bait. By using this system, several substrate candidates for PTPζ were isolated. Among them, GIT1/Cat-1 (G protein-coupled receptor kinase-interactor 1/Cool-associated, tyrosine-phosphorylated 1) was examined further. GIT1/Cat-1 bound to PTPζ-D1902A dependent on the substrate tyrosine phosphorylation. Tyrosine-phosphorylated GIT1/Cat-1 was dephosphorylated by PTPζ in vitro. Immunoprecipitation experiments indicated that PTPζ-D1902A and GIT1/Cat-1 form a stable complex also in mammalian cells. Immunohistochemical analyses revealed that PTPζ and GIT1/Cat-1 were colocalized in the processes of pyramidal cells in the hippocampus and neocortex in rat brain. Subcellular colocalization was further verified in the growth cones of mossy fibers from pontine explants and in the ruffling membranes and processes of B103 neuroblastoma cells. Moreover, pleiotrophin, a ligand for PTPζ, increased tyrosine phosphorylation of GIT1/Cat-1 in B103 cells. All these results indicate that GIT1/Cat-1 is a substrate molecule of PTPζ.

Creation of a reversible on/off system for site-specific in vivo control of exogenous gene activity in the renal glomerulus.

Using genetically engineered glomerular mesangial cells, an in vivo gene transfer approach was developed that specifically targets the renal glomerulus. By combining this system with a tetracycline (Tc)-responsive promoter, the present study aimed to create a reversible on/off system for site-specific in vivo control of exogenous gene activity within the glomerulus. In the Tc regulatory system, a Tc-controlled transactivator (tTA) encoded by a regulator plasmid induces target gene transcription by binding to a tTA-responsive promoter located in a response plasmid. Tc inhibits this tTA-dependent transactivation via its affinity for tTA. In double-transfected cells, therefore, the activity of a transgene can be controlled by Tc. Cultured rat mesangial cells were cotransfected with a regulator plasmid and a response plasmid that introduces a beta-galactosidase gene. In vitro, stable double-transfectant MtTAG cells exhibited no beta-galactosidase activity in the presence of Tc. However, following withdrawal of Tc from culture media, expression of beta-galactosidase was induced within 24 h. When Tc was again added, the expression was rapidly resuppressed. Low concentrations of Tc were sufficient to maintain the silent state of tTA-dependent promoter. MtTAG cells were then transferred into the rat glomeruli via renal artery injection. In the isolated chimeric glomeruli, expression of beta-galactosidase was induced ex vivo in the absence of Tc, whereas it was repressed in its presence. When Tc-pretreated MtTAG cells were transferred into the glomeruli of untreated rats, beta-galactosidase expression was induced in vivo within 3 days. Oral administration of Tc dramatically suppressed this induction. These data demonstrate the feasibility of using mesangial cell vectors combined with the Tc regulatory system for site-specific in vivo control of exogenous gene expression in the glomerulus.

Polynitrosylated proteins: characterization, bioactivity, and functional consequences.

Chemical modification of proteins is a common theme in their regulation. Nitrosylation of protein sulfhydryl groups has been shown to confer nitric oxide (NO)-like biological activities and to regulate protein functions. Several other nucleophilic side chains -- including those with hydroxyls, amines, and aromatic carbons -- are also potentially susceptible to nitrosative attack. Therefore, we examined the reactivity and functional consequences of nitros(yl)ation at a variety of nucleophilic centers in biological molecules. Chemical analysis and spectroscopic studies show that nitrosation reactions are sustained at sulfur, oxygen, nitrogen, and aromatic carbon centers, with thiols being the most reactive functionality. The exemplary protein, BSA, in the presence of a 1-, 20-, 100-, or 200-fold excess of nitrosating equivalents removes 0.6 +/- 0.2, 3.2 +/- 0.4, 18 +/- 4, and 38 +/- 10, respectively, moles of NO equivalents per mole of BSA from the reaction medium; spectroscopic evidence shows the proportionate formation of a polynitrosylated protein. Analogous reaction of tissue-type plasminogen activator yields comparable NO protein stoichiometries. Disruption of protein tertiary structure by reduction results in the preferential nitrosylation of up to 20 thus-exposed thiol groups. The polynitrosylated proteins exhibit antiplatelet and vasodilator activity that increases with the degree of nitrosation, but S-nitroso derivatives show the greatest NO-related bioactivity. Studies on enzymatic activity of tissue-type plasminogen activator show that polynitrosylation may lead to attenuated function. Moreover, the reactivity of tyrosine residues in proteins raises the possibility that NO could disrupt processes regulated by phosphorylation. Polynitrosylated proteins were found in reaction mixtures containing interferon-gamma/lipopolysaccharide-stimulated macrophages and in tracheal secretions of subjects treated with NO gas, thus suggesting their physiological relevance. In conclusion, multiple sites on proteins are susceptible to attack by nitrogen oxides. Thiol groups are preferentially modified, supporting the notion that S-nitrosylation can serve to regulate protein function. Nitrosation reactions sustained at additional nucleophilic centers may have (patho)physiological significance and suggest a facile route by which abundant NO bioactivity can be delivered to a biological system, with specificity dictated by protein substrate.

Identification of receptor ligands and receptor subtypes using antagonists in a capillary electrophoresis single-cell biosensor separation system.

