Dynamic coupling between the LID and NMP domain motions in the catalytic conversion of ATP and AMP to ADP by adenylate kinase

The catalytic conversion of adenosine triphosphate (ATP) and adenosine monophosphate (AMP) to adenosine diphosphate (ADP) by adenylate kinase (ADK) involves large amplitude, ligand induced domain motions, involving the opening and the closing of ATP binding domain (LID) and AMP binding domain (NMP) domains, during the repeated catalytic cycle. We discover and analyze an interesting dynamical coupling between the motion of the two domains during the opening, using large scale atomistic molecular dynamics trajectory analysis, covariance analysis, and multidimensional free energy calculations with explicit water. Initially, the LID domain must open by a certain amount before the NMP domain can begin to open. Dynamical correlation map shows interesting cross-peak between LID and NMP domain which suggests the presence of correlated motion between them. This is also reflected in our calculated two-dimensional free energy surface contour diagram which has an interesting elliptic shape, revealing a strong correlation between the opening of the LID domain and that of the NMP domain. Our free energy surface of the LID domain motion is rugged due to interaction with water and the signature of ruggedness is evident in the observed root mean square deviation variation and its fluctuation time correlation functions. We develop a correlated dynamical disorder-type theoretical model to explain the observed dynamic coupling between the motion of the two domains in ADK. Our model correctly reproduces several features of the cross-correlation observed in simulations. (C) 2011 American Institute of Physics. doi:10.1063/1.3516588]

A dynamic coupling model for hybrid atomistic-continuum computations

A dynamic coupling model is developed for a hybrid atomistic-continuum computation in micro- and nano-fluidics. In the hybrid atomistic-continuum computation, a molecular dynamics (MD) simulation is utilized in one region where the continuum assumption breaks down and the Navier-Stokes (NS) equations are used in another region where the continuum assumption holds. In the overlapping part of these two regions, a constrained particle dynamics is needed to couple the MD simulation and the NS equations. The currently existing coupling models for the constrained particle dynamics have a coupling parameter, which has to be empirically determined. In the present work, a novel dynamic coupling model is introduced where the coupling parameter can be calculated as the computation progresses rather than inputing a priori. The dynamic coupling model is based on the momentum constraint and exhibits a correct relaxation rate. The results from the hybrid simulation on the Couette flow and the Stokes flow are in good agreement with the data from the full MD simulation and the solutions of the NS equations, respectively. (c) 2007 Elsevier Ltd. All rights reserved.

Linear multimodal actuation through discrete coupling

Due to technological limitations, robot actuators are often designed for specific tasks with narrow performance goals, whereas a wide range of behaviors is necessary for autonomous robots in uncertain complex environments. In an effort to increase the versatility of actuators, we introduce a new concept of multimodal actuation (MMA) that employs dynamic coupling in the form of clutches and brakes to change its mode of operation. The dynamic coupling allows motors and passive elements such as springs to be engaged and disengaged within a single actuator. We apply the concept to a linear series elastic actuator which uses friction brakes controlled online for the dynamic coupling. With this prototype, we are able to demonstrate several modes of operation including stiff position control, series elastic actuation as well as the possibility to store and release energy in a controlled manner for explosive tasks such as jumping. In this paper, we model the proposed concept of actuation and show a systematic performance analysis of the physical prototype that we developed in our laboratory. © 1996-2012 IEEE.

Application of a dynamic event tree methodolgy to steam generator tube rupture sequences

The Integrated Safety Assessment (ISA) methodology, developed by the Spanish Nuclear Safety Council (CSN), has been applied to a thermo-hydraulical analysis of a Westinghouse 3-loop PWR plant by means of the dynamic event trees (DET) for Steam Generator Tube Rupture (SGTR) sequences. The ISA methodology allows obtaining the SGTR Dynamic Event Tree taking into account the operator actuation times. Simulations are performed with SCAIS (Simulation Code system for Integrated Safety Assessment), which includes a dynamic coupling with MAAP thermal hydraulic code. The results show the capability of the ISA methodology and SCAIS platform to obtain the DET of complex sequences.

