Dynamic Response Optimization of Vehicles through Efficient Multibody Formulations and Automatic Differentiation Techniques

El diseño y desarrollo de sistemas de suspensión para vehículos se basa cada día más en el diseño por ordenador y en herramientas de análisis por ordenador, las cuales permiten anticipar problemas y resolverlos por adelantado. El comportamiento y las características dinámicas se calculan con precisión, bajo coste, y recursos y tiempos de cálculo reducidos. Sin embargo, existe una componente iterativa en el proceso, que requiere la definición manual de diseños a través de técnicas “prueba y error”. Esta Tesis da un paso hacia el desarrollo de un entorno de simulación eficiente capaz de simular, analizar y evaluar diseños de suspensiones vehiculares, y de mejorarlos hacia la solución optima mediante la modificación de los parámetros de diseño. La modelización mediante sistemas multicuerpo se utiliza aquí para desarrollar un modelo de autocar con 18 grados de libertad, de manera detallada y eficiente. La geometría y demás características de la suspensión se ajustan a las del vehículo real, así como los demás parámetros del modelo. Para simular la dinámica vehicular, se utiliza una formulación multicuerpo moderna y eficiente basada en las ecuaciones de Maggi, a la que se ha incorporado un visor 3D. Así, se consigue simular maniobras vehiculares en tiempos inferiores al tiempo real. Una vez que la dinámica está disponible, los análisis de sensibilidad son cruciales para una optimización robusta y eficiente. Para ello, se presenta una técnica matemática que permite derivar las variables dinámicas dentro de la formulación, de forma algorítmica, general, con la precisión de la maquina, y razonablemente eficiente: la diferenciación automática. Este método propaga las derivadas con respecto a las variables de diseño a través del código informático y con poca intervención del usuario. En contraste con otros enfoques en la bibliografía, generalmente particulares y limitados, se realiza una comparación de librerías, se desarrolla una formulación híbrida directa-automática para el cálculo de sensibilidades, y se presentan varios ejemplos reales. Finalmente, se lleva a cabo la optimización de la respuesta dinámica del vehículo citado. Se analizan cuatro tipos distintos de optimización: identificación de parámetros, optimización de la maniobrabilidad, optimización del confort y optimización multi-objetivo, todos ellos aplicados al diseño del autocar. Además de resultados analíticos y gráficos, se incluyen algunas consideraciones acerca de la eficiencia. En resumen, se mejora el comportamiento dinámico de vehículos por medio de modelos multicuerpo y de técnicas de diferenciación automática y optimización avanzadas, posibilitando un ajuste automático, preciso y eficiente de los parámetros de diseño. ABSTRACT Each day, the design and development of vehicle suspension systems relies more on computer-aided design and computer-aided engineering tools, which allow anticipating the problems and solving them ahead of time. Dynamic behavior and characteristics are thus simulated accurately and inexpensively with moderate computational times and resources. There is, however, an iterative component in the process, which involves the manual definition of designs in a trialand-error manner. This Thesis takes a step towards the development of an efficient simulation framework capable of simulating, analyzing and evaluating vehicle suspension designs, and automatically improving them by varying the design parameters towards the optimal solution. The multibody systems approach is hereby used to model a three-dimensional 18-degrees-of-freedom coach in a comprehensive yet efficient way. The suspension geometry and characteristics resemble the ones from the real vehicle, as do the rest of vehicle parameters. In order to simulate vehicle dynamics, an efficient, state-of-the-art multibody formulation based on Maggi’s equations is employed, and a three-dimensional graphics viewer is developed. As a result, vehicle maneuvers can be simulated faster than real-time. Once the dynamics are ready, a sensitivity analysis is crucial for a robust optimization. To that end, a mathematical technique is introduced, which allows differentiating the dynamic variables within the multibody formulation in a general, algorithmic, accurate to machine precision, and reasonably efficient way: automatic differentiation. This method propagates the derivatives with respect to the design parameters throughout the computer code, with little user interaction. In contrast with other attempts in the literature, mostly not generalpurpose, a benchmarking of libraries is carried out, a hybrid direct-automatic differentiation approach for the computation of sensitivities is developed, and several real-life examples are analyzed. Finally, a design optimization process of the aforementioned vehicle is carried out. Four different types of dynamic response optimization are presented: parameter identification, handling optimization, ride comfort optimization and multi-objective optimization; all of which are applied to the design of the coach example. Together with analytical and visual proof of the results, efficiency considerations are made. In summary, the dynamic behavior of vehicles is improved by using the multibody systems approach, along with advanced differentiation and optimization techniques, enabling an automatic, accurate and efficient tuning of design parameters.

