Automorphisms of Partially Commutative Groups II: Combinatorial Subgroups

We define several "standard" subgroups of the automorphism group Aut(G) of a partially commutative (right-angled Artin) group and use these standard subgroups to describe decompositions of Aut(G). If C is the commutation graph of G, we show how Aut(G) decomposes in terms of the connected components of C: obtaining a particularly clear decomposition theorem in the special case where C has no isolated vertices. If C has no vertices of a type we call dominated then we give a semi-direct decompostion of Aut(G) into a subgroup of locally conjugating automorphisms by the subgroup stabilising a certain lattice of "admissible subsets" of the vertices of C. We then characterise those graphs for which Aut(G) is a product (not necessarily semi-direct) of two such subgroups.Comment: 7 figures, 63 pages. Notation and definitions clarified and typos corrected. 2 new figures added. Appendix containing details of presentation and proof of a theorem adde

Thermal Conductivity of Ordered Mesoporous Nanocrystalline Silicon Thin Films Made from Magnesium Reduction of Polymer-Templated Silica

This paper reports the cross-plane thermal conductivity of ordered mesoporous nanocrystalline silicon thin films between 25 and 315 K. The films were produced by evaporation induced self-assembly of mesoporous silica followed by magnesium reduction. The periodic ordering of pores in mesoporous silicon was characterized by X-ray diffraction and direct SEM imaging. The average crystallite size, porosity, and film thickness were about 13 nm, 25-35%, and 140-340 nm, respectively. The pores were arranged in a face-centered cubic lattice. The cross-plane thermal conductivity of the mesoporous silicon thin films was measured using the 3ω method. It was between 3 and 5 orders of magnitude smaller than that of bulk single crystal silicon in the temperature range considered. The effects of temperature, film thickness, and copolymer template on the thermal conductivity were investigated. A model based on kinetic theory was used to accurately predict the measured thermal conductivity for all temperatures. On the one hand, both the measured thermal conductivity and the model predictions showed a temperature dependence of k proportional to T2 at low temperatures, typical of amorphous and strongly disordered materials. On the other hand, at high temperatures the thermal conductivity of mesoporous silicon films reached a maximum, indicating a crystalline-like behavior. These results will be useful in designing mesoporous silicon with desired thermal conductivity by tuning its morphology for various applications

Reductive electrosynthesis of crystalline metal-organic frameworks

Electroreduction of oxoanions affords hydroxide equivalents that induce selective deposition of crystalline metal–organic frameworks (MOFs) on conductive surfaces. The method is illustrated by cathodic electrodeposition of Zn[subscript 4]O(BDC)[subscript 3] (MOF-5; BDC = 1,4-benzenedicarboxylate), which is deposited at room temperature in only 15 min under cathodic potential. Although many crystalline phases are known in the Zn[superscript 2+]/BDCsuperscript 2–] system, MOF-5 is the only observed crystalline MOF phase under these conditions. This fast and mild method of synthesizing MOFs is amenable to direct surface functionalization and could impact applications requiring conformal coatings of microporous MOFs, such as gas separation membranes and electrochemical sensors.Massachusetts Institute of Technology. Energy Initiative (Seed Fund Program)National Science Foundation (U.S.) (Grant CHE-9808061)National Science Foundation (U.S.) (Grant DBI-9729592)National Science Foundation (U.S.) (Grant DMR- 0819762

Portability of scientific workflows in NGS data analysis: a case study

The analysis of next-generation sequencing (NGS) data requires complex computational workflows consisting of dozens of autonomously developed yet interdependent processing steps. Whenever large amounts of data need to be processed, these workflows must be executed on a parallel and/or distrib-uted systems to ensure reasonable runtime. To simplify the development and parallel execution of workflows, researchers rely on existing services such as distributed file systems, specialized workflow languages, resource managers, or workflow scheduling tools. Systems that cover some or all of these functionalities are categorized under labels like scientific workflow management systems, big data pro-cessing frameworks, or batch-queuing systems. Porting a workflow developed for a particular system on a particular hardware infrastructure to another system or to another infrastructure is non-trivial, which poses a major impediment to the scientific necessities of workflow reproducibility and workflow reusability. In this work, we describe our efforts to port a state-of -the-art workflow for the detection of specific variants in whole-exome sequencing of mice. The workflow originally was developed in the scientific workflow system snakemake for execution on a high-performance cluster controlled by Sun Grid En-gine. In the project, we ported it to the scientific workflow system SaasFee that can execute workflows on (multi-core) stand-alone servers or on clusters of arbitrary sizes using the Hadoop cluster manage-ment software. The purpose of this port was that also owners of low-cost hardware infrastructures, for which Hadoop was made for, become able to use the workflow. Although both the source and the target system are called scientific workflow systems, they differ in numerous aspects, ranging from the workflow languages to the scheduling mechanisms and the file access interfaces. These differences resulted in various problems, some expected and more unexpected, that had to be resolved before the workflow could be run with equal semantics. As a side-effect, we also report cost/runtime ratios for a state-of -the-art NGS workflow on very different hardware platforms: A comparably cheap stand-alone server (80 threads), a mid-cost, mid-sized cluster (552 threads), and a high-end HPC system (3784 threads)