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.

On the maximum energy of shock-accelerated cosmic rays at ultra-relativistic shocks

The maximum energy to which cosmic rays can be accelerated at weakly magnetised ultra-relativistic shocks is investigated. We demonstrate that for such shocks, in which the scattering of energetic particles is mediated exclusively by ion skin-depth scale structures, as might be expected for a Weibel-mediated shock, there is an intrinsic limit on the maximum energy to which particles can be accelerated. This maximum energy is determined from the requirement that particles must be isotropized in the downstream plasma frame before the mean field transports them far downstream, and falls considerably short of what is required to produce ultra-high-energy cosmic rays. To circumvent this limit, a highly disorganized field is required on larger scales. The growth of cosmic ray-induced instabilities on wavelengths much longer than the ion-plasma skin depth, both upstream and downstream of the shock, is considered. While these instabilities may play an important role in magnetic field amplification at relativistic shocks, on scales comparable to the gyroradius of the most energetic particles, the calculated growth rates have insufficient time to modify the scattering. Since strong modification is a necessary condition for particles in the downstream region to re-cross the shock, in the absence of an alternative scattering mechanism, these results imply that acceleration to higher energies is ruled out. If weakly magnetized ultra-relativistic shocks are disfavoured as high-energy particle accelerators in general, the search for potential sources of ultra-high-energy cosmic rays can be narrowed.

AcT-2: A Novel Myotropic and Antimicrobial Type 2 Tryptophyllin from the Skin Secretion of the Central American Red-Eyed Leaf Frog, Agalychnis callidryas

Tryptophyllins are a diverse family of amphibian peptides originally found in extracts of phyllomedusine frog skin by chemical means. Their biological activities remain obscure. Here we describe the isolation and preliminary pharmacological characterization of a novel type 2 tryptophyllin, named AcT-2, from the skin secretion of the red-eyed leaf frog, Agalychnis callidryas. The peptide was initially identified during smooth muscle pharmacological screening of skin secretion HPLC fractions and the unique primary structure—GMRPPWF-NH2—was established by both Edman degradation and electrospray MS/MS fragmentation sequencing. A. cDNA encoding the biosynthetic precursor of AcT-2 was successfully cloned from a skin secretion-derived cDNA library by means of RACE PCR and this contained an open-reading frame consisting of 62 amino acid residues with a single AcT-2 encoding sequence located towards the C-terminus. A synthetic replicate of AcT-2 was found to relax arterial smooth muscle (EC50 = 5.1 nM) and to contract rat urinary bladder smooth muscle (EC50 = 9.3 μM). The peptide could also inhibit the growth of the microorganisms, Staphylococcus aureus, (MIC = 256 mg/L) Escherichia coli (MIC = 512 mg/L), and Candida albicans (128 mg/L). AcT-2 is thus the first amphibian skin tryptophyllin found to possess both myotropic and antimicrobial activities.

Variability of the high-velocity outflow in the quasar PDS 456

We present a comparison of two Suzaku X-ray observations of the nearby (z = 0.184), luminous (L ∼ 10 erg s) type I quasar, PDS 456. A new 125 ks Suzaku observation in 2011 caught the quasar during a period of low X-ray flux and with a hard X-ray spectrum, in contrast with a previous 190 ks Suzaku observation in 2007 when the quasar appeared brighter and had a steep (Γ > 2) X-ray spectrum. The 2011 X-ray spectrum contains a pronounced trough near 9 keV in the quasar rest frame, which can be modeled with blueshifted iron K-shell absorption, most likely from the He- and H-like transitions of iron. The absorption trough is observed at a similar rest-frame energy as in the earlier 2007 observation, which appears to confirm the existence of a persistent high-velocity wind in PDS 456, at an outflow velocity of 0.25-0.30c. The spectral variability between 2007 and 2011 can be accounted for by variations in a partial covering absorber, increasing in covering fraction from the brighter 2007 observation to the hard and faint 2011 observation. Overall, the low-flux 2011 observation can be explained if PDS 456 is observed at relatively low inclination angles through a Compton-thick wind, originating from the accretion disk, which significantly attenuates the X-ray flux from the quasar. © 2014. The American Astronomical Society. All rights reserved.