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.

hMutSα- and hMutLα-dependent phosphorylation of p53 in response to DNA methylator damage

hMSH2⋅hMSH6 heterodimer (hMutSα) and hMLH1⋅hPMS2 complex (hMutLα) have been implicated in the cytotoxic response of mammalian cells to a number of DNA-damaging compounds, including methylating agents that produce O6-methylguanine (O6MeG) adducts. This study demonstrates that O6MeG lesions, in which the damaged base is paired with either T or C, are subject to excision repair in a reaction that depends on a functional mismatch repair system. Furthermore, treatment of human cells with the SN1 DNA methylators N-methyl-N-nitrosourea or N-methyl-N′-nitro-N-nitrosoguanidine results in p53 phosphorylation on serine residues 15 and 392, and these phosphorylation events depend on the presence of functional hMutSα and hMutLα. Coupled with the previous demonstration that O6MeG⋅T and O6MeG⋅C pairs are recognized by hMutSα, these results implicate action of the mismatch repair system in the initial step of a damage-signaling cascade that can lead to cell-cycle checkpoint activation or cell death in response to DNA methylator damage.

The 9-cis-epoxycarotenoid cleavage reaction is the key regulatory step of abscisic acid biosynthesis in water-stressed bean

Abscisic acid (ABA), a cleavage product of carotenoids, is involved in stress responses in plants. A well known response of plants to water stress is accumulation of ABA, which is caused by de novo synthesis. The limiting step of ABA biosynthesis in plants is presumably the cleavage of 9-cis-epoxycarotenoids, the first committed step of ABA biosynthesis. This step generates the C15 intermediate xanthoxin and C25-apocarotenoids. A cDNA, PvNCED1, was cloned from wilted bean (Phaseolus vulgaris L.) leaves. The 2,398-bp full-length PvNCED1 has an ORF of 615 aa and encodes a 68-kDa protein. The PvNCED1 protein is imported into chloroplasts, where it is associated with the thylakoids. The recombinant protein PvNCED1 catalyzes the cleavage of 9-cis-violaxanthin and 9′-cis-neoxanthin, so that the enzyme is referred to as 9-cis-epoxycarotenoid dioxygenase. When detached bean leaves were water stressed, ABA accumulation was preceded by large increases in PvNCED1 mRNA and protein levels. Conversely, rehydration of stressed leaves caused a rapid decrease in PvNCED1 mRNA, protein, and ABA levels. In bean roots, a similar correlation among PvNCED1 mRNA, protein, and ABA levels was observed. However, the ABA content was much less than in leaves, presumably because of the much smaller carotenoid precursor pool in roots than in leaves. At 7°C, PvNCED1 mRNA and ABA were slowly induced by water stress, but, at 2°C, neither accumulated. The results provide evidence that drought-induced ABA biosynthesis is regulated by the 9-cis-epoxycarotenoid cleavage reaction and that this reaction takes place in the thylakoids, where the carotenoid substrate is located.

Fluid-Phase Markers in the Basolateral Endocytic Pathway Accumulate in Response to the Actin Assembly-promoting Drug Jasplakinolide

