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Ongoing Research Projects supported by Research IT

Listing of project codes and abstracts, describing work undertaken which use the resources of the compute clusters hosted by the Research IT team.

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Showing 10 of 419 Results
Project Title Development of Exciton Code in HPC MSc project
Project Code HPC_17_00981
Principal Investigator Dr Charles Patterson
Start Date 2017-06-22
End Date 2017-08-31
Abstract The Exciton code written by the PI for this project uses an MPI_Window system for parallelism in GW and Bethe-Salpeter Equation calculations. The aim of this project is to investigate the efficiency of combining local generation of components of a large matrix with SCALAPACK as an alternative to the MPI_Window approach which is currently used.
Project Title Potential Energy Surfaces and Solvation Models for the Chemical Conversion of Lignocellulosic Sugars to Liquid Transport
Project Code HPC_17_00980
Principal Investigator Dr Stephen Dooley
Start Date 2017-07-01
End Date 2018-06-30
Abstract The reaction pathways accounting for the chemical conversion of non-food biomass derived sugars into carbon neutral transportation fuel molecules by reaction with hydrogen cations in various solvent media is studied. To this purpose, condensed phase catalytic platforms for the selective removal of oxygen atoms from the biomass derived sugars are pursued. To understand how these transformations occur, and how to better control them to produce preferred fuel molecules in maximal quantities, a series of Electron Density Functional Theory calculations are performed with the assistance of TCHPC. The calculations determine fundamental thermodynamic quantities that dictate the energetic and mechanistic landscape of these transformations. These quantities are used as inputs into reaction engineering kinetic models which can predict the conditions that allow for the identification of both optimal fuel components and for the identification of optimal reaction conditions for their production.
Project Title Adsorption of picricacid on Troger's base-covalent organic polymer
Project Code HPC_17_00979
Principal Investigator Prof. Thorri Gunnlaugsson
Start Date 2017-06-13
End Date 2018-06-13
Abstract Density functional theory will be employed to understand the mechanism of Troger's base-covalent organic polymer (TB-COP) binding with picric acid (PA). We considered one monomer unit of the covalent organic polymer as a model system. Various possible orientations of the PA on TB-COP will be considered and the minium energy orientation will be reported. The mechanism of binding will be further analysed by the frontier orbital energy diagrams and charge distribution analysis.
Project Title Simulations of Geomagnetically Induced Currents in the Fully Resolved Irish Power Network over 25 Years
Project Code HPC_17_00978
Principal Investigator Dr Peter Gallagher
Start Date 2013-10-01
End Date 2017-09-30
Abstract Geomagnetically Induced Currents (GICs) are a well-known terrestrial space weather hazard. They occur in power transmission networks and are known to have adverse effects in both high and midlatitude countries. Here we study GICs in the Irish power transmission network over 25 years, to better know their impact in Ireland. The calculated GICs will be used to form the basis of a statistical analysis of the phenomena in Ireland.
Project Title The Neurocognitive Bases Depressive Symptoms across Development
Project Code HPC_17_00977
Principal Investigator Assistant Professor Clare Kelly
Start Date 2017-06-08
End Date 2018-06-07
Abstract Depression is increasingly recognized as a neurodevelopmental disorder. Yet, its neurodevelopmental course remains unspecified, and the search for neurocognitive markers of vulnerability has not yet filled the “explanatory gap” in our ability to predict who will become depressed, when, and why. The rising prevalence of depressive symptoms among youth, particularly among females, highlights the urgent need to consider multiple aetiologies and to explore novel neurocognitive dimensions. The goal of this project is to use functional neuroimaging and a novel translational assay of an individual’s ability to cope under stress to examine how the neurocognitive bases of coping are affected by depressive symptoms and development during adolescence. Thirty female adolescents (aged 13-17 years) with depressive symptoms (DS) and 30 typically developing age, IQ, and SES group-matched female controls (TC) are participating in at least one fMRI scan session during which a set of anatomical and functional MRI scans are acquired. In addition, an existing set of resting state fMRI data collected from depressed adults will be examined. The aims of this project are to: (1) Examine active coping in individuals with and without depressive symptoms. We hypothesize (H1) that adolescents with depressive symptoms will exhibit impairments in AC performance and abnormalities in AMYG-mPFC circuitry underlying emotion regulation. (2) Examine effects of age on task performance, activation, and functional connectivity to delineate developmental trends in coping and regulation abilities and circuitry. We hypothesize (H2) age-related improvements in coping task performance associated with maturational changes in AMYG-mPFC circuitry.
