9,821 research outputs found

    A family of total Lagrangian Petrov-Galerkin Cosserat rod finite element formulations

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    The standard in rod finite element formulations is the Bubnov-Galerkin projection method, where the test functions arise from a consistent variation of the ansatz functions. This approach becomes increasingly complex when highly nonlinear ansatz functions are chosen to approximate the rod's centerline and cross-section orientations. Using a Petrov-Galerkin projection method, we propose a whole family of rod finite element formulations where the nodal generalized virtual displacements and generalized velocities are interpolated instead of using the consistent variations and time derivatives of the ansatz functions. This approach leads to a significant simplification of the expressions in the discrete virtual work functionals. In addition, independent strategies can be chosen for interpolating the nodal centerline points and cross-section orientations. We discuss three objective interpolation strategies and give an in-depth analysis concerning locking and convergence behavior for the whole family of rod finite element formulations.Comment: arXiv admin note: text overlap with arXiv:2301.0559

    Application of advanced fluorescence microscopy and spectroscopy in live-cell imaging

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    Since its inception, fluorescence microscopy has been a key source of discoveries in cell biology. Advancements in fluorophores, labeling techniques and instrumentation have made fluorescence microscopy a versatile quantitative tool for studying dynamic processes and interactions both in vitro and in live-cells. In this thesis, I apply quantitative fluorescence microscopy techniques in live-cell environments to investigate several biological processes. To study Gag processing in HIV-1 particles, fluorescence lifetime imaging microscopy and single particle tracking are combined to follow nascent HIV-1 virus particles during assembly and release on the plasma membrane of living cells. Proteolytic release of eCFP embedded in the Gag lattice of immature HIV-1 virus particles results in a characteristic increase in its fluorescence lifetime. Gag processing and rearrangement can be detected in individual virus particles using this approach. In another project, a robust method for quantifying Förster resonance energy transfer in live-cells is developed to allow direct comparison of live-cell FRET experiments between laboratories. Finally, I apply image fluctuation spectroscopy to study protein behavior in a variety of cellular environments. Image cross-correlation spectroscopy is used to study the oligomerization of CXCR4, a G-protein coupled receptor on the plasma membrane. With raster image correlation spectroscopy, I measure the diffusion of histones in the nucleoplasm and heterochromatin domains of the nuclei of early mouse embryos. The lower diffusion coefficient of histones in the heterochromatin domain supports the conclusion that heterochromatin forms a liquid phase-separated domain. The wide range of topics covered in this thesis demonstrate that fluorescence microscopy is more than just an imaging tool but also a powerful instrument for the quantification and elucidation of dynamic cellular processes

    Full stack development toward a trapped ion logical qubit

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    Quantum error correction is a key step toward the construction of a large-scale quantum computer, by preventing small infidelities in quantum gates from accumulating over the course of an algorithm. Detecting and correcting errors is achieved by using multiple physical qubits to form a smaller number of robust logical qubits. The physical implementation of a logical qubit requires multiple qubits, on which high fidelity gates can be performed. The project aims to realize a logical qubit based on ions confined on a microfabricated surface trap. Each physical qubit will be a microwave dressed state qubit based on 171Yb+ ions. Gates are intended to be realized through RF and microwave radiation in combination with magnetic field gradients. The project vertically integrates software down to hardware compilation layers in order to deliver, in the near future, a fully functional small device demonstrator. This thesis presents novel results on multiple layers of a full stack quantum computer model. On the hardware level a robust quantum gate is studied and ion displacement over the X-junction geometry is demonstrated. The experimental organization is optimized through automation and compressed waveform data transmission. A new quantum assembly language purely dedicated to trapped ion quantum computers is introduced. The demonstrator is aimed at testing implementation of quantum error correction codes while preparing for larger scale iterations.Open Acces

    Coding Christianity: Negotiating Religious Dialogue in Online Participatory Spaces

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    This dissertation examines rhetorical conditions and internet-mediated communication strategies that open and close dialogue between individuals with diverse and conflicting worldviews. The author illustrates this tension through sacred-secular interactions in college composition classrooms and online environments, positing that navigating conflict between these discourses—namely those espoused by religiously committed students and public university instructors—often requires stepping outside of adversarial communication frameworks. This project makes a case for models of civic engagement that use more deliberative rhetorical approaches prioritizing empathy over defensiveness and understanding before persuasion. To develop these non-adversarial communication approaches for the composition classroom, the author looks to participatory media for insights and studies the negotiation strategies of Christian and atheist YouTube users who leverage the affordances of the video medium, internet logics, and invitational rhetorical strategies to engage ideological differences in their respective online communities. Through mixed methods research involving in-depth interviews with five YouTube vloggers, netnographic study of over 3,000 videos, and statistical analysis of 76,000+ user comments, Coding Christianity finds that perspective-taking in conflict-ridden environments can happen between netizens when content creators opt out of “flame wars” and, instead, explicitly model critical openness and charitable listening to perceived “others.” The author ultimately suggests that sacred-secular tension in both academic and digital environments be used, not diffused, to negotiate conflicting values and engage in rigorous, civil dialogues

