Comparative kinetic analysis of two fungal β-glucosidases

<p>Abstract</p> <p>Background</p> <p>The enzymatic hydrolysis of cellulose is still considered as one of the main limiting steps of the biological production of biofuels from lignocellulosic biomass. It is a complex multistep process, and various kinetic models have been proposed. The cellulase enzymatic cocktail secreted by <it>Trichoderma reesei </it>has been intensively investigated. β-glucosidases are one of a number of cellulolytic enzymes, and catalyze the last step releasing glucose from the inhibitory cellobiose. β-glucosidase (BGL1) is very poorly secreted by <it>Trichoderma reesei </it>strains, and complete hydrolysis of cellulose often requires supplementation with a commercial β-glucosidase preparation such as that from <it>Aspergillus niger </it>(Novozymes SP188). Surprisingly, kinetic modeling of β-glucosidases lacks reliable data, and the possible differences between native <it>T. reesei </it>and supplemented β-glucosidases are not taken into consideration, possibly because of the difficulty of purifying BGL1.</p> <p>Results</p> <p>A comparative kinetic analysis of β-glucosidase from <it>Aspergillus niger </it>and BGL1 from <it>Trichoderma reesei</it>, purified using a new and efficient fast protein liquid chromatography protocol, was performed. This purification is characterized by two major steps, including the adsorption of the major cellulases onto crystalline cellulose, and a final purification factor of 53. Quantitative analysis of the resulting β-glucosidase fraction from <it>T. reesei </it>showed it to be 95% pure. Kinetic parameters were determined using cellobiose and a chromogenic artificial substrate. A new method allowing easy and rapid determination of the kinetic parameters was also developed. β-Glucosidase SP188 (K_m= 0.57 mM; K_p= 2.70 mM) has a lower specific activity than BGL1 (K_m= 0.38 mM; K_p= 3.25 mM) and is also more sensitive to glucose inhibition. A Michaelis-Menten model integrating competitive inhibition by the product (glucose) has been validated and is able to predict the β-glucosidase activity of both enzymes.</p> <p>Conclusions</p> <p>This article provides a useful comparison between the activity of β-glucosidases from two different fungi, and shows the importance of fully characterizing both enzymes. A Michaelis-Menten model was developed, including glucose inhibition and kinetic parameters, which were accurately determined and compared. This model can be further integrated into a cellulose hydrolysis model dissociating β-glucosidase activity from that of other cellulases. It can also help to define the optimal enzymatic cocktails for new β-glucosidase activities.</p

Fine-grained Simulation in the Design of Automotive Communication Systems

International audienceEarly in the design cycle, the two main approaches for verifying timing constraints and di- mensioning automotive embedded networks are worst-case schedulability analysis and simulation. The first aim of the paper is to demonstrate that both provide complementary results and that, most often, none of them alone is sufficient. In this paper, we present a simulation approach accounting for the clock drifts that occur on the network nodes at run- time and evaluate the extent to which the results ob- tained with this approach are relevant for the design- ers in order to validate the performances of a CAN- based communication system. One of the practical outcome of this study is to show that initial phasings between nodes, as well as the values of the clock drifts, do not significantly impact the frame response time distributions that can be observed on the long run

Multi-source and multicore automotive ECUs - OS protection mechanisms and scheduling

International audienceAs the demand for computing power is quickly increasing in the automotive domain, car manufacturers and tier-one suppliers are gradually introducing multicore ECUs in their electronic architectures. Additionally, these multicore ECUs offer new features such as higher levels of parallelism which ease the respect of the safety requirements such as the ISO 26262 and the implementation of other automotive use-cases. These new features involve also more complexity in the design, development and verification of the software applications. Hence, OEMs and suppliers will require new tools and methodologies for deployment and validation. In this paper, we review the operating system protection mechanisms (e.g., memory, timing), needed for multi-source software in a safety critical context, with a clear focus on AUTOSAR OS which is the upcoming de-facto standard for automotive ECUs. We then identify the main use cases for multicore ECUs and eventually focus on one of them. Precisely, we address the problem of scheduling numerous elementary software components, called runnables, on a limited set of identical cores. In the context of an automotive design, we assume the use of the static task partitioning scheme which provides simplicity and better predictability for the ECU designers by comparison with a global scheduling approach. We show how the global scheduling problem can be addressed as two sub-problems: partitioning the set of runnables and building the schedule on each core. Then, we prove that each of the sub-problems cannot be solved optimally due to their algorithmic complexity. We then present low complexity heuristics to partition and build a schedule of the runnable set on each core before discussing schedulability verification methods. Finally, we assess the performance of our approach on a case-study