Project Title Reward and Attentional Circuitry in ADHD
Project Code HPC_17_00976
Principal Investigator Assistant Professor Clare Kelly
Start Date 0000-00-00
End Date 0000-00-00
Abstract Individuals with ADHD exhibit altered reward learning and impaired executive function (e.g., attentional control, working memory). In this project, we are using task-based and task-independent (resting state) approaches to investigate reward and attentional circuit function in individuals with and without ADHD. We are examining the hypothesis that individuals with ADHD are at the mercy of previously learned reward associations to a greater extent than non-ADHD comparisons. We are also examining the extent to which reward learning in ADHD is affected by moment-to-moment variability in response times (RTV), whereby increased RTV reflects impairments in executive function and cognitive control of behaviour. Participants in the project take part in an fMRI scan, during which anatomical and 6 runs of functional data are acquired.
Project Title CFD analysis of pulmonary airflow
Project Code HPC_17_00975
Principal Investigator Dr Colleen Farmer
Start Date 2017-06-02
End Date 2018-06-02
Abstract This project aims to model airflow in the lungs of a range of vertebrates to understand basic structure-function questions. The overarching objective is to expand our knowledge of the evolution of the vertebrate respiratory system.
Project Title Ion migration
Project Code HPC_17_00974
Principal Investigator Prof Khurshid Ahmad
Start Date 0000-00-00
End Date 0000-00-00
Abstract I use molecular dynamics and quantum chemistry to simulate the migration of ions in molecular channels.
Project Title In silico modelling of arterial disease
Project Code HPC_17_00973
Principal Investigator Prof Caitriona Lally
Start Date 2017-06-02
End Date 2018-06-02
Abstract Each year cardiovascular diseases such as atherosclerosis and aneurysms cause 48% of all deaths in Europe. Arteries may be regarded as fibre-reinforced materials, with the stiffer collagen fibres present in the arterial wall bearing most of the load during pressurisation. Degenerative vascular diseases such as atherosclerosis and aneurysms alter the macroscopic mechanical properties of arterial tissue and therefore change the arterial wall composition and the quality and orientation of the underlying fibrous architecture. Information on the complex fibre architecture of arterial tissues is therefore at the core of understanding the aetiology of vascular diseases. The current proposal aims to use a combination of in vivo Diffusion Tensor Magnetic Resonance Imaging, with parallel in silico modelling, to non-invasively identify differences in the fibre architecture of human carotid arteries which can be directly linked with carotid artery disease and hence used to diagnose vulnerable plaque rupture risk. Knowledge of arterial fibre patterns, and how these fibres alter in response to their mechanical environment, also provides a means of understanding remodelling of tissue engineered vessels. Therefore, in the second phase of this project, this novel imaging framework will be used to determine fibre patterns of decellularised arterial constructs in vitro with a view to directing mesenchymal stem cell growth and differentiation and creating a biologically and mechanically compatible tissue engineered vessel. In silico mechanobiological models will also be used to help identify the optimum loading environment for the vessels to encourage cell repopulation but prevent excessive intimal hyperplasia. This combination of novel in vivo, in vitro and in silico work has the potential to revolutionise approaches to early diagnosis of vascular diseases and vascular tissue engineering strategies.
Project Title Muon g-2 and the isospin breaking corrections to the hadronic contributions
Project Code HPC_17_00970
Principal Investigator Assistant Professor Marina Krstic Marinkovic
Start Date 2017-05-23
End Date 2018-05-22
Abstract Several leading lattice collaborations are investing significant efforts to reduce the uncertainty in the lattice computation of the leading hadronic contribution to the muon anomalous magnetic moment to a sub- percent level in order to verify weather the current discrepancy between the standard model estimate and the experimental measurements is a sign of new physics beyond the standard model. In order to achieve this goal, giving a precise estimate of the size of the isospin breaking effects becomes relevant. Several lattice collaborations are currently competing to estimate of this important effect and TCD researchers are part of these cutting-edge efforts. We therefore apply here for computer time to measure the isospin breaking effects of the connected part of the hadronic vacuum polarisation from the lattice by applying the recently proposed method of R123 collaboration. The decisive point of this approach is defining the leading isospin breaking effects (LIBE) of an observable, by expanding in powers of the fine structure constant alpha_em, and up and down quark mass differences, mu-md. This method is developed to enable the computation of the isospin breaking corrections order by order, and its advantage with respect to the conventional methods is that it factorises the small coefficients, which in turn amounts to relatively large signal to noise ratios. Additionally, this method is not susceptible to the systematics associated with extrapolation to the physical value of the fine structure constant. On the other hand, the fact that one has to compute a significantly larger number of quark and photon propagators than in the standard approach of quenched and full QED+QCD simulations might be considered a disadvantage. However, this can be overcome by using highly optimal inverter and careful organisation of the computation of the diagrams that is being followed in this work.