An Atomistic-Continuum Hybrid Simulation Of Fluid Flows Over Superhydrophobic Surfaces

Recent experiments have found that slip length could be as large as on the order of 1 mu m for fluid flows over superhydrophobic surfaces. Superhydrophobic surfaces can be achieved by patterning roughness on hydrophobic surfaces. In the present paper, an atomistic-continuum hybrid approach is developed to simulate the Couette flows over superhydrophobic surfaces, in which a molecular dynamics simulation is used in a small region near the superhydrophobic surface where the continuum assumption is not valid and the Navier-Stokes equations are used in a large region for bulk flows where the continuum assumption does hold. These two descriptions are coupled using the dynamic coupling model in the overlap region to ensure momentum continuity. The hybrid simulation predicts a superhydrophobic state with large slip lengths, which cannot be obtained by molecular dynamics simulation alone.

An atomistic-continuum hybrid simulation of fluid flows over superhydrophobic surfaces

Recent experiments have found that slip length could be as large as on the order of 1 mu m for fluid flows over superhydrophobic surfaces. Superhydrophobic surfaces can be achieved by patterning roughness on hydrophobic surfaces. In the present paper an atomistic-continuum hybrid approach is developed to simulate the Couette flows over superhydrophobic surfaces in which a molecular dynamics simulation is used in a small region near the superhydrophobic surface where the continuum assumption is not valid and the Navier-Stokes equations are used in a large region for bulk flows where the continuum assumption does hold. These two descriptions are coupled using the dynamic coupling model in the overlap region to ensure momentum continuity. The hybrid simulation predicts a superhydrophobic state with large slip lengths which cannot be obtained by molecular dynamics simulation alone.

Size-related shifts in reliance on benthic and pelagic food webs by lake anchovy

This paper reports large variations in stable carbon and nitrogen isotope ratios of lake anchovy (Coilia ectenes taihuensis) from Lake Chaohu, China. The lake anchovy exhibited a significant C-13- and N-15- enrichment in relation to increasing fish length, and the isotopic compositions of small lake anchovy (<= 130 mm) were significantly more enriched than those of large lake anchovy (> 130 mm). The significant differences in the isotopic compositions of small and large lake anchovy suggested that their assimilated diets differed over a period of time and reflected the size-related diet shift of this fish. Bellamya aeruginosa and Corbicula fluminea were used to establish the baseline carbon signal of benthic and pelagic food webs, and these data were used to parameterize a 2-source mixing model to estimate in consumers the contribution of carbon derived from benthic versus pelagic food webs. Mixing models showed that small lake anchovy derived only 37% of their carbon from benthic food web, indicating increased reliance on pelagic prey, whereas benthic prey contributed 71% of large lake anchovy diet, suggesting greater use of benthic sources. These data indicate that there was a change in lake anchovy feeding strategy related to their size, suggesting a role in dynamic coupling between pelagic and benthic food chains. The trophic position of small lake anchovy averaged 3.0, indicating a zooplankton-based diet, compared with 3.6 in large lake anchovy, indicative of an increase in piscivorous diet. Overlap in the isotopic compositions of small and large lake anchovy probably indicated that these fish occasionally shared common diets, as suggested by stomach content studies, and/or resulted from the differences in the rate of isotopic turnover depending on differences in growth rate and metabolic turnover between small and large anchovy during diet shift from pelagic to benthic food webs. This study presents the contributions of benthic and pelagic food webs supporting lake anchovy and indicates that the intraspecific isotopic dynamic should be considered when applying stable isotope analyses to infer trophic interactions in aquatic ecosystems.

