41 research outputs found
oxDNA: coarse-grained simulations of nucleic acids made simple
No full textThe fields of DNA and RNA nanotechnology have progressed from pioneering, proof-of-principle experiments to fully-fledged applications in material science, biology and medicine. These applications exploit the intrinsic programmability of nucleic acids to generate nano- and even micro-scale structures with tailored properties. However, the design of the DNA/RNA sequences that self-assemble into a desired structure is not straightforward and often relies on expensive trial-and-error experimental protocols. A complementary approach is provided by computer simulations, which can model biomacromolecules at different levels of detail, ranging from atomistic to continuous, and can be leveraged to investigate the whole range of time- and length-scales relevant for applications. Here we present oxDNA, a software package that has been designed to efficiently run coarse-grained simulations of DNA and RNA and also features an analysis suite aimed at post-processing the analysis of oxDNA/oxRNA trajectories
The engineering of generic requirements for failure management
No full textWe consider the failure detection and management function for engine control systems as an application domain where product line engineering is indicated. The need to develop a generic requirement set - for subsequent system instantiation - is complicated by the addition of the high levels of verification demanded by this safety-critical domain, subject to avionics industry standards. We present our case study experience in this area as a candidate methodology for the engineering, validation and verification of generic requirements using domain engineering and Formal Methods techniques and tools. For a defined class of systems, the case study produces a generic requirement set in UML and an example instantiation in tabular form. Domain analysis and engineering produce a model which is integrated with the formal specification/ verification method B by the use of our UML-B profile. The formal verification both of the generic requirement set, and of a simple system instance, is demonstrated using our U2B and ProB tools. This work is a demonstrator for a tool-supported method which will be an output of EU project RODIN. The method, based in the dominant UML standard, will exploit formal verification technology largely as a "black box" for this novel combination of product line, failure management and safety-critical engineering
The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami
No full text: This chapter introduces how to run molecular dynamics simulations for DNA origami using the oxDNA coarse-grained model
A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower - MD simulation data
No full textSimulation data used in the MD simulation portions of "A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower" by M. Centola et. al
TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami
No full textSimulations of nucleic acids at different levels of structural details are increasingly used to complement and interpret experiments in different fields, from biophysics to medicine and materials science. However, the various structural models currently available for DNA and RNA and their accompanying suites of computational tools can be very rarely used in a synergistic fashion. The tacoxDNA webserver and standalone software package presented here are a step toward a long-sought interoperability of nucleic acids models. The webserver offers a simple interface for converting various common input formats of DNA structures and setting up molecular dynamics (MD) simulations. Users can, for instance, design DNA rings with different topologies, such as knots, with and without supercoiling, by simply providing an XYZ coordinate file of the DNA centre-line. More complex DNA geometries, as designable in the cadnano, CanDo and Tiamat tools, can also be converted to all-atom or oxDNA representations, which can then be used to run MD simulations. Though the latter are currently geared toward the native and LAMMPS oxDNA representations, the open-source package is designed to be further expandable. TacoxDNA is available at http://tacoxdna.sissa.it. © 2019 Wiley Periodicals, Inc
Unified Nanotechnology Format: One Way to Store Them All
No full textThe domains of DNA and RNA nanotechnology are steadily gaining in popularity while proving their value with various successful results, including biosensing robots and drug delivery cages. Nowadays, the nanotechnology design pipeline usually relies on computer-based design (CAD) approaches to design and simulate the desired structure before the wet lab assembly. To aid with these tasks, various software tools exist and are often used in conjunction. However, their interoperability is hindered by a lack of a common file format that is fully descriptive of the many design paradigms. Therefore, in this paper, we propose a Unified Nanotechnology Format (UNF) designed specifically for the biomimetic nanotechnology field. UNF allows storage of both design and simulation data in a single file, including free-form and lattice-based DNA structures. By defining a logical and versatile format, we hope it will become a widely accepted and used file format for the nucleic acid nanotechnology community, facilitating the future work of researchers and software developers. Together with the format description and publicly available documentation, we provide a set of converters from existing file formats to simplify the transition. Finally, we present several use cases visualizing example structures stored in UNF, showcasing the various types of data UNF can handle
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Automated categorisation of e-journals by synonym analysis of n-grams
No full textAutomatic keyword or keyphrase extraction is concerned with assigning keyphrases to documents based on words from within the document. Previous studies have shown that in a significant number of cases author-supplied keywords are not appropriate for the document to which they are attached. This can either be because they represent what the author believes a paper is about not what it actually is, or because they include keyphrases which are more classificatory than explanatory e.g., “University of Poppleton” instead of “Knowledge Discovery in Databases”. Thus, there is a need for a system that can generate an appropriate and diverse range of keyphrases that reflect the document. This paper proposes two possible solutions that examine the synonyms of words and phrases in the document to find the underlying themes, and presents these as appropriate keyphrases. Using three different freely available thesauri, the work undertaken examines two different methods of producing keywords and compares the outcomes across multiple strands in the timeline. The primary method explores taking n-grams of the source document phrases, and examining the synonyms of these, while the secondary considers grouping outputs by their synonyms. The experiments undertaken show the primary method produces good results and that the secondary method produces both good results and potential for future work. In addition, the different qualities of the thesauri are examined and it is concluded that the more entries in a thesaurus, the better it is likely to perform. The age of the thesaurus or the size of each entry does not correlate to performance
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Keyphrase extraction by synonym analysis of n-grams for e-journals categorisation
No full textAutomatic keyword or keyphrase extraction is concerned with assigning keyphrases to documents based on words from within the document. Previous studies have shown that in a significant number of cases author-supplied keywords are not appropriate for the document to which they are attached. This can either be because they represent what the author believes the paper is about not what it actually is, or because they include keyphrases which are more classificatory than explanatory e.g., “University of Poppleton” instead of “Knowledge Discovery in Databases”. Thus, there is a need for a system that can generate appropriate and diverse range of keyphrases that reflect the document. This paper proposes a solution that examines the synonyms of words and phrases in the document to find the underlying themes, and presents these as appropriate keyphrases. The primary method explores taking n-grams of the source document phrases, and examining the synonyms of these, while the secondary considers grouping outputs by their synonyms. The experiments undertaken show the primary method produces good results and that the secondary method produces both good results and potential for future work
The nature, causes and consequences of harm in emotionally-demanding occupations
No full textTraditional approaches to understanding psychosocial job characteristics and well-being have been quite general in that they explore links between general job characteristics such as workload and control on workers in many different sorts of occupations. One example of a more specific approach can be found in research into emotional labour - the requirement to regulate both feelings and the expression of feelings for organizational goals. Early research into emotional labour focused on customer service workers (CSW) but has more recently also considered human service workers (HSW) such as nurses and social workers. A more specific approach to thinking about the outcomes of demanding psychosocial job characteristics can be found in research on burnout which is thought to have three elements: emotional exhaustion, depersonalization (also labelled cynicism), and (low) accomplishment (also called professional efficacy). Much recent research has started to explore the links between emotional demands and burnout. The main aim of this project is therefore to explore the nature of such links through undertaking three distinct tasks. The first is a literature review of evidence and theory while the second two tasks comprise two empirical studies examining several key issues in burnout research.
This report and the work it describes were funded by the Health and Safety Executive (HSE). Its contents, including any opinions and/or conclusions expressed, are those of the author alone and do not necessarily reflect HSE policy