To investigate the role of filamentous actin in the endocytic pathway, we used the cell-permeant drug Jasplakinolide (JAS) to polymerize actin in intact polarized Madin–Darby canine kidney (MDCK) cells. The uptake and accumulation of the fluid-phase markers fluorescein isothiocyanate (FITC)-dextran and horseradish peroxidase (HRP) were followed in JAS-treated or untreated cells with confocal fluorescence microscopy, biochemical assays, and electron microscopy. Pretreatment with JAS increased the uptake and accumulation of fluid-phase markers in MDCK cells. JAS increased endocytosis in a polarized manner, with a marked effect on fluid-phase uptake from the basolateral surface but not from the apical surface of polarized MDCK cells. The early uptake of FITC-dextran and HRP was increased more than twofold in JAS-treated cells. At later times, FITC-dextran and HRP accumulated in clustered endosomes in the basal and middle regions of JAS-treated cells. The large accumulated endosomes were similar to late endosomes but they were not colabeled for other late endosome markers, such as rab7 or mannose-6-phosphate receptor. JAS altered transport in the endocytic pathway at a later stage than the microtubule-dependent step affected by nocodazole. JAS also had a notable effect on cell morphology, inducing membrane bunching at the apical pole of MDCK cells. Although other studies have implicated actin in endocytosis at the apical cell surface, our results provide novel evidence that filamentous actin is also involved in the endocytosis of fluid-phase markers from the basolateral membrane of polarized cells.

Guanidine hydrochloride blocks a critical step in the propagation of the prion-like determinant [PSI+] of Saccharomyces cerevisiae

The cytoplasmic heritable determinant [PSI+] of the yeast Saccharomyces cerevisiae reflects the prion-like properties of the chromosome-encoded protein Sup35p. This protein is known to be an essential eukaryote polypeptide release factor, namely eRF3. In a [PSI+] background, the prion conformer of Sup35p forms large oligomers, which results in the intracellular depletion of functional release factor and hence inefficient translation termination. We have investigated the process by which the [PSI+] determinant can be efficiently eliminated from strains, by growth in the presence of the protein denaturant guanidine hydrochloride (GuHCl). Strains are “cured” of [PSI+] by millimolar concentrations of GuHCl, well below that normally required for protein denaturation. Here we provide evidence indicating that the elimination of the [PSI+] determinant is not derived from the direct dissolution of self-replicating [PSI+] seeds by GuHCl. Although GuHCl does elicit a moderate stress response, the elimination of [PSI+] is not enhanced by stress, and furthermore, exhibits an absolute requirement for continued cell division. We propose that GuHCl inhibits a critical event in the propagation of the prion conformer and demonstrate that the kinetics of curing by GuHCl fit a random segregation model whereby the heritable [PSI+] element is diluted from a culture, after the total inhibition of prion replication by GuHCl.

Virus-encoded suppressor of posttranscriptional gene silencing targets a maintenance step in the silencing pathway

Certain plant viruses encode suppressors of posttranscriptional gene silencing (PTGS), an adaptive antiviral defense response that limits virus replication and spread. The tobacco etch potyvirus protein, helper component-proteinase (HC-Pro), suppresses PTGS of silenced transgenes. The effect of HC-Pro on different steps of the silencing pathway was analyzed by using both transient Agrobacterium tumefaciens-based delivery and transgenic systems. HC-Pro inactivated PTGS in plants containing a preexisting silenced β-glucuronidase (GUS) transgene. PTGS in this system was associated with both small RNA molecules (21–26 nt) corresponding to the 3′ proximal region of the transcribed GUS sequence and cytosine methylation of specific sites near the 3′ end of the GUS transgene. Introduction of HC-Pro into these plants resulted in loss of PTGS, loss of small RNAs, and partial loss of methylation. These results suggest that HC-Pro targets a PTGS maintenance (as opposed to an initiation or signaling) component at a point that affects accumulation of small RNAs and methylation of genomic DNA.

STAT3 activation is a critical step in gp130-mediated terminal differentiation and growth arrest of a myeloid cell line.

Myeloid leukemia M1 cells can be induced for growth arrest and terminal differentiation into macrophages in response to interleukin 6 (IL-6) or leukemia inhibitory factor (LIF). Recently, a large number of cytokines and growth factors have been shown to activate the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling pathway. In the case of IL-6 and LIF, which share a signal transducing receptor gp130, STAT3 is specifically tyrosine-phosphorylated and activated by stimulation with each cytokine in various cell types. To know the role of JAK-STAT pathway in M1 differentiation, we have constructed dominant negative forms of STAT3 and established M1 cell lines that constitutively express them. These M1 cells that overexpressed dominant negative forms showed no induction of differentiation-associated markers including Fc gamma receptors, ferritin light chain, and lysozyme after treatment with IL-6. Expression of either c-myb or c-myc was not downregulated. Furthermore, IL-6- and LIF-mediated growth arrest and apoptosis were completely blocked. Thus these findings demonstrate that STAT3 activation is the critical step in a cascade of events that leads to terminal differentiation of M1 cells.

Ethanol inhibits luteinizing hormone-releasing hormone (LHRH) secretion by blocking the response of LHRH neuronal terminals to nitric oxide.

It has previously been shown that alcohol can suppress reproduction in humans, monkeys, and small rodents by inhibiting release of luteinizing hormone (LH). The principal action is via suppression of the release of LH-releasing hormone (LHRH) both in vivo and in vitro. The present experiments were designed to determine the mechanism by which alcohol inhibits LHRH release. Previous research has indicated that the release of LHRH is controlled by nitric oxide (NO). The proposed pathway is via norepinephrine-induced release of NO from NOergic neurons, which then activates LHRH release. In the present experiments, we further evaluated the details of this mechanism in male rats by incubating medial basal hypothalamic (MBH) explants in vitro and examining the release of NO, prostaglandin E2 (PGE2), conversion of arachidonic acid to prostanoids, and production of cGMP. The results have provided further support for our theory of LHRH control. Norepinephrine increased the release of NO as measured by conversion of [14C]arginine to [14C]citrulline, and this increase was blocked by the alpha 1 receptor blocker prazosin. Furthermore, the release of LHRH induced by nitroprusside (NP), a donor of NO, is related to the activation of soluble guanylate cyclase by NO since NP increased cGMP release from MBHs and cGMP also released LHRH. Ethanol had no effect on the production of NO by MBH explants or the increased release of NO induced by norepinephrine. Therefore, it does not act at that step in the pathway. Ethanol also failed to affect the increase in cGMP induced by NP. On the other hand, as might be expected from previous experiments indicating that LHRH release was brought about by PGE2, NP increased the conversion of [14C]arachidonic acid to its metabolites, particularly PGE2. Ethanol completely blocked the release of LHRH induced by NP and the increase in PGE2 induced by NP. Therefore, the results support the theory that norepinephrine acts to stimulate NO release from NOergic neurons. This NO diffuses to the LHRH terminals where it activates guanylate cyclase, leading to an increase in cGMP. At the same time, it also activates cyclooxygenase. The increase in cGMP increases intracellular free calcium, activating phospholipase A2 to provide arachidonic acid, the substrate for conversion by the activated cyclooxygenase to PGE2, which then activates the release of LHRH. Since alcohol inhibits the conversion of labeled arachidonic acid to PGE2, it must act either directly to inhibit cyclooxygenase or perhaps it may act by blocking the increase in intracellular free calcium induced by cGMP, which is crucial for activation of of both phospholipase A2 and cyclooxygenase.

Influence of Incidence Angle on the Coherent Copolar Polarimetric Response of Rice at X-Band

The coherent nature of the acquisition by TerraSAR-X of both copolar channels (HH and VV) enables the generation of many different polarimetric observables with physical interpretation, as have recently been used for monitoring rice fields. In this letter, the influence of incidence angle upon these polarimetric observables is analyzed by comparing three stacks of images that were acquired simultaneously at different incidence angles (22°, 30°, and 40°) during a whole cultivation campaign. We show that the response of observables related to dominance (entropy, ratios of components) and type of scattering mechanisms (alpha angles) is not greatly influenced by incidence angle at some stages: early and advanced vegetative phases, and maturation. Moreover, the acquisition geometry drives the sensitivity to the presence of the initial stems and tillers, being detected earlier at shallower angles. This analysis is a necessary step before studying potential methodologies for combining different orbits and beams for reducing the time between acquisitions for monitoring purposes.