Robust Control of Systems Subjected to Uncertain Disturbances and Actuator Dynamics

Esta tesis está enfocada al diseño y validación de controladores robustos que pueden reducir de una manera efectiva las vibraciones structurales producidas por perturbaciones externas tales como terremotos, fuertes vientos o cargas pesadas. Los controladores están diseñados basados en teorías de control tradicionalamente usadas en esta area: Teoría de estabilidad de Lyapunov, control en modo deslizante y control clipped-optimal, una técnica reciente mente introducida : Control Backstepping y una que no había sido usada antes: Quantitative Feedback Theory. La principal contribución al usar las anteriores técnicas, es la solución de problemas de control estructural abiertos tales como dinámicas de actuador, perturbaciones desconocidas, parametros inciertos y acoplamientos dinámicos. Se utilizan estructuras típicas para validar numéricamente los controladores propuestos. Especificamente las estructuras son un edificio de base aislada, una plataforma estructural puente-camión y un puente de 2 tramos, cuya configuración de control es tal que uno o mas problemas abiertos están presentes. Se utilizan tres prototipos experimentales para implementar los controladores robustos propuestos, con el fin de validar experimentalmente su efectividad y viabilidad. El principal resultado obtenido con la presente tesis es el diseño e implementación de controladores estructurales robustos que resultan efectivos para resolver problemas abiertos en control estructural tales como dinámicas de actuador, parámetros inciertos, acoplamientos dinámicos, limitación de medidas y perturbaciones desconocidas.

Luminescence of Eu(III) beta-diketone complex supported on functionalized macroporous silica matrix

This work reports on the photoluminescent properties of the complex diequatris(thenoyltrifluoroacetonate) europium(III), which was adsorbed or supported on tubes of modified surface silica matrix. The luminescence data and the experimental intensity parameter results evidence the existence of high interactions between the complex [Eu(tta)(3)(H2O)(2)] and the modified surface matrix. The anchored complex on macroporous silica shows higher intensity parameter values suggesting that the Eu-0 bond becomes more covalent than the adsorbed one. Therefore, the hypersensitive character of the D-5(0) --> F-7(2) transition increases evidencing a high contribution of the dynamic coupling mechanism possibly due to highly polarizable chemical environments occupied by europium(III) ion. The lifetimes of the complex on silica matrices were measured. (C) 2001 Elsevier B.V. Ltd. All rights reserved.

The theory of vibronic transitions in rare earth compounds

The theory of vibronic transitions in rare earth compounds is re-examined in the light of a more reliable representation for the ligand field Hamiltonian than the crude electrostatic model. General expressions that take into account the relevant contributions from the forced electric dipole and dynamic coupling mechanisms are derived for the vibronic intensity parameters. These include additional terms, from charge and polarizability gradients, which have not been considered in previous work. Emphasis is given to the relative signs of these various contributions. Under certain approximations these expressions may be conveniently written in terms of accessible ligand field parameters. A comparison with experimental values for the compounds Cs2NaEuCl6 and LiEuF4 is made and satisfactory agreement between theory and experiment is found. A discussion is given on the sensitivity of the calculated intensities to the values of radial integrals, interconfigurational energy differences and ligand field parameters that may be used. Finally, the problem in which a vibronic and an electronic level are in resonance, or near resonance, is analyzed. Suitable expressions to describe the effects of the even-rank components of the vibronic Hamiltonian are obtained. It is found that, depending on the strength of the vibronic interaction and the resonance conditions, the admixture between these two levels may lead to intensities of nearly equal values. © 1995.

Spectroscopic study of the interaction of Nd3+ with amino acids: Phenomenological 4f-4f intensity parameters

We have studied the bevahior of the phenomenological 4f-4f intensity parameters in compounds of the Nd ion with glycine, L-aspartic acid, L-glutamic acid, L-histidine, DL-malic acid and Aspartame™ in aqueous solution, as a function of the pK values and partial charges on the oxygens of the carboxylate groups of these molecules. The results are discussed and qualitatively interpreted in terms of the forced electric dipole and dynamic coupling mechanisms of the 4f-4f intensities, thus indicating that the forced electric dipole mechanism is dominant.

