Relative size selection of a conjugated polyelectrolyte in virus-like protein structures

A conjugated polyelectrolyte poly[(2-methoxy-5-propyloxy sulfonate)-phenyl-ene vinylene] (MPS-PPV) drives the assembly of virus capsid proteins to form single virus-like particles (VLPs) and aggregates with more than two VLPs, with a relative selection of high molecular weight polymer in the latter.     

Catalytic conversion of methane to methanol over Cu-mordenite

Methane can be converted to methanol over copper-exchanged mordenite at 200 °C. Methanol could be recovered at the end of the reactor. This multi-step reaction opens the possibility for methane to methanol conversion in a closed catalytic cyclic reaction system.     

A sparse octree gravitational N-body code that runs entirely on the GPU processor

We present the implementation and performance of a new gravitational N-body tree-code that is specifically designed for the graphics processing unit (GPU).¹ All parts of the tree-code algorithm are executed on the GPU. We present algorithms for parallel construction and traversing of sparse octrees. These algorithms are implemented in CUDA and tested on NVIDIA GPUs, but they are portable to OpenCL and can easily be used on many-core devices from other manufacturers. This portability is achieved by using general parallel-scan and sort methods. The gravitational tree-code outperforms tuned CPU code during the tree-construction and shows a performance improvement of more than a factor 20 overall, resulting in a processing rate of more than 2.8 million particles per second.     

Universal Behaviour of Extreme Value Statistics for Selected Observables of Dynamical Systems

The main results of the extreme value theory developed for the investigation of the observables of dynamical systems rely, up to now, on the block maxima approach. In this framework, extremes are identified with the block maxima of the time series of the chosen observable, in the limit of infinitely long blocks. It has been proved that, assuming suitable mixing conditions for the underlying dynamical systems, the extremes of a specific class of observables are distributed according to the so called Generalised Extreme Value (GEV) distribution. Direct calculations show that in the case of quasi-periodic dynamics the block maxima are not distributed according to the GEV distribution. In this paper we show that considering the exceedances over a given threshold instead of the block-maxima approach it is possible to obtain a Generalised Pareto Distribution also for extremes computed in systems which do not satisfy mixing conditions. Requiring that the invariant measure locally scales with a well defined exponent—the local dimension—, we show that the limiting distribution for the exceedances of the observables previously studied with the block maxima approach is a Generalised Pareto distribution where the parameters depend only on the local dimensions and the values of the threshold but not on the number of observations considered. We also provide connections with the results obtained with the block maxima approach. In order to provide further support to our findings, we present the results of numerical experiments carried out considering the well-known Chirikov standard map.     

Amylose and Amylopectin Hybrid Materials via Enzymatic Pathways

Summary: Oligo- and polysaccharides are important macromolecules in living systems, showing their multifunctional characteristics in the construction of cell walls, energy storage, cell recognition and their immune response. Saccharides as organic raw materials can open new perspectives on the way to new biocompatible and biodegradable products which could help to overcome the problems resulting from the upcoming restrictions of petrochemical resources. Construction of well-defined carbohydrate polymer backbones is very challenging as it is difficult to realize complete regio and stereo-control of the glycosylating process. Most synthetic approaches are therefore based on the modification or degradation of naturally occurring polysaccharides resulting in less then perfect products. Enzymes have several remarkable catalytic properties compared with other types of catalysts in terms of their selectivity, high catalytic activity, lack of undesirable side reactions and operation under mild conditions. A biocatalytic pathway to synthesize saccharides is therefore very attractive as it results in well-defined polysaccharides avoiding the above drawbacks. When biogenic polysaccharides are combined with synthetic macromolecules, surfaces etc. materials with new interesting properties arise and the processability of the designed hybrid materials is facilitated. Amylose and amylopectin hybrid materials can be synthesized via enzymatic polymerization routes utilizing transferases. This approach opens access to well-defined hybrid structures bearing amylase or amylopectin moieties that cannot be synthesized by any other means.     

Development of Non-Hydrolysable Oligosaccharide Activity-Based Inactivators for Endoglycanases: A Case Study on α-1,6 Mannanases

There is a vast genomic resource for enzymes active on carbohydrates. Lagging far behind, however, are functional chemical tools for the rapid characterization of carbohydrate-active enzymes. Activity-based probes (ABPs) offer one chemical solution to these issues with ABPs based upon cyclophellitol epoxide and aziridine covalent and irreversible inhibitors representing a potent and widespread approach. Such inhibitors for enzymes active on polysaccharides are potentially limited by the requirement for several glycosidic bonds, themselves substrates for the enzyme targets. Here, it is shown that non-hydrolysable trisaccharide can be synthesized and applied even to enzymes with challenging subsite requirements. It was found that incorporation of carbasugar moieties, which was accomplished by cuprate-assisted regioselective trans-diaxial epoxide opening of carba-mannal synthesised for this purpose, yields inactivators that act as powerful activity-based inhibitors for α-1,6 endo-mannanases. 3-D structures at 1.35–1.47 Å resolutions confirm the design rationale and binding to the enzymatic nucleophile. Carbasugar oligosaccharide cyclophellitols offer a powerful new approach for the design of robust endoglycosidase inhibitors, while the synthesis procedures presented here should allow adaptation towards activity-based endoglycosidase probes as well as configurational isosteres targeting other endoglycosidase families.     

In Europe

Physics in Perspective - As the History of Science Society, which is based in America, holds its annual meeting in Utrecht, one of the key academic centers on the European continent, one may...     

1,2- or 1,3-Hydride Shifts: What Controls Guaiane Biosynthesis?

A systematic computational study addressing the entire chemical space of guaianes in conjunction with an analysis of all known compounds shows that 1,3-hydride shifts are rare events in guaiane biosynthesis. As demonstrated here, 1,3-hydride shifts towards guaianes can only be realized for two stereochemically well defined out of numerous possible stereoisomeric skeletons. One example is given by the mechanism of guaia-4(15)-en-11-ol synthase from California poplar, an enzyme that yields guaianes with unusual stereochemical properties. The general results from DFT calculations were experimentally verified through isotopic-labeling experiments with guaia-4(15)-en-11-ol synthase.     

A systematic approach to parameter optimization and its application to flight schedule simulation software

Journal of Heuristics - Industrial software often has many parameters that critically impact performance. Frequently, these are left in a sub-optimal configuration for a given application because...