    The Angel of Art Sees the Future Even as She Flies Backwards: Enabling Deep Relational Encounter Through Participatory Practice-Based Research

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    The reading of this textual exegesis is deepened in conjunction with viewing the practice-based artefacts referenced within the text. These are contained within an accompanying Multi-Media resource (MMR). Elements from the MMR can also be accessed (or requested) from my website at www.alicecharlottebell.com and on Vimeo at Dr Alice Charlotte Bell https://vimeo.com/user161523908 and on You Tube at Alice Charlotte Bell https://youtube.com/playlist?list=PLnqD-anWUT3U5gIBP2KIR7tkDdrXUAhIBThis research addresses the current lack of opportunity within interdisciplinary arts practices for deep one-to-one relational encounters between creative practitioners operating in applied arts, performance, and workshop contexts with participant-subjects. This artistic problem is situated within the wider culture of pervasive social media, which continues to shape our interactions into forms that are characteristically faster, shorter, and more fragmented than ever before. Such dispersal of our attention is also accelerating our inability to deeply focus or relate for any real length of time. These modes of engaging within our technologically permeated, cosmopolitan and global society is escalating relational problems. Coupled with a constant bombardment of unrealistic visual images, mental health difficulties are also consequently rising, cultivating further issues such as identity ‘splitting’, (Lopez-Fernandez, 2019). In the context of the arts, this thesis proposes that such relational lack cannot be solved by one singular art form, one media modality, one existing engagement approach, or within a short participatory timeframe. Key to the originality of my thesis is the deliberate embodiment of a maternal experience. Feminist Lise Haller-Ross’ proposes that there is a ‘mother shaped hole in the art world’ and that, ‘as with the essence of the doughnut – we don’t need another hole for the doughnut, we need a whole new recipe’ (conference address, 2015). Indeed, her assertion encapsulates a need for different types of artistic and relational ingredients to be found. I propose these can be discovered within particular forms of maternal love; nurture; caring, and through conceptual relational states of courtship; intercourse; gestation, and birth. Furthermore, my maternal emphasis builds on: feminist, artist, and psychotherapist Bracha Ettinger’s (2006; 2015) notions of maternal, cohabitation and carrying; architect and phenomenologist Juhani Pallasmaa’s (2012) views on sensing and feeling; child psychoanalyst Donald Winnicott’s (1971) thoughts on transitional phenomena and perceptions of holding. Such psychotherapeutic and phenomenological theories are imbricated in-action within my multimodal arts processes. Additionally, by deliberately not privileging the ocular, I engage all my project participants senses and distil their multimodal data through an extended form of somatic and artistic Interpretive Phenomenological Analysis (IPA), (Smith, Flowers, and Larkin, 2009). IPA usefully focuses on the importance of the thematic and idiographic in terms of new knowledge generation, with an analytical focus on lived experience. Indeed, whilst the specifics of the participants in my minor and major projects are unique, my research activates and makes valid, findings that are collectively beneficial to the disciplines of applied and interdisciplinary arts; the field of practice-based research, and beyond. My original contribution to new knowledge as argued by this thesis, comprises both this text exposition and my practice. This sees the final generation of a new multimodal arts Participatory Practice-Based Framework (PartPb). Through this framework, the researcher-practitioner is seen to adopt a maternal role to gently guide project participants through four phases of co-created multimodal artwork generation. The four participatory ‘Phases’ are: Phase 1: Courtship – Digital Dialogues; Phase 2: Intercourse – Performative Encounters; Phase 3: Gestation – Screen Narratives; Phase 4: Birth – Relational Artworks. The framework also contains six researcher-only ‘Stages’: Stage 1: Participant Selection; Stage 2: Checking Distilled Themes; Stage 3: Location and Object Planning; Stage 4: Noticing, Logging, Sourcing; Stage 5: Collaboration and Construction; Stage 6: Releasing, Gifting, Recruiting. This new PartPb framework, is realised within a series of five practice-based (Pb) artworks called, ‘Minor Projects 1-5’, (2015-16) and Final Major Project, ‘Transformational Encounters: Touch, Traction, Transform’ (TETTT), (2018). These projects are likewise shaped through action-research processes of iterative testing, as developed from Candy and Edmonds (2010) Practice-based Research (PbR) trajectory. In my new PartPb framework, Candy, and Edmonds’ PbR processes are originally combined with a form of Fritz and Laura Perl’s Gestalt Experience Cycle (1947). This innovative fusion I come to term as a form of ‘Feeling Architecture,’ which is procedurally proven to hold and carry both researcher and participants alike, safely, ethically, and creatively through all Phases and Stages of artefact generation. Specifically, my new multimodal PartPb framework offers new knowledge to the field of Practice-Based Research (PbR) and practitioners working in multimodal arts and applied performance contexts. Due to its participatory focus, I develop on the term Practice-Based Research, (Candy and Edmonds, 2010) to coin the term Participatory Practice-Based Research, (PartPbR). The unique combination of multimodal arts and social-psychological methodologies underpinning my framework also has the potential to contribute to broader Arts, Well-Being, and Creative Health agendas, such as the UK government’s Social Prescribing and Arts and Health initiatives. My original framework offers future researchers’ opportunities to further develop, enhance and enrich individual and community well-being through its application to their own projects, and, in doing so, also starts to challenge unhelpful art binaries that still position community arts practices as somehow lesser to higher art disciplines.Fully funded scholarship in Contemporary Performance from De Montfort University. Final PbR output in the form of the exhibition ‘Transformational Encounters: Touch, Traction, Transform’ (TETTT), sponsored by Design Alliance Ltd. www.designalliance.c