Análisis Integrado de Seguridad de un accidente de SGTR en un reactor nuclear tipo PWR

El accidente de rotura de tubos de un generador de vapor (Steam Generator Tube Rupture, SGTR) en los reactores de agua a presión es uno de los transitorios más exigentes desde el punto de vista de operación. Los transitorios de SGTR son especiales, ya que podría dar lugar a emisiones radiológicas al exterior sin necesidad de daño en el núcleo previo o sin que falle la contención, ya que los SG pueden constituir una vía directa desde el reactor al medio ambiente en este transitorio. En los análisis de seguridad, el SGTR se analiza desde un punto determinista y probabilista, con distintos enfoques con respecto a las acciones del operador y las consecuencias analizadas. Cuando comenzaron los Análisis Deterministas de Seguridad (DSA), la forma de analizar el SGTR fue sin dar crédito a la acción del operador durante los primeros 30 min del transitorio, lo que suponía que el grupo de operación era capaz de detener la fuga por el tubo roto dentro de ese tiempo. Sin embargo, los diferentes casos reales de accidentes de SGTR sucedidos en los EE.UU. y alrededor del mundo demostraron que los operadores pueden emplear más de 30 minutos para detener la fuga en la vida real. Algunas metodologías fueron desarrolladas en los EEUU y en Europa para abordar esa cuestión. En el Análisis Probabilista de Seguridad (PSA), las acciones del operador se tienen en cuenta para diseñar los cabeceros en el árbol de sucesos. Los tiempos disponibles se utilizan para establecer los criterios de éxito para dichos cabeceros. Sin embargo, en una secuencia dinámica como el SGTR, las acciones de un operador son muy dependientes del tiempo disponible por las acciones humanas anteriores. Además, algunas de las secuencias de SGTR puede conducir a la liberación de actividad radiológica al exterior sin daño previo en el núcleo y que no se tienen en cuenta en el APS, ya que desde el punto de vista de la integridad de núcleo son de éxito. Para ello, para analizar todos estos factores, la forma adecuada de analizar este tipo de secuencias pueden ser a través de una metodología que contemple Árboles de Sucesos Dinámicos (Dynamic Event Trees, DET). En esta Tesis Doctoral se compara el impacto en la evolución temporal y la dosis al exterior de la hipótesis más relevantes encontradas en los Análisis Deterministas a nivel mundial. La comparación se realiza con un modelo PWR Westinghouse de tres lazos (CN Almaraz) con el código termohidráulico TRACE, con hipótesis de estimación óptima, pero con hipótesis deterministas como criterio de fallo único o pérdida de energía eléctrica exterior. Las dosis al exterior se calculan con RADTRAD, ya que es uno de los códigos utilizados normalmente para los cálculos de dosis del SGTR. El comportamiento del reactor y las dosis al exterior son muy diversas, según las diferentes hipótesis en cada metodología. Por otra parte, los resultados están bastante lejos de los límites de regulación, pese a los conservadurismos introducidos. En el siguiente paso de la Tesis Doctoral, se ha realizado un análisis de seguridad integrado del SGTR según la metodología ISA, desarrollada por el Consejo de Seguridad Nuclear español (CSN). Para ello, se ha realizado un análisis termo-hidráulico con un modelo de PWR Westinghouse de 3 lazos con el código MAAP. La metodología ISA permite la obtención del árbol de eventos dinámico del SGTR, teniendo en cuenta las incertidumbres en los tiempos de actuación del operador. Las simulaciones se realizaron con SCAIS (sistema de simulación de códigos para la evaluación de la seguridad integrada), que incluye un acoplamiento dinámico con MAAP. Las dosis al exterior se calcularon también con RADTRAD. En los resultados, se han tenido en cuenta, por primera vez en la literatura, las consecuencias de las secuencias en términos no sólo de daños en el núcleo sino de dosis al exterior. Esta tesis doctoral demuestra la necesidad de analizar todas las consecuencias que contribuyen al riesgo en un accidente como el SGTR. Para ello se ha hecho uso de una metodología integrada como ISA-CSN. Con este enfoque, la visión del DSA del SGTR (consecuencias radiológicas) se une con la visión del PSA del SGTR (consecuencias de daño al núcleo) para evaluar el riesgo total del accidente. Abstract Steam Generator Tube Rupture accidents in Pressurized Water Reactors are known to be one of the most demanding transients for the operating crew. SGTR are special transient as they could lead to radiological releases without core damage or containment failure, as they can constitute a direct path to the environment. The SGTR is analyzed from a Deterministic and Probabilistic point of view in the Safety Analysis, although the assumptions of the different approaches regarding the operator actions are quite different. In the beginning of Deterministic Safety Analysis, the way of analyzing the SGTR was not crediting the operator action for the first 30 min of the transient, assuming that the operating crew was able to stop the primary to secondary leakage within that time. However, the different real SGTR accident cases happened in the USA and over the world demonstrated that operators can took more than 30 min to stop the leakage in actual sequences. Some methodologies were raised in the USA and in Europe to cover that issue. In the Probabilistic Safety Analysis, the operator actions are taken into account to set the headers in the event tree. The available times are used to establish the success criteria for the headers. However, in such a dynamic sequence as SGTR, the operator actions are very dependent on the time available left by the other human actions. Moreover, some of the SGTR sequences can lead to offsite doses without previous core damage and they are not taken into account in PSA as from the point of view of core integrity are successful. Therefore, to analyze all this factors, the appropriate way of analyzing that kind of sequences could be through a Dynamic Event Tree methodology. This Thesis compares the impact on transient evolution and the offsite dose of the most relevant hypothesis of the different SGTR analysis included in the Deterministic Safety Analysis. The comparison is done with a PWR Westinghouse three loop model in TRACE code (Almaraz NPP), with best estimate assumptions but including deterministic hypothesis such as single failure criteria or loss of offsite power. The offsite doses are calculated with RADTRAD code, as it is one of the codes normally used for SGTR offsite dose calculations. The behaviour of the reactor and the offsite doses are quite diverse depending on the different assumptions made in each methodology. On the other hand, although the high conservatism, such as the single failure criteria, the results are quite far from the regulatory limits. In the next stage of the Thesis, the Integrated Safety Assessment (ISA) methodology, developed by the Spanish Nuclear Safety Council (CSN), has been applied to a thermohydraulical analysis of a Westinghouse 3-loop PWR plant with the MAAP code. The ISA methodology allows obtaining the SGTR Dynamic Event Tree taking into account the uncertainties on the operator actuation times. Simulations are performed with SCAIS (Simulation Code system for Integrated Safety Assessment), which includes a dynamic coupling with MAAP thermal hydraulic code. The offsite doses are calculated also with RADTRAD. The results shows the consequences of the sequences in terms not only of core damage but of offsite doses. This Thesis shows the need of analyzing all the consequences in an accident such as SGTR. For that, an it has been used an integral methodology like ISA-CSN. With this approach, the DSA vision of the SGTR (radiological consequences) is joined with the PSA vision of the SGTR (core damage consequences) to measure the total risk of the accident.

