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Trinity College Dublin

Ongoing Research Projects supported by TCHPC

TCHPC allocates resources to assist research in many different fields. Below is a list of current projects been undertaken with the help of TCHPC.
  • Engineering
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    Dr. Dermot O'Dwyer
    Trinity College Dublin
    Cantilevered stone stairs do not generally cantilever. Each stone tread transfers load applied to it from the tread above to the tread below and the wall support. The predominant resulting force developed within the tread is a torque.Assessing cantilevered stone stairs is complex because they are highly statically indeterminate. The support conditions at the wall are difficult to assess and the treads are carved from stone which is a natural and often highly variable material. In addition, many stairs have undergone repairs, which in some cases have weakened them.In proposing a simple method for analysing a flight of cantilevered stone stairs, the statically indeterminate problem is made determinate by assuming the support condition and location of the resultant contact force between the treads. This study should establish the range of these values in different stairs with different support condition and geometries.In this project, detailed finite element model capable of modelling the contact forces between individual tread and capable of modelling varieties of wall support conditions has been developed using ANSYS.
  • Chemistry
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    Prof. Graeme Watson
    Trinity College Dublin
    Nitrogen oxide based emissions from combustion engines have become a topic of concern in recent years, due to the harmful effects they have on the environment. Decomposition of NOx (x = 1,2) (deNOx) leads to the emissions of N2O and NO2 which damage the ozone layer. As a result, strict regulations have been imposed on NOx (x = 1, 2) emissions, leading to the development of three way car catalysts (TWC). The active metals used in TWC’s are Rh, Pd and Pt. Extensive research has shown that Rh is a more effective active metal at deNOx, however it is rare and expensive. Furthermore, research into the mechanism of deNOx on the active support metals in TWC’s, to fully understand the reduction of NOx emissions to nitrogen and oxygen gas is in heated debate. Hence, elucidation of the mechanism on Rh, Pd and Pt active metal surfaces will help to understand the decomposition process and develop new low-cost metal catalysts to fully reduce nitrogen based emissions. We will explore adsorption of O, NO and NO2 on the low index surfaces of Rh, Pd and Pt using DFT: GGA calculations as the first step in understanding the mechanism of the NO and NO2 decomposition processes.
  • Chemistry
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    Prof. Graeme Watson
    Trinity College Dublin
    In 1997, Hosono and co-workers first reported p-type conductivity and transparency in thin films of delafossite CuAlO2. Since then, there has been an explosion of interest in developing p-type TCOs to rival the industry standard n-type TCOs. