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.

Promoting multicultural education in the primary classroom:Broadband videoconferencing facilities and digital video

The aim of this study was to explore the impact of interaction (through gathering local field data and engaging in remote reciprocal presentations) on aspects of multicultural awareness. Sixty-six 11-12-year-old Scottish primary school pupils collected data in the field from their local community through questionnaires, interviews, direct observation, digital images and video. From this they distilled a multimedia presentation, delivered by videoconference to a partner school in the USA, who reciprocated. There was some evidence of pre-post project gains in the complexity of the children's perceptions of their community environment, the ethnicity of their community, their own ethnicity, and news images. The children's use of language to define ethnicity also became more complex and their attitudes toward ethnic minorities became more inclusive. The implications for practice, policy and future research were explored. © 2004 Elsevier Ltd. All rights reserved.

The role of facilities manager in sustainable practice in the UK and Ireland

Purpose – The purpose of this paper is to explore the role of facilities managers in sustainable practice. It also analyzes the change in facilities management (FM) in terms of sustainability.

Design/methodology/approach – This research adopted a combination of literature review and expert interviews. Empirical data were collected through in-depth interviews with 40 industrial experts in the UK and Ireland.

Findings – The analysis of interview results shows a sustainable movement in the context of FM. Facilities managers play important roles in sustainable practice, including integrating all sustainability considerations, linking strategic level with operational level, incorporating FM knowledge and experience into design, disseminating sustainable knowledge and educating people and encouraging sustainability through innovation.

Research limitations/implications – This research goes beyond the limitations of existing studies that are characterized by a lack of positioning facilities managers in sustainability.

Practical implications – Sustainable delivery represents a direction of FM development. This research describes what facilities managers can do and how they should do for sustainable delivery of FM, based on which improvements are made and benefits are maximized.

Originality/value – This research provides a deeper insight into the FM role in the sustainable agenda. The findings of this research help industrial practitioners and academic researchers to better understand sustainable FM.

Material Logistics in Urban Construction Sites: A Structural Equation Model

Aim: The aim of this paper is to identify best practice relating to the effective management of materials in an urban, confined construction site, using structural equation modelling.

Methodology: A literature review, case study analysis and questionnaire survey are employed, with the results scrutinised using confirmatory factor analysis in the form of structural equation modelling.

Results: The following are the leading strategies in the management of materials in a confined urban site environment; (1) Consult and review the project programme, (2) Effective communication and delivery, (3) Implement site safety management plans, and (4) Proactive spatial monitoring and control.

Implication for Practice: With the relentless expansion of urban centres and the increasing high cost of materials, any potential savings made on-site would translate into significant monetary concessions on completion of a development.

Originality/Value: As on-site project management professionals successfully identify and implement the various strategies in the management of plant and materials on a confined urban site, successful resource management in this restrictive environment is attainable.

Innovative Aspect of Paper: An empirical study of three different construction sites in three different countries (Ireland, England and USA) together with a questionnaire survey from the industry, investigating the managerial strategies in the management of plant and material in confined urban site environments

The effects of stepped sites and ruthenium adatom decoration on methanol dehydrogenation over platinum-based catalyst surfaces

A density functional theory study of methanol dehydrogenation over stepped Pt(2 1 1) surfaces without and with Ru modification was carried out to understand fuel catalytic reactions on Pt-based catalysts. Two main pathways of the CH3OH dehydrogenation were examined: the O–H pathway which was initiated by O–H bond scission to form the methoxy (CH3O) intermediate followed by sequential cleavage of C–H bonds to CO, and the C–H pathway which was initiated by C–H bond scission to form the hydroxymethyl (CH2OH) followed by two C–H bond cleavages to COH and then CO. Possible crossover reactions between the O–H and C–H pathways were also computed. Compared to flat Pt(1 1 1), stepped Pt(2 1 1) increases the adsorption energies of intermediates, making no significant contribution to decreasing the reaction barriers of most elementary steps involved, except in the first hydrogen scission. However, on the Ru-modified surface, a significant reduction was found in reaction barriers for the first step of the C–H bond scission and a number of further dehydrogenation steps crossing over to the O–H pathway, with the most facile paths identified. Our data reveals the complexity of methanol catalytic reaction processes at the atomic level and contributes to a fundamental understanding of fuel reactions on Pt-based catalysts.

Integrated Earth Resistivity Tomography (ERT) and Multilevel Gas Sampling: A Tool to Map Geogenic and Anthropogenic Methane Accumulation on Brownfield Sites

Soil gas emissions of methane and carbon dioxide on brownfield sites are usually attributed to anthropogenic activities; however geogenic sources of soil gas are often not considered during site investigation and risk management strategies. This paper presents a field study at a redeveloped brownfield site on a flood plain to identify accumulations of methane biogas trapped in underlying sediments. The investigation is based on a multidisciplinary approach using direct multi-level sampling measurements and Earth resistivity tomography . Resistivity imaging was applied to evaluate the feasibility of identifying the size and spatial continuity of soil gas accumulations in anthropogenic and naturally occurring deposits. As a result, biogas accumulations are described within both anthropogenic deposits and pristine organic sediments. This result is important to identify the correct approaches to identify and manage risks associated with soil gas emissions on brownfield and pristine sites. The organic-rich sediments in Quaternary fluvial environments of São Paulo Basin in particular the Tietê River, biogas reservoirs can be generated and trapped beneath geogenic and anthropogenic layers, potentially requiring the management of brownfield developments across this region.

A carefully curated collection: female figures as sites of inscription in Gautier’s Émaux et Camées

This article examines the ways in which female figures function as additional sites for poetic inscription in Gautier's Émaux et Camées. Although considerable attention has already been paid to the numerous and varied objects catalogued in the collection and, indeed, to the notion of the poems themselves as objects, the present study aims to expand upon such interpretations of the work by focusing on three texts, "Le Poëme de la femme", "Étude de mains : Impéria" and "La fellah". In these poems, female figures who, while they may at first be granted some agency (and be represented going about the business of daily, if highly stylized, life), are finally immobilized within the verse as their bodies, and particularly their pristine skin, ultimately function as an additional paper-like surface for the poet, permitting their assimilation into Gautier's diminutive private collection.