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1701 Publications visible to you, out of a total of 1701
The Shape of Protein Crowders is a Major Determinant of Protein Diffusion

Abstract

Not specified

Authors: Jessica Balbo, Paolo Mereghetti, Dirk-Peter Herten, Rebecca C. Wade

Date Published: 1st Apr 2013

Publication Type: Journal

Translational repression of thymidylate synthase by targeting its mRNA

Abstract

Not specified

Authors: Divita Garg, Alexander V. Beribisky, Glauco Ponterini, Alessio Ligabue, Gaetano Marverti, Andrea Martello, M. Paola Costi, Michael Sattler, Rebecca C. Wade

Date Published: 1st Apr 2013

Publication Type: Journal

Biggest challenges in bioinformatics

Abstract (Expand)

The third Heidelberg Unseminars in Bioinformatics (HUB) was held on 18th October 2012, at Heidelberg University, Germany. HUB brought together around 40 bioinformaticians from academia and industry to … discuss the ‘Biggest Challenges in Bioinformatics’ in a ‘World Café’ style event.

Authors: Jonathan C Fuller, Pierre Khoueiry, Holger Dinkel, Kristoffer Forslund, Alexandros Stamatakis, Joseph Barry, Aidan Budd, Theodoros G Soldatos, Katja Linssen, Abdul Mateen Rajput

Date Published: 15th Mar 2013

Publication Type: Journal

Ligand-based discovery of N-(1,3-dioxo-1H,3H-benzo[de]isochromen-5-yl)-carboxamide and sulfonamide derivatives as thymidylate synthase A inhibitors

Abstract

Not specified

Authors: Stefania Ferrari, Marco Ingrami, Fabrizia Soragni, Rebecca C. Wade, M. Paola Costi

Date Published: 1st Feb 2013

Publication Type: Journal

On GPU-Based Nearest Neighbor Queries for Large-Scale Photometric Catalogs in Astronomy

Abstract (Expand)

Nowadays astronomical catalogs contain patterns of hundreds of millions of objects with data volumes in the terabyte range. Upcoming projects will gather such patterns for several billions of objects … with peta- and exabytes of data. From a machine learning point of view, these settings often yield unsupervised, semi-supervised, or fully supervised tasks, with large training and huge test sets. Recent studies have demonstrated the effectiveness of prototype-based learning schemes such as simple nearest neighbor models. However, although being among the most computationally efficient methods for such settings (if implemented via spatial data structures), applying these models on all remaining patterns in a given catalog can easily take hours or even days. In this work, we investigate the practical effectiveness of GPU-based approaches to accelerate such nearest neighbor queries in this context. Our experiments indicate that carefully tuned implementations of spatial search structures for such multi-core devices can significantly reduce the practical runtime. This renders the resulting frameworks an important algorithmic tool for current and upcoming data analyses in astronomy.

Authors: Justin Heinermann, Oliver Kramer, Kai Lars Polsterer, Fabian Gieseke

Date Published: 2013

Publication Type: InProceedings

Finding new high-redshift quasars by asking the neighbours

Abstract

Not specified

Authors: Kai Lars Polsterer, Peter-Christian Zinn, Fabian Gieseke

Date Published: 2013

Publication Type: Journal

Which Side-Reactions Compromise Nitroxide Mediated Polymerization?

Abstract (Expand)

The mechanism of the nitroxide mediated polymerization (NMP) is well understood, however less is known about the side-reactions that interfere and in certain cases severely compromise it. Experimental … studies inevitably involve model fitting leading to at times contradictory conclusions as to which elementary side-reactions are behind the failure of a given NMP system. In the present work we use high-level quantum-chemical calculations to obtain the rate coefficients of the various side-reactions, both suggested previously and considered here for the first time, and first principles PREDICI kinetic simulations to identify the most deleterious side-reactions involved in the TEMPO, SG1 and DPAIO mediated polymerization of styrene, acrylate and methacrylate monomers. We show that the core mechanism for the thermal decomposition of alkoxyamines differs between the uni- and polymeric species, which often makes such experiments not suitable for modelling the NMP conditions. We also find that the main side-reaction responsible for the failure of TEMPO and SG1 in methacrylate homopolymerization is an intramolecular alkoxyamine decomposition (often referred to as ‘disproportionation’) via a Cope-type elimination, however in the case of SG1 the polymerization outcome is additionally affected by the equilibrium constant of alkoxyamine bond homolysis. On the basis of these findings, complemented by a thorough analysis of available experimental data, we define guidelines for minimising occurrence of the side-reactions and thus improving NMP. Finally, the accurate first principles rate parameters reported in this study should prove useful for subsequent kinetic modelling oriented at optimising different polymerization conditions.

Authors: Ganna Gryn'ova, Ching Yeh Lin, Michelle L. Coote

Date Published: 2013

Publication Type: Journal

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