Performance of a Sequential Reactive Barrier for Bioremediation of Coal Tar Contaminated Groundwater

Following a thorough site investigation, a biological Sequential Reactive Barrier (SEREBAR), designed to remove Polycyclic Aromatic Hydrocarbons (PAHs) and BTEX compounds, was installed at a Former Manufactured Gas Plant (FMGP) site. The novel design of the barrier comprises, in series, an interceptor and six reactive chambers. The first four chambers (2 nonaerated-2 aerated) were filled with sand to encourage microbial colonization. Sorbant Granular Activated Carbon (GAC) was present in the final two chambers in order to remove any recalcitrant compounds. The SEREBAR has been in continuous operation for 2 years at different operational flow rates (ranging from 320 L/d to 4000 L/d, with corresponding residence times in each chamber of 19 days and 1.5 days, respectively). Under low flow rate conditions (320-520 L/d) the majority of contaminant removal (>93%) occurred biotically within the interceptor and the aerated chambers. Under high flow rates (1000-4000 L/d) and following the installation of a new interceptor to prevent passive aeration, the majority of contaminant removal (>80%) again occurred biotically within the aerated chambers. The sorption zone (GAC) proved to be an effective polishing step, removing any remaining contaminants to acceptable concentrations before discharge down-gradient of the SEREBAR (overall removals >95%).

Ion-Atom/Argon - Calculation of ionization cross sections by fast ion impact for neutral target atoms ranging from hydrogen to argon

A FORTRAN 90 program is presented which calculates the total cross sections, and the electron energy spectra of the singly and doubly differential cross sections for the single target ionization of neutral atoms ranging from hydrogen up to and including argon. The code is applicable for the case of both high and low Z projectile impact in fast ion-atom collisions. The theoretical models provided for the program user are based on two quantum mechanical approximations which have proved to be very successful in the study of ionization in ion-atom collisions. These are the continuum-distorted-wave (CDW) and continuum-distorted-wave eikonal-initial-state (CDW-EIS) approximations. The codes presented here extend previously published. codes for single ionization of. target hydrogen [Crothers and McCartney, Comput. Phys. Commun. 72 (1992) 288], target helium [Nesbitt, O'Rourke and Crothers, Comput. Phys. Commun. 114 (1998) 385] and target atoms ranging from lithium to neon [O'Rourke, McSherry and Crothers, Comput. Phys. Commun. 131 (2000) 129]. Cross sections for all of these target atoms may be obtained as limiting cases from the present code. Title of program: ARGON Catalogue identifier: ADSE Program summary URL: http://cpc.cs.qub.ac.uk/cpc/summaries/ADSE Program obtainable from: CPC Program Library Queen's University of Belfast, N. Ireland Licensing provisions: none Computer for which the program is designed and others on which it is operable: Computers: Four by 200 MHz Pro Pentium Linux server, DEC Alpha 21164; Four by 400 MHz Pentium 2 Xeon 450 Linux server, IBM SP2 and SUN Enterprise 3500 Installations: Queen's University, Belfast Operating systems under which the program has been tested: Red-hat Linux 5.2, Digital UNIX Version 4.0d, AIX, Solaris SunOS 5.7 Compilers: PGI workstations, DEC CAMPUS Programming language used: FORTRAN 90 with MPI directives No. of bits in a word: 64, except on Linux servers 32 Number of processors used: any number Has the code been vectorized or parallelized? Parallelized using MPI No. of bytes in distributed program, including test data, etc.: 32 189 Distribution format: tar gzip file Keywords: Single ionization, cross sections, continuum-distorted-wave model, continuum- distorted-wave eikonal-initial-state model, target atoms, wave treatment Nature of physical problem: The code calculates total, and differential cross sections for the single ionization of target atoms ranging from hydrogen up to and including argon by both light and heavy ion impact. Method of solution: ARGON allows the user to calculate the cross sections using either the CDW or CDW-EIS [J. Phys. B 16 (1983) 3229] models within the wave treatment. Restrictions on the complexity of the program: Both the CDW and CDW-EIS models are two-state perturbative approximations. Typical running time: Times vary according to input data and number of processors. For one processor the test input data for double differential cross sections (40 points) took less than one second, whereas the test input for total cross sections (20 points) took 32 minutes. Unusual features of the program: none (C) 2003 Elsevier B.V All rights reserved.

Sounds of the City

“Sounds of the City” is a large-scale community project and exhibition commissioned by the Metropolitan Arts Centre (MAC) and led by artists from the Sonic Arts Research Centre (SARC), Queen’s University Belfast. Over a four-month period, the artists worked together with two intergenerational groups in Belfast with the aim of addressing specific sound qualities of places, events and stories. Themes that surfaced from this process constitute the basis for the exhibition which promotes listening as a form of intersecting daily life, identity and memory. Five installations address aural contexts ranging from Belfast’s industrial heritage to the local family home. These are shaped by present and past experiences of workshop participants at Dee Street Community Centre in East Belfast and Tar Isteach in North Belfast. The themes and contents of these installations center upon the relationship between sound and memory, sound and place, and the documentation of everyday personal auditory experience.
All materials exhibited have emerged through workshops, interviews and field-recording sessions. Workshops acted as a basis from which to inform each group about the project’s aims, methods of listening, methods of documenting sound and the wider areas of soundscape studies and acoustic ecology. They also provided a central point allowing participants to organize outside activities and share material for exhibition.
“Sounds of the City” explores the relationship between sound and community through everyday life and presents a dynamic and ever-changing soundscape that shapes Belfast’s identity.

Sounds of the City has been exhibited at the MAC, Belfast 2012 and at Espaço Ecco, Brasilia 2013.

PLUMED 2: New feathers for an old bird

Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here a,complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

Program summary

Program title: PLUMED 2

Catalogue identifier: AEEE_v2_0

Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.html

Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland

Licensing provisions: Yes

No. of lines in distributed program, including test data, etc.: 700646

No. of bytes in distributed program, including test data, etc.: 6618136

Distribution format: tar.gz

Programming language: ANSI-C++.

Computer: Any computer capable of running an executable produced by a C++ compiler.

Operating system: Linux operating system, Unix OSs.

Has the code been vectorized or parallelized?: Yes, parallelized using MPI.

RAM: Depends on the number of atoms, the method chosen and the collective variables used.

Classification: 3, 7.7, 23. Catalogue identifier of previous version: AEEE_v1_0.

Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1961.

External routines: GNU libmatheval, Lapack, Bias, MPI. (C) 2013 Elsevier B.V. All rights reserved.

Thermal decomposition mechanism of levoglucosan during cellulose pyrolysis

Levoglucosan (1,6-anhydro-β-d-glucopyranose) decomposition is an important step during cellulose pyrolysis and for secondary tar reactions. The mechanism of levoglucosan thermal decomposition was studied in this paper using density functional theory methods. The decomposition included direct CO bond breaking, direct CC bond breaking, and dehydration. In total, 9 different pathways, including 16 elementary reactions, were studied, in which levoglucosan serves as a reactant. The properties of the reactants, transition states, intermediates, and products for every elementary reaction were obtained. It was found that 1-pentene-3,4-dione, acetaldehyde, 2,3-dihydroxypropanal, and propanedialdehyde can be formed from the CO bond breaking decomposition reactions. 1,2-Dihydroxyethene and hydroxyacetic acid vinyl ester can be formed from the CC bond breaking decomposition reactions. It was concluded that CO bond breaking is easier than CC bond breaking due to a lower activation energy and a higher released energy. During the 6 levoglucosan dehydration pathways, one water molecule which composed of a hydrogen atom from C3 and a hydroxyl group from C2 is the preferred pathway due to a lower activation energy and higher product stability. © 2012 Elsevier B.V. All rights reserved.

samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files

MOTIVATION: Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However, the reproducibility and robustness of RNA-seq data analysis results is often unclear. This is in part attributed to the two counter acting goals of (a) a cost efficient and (b) an optimal experimental design leading to a compromise, e.g., in the sequencing depth of experiments.

RESULTS: We introduce an R package called samExploreR that allows the subsampling (m out of n bootstraping) of short-reads based on SAM files facilitating the investigation of sequencing depth related questions for the experimental design. Overall, this provides a systematic way for exploring the reproducibility and robustness of general RNA-seq studies. We exemplify the usage of samExploreR by studying the influence of the sequencing depth and the annotation on the identification of differentially expressed genes.

AVAILABILITY: Availability: samExploreR is available as an R package from Bioconductor (after acceptance of the paper, download link: http://www.bio-complexity.com/samExploreR_1.0.0.tar.gz).