Ornithokinin (avian bradykinin) from the skin of the Chinese bamboo odorous frog, Odorrana versabilis

One of the most widespread and abundant families of pharmacologically active peptides in amphibian defensive skin secretions is the bradykinins and related peptides. Despite retaining certain primary structural attributes that assign them to this peptide family, bradykinins and related peptides are unique among amphibian skin peptides in that they exhibit a wide range of primary structural variations, post-translational modifications and/or N-terminal or C-terminal extensions. Initially it was believed that their high degree of primary structural heterogeneity was reflective of random gene mutations within species, but latterly, there is an increasing body of evidence that the spectrum of structural modifications found within this peptide family is reflective of the vertebrate predator spectrum of individual species. Here we report the discovery of ornithokinin (avian bradykinin – Thr6, Leu8-bradykinin) in the skin secretion of the Chinese bamboo odorous frog, Odorrana versabilis. Molecular cloning of its biosynthetic precursor-encoding cDNA from a skin secretion-derived cDNA library revealed a deduced open-reading frame of 86 amino acid residues, encoding a single copy of ornithokinin towards its C-terminus. The domain architecture of this ornithokinin precursor protein was consistent with that of a typical amphibian skin peptide and quite different to that of the ornithokininogen from chicken plasma. Ornithokinin was reported to induce hypotension in the chicken and to contract the chicken oviduct but to have no obvious effect on the rat uterus. However, in this study, synthetic ornithokinin was found to contract the rat ileum (EC50 = 539 nM) and to increase contraction frequency in the rat uterus (EC50 = 1.87 μM).

Molecular Cloning of a Novel Tryptophyllin Peptide from the Skin of the Orange-Legged Monkey Frog, Phyllomedusa hypochondrialis

Tryptophyllins are a group of small (4–14 amino acids), heterogenous peptides, mostly from the skins of hylid frogs from the genera, Phyllomedusa and Litoria. To date, more than forty TPHs have been discovered in species from these two genera. Here, we describe the identification of a novel tryptophyllin type 3 peptide, PhT-3, from the extracts of skin of the orange-legged monkey frog, Phyllomedusa hypochondrialis, and molecular cloning of its precursor-encoding cDNA from a cDNA library constructed from the same skin sample. Full primary structural characterization was achieved using a combination of direct Edman degradation, mass spectrometry and deduction from cloned skin-derived cDNA. The open-reading frame of the precursor cDNA was found to consist of 63 amino acid residues. The mature peptide arising from this precursor contains a post-translationally modified N-terminal pyroglutamate (pGlu) residue, formed from acid-mediated cyclization of an N-terminal Gln (Q) residue, and with the structure: pGlu-Asp-Lys-Pro-Phe-Trp-Pro-Pro-Pro-Ile-Tyr-Pro-Met. Pharmacological assessment of a synthetic replicate of this peptide on phenylephrine preconstricted rat tail artery segments, revealed a reduction in relaxation induced by bradykinin. PhT-3 was also found to mediate antiproliferative effects on human prostate cancer cell lines.

Dissidents with an innovation cause? Non-institutionalized actors ’ online social knowledge sharing, solution-finding tensions and technology management innovation

Purpose
– Traditionally, most studies focus on institutionalized management-driven actors to understand technology management innovation. The purpose of this paper is to argue that there is a need for research to study the nature and role of dissident non-institutionalized actors’ (i.e. outsourced web designers and rapid application software developers). The authors propose that through online social knowledge sharing, non-institutionalized actors’ solution-finding tensions enable technology management innovation.

Design/methodology/approach
– A synthesis of the literature and an analysis of the data (21 interviews) provided insights in three areas of solution-finding tensions enabling management innovation. The authors frame the analysis on the peripherally deviant work and the nature of the ways that dissident non-institutionalized actors deviate from their clients (understood as the firm) original contracted objectives.

Findings
– The findings provide insights into the productive role of solution-finding tensions in enabling opportunities for management service innovation. Furthermore, deviant practices that leverage non-institutionalized actors’ online social knowledge to fulfill customers’ requirements are not interpreted negatively, but as a positive willingness to proactively explore alternative paths.

