1,124 research outputs found
Kinetic self-organization of trenched templates for the fabrication of versatile ferromagnetic nanowires
We have self-organized versatile magnetic nanowires, ie with variable period
and adjustable magnetic anisotropy energy (MAE). First, using the kinetic
roughening of W(110) uniaxial templates of trenches were grown on commercial
Sapphire wafers. Unlike most templates used for self-organization, those have a
variable period, 4-12nm are demonstrated here. Fe deposition then results in
the formation of wires in the trenches. The magnitude of MAE could be
engineered up or down by changing the capping- or underlayer, in turn affecting
the mean superparamagnetic temperature, raised to 175K so far.Comment: 3 page
Mechanical properties of the elemental nanocomponents of nacre structure
Sheet nacre is a nanocomposite with a multiscale structure displaying a lamellar âbricks and mortarâ microarchitecture. In this latter, the brick refer to aragonite platelets and the mortar to a soft organic biopolymer. However, it appears that each brick is also a nanocomposite constituted as CaCO3 nanoparticles reinforced organic composite material. What is the role of this âintracrystallineâ organic phase in the deformation of platelet? How does this nanostructure control the mechanical behaviour of sheet nacre at the macroscale? To answer these questions, the mechanical properties of each nanocomponents are successively investigated and computed using spherical and sharp nanoindentation tests combined with a structural model of the organomineral platelets built from AFM investigations
Flot de conception automatique pour circuits commutables
National audienceLes FPGA, ou puces reconfigurables, nâont pas cessĂ© dâĂ©voluer depuis leur crĂ©ation et sont dĂ©sormais utilisĂ©s dans des systĂšmes complets (Xilinx Zynq ou Altera Stratix). MalgrĂ© tout, il reste de nombreux champs applicatifs desquels ils sont absents, et Ă tort. Utiliser les FPGA de maniĂšre plus intense au sein de systĂšmes complets est possible, mais il faut pour cela dĂ©velopper les capacitĂ©s multi-utilisateurs de ces plateformes. Donner la capacitĂ© Ă une application sâexĂ©cutant sur un FPGA de se stopper pour, par exemple, laisser sâexĂ©cuter dâautres applications jugĂ©es prioritaires est particuliĂšrement intĂ©ressant. Une telle action est qualifiĂ©e de « changement de contexte » (en anglais context-switch).Dans cet article, nous prĂ©sentons une mĂ©thode et un outil permettant de donner cette capacitĂ© Ă des circuits fonctionnant sur cible reconfigurable. Le flot de conception prĂ©sentĂ© sâappuie sur un logiciel de synthĂšse de haut niveau et offre automatiquement la capacitĂ© de commutation aux circuits synthĂ©tisĂ©s. Les expĂ©riences menĂ©es sur un panel de circuits classiques montrent que lâajout de cette capacitĂ© Ă un coĂ»t relativement faible ainsi quâune rapiditĂ© de commutation sans Ă©gale dans la littĂ©rature
Automatic High-Level Hardware Checkpoint Selection for Reconfigurable Systems
International audienceâModern FPGAs provide great computational power and flexibility but there is still room for improving their performances. For example multiuser approaches are particularly underdeveloped as they require specific mechanisms still to be automated. Sharing an FPGA resource between applications or users requires a context switch ability. The latter enables pausing and resuming applications at system demand. This paper presents a method that automatically selects a good execution point, called hardware checkpoint, to perform a context switch on an FPGA. The method relies on a static analysis of the finite state machine of a circuit to select the checkpoint states. The obtained selection ensures that the context switch mechanism respects a given latency and tries to minimize the mechanism costs. The method takes advantage of its integration in an open-source HLS tool and preliminary results highlight its efficiency. Index TermsâFPGA, HLS, CAD, hardware context switc
Topology Construction in RPL Networks over Beacon-Enabled 802.15.4
In this paper, we propose a new scheme that allows coupling beacon-enabled
IEEE 802.15.4 with the RPL routing protocol while keeping full compliance with
both standards. We provide a means for RPL to pass the routing information to
Layer 2 before the 802.15.4 topology is created by encapsulating RPL DIO
messages in beacon frames. The scheme takes advantage of 802.15.4 command
frames to solicit RPL DIO messages. The effect of the command frames is to