    A high-performance open-source framework for multiphysics simulation and adjoint-based shape and topology optimization

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    The first part of this thesis presents the advances made in the Open-Source software SU2, towards transforming it into a high-performance framework for design and optimization of multiphysics problems. Through this work, and in collaboration with other authors, a tenfold performance improvement was achieved for some problems. More importantly, problems that had previously been impossible to solve in SU2, can now be used in numerical optimization with shape or topology variables. Furthermore, it is now exponentially simpler to study new multiphysics applications, and to develop new numerical schemes taking advantage of modern high-performance-computing systems. In the second part of this thesis, these capabilities allowed the application of topology optimiza- tion to medium scale fluid-structure interaction problems, using high-fidelity models (nonlinear elasticity and Reynolds-averaged Navier-Stokes equations), which had not been done before in the literature. This showed that topology optimization can be used to target aerodynamic objectives, by tailoring the interaction between fluid and structure. However, it also made ev- ident the limitations of density-based methods for this type of problem, in particular, reliably converging to discrete solutions. This was overcome with new strategies to both guarantee and accelerate (i.e. reduce the overall computational cost) the convergence to discrete solutions in fluid-structure interaction problems.Open Acces

    Principles of Massively Parallel Sequencing for Engineering and Characterizing Gene Delivery

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    The advent of massively parallel sequencing and synthesis technologies have ushered in a new paradigm of biology, where high throughput screening of billions of nucleid acid molecules and production of libraries of millions of genetic mutants are now routine in labs and clinics. During my Ph.D., I worked to develop data analysis and experimental methods that take advantage of the scale of this data, while making the minimal assumptions necessary for deriving value from their application. My Ph.D. work began with the development of software and principles for analyzing deep mutational scanning data of libraries of engineered AAV capsids. By looking at not only the top variant in a round of directed evolution, but instead a broad distribution of the variants and their phenotypes, we were able to identify AAV variants with enhanced ability to transduce specific cells in the brain after intravenous injection. I then shifted to better understand the phenotypic profile of these engineered variants. To that end, I turned to single-cell RNA sequencing to seek to identify, with high resolution, the delivery profile of these variants in all cell types present in the cortex of a mouse brain. I began by developing infrastructure and tools for dealing with the data analysis demands of these experiments. Then, by delivering an engineered variant to the animal, I was able to use the single-cell RNA sequencing profile, coupled with a sequencing readout of the delivered genetic cargo present in each cell type, to define the variant’s tropism across the full spectrum of cell types in a single step. To increase the throughput of this experimental paradigm, I then worked to develop a multiplexing strategy for delivering up to 7 engineered variants in a single animal, and obtain the same high resolution readout for each variant in a single experiment. Finally, to take a step towards translation to human diagnostics, I leveraged the tools I built for scaling single-cell RNA sequencing studies and worked to develop a protocol for obtaining single-cell immune profiles of low volumes of self-collected blood. This study enabled repeat sampling in a short period of time, and revealed an incredible richness in individual variability and time-of-day dependence of human immune gene expression. Together, my Ph.D. work provides strategies for employing massively parallel sequencing and synthesis for new biological applications, and builds towards a future paradigm where personalized, high-resolution sequencing might be coupled with modular, customized gene therapy delivery.</p

    The Angel of Art Sees the Future Even as She Flies Backwards: Enabling Deep Relational Encounter Through Participatory Practice-Based Research.