Research limitations/implications
– The findings demonstrate the importance of dissident non-institutionalized actors in technology management innovation. However, this work is based on a single country (USA) and additional research is needed to validate and generalize the findings in other cultural and institutional settings.

Originality/value
– This paper provides new insights into the perceptions of dissident non-institutionalized actors in the practice of IT managerial decision making. The work departs from, but also extends, the previous literature, demonstrating that peripherally deviant work in solution-finding practice creates tensions, enabling management innovation between IT providers and users.

An accelerated method of developing DBT projects using CDIO partner institutions as parallel processors

The cycle of the academic year impacts on efforts to refine and improve major group design-build-test (DBT) projects since the time to run and evaluate projects is generally a full calendar year. By definition these major projects have a high degree of complexity since they act as the vehicle for the application of a range of technical knowledge and skills. There is also often an extensive list of desired learning outcomes which extends to include professional skills and attributes such as communication and team working. It is contended that student project definition and operation, like any other designed product, requires a number of iterations to achieve optimisation. The problem however is that if this cycle takes four or more years then by the time a project’s operational structure is fine tuned it is quite possible that the project theme is no longer relevant. The majority of the students will also inevitably experience a sub-optimal project experience over the 5 year development period. It would be much better if the ratio were flipped so that in 1 year an optimised project definition could be achieved which had sufficient longevity that it could run in the same efficient manner for 4 further years. An increased number of parallel investigators would also enable more varied and adventurous project concepts to be examined than a single institution could undertake alone in the same time frame.
This work-in-progress paper describes a parallel processing methodology for the accelerated definition of new student DBT project concepts. This methodology has been devised and implemented by a number of CDIO partner institutions in the UK & Ireland region. An agreed project theme was operated in parallel in one academic year with the objective of replacing a multi-year iterative cycle. Additionally the close collaboration and peer learning derived from the interaction between the coordinating academics facilitated the development of faculty teaching skills in line with CDIO standard 10.

Masks as methodology and the phenomenological turn: issues of interpretation

The purposes of this chapter are to argue for (i) the heuristic value of the concept of mask and masking in research which has its basis in psychodynamic theory but relating it to socio-cultural theory as means to understanding self-experience (ii) the value of creating and performing masks as one valuable methodological ‘embodied’ form in social and educational research that represent individuals’ richly textured self-other constructions and allow for the interrogation of any simplistic dichotomies associated with notions of ‘inside’ ‘outside’ categories (iii) exploring possibilities and dilemmas of interpretation within this frame

The student experience in Objective Structured Clinical Examinations (OSCEs): phenomenological analysis

Background and purpose
The dominant psychometric discourse of OSCEs may lead to unexpected problems, such as a checklist-based student performance1 which under emphasises the clinical relationship with student and standardised patient (SP). Such encounters can be dehumanising for SPs2 and have implications for what students learn about relational skills through the assessment process. In this study we explore medical students’ experiences of undertaking OSCEs using a phenomenological frame.
Methodology
Interpretative phenomenological analysis is a form of qualitative methodology which has strong resonance with existentialism and focuses on the lived experience without significant reference to external political or discursive
forces.
Six 4th year undergraduate medical students from Queen’s University Belfast were recruited in December 2013. Maximum variation sampling was used. Students were interviewed by a researcher in the week prior to the
OSCE and then again in the week following the OSCE in Jan 2014. Interviews were minimally structured in order to be open to respondents, rather than adhering to a fixed topic guide, but focussed on participants’ experiences, thoughts and feelings about taking part in OSCEs. Interviews were audio-recorded and
transcribed. Students were also asked to complete a short diary entry in the days prior to the OSCEs and another immediately following. Diary entries were written, emailed or audio-recorded at student’s preference.
Results
Transcripts are currently being analysed by interpretative phenomenological analysis. Preliminary analysis has demonstrated the significance of students’ relationships within the OSCE triad (student, SP and examiner); the effect of the immediate examination environment; realism versus roleplay; students’ perceptions of the purpose of assessment; and coping mechanisms.
Full results will be available by the time of the conference.
Conclusion and Discussion
Understanding the student experience in OSCEs is a crucial step in understanding the complex construction of relationships within the OSCE triad. The focus in OSCEs is typically on standardisation and reliability, but in exploring social interactions we may refocus attention on their inherent potential for learning and effects on both students and patients.
References
1. Hodges B. Medical education and the maintenance of incompetence. Med Teach 2006;28(8):690-6
2. Johnston JL, Lundy G, McCullough M, Gormley GJ. The view from over there: reframing the OSCE through the experience of standardised patient
raters. Med Educ 2013;47(9):899-909