reset the Trickle timer that governs sending DIO messages. We provide a
detailed analysis of the overhead incurred by the proposed scheme to understand
topology construction costs. We have evaluated the scheme using Contiki and the
instruction-level Cooja simulator and compared our results against the most
common scheme used for dissemination of the upper-layer information in
beacon-enabled PANs. The results show energy savings during the topology
construction phase and in the steady state
Study of overland flow with uncertain infiltration using stochastic tools
The saturated hydraulic conductivity is one of the key parameters in the modelling of overland flow water fluxes. In this study, this parameter is defined as a stochastic parameter, idealized as a piecewise constant random field with uniform distribution. This paper aims at investigating the effects of the spatial and temporal scales in uncertainty propagation within overland flow models, and at identifying the localization of the most influential saturated hydraulic conductivity using sensitivity analysis. The results show that the influence of saturated hydraulic conductivity depends on the soil saturation and its spatial localization. For instance, in case of low saturated soils, the most influent parameter is the one located downslope, whereas in case of high saturated soils, the most influent one is either the most infiltrating or the intermediate one. The results indicate where efforts should be concentrate when collecting input parameters to reduce modelling uncertainties
Accélération de l'exploration de l'espace chimique du cytochrome P450 BM3 par des méthodes de criblage à haut débit et bio-informatiques
Lâapplication de la chimie organique est prĂ©pondĂ©rante dans plusieurs secteurs industriels tels que le pharmaceutique, le cosmĂ©tique, lâalimentaire ou les produits mĂ©nagers. La chimie organique Ă©volue sans cesse pour rendre les synthĂšses plus efficaces et moins dispendieuses. Cependant, lâamĂ©lioration de voies de synthĂšse se fait souvent sans Ă©gard Ă leur effet sur lâenvironnement. Ceci a entrainĂ© lâĂ©mergence de la chimie verte pour rĂ©duire leur impact environnemental. Ă cette fin, lâune des stratĂ©gies employĂ©es est la biocatalyse : lâutilisation dâenzymes due Ă leurs propriĂ©tĂ©s âvertesâ et leur grande efficacitĂ© rĂ©actionnelle.
Les oxydases de type cytochrome P450 sont reconnues pour leur grande promiscuitĂ©, liĂ©e Ă leur rĂŽle dans la dĂ©toxification de composĂ©s xĂ©nobiotiques et de molĂ©cules endogĂšnes dans le corps. Cette superfamille dâenzymes accomplit une diversitĂ© de rĂ©actions dâoxydations en une seule Ă©tape telles que lâhydroxylation, lâĂ©poxidation, la dĂ©samination, la dĂ©shalogĂ©nation et la cyclopropanation. La P450 BM3 (P450 BM3) de Bacillus megaterium possĂšde lâune des plus grandes activitĂ©s catalytiques de sa famille, justifiant lâintĂ©rĂȘt grandissant de ses applications industrielles. Ce mĂ©moire se penche sur la nĂ©cessitĂ© dâamĂ©liorer les essais afin dâaugmenter la capacitĂ© de criblage pour obtenir une plus grande proportion de variants capable de catalyser une rĂ©action dĂ©sirĂ©e.
Il a Ă©tĂ© proposĂ© que la synthĂšse de lâindigo par les variants de P450 BM3 soit un indicateur de promiscuitĂ© envers de nouveaux substrats. Nous avons explorĂ© lâespace mutationnel de P450 BM3 pour la synthĂšse de lâindigo en comparant diffĂ©rentes mĂ©thodes de criblage de librairies de variants. Dans un premier temps, des librairies de variants furent crĂ©Ă©es par mutagĂ©nĂšse par saturation de site. Cela permet dâobtenir une reprĂ©sentation uniforme des variants Ă chaque position sĂ©lectionnĂ©e plus rapidement et Ă un coĂ»t modique. Ensuite, des mĂ©thodes de criblage furent optimisĂ©es pour quantifier les variants de P450 BM3 et les cribler de deux façons. Nous avons comparĂ© un essai colorimĂ©trique direct grĂące Ă lâabsorbance de lâindigo avec un essai gĂ©nĂ©ral indirect combinant la fluorescence du cofacteur NADPH et la spectromĂ©trie de masse (LC-MS, GC-MS et LC prĂ©parative). Cette deuxiĂšme approche permet de cribler les variants indĂ©pendamment du substrat. Afin dâaugmenter le dĂ©bit du criblage, nous avons optimisĂ© les mĂ©thodes en utilisant des plaques 96 puits avec une station de pipetage automatisĂ©e. Nous avons dĂ©couvert de multiples nouveaux variants de P450 BM3 synthĂ©tisant lâindigo dont une forte fraction de ces derniers sâest rĂ©vĂ©lĂ©e aptes Ă synthĂ©tiser une molĂ©cule de valeur Ă©levĂ©e en industrie : la cĂ©tone de framboise.