    Get PDF
    This research addresses the current lack of opportunity within interdisciplinary arts practices for deep one-to-one relational encounters between creative practitioners operating in applied arts, performance, and workshop contexts with participant-subjects. This artistic problem is situated within the wider culture of pervasive social media, which continues to shape our interactions into forms that are characteristically faster, shorter, and more fragmented than ever before. Such dispersal of our attention is also accelerating our inability to deeply focus or relate for any real length of time. These modes of engaging within our technologically permeated, cosmopolitan and global society is escalating relational problems. Coupled with a constant bombardment of unrealistic visual images, mental health difficulties are also consequently rising, cultivating further issues such as identity ‘splitting’, (Lopez-Fernandez, 2019). In the context of the arts, this thesis proposes that such relational lack cannot be solved by one singular art form, one media modality, one existing engagement approach, or within a short participatory timeframe. Key to the originality of my thesis is the deliberate embodiment of a maternal experience. Feminist Lise Haller-Ross’ proposes that there is a ‘mother shaped hole in the art world’ and that, ‘as with the essence of the doughnut – we don’t need another hole for the doughnut, we need a whole new recipe’ (conference address, 2015). Indeed, her assertion encapsulates a need for different types of artistic and relational ingredients to be found. I propose these can be discovered within particular forms of maternal love; nurture; caring, and through conceptual relational states of courtship; intercourse; gestation, and birth. Furthermore, my maternal emphasis builds on: feminist, artist, and psychotherapist Bracha Ettinger’s (2006; 2015) notions of maternal, cohabitation and carrying; architect and phenomenologist Juhani Pallasmaa’s (2012) views on sensing and feeling; child psychoanalyst Donald Winnicott’s (1971) thoughts on transitional phenomena and perceptions of holding. Such psychotherapeutic and phenomenological theories are imbricated in-action within my multimodal arts processes. Additionally, by deliberately not privileging the ocular, I engage all my project participants senses and distil their multimodal data through an extended form of somatic and artistic Interpretive Phenomenological Analysis (IPA), (Smith, Flowers, and Larkin, 2009). IPA usefully focuses on the importance of the thematic and idiographic in terms of new knowledge generation, with an analytical focus on lived experience. Indeed, whilst the specifics of the participants in my minor and major projects are unique, my research activates and makes valid, findings that are collectively beneficial to the disciplines of applied and interdisciplinary arts; the field of practice-based research, and beyond. My original contribution to new knowledge as argued by this thesis, comprises both this text exposition and my practice. This sees the final generation of a new multimodal arts Participatory Practice-Based Framework (PartPb). Through this framework, the researcher-practitioner is seen to adopt a maternal role to gently guide project participants through four phases of co-created multimodal artwork generation. The four participatory ‘Phases’ are: Phase 1: Courtship – Digital Dialogues; Phase 2: Intercourse – Performative Encounters; Phase 3: Gestation – Screen Narratives; Phase 4: Birth – Relational Artworks. The framework also contains six researcher-only ‘Stages’: Stage 1: Participant Selection; Stage 2: Checking Distilled Themes; Stage 3: Location and Object Planning; Stage 4: Noticing, Logging, Sourcing; Stage 5: Collaboration and Construction; Stage 6: Releasing, Gifting, Recruiting. This new PartPb framework, is realised within a series of five practice-based (Pb) artworks called, ‘Minor Projects 1-5’, (2015-16) and Final Major Project, ‘Transformational Encounters: Touch, Traction, Transform’ (TETTT), (2018). These projects are likewise shaped through action-research processes of iterative testing, as developed from Candy and Edmonds (2010) Practice-based Research (PbR) trajectory. In my new PartPb framework, Candy, and Edmonds’ PbR processes are originally combined with a form of Fritz and Laura Perl’s Gestalt Experience Cycle (1947). This innovative fusion I come to term as a form of ‘Feeling Architecture,’ which is procedurally proven to hold and carry both researcher and participants alike, safely, ethically, and creatively through all Phases and Stages of artefact generation. Specifically, my new multimodal PartPb framework offers new knowledge to the field of Practice-Based Research (PbR) and practitioners working in multimodal arts and applied performance contexts. Due to its participatory focus, I develop on the term Practice-Based Research, (Candy and Edmonds, 2010) to coin the term Participatory Practice-Based Research, (PartPbR). The unique combination of multimodal arts and social-psychological methodologies underpinning my framework also has the potential to contribute to broader Arts, Well-Being, and Creative Health agendas, such as the UK government’s Social Prescribing and Arts and Health initiatives. My original framework offers future researchers’ opportunities to further develop, enhance and enrich individual and community well-being through its application to their own projects, and, in doing so, also starts to challenge unhelpful art binaries that still position community arts practices as somehow lesser to higher art disciplines
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