On-chip CMOS-compatible all-optical integrator

One reason for using photonic devices is their speed—much faster than electronic circuits—but there are many challenges in integrating the two technologies. Ferrera et al. construct a CMOS-compatible monolithic optical waveform integrator, a key building block for photonic circuits

Gorenstein homological algebra and universal coefficient theorems

We study criteria for a ring—or more generally, for a small category—to be Gorenstein and for a module over it to be of finite projective dimension. The goal is to unify the universal coefficient theorems found in the literature and to develop machinery for proving new ones. Among the universal coefficient theorems covered by our methods we find, besides all the classic examples, several exotic examples arising from the KK-theory of C*-algebras and also Neeman’s Brown–Adams representability theorem for compactly generated categories

Lattice Boltzmann simulations of soft matter systems

This article concerns numerical simulations of the dynamics of particles immersed in a continuum solvent. As prototypical systems, we consider colloidal dispersions of spherical particles and solutions of uncharged polymers. After a brief explanation of the concept of hydrodynamic interactions, we give a general overview over the various simulation methods that have been developed to cope with the resulting computational problems. We then focus on the approach we have developed, which couples a system of particles to a lattice Boltzmann model representing the solvent degrees of freedom. The standard D3Q19 lattice Boltzmann model is derived and explained in depth, followed by a detailed discussion of complementary methods for the coupling of solvent and solute. Colloidal dispersions are best described in terms of extended particles with appropriate boundary conditions at the surfaces, while particles with internal degrees of freedom are easier to simulate as an arrangement of mass points with frictional coupling to the solvent. In both cases, particular care has been taken to simulate thermal fluctuations in a consistent way. The usefulness of this methodology is illustrated by studies from our own research, where the dynamics of colloidal and polymeric systems has been investigated in both equilibrium and nonequilibrium situations.Comment: Review article, submitted to Advances in Polymer Science. 16 figures, 76 page

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

THE PRODUCT POLARIZATION OF CHEMILUMINESCENT REACTIONS OF ORBITAL ALIGNED CA(1P1) WITH CH3I AND C2H5I

The product polarization in the beam-gas chemiluminescent reactions Ca(P-1(1)) + RI --> CaI* + R for different initial Ca electronic orbital alignments are both probed experimentally and calculated with the DIP extension of the DIPR model (the direct interaction with product repulsion (DIPR) model, with product repulsion distributed as in photodissociation (DIP) model). The experimental results show that the product rotational alignment is independent of the Ca(P-1(1)) orbital alignment and that the distribution of the product rotational vector becomes less anisotropic as the number of carbon atoms in R increased. The reagent alignment sensitivity factors of the reaction Ca(P-1(1)) + CH3I --> CaI* + CH3 are also investigated

Reagent orbital alignment effect in chemiluminescence reactions Ca(P-1(1))+CH3X (X = Cl, I)

Reagent orbital alignment effects in chemiluminescence reactions Ca(P-1(1)) + CH3X (X = Cl, I) are studied in a beam-gas apparatus. Stronger alignment dependence is found in the reaction Ca(P-1(1)) + CH3CI. For an ideal case, a simple expression is derived to calculate the reagent alignment sensitivity factor. This analysis shows that the primary reasons for the different alignment dependence between Ca(P-1(1)) + CH3CI and Ca(P-1(1)) + CH3I lie in two facts: one is the larger reaction radius for the latter reaction, and the other is the larger potential splitting V-Pi-V-Sigma for the former reaction

Product rotational alignment of orbital aligned Ca(P-1(1)) with CnH2n+1Br (n=1, 2, 3) reactions

The product rotational alignment of Ca(P-1(1)) with CnH2n+1Br (n = 1, 2, 3) for different initial Ca(P-1(1)) electronic orbital alignment is probed by means of laser-induced chemiluminescence in beam-gas apparatus. And the product rotational alignment of these reactions is calculated with an extended direct interaction with product repulsion (DIPR) model. The effects of the magnitude of the repulsive energy and the reagent approach geometry on the title reactions are also studied

Climate extremes in Loess of China coupled with the strength of deep-water formation in the North Atlantic

The loess-paleosol sequences of the last 1.2 Ma in China have recorded two kinds of climate extremes: the strongly developed S4, S5-1 and S5-3 soils (corresponding to the marine delta(18)O stages 11, 13, and 15, respectively) as evidence of three episodes of great warmth and two coarse-grained loess units (L9 and L15, corresponding to the marine delta(18)O stages 22, 23, 24 and 38, respectively) which indicate severest glacial conditions. The climatic and geographical significance of these events are still unclear, and their cause remains a puzzle. Paleopedological, geochemical and magnetic susceptibility data from three loess sections (Xifeng, Changwu and Weinan) suggest that the S4, S5-1 and S5-3 soils were formed under sub-tropical semi-humid climates with a tentatively estimated mean annual temperature (MAT) of at least 4-6 degrees C higher and a mean annual precipitation (MAP) of 200-300 mm higher than for the present-day, indicating a much strengthened summer monsoon. The annual rainfall was particularly accentuated for the southern-most part of the Loess Plateau, suggesting that the monsoon rain belt (the contact of the monsoonal northward warm-humid air mass with the dry-cold southward one) might have stood at the southern part of the Plateau for a relatively long period each year. The loess units L9 and L15 were deposited under semi-desertic environments with a tentatively estimated MAT and MAP of only about 1.5-3 degrees C and 150-250 mm, indicating a much strengthened winter monsoon, and that the summer monsoon front could rarely penetrate into the Loess Plateau region. Correlation with marine carbon isotope records suggests that these climate extremes have large regional, even global, significance rather than being local phenomena in China. They match the periods with greatest/smallest Atlantic-Pacific delta(13)C gradients, respectively, indicating their relationships with the strength of Deep Water (NADW) production in the North Atlantic. These results suggest that the monsoon climate in the Loess Plateau region was significantly linked with the North Atlantic thermohaline circulation on timescales of 10(4) years. (C) 1998 Elsevier Science B.V. All rights reserved