Controle subótimo de manipuladores subatuados via redundância de atuação

Este trabalho apresenta uma metodologia de controle de posição das juntas passivas de um manipulador subatuado de uma maneira subótima. O termo subatuado se refere ao fato de que nem todas as juntas ou graus de liberdade do sistema serem equipados com atuadores, o que ocorre na prática devido a falhas ou como resultado de projeto. As juntas passivas de manipuladores desse tipo são indiretamente controladas pelo movimento das juntas ativas usando as características de acoplamento da dinâmica de manipuladores. A utilização de redundância de atuação das juntas ativas permite a minimização de alguns critérios, como consumo de energia, por exemplo. Apesar da estrutura cinemática de manipuladores subatuados ser idêntica a do totalmente atuado, em geral suas características dinâmicas diferem devido a presença de juntas passivas. Assim, apresentamos a modelagem dinâmica de um manipulador subatuado e o conceito de índice de acoplamento. Este índice é utilizado na seqüência de controle ótimo do manipulador. A hipótese de que o número de juntas ativas seja maior que o número de passivas permite o controle ótimo das juntas passivas, uma vez que na etapa de controle destas há mais entradas (torques nos atuadores das juntas ativas), que elementos a controlar (posição das juntas passivas). Neste ponto reside a contribuição desta tese ao estado da arte, uma vez que não há até o momento publicação que proponha o controle ótimo das juntas passivas neste caso.