La corrĂ©lation de lâactivitĂ© de P450 BM3 avec lâindigo et la cĂ©tone de framboise justifie lâexploration plus profonde de lâespace mutationnel de P450 BM3. La comprĂ©hension de cette corrĂ©lation permettrait de guider dâavantage lâingĂ©nierie de P450 BM3 vers de nouveaux substrats. Ă cette fin, nous tentons dâexpliquer la relation entre la structure, le dynamisme et lâactivitĂ© des variants de P450 BM3. Les mĂ©thodes de criblage conventionnelles ne sont pas assez efficaces pour gĂ©nĂ©rer de grandes sĂ©ries de donnĂ©es (« Big Data »). Nous appliquons le sĂ©quençage de nouvelle gĂ©nĂ©ration afin dâidentifier >104 variants simultanĂ©ment pour relier le gĂ©notype (ADN) au phĂ©notype (synthĂšse dâindigo). Lâanalyse de ces donnĂ©es nĂ©cessite lâutilisation dâoutils statistiques et informatiques tels que la modĂ©lisation, la dynamique molĂ©culaire et lâanalyse de composantes indĂ©pendantes du temps et de la structure (tICA). Nous observons une tendance commune des variants actifs de P450 BM3 reprĂ©sentĂ© par un changement dâĂ©quilibre entre ses deux conformations majeures. Ce changement conformationnel pourrait expliquer la propension de P450 BM3 Ă synthĂ©tiser lâindigo.
Ce mĂ©moire prĂ©sente ainsi des mĂ©thodes permettant dâaccĂ©lĂ©rer la dĂ©couverte de variants actifs de P450 BM3 pour diverses rĂ©actions dâintĂ©rĂȘt en industrie. Les mĂ©thodologies ci-dĂ©veloppĂ©es pourront ensuite guider lâingĂ©nierie dâautres systĂšmes enzymatiques.Organic chemistry plays a major role in the pharmaceutical, cosmetic, food and household product industries. Industrial organic synthesis has constantly evolved to be more efficient and less cost-effective. However, those improvements were often made regardless of their impact on the environment, spawning the creation of the discipline of Green Chemistry. One among many strategies to make chemistry more innocuous to the environment is to apply biocatalysis: the use of enzymes for their âgreenâ properties and catalytic efficacy.
Cytochrome P450 oxidases are well known for their substrate promiscuity in detoxification of xenobiotics and endogenous molecules in the body. This superfamily of enzymes catalyzes a diversity of oxidation reactions in a single step, including hydroxylations, epoxidations, deaminations, dehalogenations and cyclopropanations. Cytochrome P450 BM3 (P450 BM3) from Bacillus megaterium is one of the most efficient of its family, justifying the growing interest for its industrial applications. This thesis considers the necessity to improve assays in order to increase the throughput of enzyme library screening and to improve the ratio of active variants.
Indigo synthesis has been proposed to be an efficient predictor of promiscuity towards novel substrates of P450 BM3. We explore the mutational space of P450 BM3 for indigo synthesis and compare screening methods. We made variant libraries using site-directed saturation mutagenesis to obtain a uniform distribution of mutations at each position and reduce cost and time. We optimized a method to quantify P450 BM3 variants and two different screening methods. We compared a direct colorimetric assay using indigo absorbance and an indirect assay using NADPH fluorescence coupled with mass spectrometry (LC-MS, GC-MS and LC prep). This second approach circumvents the need to develop an assay dependent of the substrate. To increase screening throughput, we optimized methods in a 96-well plate format and use an automated pipetting station. We confirm the discovery of new indigo-producing variants. We further demonstrate that indigo can serve as a strong predictor of raspberry ketone production, a high value industrial compound.
The correlation of the activity of P450 BM3 with indigo and raspberry ketone justifies the exploration of the fitness landscape P450 BM3. Understanding this correlation would accelerate engineering of P450 BM3 for reaction with novel substrates. We attempt to explain the relationship between the structure, dynamism and activity through deep-mutational scanning of P450 BM3. Conventional screening methods are not sufficient to produce large datasets (Big Data); we apply next-generation sequencing (NGS) to identify >104 variants simultaneously and to link the genotype (DNA) and the phenotype (indigo production). Analysis of NGS for enzyme engineering required the development of statistical and bioinformatics tools such as modeling, molecular dynamics and time-structure independent component analysis (tICA). Those methods allowed us to observe conformational perturbations that were shared between the active variants represented as a shift of equilibrium between two major conformations. This shift may explain the propensity of diverse P450 BM3 variants to synthesize indigo.
This masterâs thesis successfully demonstrates the accelerated discovery of engineered variants of P450 BM3 with activity for industrially relevant reactions. The methodologies we have developed contribute to knowledge on enzyme engineering and have the potential to be applied more broadly in other enzyme systems
Quelques propriétés du complexe de Morse-Novikov
Mémoire numérisé par la Direction des bibliothÚques de l'Université de Montréal
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