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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 423 Results
Project Title Effect of Environmental Stochasticity on Ecosystem Stability
Project Code HPC_17_00985
Principal Investigator Dr. Ian Donohue
Start Date 2017-07-05
End Date 2017-09-30
Abstract How environmental stochasticity will affect the successful predication of ecological process of natural systems is essential for ecosystem management facing unregulated climate change. Ecological stability determines the sustainability of ecological functioning and services, but little is known about its predictability in a stochastic environment. Here we present the first holistic demonstration of how environmental stochasticity regulate the predication of three types of ecological stabilities including variability, resistance, and recovery time, which are of profound conservation applications. Using stochastic models of food webs, we show the huge discrepancy in their predictabilities with environmental stochasticity.
Project Title Role of septal region in the integration of spatial and reward information
Project Code HPC_17_00984
Principal Investigator Dr Marian Tsanov
Start Date 2017-07-04
End Date 2017-08-31
Abstract Hippocampus mediate episodic memory formation but the neurophysiological mechanisms that integrate the spatial and reinforcement components of episodic memories are scarcely understood. The hippocampal system encodes the spatial location within the environment, while the tegmental dopaminergic system mediates the signal processing of rewards. There is, however, limited information about how hippocampal spatial and tegmental reward systems maintain feedback loop to synchronise their activity for place and reward. The lateral septum is the only major non-hippocampal target of hippocampal CA3 area. That makes the septal region a likely locus of integration between reward and spatial information. A Recent study has identified a circuit from area CA3 of dorsal hippocampus to ventral tegmental area (VTA) that uses lateral septum as a relay. However, the functional role of this connection is still unclear. Using electrophysiological recordings from rats performing spatial and reinforcement tasks I plan to identify the signal processing of the space and reward for each septal sub-region. Our optogenetic stimulation design will aim to investigate the role of tegmental dopaminergic inputs on septal neuronal responses and to what degree the optogenetic stimulation regulates the spatial features of septal signal processing
Project Title Investigation of brain structure and connectivity in ASD
Project Code HPC_17_00983
Principal Investigator Prof Louise Gallagher
Start Date 2017-06-27
End Date 2018-09-30
Abstract Autistic spectrum disorders (ASDs) are devastating neurodevelopmental disorders of childhood, characterised by deficits in social interaction, communication and restricted, repetitive patterns of behaviour. Despite unknown aetiology, reports of deficits in functional and structural connectivity lend support to an emerging theory of altered cortical connectivity. In autism, specific structural abnormalities have been described in the frontal lobe, anterior cingulate and parietal cortex. These regions are required for successful attention orienting and set shifting, cognitive functions that are reported to be impaired in ASD which are proposed to contribute to social communication deficits (attention orienting) and restrictive, repetitive behaviours (set shifting) which are characteristic of autism. In this study we hypothesise that specific deficits in attention orienting and set shifting in high functioning autism (HFA) are associated with underlying structural and functional brain abnormalities including abnormal interregional connectivity. We aim to test the abnormal cortical connectivity hypothesis of HFA by using multiple neuroimaging techniques. Specifically we will: • Characterise neuropsychological functions of attention orienting and set shifting in an ASD sample. Investigate differences in brain structure and function between cases and controls, using, voxel-based-morphometry (VBM), diffusion-tensor-imaging (DTI), functional MRI (fMRI) and cortical thickness during attention orienting and set-shifting tasks. • Relate brain activation (function) during task performance analytically to anatomical brain structure to investigate whether abnormalities detected by fMRI correlate with abnormalities detected by structural neuroimaging. • Investigate levels of synchronisation of neural networks activated during these tasks in subjects with HFA compared with controls, using functional connectivity analyses.
Project Title Exploration of the Computational Potential of Kelvin
Project Code HPC_17_00982
Principal Investigator Dr Ruth Britto
Start Date 2017-06-22
End Date 2017-11-01
Abstract In this work, we will perform a preliminary investigation to determine the long-term potential of the Kelvin cluster for higher-loop perturbative calculations.
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.