Non-adiabatic cluster expansion after ultrashort laser interaction

AbstractWe used X-ray spectroscopy as a diagnostic tool for investigating the properties of laser-cluster interactions at the stage in which non-adiabatic cluster expansion takes place and a quasi-homogeneous plasma is produced. The experiment was carried out with a 10 TW, 65 fs Ti:Sa laser focused on CO2 cluster jets. The effect of different laser-pulse contrast ratios and cluster concentrations was investigated. The X-ray emission associated to the Rydberg transitions allowed us to retrieve, through the density and temperature of the emitting plasma, the time after the beginning of the interaction at which the emission occurred. The comparison of this value with the estimated time for the "homogeneous" plasma formation shows that the degree of adiabaticity depends on both the cluster concentration and the pulse contrast. Interferometric measurements support the X-ray data concerning the plasma electron density

Frame latency evaluation: when simulation and analysis alone are not enough

International audienceThis talk is about temporal verification in real-time communication systems. Early in the design cycle, the two main approaches for verifying timing constraints and dimensioning the networks are worst-case schedulability analysis and simulation. The aim of the talk is to demonstrate that both provide complementary results and that, most often, none of them alone is sufficient. In particular, it will be shown that response time distributions that can be derived from simulations cannot replace worst-case analysis. This will be done on automotive case-studies using analysis and simulation software tools

Impact of clock drifts on CAN frame response time distributions

Abstract: The response time distributions of the frames sent on a Controller Area Network (CAN) bus are of prime interest to dimension and validate automotive electronic architectures. However, the existing work on the timing behaviour of the CAN network does not take into account that all the data exchanges between the Electronic Control Units (ECUs) are driven by different and independent clocks which are subject to clock drifts. This paper proposes a model for clock drifts and describes their impact on the CAN frame response time distributions. By implementing the clock drifts in a CAN simulation tool, we show experimentally that the response time distributions converge, for drift values chosen randomly within the same range on all ECUs, whatever the initial phasings between the sending nodes. Furthermore, we show that, as a result of the clock drifts, the situations leading to the worst case response times are transient. A. Context of the study. I

Vérification des contraintes temporelles de bout-en-bout dans le contexte AutoSar

