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Path Integral Approaches and Graphics Processing Unit Tools for Quantum Molecular Dynamics SimulationsConstable, Stephen Joel January 2012 (has links)
This thesis details both the technical and theoretical aspects of performing path integrals through classical Molecular Dynamics (MD) simulations. In particular, Graphics Processing Unit (GPU) computing is used to augment the Path Integral Molecular Dynamics (PIMD) portion of the widely available Molecular Modelling Tool Kit (MMTK) library. This same PIMD code is also extended in a different direction: a novel method for nuclear ground state property prediction is introduced that closely mimics existing code in functional form.
In order to add GPU computing capabilities to the existing MMTK codebase, the open source Open Molecular Mechanics (OpenMM) library was used. OpenMM provides high performance implementations of a variety of commonly used MD algorithms, with the goal of supporting current and future specialized hardware. Due to the object oriented nature of both codes, and the use of SI units in each, the development process was rather painless. The integration of OpenMM with MMTK is seamless, and arbitrary systems are supported without the user even needing to know that GPU acceleration is being used. The hybrid OpenMM-MMTK code is benchmarked against the vanilla MMTK code in terms of speed and accuracy, and the results show that GPU computing is the obvious choice for PIMD simulations.
Starting with a desire to apply the highly efficient Path Integral Langevin Equation (PILE) thermostat to the Path Integral Ground State (PIGS) problem, a new hybrid PILE-PIGS, or LE-PIGS, method was developed. This thesis describes the theoretical justification for this method, including the introduction of a modified normal mode representation based on the Discrete Cosine Transform (DCT). It is shown that in DCT space, the equations of motion of a PIGS system are virtually identical to the equations of motion of a PIMD system in Fourier space. This leads to direct reuse of existing PILE code in MMTK, and options to extend this ground state problem to OpenMM for the purpose of GPU acceleration. The method is applied to a series of model systems, and in each case convergence to the exact ground state energy is observed.
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Path Integral Approaches and Graphics Processing Unit Tools for Quantum Molecular Dynamics SimulationsConstable, Stephen Joel January 2012 (has links)
This thesis details both the technical and theoretical aspects of performing path integrals through classical Molecular Dynamics (MD) simulations. In particular, Graphics Processing Unit (GPU) computing is used to augment the Path Integral Molecular Dynamics (PIMD) portion of the widely available Molecular Modelling Tool Kit (MMTK) library. This same PIMD code is also extended in a different direction: a novel method for nuclear ground state property prediction is introduced that closely mimics existing code in functional form.
In order to add GPU computing capabilities to the existing MMTK codebase, the open source Open Molecular Mechanics (OpenMM) library was used. OpenMM provides high performance implementations of a variety of commonly used MD algorithms, with the goal of supporting current and future specialized hardware. Due to the object oriented nature of both codes, and the use of SI units in each, the development process was rather painless. The integration of OpenMM with MMTK is seamless, and arbitrary systems are supported without the user even needing to know that GPU acceleration is being used. The hybrid OpenMM-MMTK code is benchmarked against the vanilla MMTK code in terms of speed and accuracy, and the results show that GPU computing is the obvious choice for PIMD simulations.
Starting with a desire to apply the highly efficient Path Integral Langevin Equation (PILE) thermostat to the Path Integral Ground State (PIGS) problem, a new hybrid PILE-PIGS, or LE-PIGS, method was developed. This thesis describes the theoretical justification for this method, including the introduction of a modified normal mode representation based on the Discrete Cosine Transform (DCT). It is shown that in DCT space, the equations of motion of a PIGS system are virtually identical to the equations of motion of a PIMD system in Fourier space. This leads to direct reuse of existing PILE code in MMTK, and options to extend this ground state problem to OpenMM for the purpose of GPU acceleration. The method is applied to a series of model systems, and in each case convergence to the exact ground state energy is observed.