River and Hillslope Response to Localized Uplift Along a Left Bend of the San Andreas Fault, Santa Cruz Mountains, CA

Studying landscape evolution of the Earthís surface is difficult because both tectonic forces and surface processes control its response to perturbation, and ultimately, its shape and form. Researchers often use numerical models to study erosional response to deformation because there are rarely natural settings in which we can evaluate both tectonic activity and topographic response over appropriate time scales (103-105 years). In certain locations, however, geologic conditions afford the unique opportunity to study the relationship between tectonics and topography. One such location is along the Dragonís Back Pressure Ridge in California, where the landscape moves over a structural discontinuity along the San Andreas Fault and landscape response to both the initiation and cessation of uplift can be observed. In their landmark study, Hilley and Arrowsmith (2008) found that geomorphic metrics such as channel steepness tracked uplift and that hillslope response lagged behind that of rivers. Ideal conditions such as uniform vegetation density and similar lithology allowed them to view each basin as a developmental stage of response to uplift only. Although this work represents a significant step forward in understanding landscape response to deformation, it remains unclear how these results translate to more geologically complex settings. In this study, I apply similar methodology to a left bend along the San Andreas Fault in the Santa Cruz Mountains, California. At this location, the landscape is translated through a zone of localized uplift caused by the bend, but vegetation, lithology, and structure vary. I examine the geomorphic response to uplift along the San Andreas Fault bend in order to determine whether predicted landscape patterns can be observed in a larger, more geologically complex setting than the Dragonís Back Pressure Ridge. I find that even with a larger-scale and a more complex setting, geomorphic metrics such as channel steepness index remain useful tools for evaluating landscape evolution through time. Steepness indices in selected streams of study record localized uplift caused by the restraining bend, while hillslope adjustment in the form of landsliding occurs over longer time scales. This project illustrates that it is possible to apply concepts of landscape evolution models to complex settings and is an important contribution to the body of geomorphological study.

Effector ExoU from the type III secretion system is an important modulator of gene expression in lung epithelial cells in response to Pseudomonas aeruginosa infection

Pseudomonas aeruginosa is an important pathogen in immunocompromised patients and secretes a diverse set of virulence factors that aid colonization and influence host cell defenses. An important early step in the establishment of infection is the production of type III-secreted effectors translocated into host cells by the bacteria. We used cDNA microarrays to compare the transcriptomic response of lung epithelial cells to P. aeruginosa mutants defective in type IV pili, the type III secretion apparatus, or in the production of specific type III-secreted effectors. Of the 18,000 cDNA clones analyzed, 55 were induced or repressed after 4 It of infection and could be classified into four different expression patterns. These include (i) host genes that are induced or repressed in a type III secretion-independent manner (32 clones), (ii) host genes induced specifically by ExoU (20 clones), and (iii) host genes induced in an ExoU-independent but type III secretion dependent manner (3 clones). In particular, ExoU was essential for the expression of immediate-early response genes, including the transcription factor c-Fos. ExoU-dependent gene expression was mediated in part by early and transient activation of the AN transcription factor complex. In conclusion, the present study provides a detailed insight into the response of epithelial cells to infection and indicates the significant role played by the type III virulence mechanism in the initial host response.

Characterisation of a harvesting step for monoclonal antibodies from mammalian cell culture

