Filling of three-dimensional space by two-dimensional sheet growth.

Models of three-dimensional space filling based on growth of two-dimensional sheets are proposed. Beginning from planar Eden-style growth of sheets, additional growth modes are introduced. These enable the sheets to form layered or disordered structures. The growth modes can also be combined. An off-lattice kinetic Monte Carlo-based computer algorithm is presented and used to study the kinetics of the new models and the resulting structures. It is possible to study space filling by two-dimensional growth in a three-dimensional domain with arbitrarily oriented sheets; the results agree with previously published models where the sheets are only able to grow in a limited set of directions. The introduction of a bifurcation mechanism gives rise to complex disordered structures that are of interest as model structures for the mesostructure of calcium silicate hydrate in hardened cement paste.This research was supported by the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement 264448. AFR was supported by EPSRC grant EP/H035397/1.This is the author accepted manuscript. The final version is available from APS via http://dx.doi.org/10.1103/PhysRevE.92.04210

Methanol conversion on borocarbonitride catalysts: Identification and quantification of active sites

Borocarbonitrides (BCNs) have emerged as highly selective catalysts for the oxidative dehydrogenation (ODH) reaction. However, there is a lack of in-depth understanding of the catalytic mechanism over BCN catalysts due to the complexity of the surface oxygen functional groups. Here, BCN nanotubes with multiple active sites are synthesized for oxygen-assisted methanol conversion reaction. The catalyst shows a notable activity improvement for methanol conversion (29%) with excellent selectivity to formaldehyde (54%). Kinetic measurements indicate that carboxylic acid groups on BCN are responsible for the formation of dimethyl ether, while the redox catalysis to formaldehyde occurs on both ketonic carbonyl and boron hydroxyl (B-OH) sites. The ODH reaction pathway on the B-OH site is further revealed by in situ infrared, x-ray absorption spectra, and density functional theory. The present work provides physical-chemical insights into the functional mechanism of BCN catalysts, paving the way for further development of the underexplored nonmetallic catalytic systems

GenoQuery: a new querying module for functional annotation in a genomic warehouse

Motivation: We have to cope with both a deluge of new genome sequences and a huge amount of data produced by high-throughput approaches used to exploit these genomic features. Crossing and comparing such heterogeneous and disparate data will help improving functional annotation of genomes. This requires designing elaborate integration systems such as warehouses for storing and querying these data

Diverse soil carbon dynamics expressed at the molecular level

The stability and potential vulnerability of soil organic matter (SOM) to global change remains incompletely understood due to the complex processes involved in its formation and turnover. Here we combine compound-specific radiocarbon analysis with fraction-specific and bulk-level radiocarbon measurements in order to further elucidate controls on SOM dynamics in a temperate and sub-alpine forested ecosystem. Radiocarbon contents of individual organic compounds isolated from the same soil interval generally exhibit greater variation than those among corresponding operationally-defined fractions. Notably, markedly older ages of long-chain plant leaf wax lipids (n-alkanoic acids) imply that they reflect a highly stable carbon pool. Furthermore, marked 14C variations among shorter- and longer-chain n-alkanoic acid homologues suggest that they track different SOM pools. Extremes in SOM dynamics thus manifest themselves within a single compound class. This exploratory study highlights the potential of compound-specific radiocarbon analysis for understanding SOM dynamics in ecosystems potentially vulnerable to global change

Determinants of legacy effects in pine trees – implications from an irrigation-stop experiment

Tree responses to altered water availability range from immediate (e.g. stomatal regulation) to delayed (e.g. crown size adjustment). The interplay of the different response times and processes, and their effects on long-term whole-tree performance, however, is hardly understood. Here we investigated legacy effects on structures and functions of mature Scots pine in a dry inner-Alpine Swiss valley after stopping an 11-yr lasting irrigation treatment. Measured ecophysiological time series were analysed and interpreted with a system-analytic tree model. We found that the irrigation stop led to a cascade of downregulations of physiological and morphological processes with different response times. Biophysical processes responded within days, whereas needle and shoot lengths, crown transparency, and radial stem growth reached control levels after up to 4 yr only. Modelling suggested that organ and carbon reserve turnover rates play a key role for a tree’s responsiveness to environmental changes. Needle turnover rate was found to be most important to accurately model stem growth dynamics. We conclude that leaf area and its adjustment time to new conditions is the main determinant for radial stem growth of pine trees as the transpiring area needs to be supported by a proportional amount of sapwood, despite the growth-inhibiting environmental conditions

Determinants of legacy effects in pine trees - implications from an irrigation-stop experiment

Tree responses to altered water availability range from immediate (e.g. stomatal regulation) to delayed (e.g. crown size adjustment). The interplay of the different response times and processes, and their effects on long-term whole-tree performance, however, is hardly understood. Here we investigated legacy effects on structures and functions of mature Scots pine in a dry inner-Alpine Swiss valley after stopping an 11-yr lasting irrigation treatment. Measured ecophysiological time series were analysed and interpreted with a system-analytic tree model. We found that the irrigation stop led to a cascade of downregulations of physiological and morphological processes with different response times. Biophysical processes responded within days, whereas needle and shoot lengths, crown transparency, and radial stem growth reached control levels after up to 4 yr only. Modelling suggested that organ and carbon reserve turnover rates play a key role for a tree's responsiveness to environmental changes. Needle turnover rate was found to be most important to accurately model stem growth dynamics. We conclude that leaf area and its adjustment time to new conditions is the main determinant for radial stem growth of pine trees as the transpiring area needs to be supported by a proportional amount of sapwood, despite the growth-inhibiting environmental conditions.Peer reviewe

Biowep: a workflow enactment portal for bioinformatics applications

<p>Abstract</p> <p>Background</p> <p>The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity in bioinformatics. ICT standards and tools, like Web Services and Workflow Management Systems (WMS), can support the creation and deployment of such systems. Many Web Services are already available and some WMS have been proposed. They assume that researchers know which bioinformatics resources can be reached through a programmatic interface and that they are skilled in programming and building workflows. Therefore, they are not viable to the majority of unskilled researchers. A portal enabling these to take profit from new technologies is still missing.</p> <p>Results</p> <p>We designed biowep, a web based client application that allows for the selection and execution of a set of predefined workflows. The system is available on-line. Biowep architecture includes a Workflow Manager, a User Interface and a Workflow Executor. The task of the Workflow Manager is the creation and annotation of workflows. These can be created by using either the Taverna Workbench or BioWMS. Enactment of workflows is carried out by FreeFluo for Taverna workflows and by BioAgent/Hermes, a mobile agent-based middleware, for BioWMS ones. Main workflows' processing steps are annotated on the basis of their input and output, elaboration type and application domain by using a classification of bioinformatics data and tasks. The interface supports users authentication and profiling. Workflows can be selected on the basis of users' profiles and can be searched through their annotations. Results can be saved.</p> <p>Conclusion</p> <p>We developed a web system that support the selection and execution of predefined workflows, thus simplifying access for all researchers. The implementation of Web Services allowing specialized software to interact with an exhaustive set of biomedical databases and analysis software and the creation of effective workflows can significantly improve automation of in-silico analysis. Biowep is available for interested researchers as a reference portal. They are invited to submit their workflows to the workflow repository. Biowep is further being developed in the sphere of the Laboratory of Interdisciplinary Technologies in Bioinformatics – LITBIO.</p