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Mealtimes and food for people with profound intellectual and multiple disabilities and dysphagia : understanding the lived experience of family carersCrawford, Hannah Grace January 2016 (has links)
This study aims to develop an understanding of the lived experience of family carers of people with PIMD and dysphagia, in relation to mealtimes and food. Policy in recent years has begun to address the inequalities faced by people with learning disabilities and it is striving to improve their lives and the services offered to them. People with profound intellectual and multiple disabilities (PIMD) often have additional eating and drinking difficulties (dysphagia). People with dysphagia require ongoing support and guidance, to maximize their health, specifically their nutrition and hydration. In order to ensure that this support is appropriate, useful and sensitive to the needs of individuals and their families, it is important to try and view mealtimes through the eyes of these individuals and their families. The aims of this study emerged from observations made during my clinical work as a Speech & Language Therapist (SLT) and from engaging in discussion with family carers. In particular it has become increasingly clear from clinical practice that family carers often have different points of view about their son or daughter with profound intellectual and multiple disabilities, than those of professionals. These different points of view are often not clearly articulated by carers or professionals, and clinical interventions may become marked with conflict. This study is sited within a mental health and learning disability NHS trust in the north east of England. It utilises a phenomenological methodology and employs mixed methods to obtain data. Data collection took place between June 2013 and August 2014. Medical descriptions do not capture how it feels to live with impairment and resulting disability. Only when we examine this and allow individuals to tell their stories, as experts in their experiences, can we understand and offer support accordingly and ensure more functional and beneficial interactions and interventions. Findings are presented around four themes – the meaning of food and mealtimes, relationships, roles within the family and challenges. Findings are discussed in relation to the existing literature and recommendations are made for practice and for future research. During this study the adult child is mainly referred to as the ‘child’. For clarity, this is not in any way meant to convey the individual’s presentation as having PIMD as akin to being a child. The term is used to represent the relationship between the parents and the child. Despite the fact that the individuals are adults, they are still the children of the parents, and the relationship is a parent-son/daughter relationship. For brevity the term ‘child’ is used in preference to ‘adult child’. The use of the term has been agreed with the parents participating in the study. All names are assumed and have been chosen by the participants. In the course of this thesis the direct giving of food to the individuals with disabilities is termed ‘feeding’. I acknowledge this term may be associated with potentially negative connotations. The term ‘feeding’ has been used because it is the term used widely in the literature, because it was used by the family carers in their narratives and because there is no other suitable substitute which adequately describes the direct provision of food from one person in to the mouth of another.
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Deltagandets kontextuella villkor : fem träningsskoleklassers pedagogiska praktikÖstlund, Daniel January 2012 (has links)
The thesis should be regarded as a contribution to the development of knowledge about the interaction taking place in the educational setting for pupils with PIMD in Sweden, the training school (Sw. Träningsskola), and the contextual and interactional conditions that characterizes this educational setting. The study is expected to contribute to a deeper understanding of the pedagogical praxis in the training School and the pupils’ possibilities to be agents within the processes of interaction, participation and learning. The thesis aims to contribute to the development of knowledge about the contextual and interactional conditions that training school pedagogic practice is characterized by. The study's overall purpose is to analyze the participation and interaction in the context of five training school classes. A particular focus is placed on teaching organization and the interaction patterns appearing in the pedagogical practice and what kind of consequences the interaction has for the pupils’ participation. Participation in this study refers to how the teams and students jointly create interaction in classrooms, the patterns produced by the interaction. The study draws on a theoretical framework that is influenced by ethnometodological work and from the dramaturgical framework by Goffman, where the participant’s social actions and methodical ways of making sense in a social setting are in focus. The design of the data collection is inspired by an ethnographic approach and is constructed as a classroom study. The empirical material was collected by classroom observations and by video recordings. The data derive from video recordings that were made during spring 2009 and spring 2010 in five training school classes and all together twenty pupils (age 8-19, eleven boys and nine girls) and 28 members from the teams (nine special teachers, two music teachers, one psychical education teacher and 16 assistants) participated in the study. The results are showing that the pedagogical practice in training school was defined by six different areas: Circle time, One-to-one tuition, Group joint education, Snack time/ lunch, Breaks and play-time and Transitions. In the interaction between the pupils and the staff the pupils’ positions was constructed as: The attentive and responsive pupil, The experiencing pupil, The choice making and autonomous pupil, The exploring pupil, The pupil that shows civil inattention, The pupil as a recipient of care and The playing pupil. A starting point for further research involves studying how students' participation is constructed in more inclusive settings i.e. in interaction with other children who do not have such extensive disabilities.
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Algorithms and computer code for ab initio path integral molecular dynamics simulationsMore, Joshua N. January 2015 (has links)
This thesis presents i-PI, a new path integral molecular dynamics code designed to capture nuclear quantum effects in ab initio electronic structure calculations of condensed phase systems. This software has an implementation of estimators used to calculate a wide range of static and dynamical properties and of state-of-the-art techniques used to increase the computational efficiency of path integral simulations. i-PI has been designed in a highly modular fashion, to ensure that it is as simple as possible to develop and implement new algorithms to keep up with the research frontier, and so that users can take maximum advantage of the numerous electronic structure programs which are freely available without needing to rewrite large amounts of code. Among the functionality of the i-PI code is a novel integrator for constant pressure dynamics, which is used to investigate the properties of liquid water at 750 K and 10 GPa, and efficient estimators for the calculation of single particle momentum distri- butions, which are used to study the properties of solid and liquid ammonia. These show respectively that i-PI can be used to make predictions about systems which are both difficult to study experimentally and highly non-classical in nature, and that it can illustrate the relative advantages and disadvantages of different theoretical methods and their ability to reproduce experimental data.