The focus of this research was defined by a poorly characterised filtration train employed to clarify culture broth containing monoclonal antibodies secreted by GS-NSO cells: the filtration train blinded unpredictably and the ability of the positively charged filters to adsorb DNA from process material was unknown. To direct the development of an assay to quantify the ability of depth filters to adsorb DNA, the molecular weight of DNA from a large-scale, fed-batch, mammalian cell culture vessel was evaluated as process material passed through the initial stages of the purification scheme. High molecular weight DNA was substantially cleared from the broth after passage through a disc stack centrifuge and the remaining low molecular weight DNA was largely unaffected by passage through a series of depth filters and a sterilising grade membrane. Removal of high molecular weight DNA was shown to be coupled with clarification of the process stream. The DNA from cell culture supernatant showed a pattern of internucleosomal cleavage of chromatin when fractionated by electrophoresis but the presence of both necrotic and apoptotic cells throughout the fermentation meant that the origin of the fragmented DNA could not be unequivocally determined. An intercalating fluorochrome, PicoGreen, was elected for development of a suitable DNA assay because of its ability to respond to low molecular weight DNA. It was assessed for its ability to determine the concentration of DNA in clarified mammalian cell culture broths containing pertinent monoclonal antibodies. Fluorescent signal suppression was ameliorated by sample dilution or by performing the assay above the pI of secreted IgG. The source of fluorescence in clarified culture broth was validated by incubation with RNase A and DNase I. At least 89.0 % of fluorescence was attributable to nucleic acid and pre-digestion with RNase A was shown to be a requirement for successful quantification of DNA in such samples. Application of the fluorescence based assay resulted in characterisation of the physical parameters governing adsorption of DNA by various positively charged depth filters and membranes in test solutions and the DNA adsorption profile of the manufacturing scale filtration train. Buffers that reduced or neutralised the depth filter or membrane charge, and those that impeded hydrophobic interactions were shown to affect their operational capacity, demonstrating that DNA was adsorbed by a combination of electrostatic and hydrophobic interactions. Production-scale centrifugation of harvest broth containing therapeutic protein resulted in the reduction of total DNA in the process stream from 79.8 μg m1-1 to 9.3 μg m1-1 whereas the concentration of DNA in the supernatant of pre-and post-filtration samples had only marginally reduced DNA content: from 6.3 to 6.0 μg m1-1 respectively. Hence the filtration train was shown to ineffective in DNA removal. Historically, blinding of the depth filters had been unpredictable with data such as numbers of viable cells, non-viable cells, product titre, or process shape (batch, fed-batch, or draw and fill) failing to inform on the durability of depth filters in the harvest step. To investigate this, key fouling contaminants were identified by challenging depth filters with the same mass of one of the following: viable healthy cells, cells that had died by the process of apoptosis, and cells that had died through the process of necrosis. The pressure increase across a Cuno Zeta Plus 10SP depth filter was 2.8 and 16.5 times more sensitive to debris from apoptotic and necrotic cells respectively, when compared to viable cells. The condition of DNA released into the culture broth was assessed. Necrotic cells released predominantly high molecular weight DNA in contrast to apoptotic cells which released chiefly low molecular weight DNA. The blinding of the filters was found to be largely unaffected by variations in the particle size distribution of material in, and viscosity of, solutions with which they were challenged. The exceptional response of the depth filters to necrotic cells may suggest the cause of previously noted unpredictable filter blinding whereby a number of necrotic cells have a more significant impact on the life of a depth filter than a similar number of viable or apoptotic cells. In a final set of experiments the pressure drop caused by non-viable necrotic culture broths which had been treated with DNase I or benzonase was found to be smaller when compared to untreated broths: the abilities of the enzyme treated cultures to foul the depth filter were reduced by 70.4% and 75.4% respectively indicating the importance of DNA in the blinding of the depth filter studied.

Target spatial frequency determines the response to conflicting defocus- and convergence-driven accommodative stimuli

Asthenopia, or visual fatigue, is a frequent complaint from observers of stereoscopic three-dimensional displays. It has been proposed that asthenopia is a consequence of anomalous oculomotor responses generated by conflict between accommodative and convergence stimuli. The hypothesis was examined by measuring accommodation and convergence continuously with a Shin-Nippon SRW5000 infrared autorefractor and a limbus tracking device. Subjects viewed a high contrast Maltese Cross target at three levels of Gaussian filter target blur under conditions of relatively low- and high-conflict between accommodation and convergence stimuli, the latter inducing the sensation of stereopsis. Under the low-conflict conditions accommodation was stable, but convergence-driven accommodation was dominant when the target was extremely blurred. Under the high-conflict conditions the role of convergence-driven accommodation increased systematically with the degree of target blur. It is proposed that defocus-driven accommodation becomes weak when the target comprises low spatial frequency components. Large accommodative overshoots to step stimuli that are not blurred or only mildly blurred were consistently observed and are attributed to the initial accommodative response being convergence-driven. Whereas the possibility that high-conflict conditions are a cause of asthenopia has been previously reported, this is the first evidence that they specifically affect accommodative responses while viewing stereoscopic displays. © 2005 Elsevier Ltd. All rights reserved.

Improving the response time of polymer optical fibre Bragg grating water activity sensors

In this work we investigate the effect of temperature and diameter size on the response time of a poly(methyl methacrylate) based, polymer optical fibre Bragg grating water activity sensor. The unstrained and etched sensor was placed in an environmental chamber to maintain controlled temperature and humidity conditions and subjected to step changes in humidity. The data show a strong correlation between decrease in diameter and shorter response time. A decrease in response time was also observed with an increase in temperature.