A capillary electrophoresis system with single-cell biosensors as a detector has been used to separate and identify ligands in complex biological samples. The power of this procedure was significantly increased by introducing antagonists that inhibited the cellular response from selected ligand-receptor interactions. The single-cell biosensor was based on the ligand-receptor binding and G-protein-mediated signal transduction pathways in PC12 and NG108-15 cell lines. Receptor activation was measured as increases in cytosolic free calcium ion concentration by using fluorescence microscopy with the intracellular calcium ion indicator fluo-3-acetoxymethyl ester. Specifically, a mixture of bradykinin (BK) and acetylcholine (ACh) was fractionated and the components were identified by inhibiting the cellular response with icatibant (HOE 140), a selective antagonist to the BK B2 receptor subtype (B2BK), and atropine, an antagonist to muscarinic ACh receptor subtypes. Structurally related forms of BK were also identified based on inhibiting B2BK receptors. Applications of this technique include identification of endogenous BK in a lysate of human hepatocellular carcinoma cells (Hep G2) and screening for bioactivity of BK degradation products in human blood plasma. The data demonstrate that the use of antagonists with a single-cell biosensor separation system aids identification of separated components and receptor subtypes.

A modified tetracycline-regulated system provides autoregulatory, inducible gene expression in cultured cells and transgenic mice.

A system for tetracycline-regulated inducible gene expression was described recently which relies on constitutive expression of a tetracycline-controlled transactivator (tTA) fusion protein combining the tetracycline repressor and the transcriptional activation domain of VP16 [Gossen, M. & Bujard, H. (1992) Proc. Natl. Acad. Sci. USA 89, 5547-5551]. This system yielded only low levels of transactivator protein, probably because tTA is toxic. To avoid this difficulty, we placed the tTA gene under the control of the inducible promoter to which tTA binds, making expression of tTA itself inducible and autoregulatory. When used to drive expression of the recombination activating genes 1 and 2 (RAG-1 and RAG-2), the autoregulatory system yielded both substantially higher levels of variable (diversity) joining [V(D)J] recombination activity (70-fold on average) and inducible expression in a much larger fraction of transfected cells (autoregulatory, 90%, vs. constitutive, 18%). In addition, this system allowed the creation of transgenic mice in which expression of a luciferase transgene was inducible tens to hundreds of times the basal levels in most tissues examined. Induced levels of expression were highest in thymus and lung and appear to be substantially higher than in previously reported inducible luciferase transgenic mice created with the constitutive system. With the modified system, inducible transactivator mRNA and protein were easily detected in cell lines by RNA and Western blotting, and transactivator mRNA was detected by RNA blotting in some tissues of transgenic mice. This autoregulatory system represents an improved strategy for tetracycline-regulated gene expression both in cultured cells and in transgenic animals.

Ocorrência e remoção dos protozoários patogênicos Giardia spp. e Cryptosporidium spp. em sistemas de tratamento de esgoto sanitário

O propósito do presente estudo foi investigar e monitorar a remoção de cistos de Giardia spp. e oocistos de Cryptosporidium spp. por diferentes processos de uma estação de tratamento de esgoto (ETE) em escala plena, composta basicamente por tratamento preliminar, reator UASB e flotador por ar dissolvido, e verificar a ocorrência desses protozoários no lodo do reator UASB e do flotador. Além disso, avaliou-se a remoção desses parasitos pelo processo de flotação por ar dissolvido em escala de bancada (equipamento Flotateste). Analisou-se a qualidade das amostras a partir de variáveis físicas e químicas, e pela detecção de microrganismos indicadores - E. coli, coliformes totais e Clostridium perfringens. Os métodos de detecção de protozoários se basearam nas etapas de concentração (tripla centrifugação ou filtração em membrana seguida de tripla centrifugação); purificação por separação imunomagnética (IMS); detecção por reação de imunofluorescência direta (RID). As recuperações de cistos variaram de 32,6 a 67,0 % dependendo do método adotado, já para os oocistos as recuperações estiveram na faixa de 5,6 a 12,0 %. Na ETE-Monjolinho foram detectadas significativas quantidades de cistos de Giardia spp. em 100% das amostras de esgoto analisadas, com concentração média de 1,89 x 104 e 2,35 x 102 cistos.L-1 no esgoto bruto e tratado, respectivamente. Já os oocistos de Cryptosporidium spp. foram detectados em 39,0 % das amostras de esgoto, com concentração média de 1,35 x 102 oocistos.L-1 no esgoto bruto e 5,87 oocistos.L-1 em esgoto tratado (após flotador). A remoção global da ETE para remoção de Giardia spp. foi em média 2,03 log. O lodo do reator UASB e lodo do flotador apresentaram altas quantidade de (oo)cistos, constatando-se a tendência desses sistemas em concentrar os (oo)cistos por seus processos físicos. Algumas correlações significativas foram encontradas, como correlação entre a concentração de cistos no lodo e a variável sólidos totais, a concentração de cistos no esgoto bruto e as variáveis cor aparente, DQO total e particulada, e a concentração de cistos no efluente UASB e o microrganismo Clostridium perfringens. Diferentemente do flotador em escala plena, o processo do flotação por ar dissolvido em escala de bancada alcançou elevadas remoções médias de cistos de Giardia spp., entre 2,5 e 2,7 log nas diferentes condições de floculação estudadas.