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Polyhandicap et évaluation cognitive : apports du paradigme d'habituation visuelle / Contributions of the visual habituation paradigme to the cognitive assessment of adults with Profound Intellectual and Multiple DisabilitiesChard, Melissa 02 December 2014 (has links)
Le polyhandicap est la conséquence d'une atteinte massive et précoce du Système Nerveux Central. Les personnes polyhandicapées présentent donc des difficultés motrices sévères ainsi qu'une déficience intellectuelle profonde, leur QI étant statistiquement estimé comme étant inférieur à 20. De ce fait, ces personnes ont besoin d'une assistance dans la réalisation des actes de la vie quotidienne, présentent des capacités d'apprentissage très limitées et n'ont pas accès à une communication symbolique. Aujourd'hui, nous ne savons que très peu de choses sur la vie cognitive des personnes polyhandicapées, et sur la manière unique et originale dont chacune d'entre elles construit ses connaissances sur le monde et développe ses propres compétences. Si l'étude et la compréhension du développement de l'enfant et du jeune polyhandicapé peut s'adosser sur les modèles et outils d'évaluation issus de la psychologie du développement, l'appréhension de sujets adultes reste, en revanche, très peu balisée. Ceci serait principalement lié au fait que chaque personne polyhandicapée présente des restrictions motrices importantes, une absence de langage oral et un répertoire de réponses comportementales dont l'interprétation va rester soumise à une importante variabilité inter-observateurs. L'objectif de ce projet de recherche est de mettre au point une méthode d'étude des compétences cognitives des personnes polyhandicapées de tout âge qui puisse tenir compte à la fois des spécificités liées à leurs handicaps multiples, tout en favorisant un cadre d'interprétation objectif des réponses comportementales de chaque personne. Pour cela, nous nous sommes donc inspirés des études menées chez des nourrissons âgés de quelques mois, basées sur le principe de l'habituation visuelle. Le paradigme d'habituation visuelle postule qu'un sujet exposé de manière répétée à un même stimulus visuel présentera un déclin progressif de la durée de fixation, correspondant à la construction et à la consolidation d'une représentation en mémoire de l'objet. La présentation d'un nouveau stimulus va donc entraîner une augmentation des temps de fixation, signe que le sujet s'est montré capable de comparer le nouvel objet à la représentation interne du précédent. Ainsi, il est possible d'étudier les capacités de discrimination et de mémorisation de sujets humains et non-humains, indépendamment de toute aptitude motrice ou verbale, seul le comportement visuel étant pris en compte. La première étape de notre travail de recherche a d'abord consisté à créer des conditions favorables à l'implémentation d'épreuves basées sur le paradigme d'habituation visuelle auprès d'un public de personnes polyhandicapées adultes. Une étude de faisabilité a donc d'abord été conduite à travers laquelle nous avons pu traiter d'aspects aussi bien matériels que méthodologiques. Nous avons ainsi pu mettre au point des conditions de passation et un matériel adapté. Ensuite, nous avons pu valider l'utilisation de cette approche auprès d'un échantillon plus large d'individus, en mettant en évidence un phénomène d'habituation et de déshabituation sur une épreuve de perception simple. Enfin, nous nous sommes penchés plus spécifiquement sur la manière dont ce paradigme pouvait s'appliquer à l'étude de certains domaines de compétences cognitives, et plus spécifiquement la perception du nombre et des quantités. Pour cela, trois tâches inspirées de la littérature en psychologie du développement ont été mises au point. Nous avons trouvé que les participants sont capables de différencier deux quantités d'objets lorsqu'aucune variable confondue n'est contrôlée, et que la position des objets reste déterminante dans leur capacité d'encodage des stimuli. Ces données nous ont conduits à réfléchir de manière plus globale sur la manière dont ces personnes peuvent construire leurs connaissances en l'absence d'action directe sur les objets de leur environnement. / L'auteur n'a pas fourni de résumé en anglais.
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I never tried the swings before : Perspectives on urban greenspace from children with profound intellectual and multiple disabilitiesHanses, Lena January 2019 (has links)
To achieve the United Nations Sustainable Development Goal 11.7 aiming to create inclusiveand accessible greenspaces, there is need to involve children with profound intellectual andmultiple disabilities in research and planning practices. The aim of this study is to explore whatexperiences of accessibility children with profound intellectual and multiple disabilities haveof greenspace. Through the qualitative method of go along interviews using augmentative andalternative communication, such as pictures and sign language, children provide their opinionsabout the public park Långbroparken in southern Stockholm, Sweden. Their experiences areanalysed through the framework of environmental justice, exploring fair distribution,recognition, capabilities and functioning. The findings demonstrate that children with profoundintellectual and multiple disabilities can indeed be included in research practices throughadapted interview situations. Either the researcher needs to be skilled and experienced inalternative and augmentative communication, and preferably have previous relations with thechildren, or be able to cooperate with someone who has such abilities and connections.Individual experiences of physical and social accessibility in the park create feelings of bothoutsideness and immersing oneself into nature and highlight the interaction of person andenvironment. In conclusion, children with profound intellectual and multiple disabilities holdvaluable explanations and experiences of what constitutes inclusive and accessible greenspacesand their perspectives are required to fulfil targets such as the United Nations SustainableDevelopment Goal 11.7.
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