Linear Response for Confined Particles

The dynamics of fluctuations is considered for electrons near a positive ion or for charges in a confining trap. The stationary nonuniform equilibrium densities are discussed and contrasted. The linear response function for small perturbations of this nonuniform state is calculated from a linear Markov kinetic theory whose generator for the dynamics is exact in the short time limit. The kinetic equation is solved in terms of an effective mean field single particle dynamics determined by the local density and dynamical screening by a dielectric function for the non-uniform system. The autocorrelation function for the total force on the charges is discussed.Comment: 4 pages, 1 figure. Results presented at the "International Conference on Strongly Coupled Coulomb Systems", Camerino, Italy, July 2008. Submitted for publication in the conference proceedings (special issue of Journal of Physics A

SAT-based optimal hypergraph partitioning with replication

We propose a methodology for optimal k-way partitioning with replication of directed hypergraphs via Boolean satisfiability. We begin by leveraging the power of existing and emerging SAT solvers to attack traditional logic bipartitioning and show good scaling behavior. We continue to present the first optimal partitioning results that admit generation and assignment of replicated nodes concurrently. Our framework is general enough that we also give the first published optimal results for partitioning with respect to the maximum subdomain degree metric and the sum of external degrees metric. We show that for the bipartitioning case we can feasibly solve problems of up to 150 nodes with simultaneous replication in hundreds of seconds. For other partitioning metrics, we are able to solve problems up to 40 nodes in hundreds of seconds

Packet Switched vs. Time Multiplexed FPGA Overlay Networks

Dedicated, spatially configured FPGA interconnect is efficient for applications that require high throughput connections between processing elements (PEs) but with a limited degree of PE interconnectivity (e.g. wiring up gates and datapaths). Applications which virtualize PEs may require a large number of distinct PE-to-PE connections (e.g. using one PE to simulate 100s of operators, each requiring input data from thousands of other operators), but with each connection having low throughput compared with the PE’s operating cycle time. In these highly interconnected conditions, dedicating spatial interconnect resources for all possible connections is costly and inefficient. Alternatively, we can time share physical network resources by virtualizing interconnect links, either by statically scheduling the sharing of resources prior to runtime or by dynamically negotiating resources at runtime. We explore the tradeoffs (e.g. area, route latency, route quality) between time-multiplexed and packet-switched networks overlayed on top of commodity FPGAs. We demonstrate modular and scalable networks which operate on a Xilinx XC2V6000-4 at 166MHz. For our applications, time-multiplexed, offline scheduling offers up to a 63% performance increase over online, packet-switched scheduling for equivalent topologies. When applying designs to equivalent area, packet-switching is up to 2× faster for small area designs while time-multiplexing is up to 5× faster for larger area designs. When limited to the capacity of a XC2V6000, if all communication is known, time-multiplexed routing outperforms packet-switching; however when the active set of links drops below 40% of the potential links, packet-switched routing can outperform time-multiplexing

SAT-based optimal hypergraph partitioning with replication

We propose a methodology for optimal k-way partitioning with replication of directed hypergraphs via Boolean satisfiability. We begin by leveraging the power of existing and emerging SAT solvers to attack traditional logic bipartitioning and show good scaling behavior. We continue to present the first optimal partitioning results that admit generation and assignment of replicated nodes concurrently. Our framework is general enough that we also give the first published optimal results for partitioning with respect to the maximum subdomain degree metric and the sum of external degrees metric. We show that for the bipartitioning case we can feasibly solve problems of up to 150 nodes with simultaneous replication in hundreds of seconds. For other partitioning metrics, we are able to solve problems up to 40 nodes in hundreds of seconds

Highly modulated supported triazolium-based ionic liquids: direct control of the electronic environment on Cu nanoparticles

A series of new triazolium-based supported ionic liquids (SILPs), decorated with Cu NPs, were successfully prepared and applied to the N-arylation of aryl halides with anilines. The triazoles moieties were functionalised using copper-catalysed azide–alkyne cycloaddition. SILP surface characterisation showed a strong correlation between the triazolium cation volume and textural properties. STEM images showed well-dispersed Cu NPs on SILPs with a mean diameter varying from 3.6 to 4.6 nm depending on the triazolium cation used. Besides, XPS results suggest that the Cu(0)/Cu(I) ratio can be modulated by the electronic density of triazolium substituents. XPS and computational analysis gave mechanistic insights into the Cu NP stabilisation pathways, where the presence of electron-rich groups attached to a triazolium ring plays a critical role in leading to a cation adsorption pathway (Eads = 72 kcal mol−1). In contrast, less electron-rich groups favour the anion adsorption pathway (Eads = 63 kcal mol−1). The Cu@SILP composite with electron-rich groups showed the highest activity for the C–N Ullmann coupling reaction, which suggests that electron-rich groups might act as an electron-like reservoir to facilitate oxidative addition for N-arylation. This strategy firmly suggests the strong dependence of the nature of triazolium-based SILPs on the Cu NP surface active sites, which may provide a new environment to confine and stabilise MNPs for catalytic applications

Predictions of CYPMediated Drug-Drug Interactions Using Cryopreserved Human Hepatocytes

consistent with an underestimation of in vitro inhibition potency in this system. In conclusion, the HHSHP system proved to be a simple, accurate predictor of DDIs for 3 major CYPs and superior to the protein-free approach

Clades of huge phages from across Earth's ecosystems.

Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems