A Metal–Organic Framework with a Hierarchical System of Pores and Tetrahedral Building Blocks

No AbstractPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/50670/1/2528_ftp.pd

A real-time proximity querying algorithm for haptic-based molecular docking

Intermolecular binding underlies every metabolic and regulatory processes of the cell, and the therapeutic and pharmacological properties of drugs. Molecular docking systems model and simulate these interactions in silico and allow us to study the binding process. Haptic-based docking provides an immersive virtual docking environment where the user can interact with and guide the molecules to their binding pose. Moreover, it allows human perception, intuition and knowledge to assist and accelerate the docking process, and reduces incorrect binding poses. Crucial for interactive docking is the real-time calculation of interaction forces. For smooth and accurate haptic exploration and manipulation, force-feedback cues have to be updated at a rate of 1 kHz. Hence, force calculations must be performed within 1ms. To achieve this, modern haptic-based docking approaches often utilize pre-computed force grids and linear interpolation. However, such grids are time-consuming to pre-compute (especially for large molecules), memory hungry, can induce rough force transitions at cell boundaries and cannot be applied to flexible docking. Here we propose an efficient proximity querying method for computing intermolecular forces in real time. Our motivation is the eventual development of a haptic-based docking solution that can model molecular flexibility. Uniquely in a haptics application we use octrees to decompose the 3D search space in order to identify the set of interacting atoms within a cut-off distance. Force calculations are then performed on this set in real time. The implementation constructs the trees dynamically, and computes the interaction forces of large molecular structures (i.e. consisting of thousands of atoms) within haptic refresh rates. We have implemented this method in an immersive, haptic-based, rigid-body, molecular docking application called Haptimol_RD. The user can use the haptic device to orientate the molecules in space, sense the interaction forces on the device, and guide the molecules to their binding pose. Haptimol_RD is designed to run on consumer level hardware, i.e. there is no need for specialized/proprietary hardware

Le chaos des subjectivités : Fauda

La série israélienne Fauda narre le quotidien de forces spéciales de l’armée israélienne, les mista’aravim (littéralement les « arabisés »), dont la mission est d’opérer incognito derrière les lignes ennemies en se déguisant en civils palestiniens. Produite en 2015 par deux vétérans de cette unité, Avi Issacharoff et Lior Raz, elle rencontre un succès planétaire. Elle a suscité des éloges appuyés aussi bien que de virulentes critiques, au point qu'en mars 2018, le mouvement « Boycott, Désinvestissement, Sanction », qui vise à faire pression sur Israël pour stopper sa politique de colonisation de la Cisjordanie, demande à Netflix de ne plus la diffuser car elle légitimerait les « crimes de guerre ». Les séries TV doivent-elles rendre fidèlement compte des réalités politiques qu’elles traitent ? En m’appuyant sur les concepts de dispositif de problématisation et d’effet de fiction, j’étudie dans un premier temps la manière dont la série s’inscrit dans l’histoire des représentations audiovisuelles israéliennes de Tsahal. Elle indique une « américanisation » des codes de représentation de l’institution militaire, en empruntant notamment à l’esthétique du western. Dans un deuxième temps, j’interroge les accusations partisanes dont a fait l'objet Fauda. Pour ses détracteurs, elle propose une vision « orientée » du conflit israélo-palestinien. Ses créateurs revendiquent au contraire la mise en récit « authentique » du travail de l’unité à partir de leur expérience de vétéran. Cependant, aux critiques pointant la disparité avec la situation quotidienne des Palestiniens, ceux-ci répondent en se retranchant derrière leur licence fictionnelle. Dans un troisième temps, je propose deux pistes pour prévenir les dilemmes éthiques posés par la représentation à l’écran d’une réalité politique sensible : la mise à contribution des sciences sociales, notamment des historiens, dans la production audiovisuelle, et la promotion d’un naturalisme participatif.The Israeli TV show Fauda depicts the daily life of the mista’aravim (literally « the Arabized »), a special force of the Israeli army whose mission is to operate incognito behind enemy lines by disguising themselves as Palestinian civilians. Produced in 2015 by two veterans of this unit, Avi Issacharoff and Lior Raz, this TV shows is a global it. It is acclaimed as well as heavily criticized. In March 2018, the movement « Boycott, Divestment, Sanction », aiming at pressuring Israel to stop its illegal settlements in the West Bank, asked Netflix to no longer broadcast a TV show that is legitimizing « war crimes ». Should TV shows accurately reflect the political realities they deal with? Drawing on the concepts of problematization and fictional effect, I first analyze how Fauda fits into the history of the Israeli representations of the IDF. I argue that Fauda represents an americanization of the IDF’s representation, borrowing in particular from the aesthetics of western. I then question the accusations made against Fauda. For its detractors, it offers an « oriented » vision of the Israeli-Palestinian conflict. Its creators, on the contrary, claim its « authenticness », based on their experience as veterans. This argument is contractor with their own declarations, when responding to critics they argue that Fauda is merely a fiction. Finally, I propose two avenues to prevent the ethical dilemmas posed by the representation of a sensitive political situation: the contribution of the social sciences, and the promotion of what I call a « participative naturalism »