Les systèmes électroniques embarqués dans les véhicules ont une complexité sans cesse croissante. Cependant, il est crucial d'en maîtriser le comportement temporel afin de garantir la sécurité ainsi que le confort des passagers. La vérification des contraintes temporelles de bout-en-bout est donc un enjeu majeur lors de la conception d'un véhicule. Dans le contexte de l'architecture logicielle AUTOSAR standard dans les véhicules, nous décomposons la vérification d'une contrainte de bout-en-bout en sous-problèmes d'ordonnancement sur les calculateurs et sur les réseaux de communication que nous traitons ensuite séparément. Dans un premier temps, nous présentons une approche permettant d'améliorer l'utilisation des calculateurs exécutant un grand nombre de composants logiciels, compatible avec l'introduction progressive des plateformes multi-coeurs. Nous décrivons des algorithmes rapides et efficaces pour lisser la charge périodique sur les calculateurs multi-coeurs en adaptant puis en améliorant une approche existant pour les bus CAN. Nous donnons également des résultats théoriques sur l'efficacité des algorithmes dans certains cas particuliers. Enfin, nous décrivons les possibilités d'utilisation de ces algorithmes en fonction des autres tâches exécutées sur le calculateur. La suite des travaux est consacrée à l'étude des distributions de temps de réponse des messages transmis sur les bus CAN. Dans un premier temps nous présentons une approche de simulation basée sur la modélisation des dérives d'horloges des calculateurs communicant sur le réseau. Nous montrons que nous obtenons des distributions de temps de réponse similaires en réalisant une longue simulation avec des dérives d'horloge ou en faisant un grand nombre de courtes simulations sans dérives d'horloge. Nous présentons enfin une technique analytique pour évaluer les distributions de temps de réponse des trames CAN. Nous présentons différents paramètres d'approximation permettant de réduire le nombre très important de calculs à effectuer en limitant la perte de précision. Enfin, nous comparons expérimentalement les résultats obtenus par analyse et simulation et décrivons les avantages et inconvénients respectifs de ces approchesThe complexity of electronic embedded systems in cars is continuously growing. Hence, mastering the temporal behavior of such systems is paramount in order to ensure the safety and comfort of the passengers. As a consequence, the verification of end-to-end real-time constraints is a major challenge during the design phase of a car. The AUTOSAR software architecture drives us to address the verification of end-to-end real-time constraints as two independent scheduling problems respectively for electronic control units and communication buses. First, we introduce an approach, which optimizes the utilization of controllers scheduling numerous software components that is compatible with the upcoming multicore architectures. We describe fast and efficient algorithms in order to balance the periodic load over time on multicore controllers by adapting and improving an existing approach used for the CAN networks. We provide theoretical result on the efficiency of the algorithms in some specific cases. Moreover, we describe how to use these algorithms in conjunction with other tasks scheduled on the controller. The remaining part of this research work addresses the problem of obtaining the response time distributions of the messages sent on a CAN network. First, we present a simulation approach based on the modelisation of clock drifts on the communicating nodes connected on the CAN network. We show that we obtain similar results with a single simulation using our approach in comparison with the legacy approach consisting in numerous short simulation runs without clock drifts. Then, we present an analytical approach in order to compute the response time distributions of the CAN frames. We introduce several approximation parameters to cope with the very high computational complexity of this approach while limiting the loss of accuracy. Finally, we compare experimentally the simulation and analytical approaches in order to discuss the relative advantages of each of the two approachesMETZ-SCD (574632105) / SudocNANCY1-Bib. numérique (543959902) / SudocNANCY2-Bibliotheque electronique (543959901) / SudocNANCY-INPL-Bib. électronique (545479901) / SudocSudocFranceF

Author manuscript, published in &quot;Embedded Real Time Software and Systems- ERTSS 2010 (2010)&quot; Multicore scheduling in automotive ECUs

Abstract: As the demand for computing power is quickly increasing in the automotive domain, car manufacturers and tier-one suppliers are gradually introducing multicore ECUs in their electronic architectures. Additionally, these multicore ECUs offer new features such as higher levels of parallelism which eases the respect of the safety requirements introduced by the ISO 26262 and can be taken advantage of in various other automotive use-cases. These new features involve also more complexity in the design, development and verification of the software applications. Hence, OEMs and suppliers will require new tools and methodologies for deployment and validation. In this paper, we present the main use cases for multicore ECUs and then focus on one of them. Precisely, we address the problem of scheduling numerous elementary software components (called runnables) on a limited set of identical cores. In the context of an automotive design, we assume the use of the static task partitioning scheme which provides simplicity and better predictability for the ECU designers by comparison with a global scheduling approach. We show how the global scheduling problem can be addressed as two subproblems: partitioning the set of runnables and building the schedule on each core. At that point, we prove that each of the sub-problems cannot be solved optimally due to their algorithmic complexity. We then present low complexity heuristics to partition and build a schedule of the runnable set on each core before discussing schedulability verification methods. Finally, we assess the performance of our approach on realistic case-studies

Partioned scheduling of tasks on automotive multicore ECUs

As the demand for computing power is quickly increasing in the automotive domain, car manufacturers and tier-one suppliers are gradually introducing multicore ECUs in their electronic architectures. In this paper we address the general problem of scheduling numerous elementary software components (called runnables) on a limited set of identical cores. In the context of an automotive design, we assume the use of the static task partitioning scheme which provides simplicity and better predictability for the ECU designers with respect to a global scheduling approach. We show how the global scheduling problem can be addressed as two sub-problems: partitioning the set of runnables and building the schedule on each core. Then, we prove that each of the sub-problems cannot be solved optimally due to their algorithmic complexity. We then present low complexity heuristics and derive lower bounds on their efficiency (i.e., competitive ratio). Finally, we assess the performance of our approach on realistic case-studies