Technology, work organisation and job quality in the service sector: an introduction’

This special issue volume is concerned with how technology is changing the nature of work and working conditions while generating new products and new forms of service delivery. The five articles included in this volume cover service work, from the routine and clerical through to highly credentialed and professional work. Although some of the established challenges concerning the impact of Information and Communication Technology (ICT) on work and workplaces are evident in the articles, it is also clear that new service delivery processes demand new skills and training to some extent. Overall findings indicate that while ICT competencies are important, they need to be supplemented by the soft skills that are crucial for effective customer interactions and more open work systems with greater autonomy and participation whereby flexible work teams can have a positive impact on job quality outcomes. This introductory article examines technology and the changing nature of work through three strands of interpretation, prior to introducing the five articles in this special issue.

Impact of offshore wind power forecast error in a carbon constraint electricity market

This paper investigates the impacts of offshore wind power forecast error on the operation and management of a pool-based electricity market in 2050. The impact from offshore wind power forecast errors of up to 2000 MW on system generation costs, emission costs, dispatch-down of wind, number of start-ups and system marginal price are analysed. The main findings of this research are an increase in system marginal prices of approximately 1% for every percentage point rise in the offshore wind power forecast error regardless of the average forecast error sign. If offshore wind power generates less than forecasted (−13%) generation costs and system marginal prices increases by 10%. However, if offshore wind power generates more than forecasted (4%) the generation costs decrease yet the system marginal prices increase by 3%. The dispatch down of large quantities of wind power highlights the need for flexible interconnector capacity. From a system operator's perspective it is more beneficial when scheduling wind ahead of the trading period to forecast less wind than will be generated.

Self-Feedback Motion Control for Cable-Driven Parallel Manipulators

This article proposes a closed-loop control scheme based on joint-angle feedback for cable-driven parallel manipulators (CDPMs), which is able to overcome various difficulties resulting from the flexible nature of the driven cables to achieve higher control accuracy. By introducing a unique structure design that accommodates built-in encoders in passive joints, the seven degrees of freedom (7-DOF) CDPM can obtain joint angle values without external sensing devices, and it is used for feedback control together with a proper closed-loop control algorithm. The control algorithm has been derived from the time differential of the kinematic formulation, which relates the joint angular velocities to the time derivative of cable lengths. In addition, the Lyapunov stability theory and Monte Carlo method have been used to mathematically verify the self-feedback control law that has tolerance for parameter errors. With the aid of co-simulation technique, the self-feedback closed-loop control is applied on a 7-DOF CDPM and it shows higher motion accuracy than the one with an open-loop control. The trajectory tracking experiment on the motion control of the 7-DOF CDPM demonstrated a good performance of the self-feedback control method.

Political Posturing or Real Powers: Control of Genetically Modified Crops by the Member States and their Regions

The cultivation of genetically modified (GM) crops in the EU is highly harmonised, involving a central authorisation procedure that aims to ensure a high level of environmental and human health protection. However conflicts over authority persist and the Commission has responded to a combination of internal and external pressures with a more flexible approach to coexistence, a proposed opt-out clause and recently a promise by the head of the Commission to review the existing EU GM legislative regime, providing an opportunity to consider and suggest paths of development. In light of the significance of multilevel governance and subsidiarity for GM cultivation, this paper considers the policy-making powers of the Member States and subnational regions in this regime, focussing upon post-authorisation options in particular. A number of core mechanisms exist, including voluntary measures, safeguard clauses, coexistence measures, a proposed express opt-out and Article 4(2) TEU on ‘national identity. These mechanisms are examined in light of the goals and challenges of multilevel governance, in order to consider whether the relevant powers are located at the appropriate level. Overall, it is apparent that the developments occurring at the EU level are strengthening multilevel governance, but with significant opportunities to improve it further through focussing on the supporting roles and the regional levels in particular.