Confluence in UnTyped Higher-Order Theories by means of Critical Pairs

User-defined higher-order rewrite rules are becoming a standard in proof assistants based on intuitionistic type theory. This raises the question of proving that they preserve the properties of beta-reductions for the corresponding type systems. We develop here techniques that reduce confluence proofs to the checking of various forms of critical pairs for higher-order rewrite rules extending beta-reduction on pure lambda-terms. The present paper concentrates on the case where rewrite rules are left-linear and critical pairs can be joined without using beta-rewrite steps. The other two cases will be addressed in forthcoming papers

ExaViz: a Flexible Framework to Analyse, Steer and Interact with Molecular Dynamics Simulations

International audienceThe amount of data generated by molecular dynamics simulations of large molecular assemblies and the sheer size and complexity of the systems studied call for new ways to analyse, steer and interact with such calculations. Traditionally, the analysis is performed off-line once the huge amount of simulation results have been saved to disks, thereby stressing the supercomputer I/O systems, and making it increasingly difficult to handle post-processing and analysis from the scientist's office. The ExaViz framework is an alternative approach developed to couple the simulation with analysis tools to process the data as close as possible to their source of creation, saving a reduced, more manageable and pre-processed data set to disk. ExaViz supports a large variety of analysis and steering scenarios. Our framework can be used for live sessions (simulations short enough to be fully followed by the user) as well as batch sessions (long time batch executions). During interactive sessions, at run time, the user can display plots from analysis, visualise the molecular system and steer the simulation with a haptic device. We also emphasise how a Cave-like immersive environment could be used to leverage such simulations, offering a large display surface to view and intuitively navigate the molecular system

Poly[[aqua­tris­(μ-benzene-1,4-dicarboxyl­ato)tricobalt(II)] methanol monosolvate monohydrate]

The asymmetric unit of the title compound, {[Co3(C8H4O4)3(H2O)]·CH3OH·H2O}n, consists of four crystallographically independent Co cations, four benzene-1,4-dicarboxyl­ate (bdc) anions, two water and one methanol solvent mol­ecule. Two of the Co cations and two of the bdc anions are located on centres of inversion, whereas all other atoms are located in general positions. In the crystal, two Co atoms are only fourfold coordinated by three O atoms from three bdc ligands and by one O atom from one coordinated water mol­ecule, while a third Co atom is coordinated by four O atoms from four bdc ligands within a strongly distorted tetra­hedral geometry. The other two Co cations are octa­hedrally coordinated by six O atoms from six bdc anions. The Co cations are linked by the bdc anions into a three-dimensional framework. From this arrangement, cavities are formed in which additional methanol and water mol­ecules are embedded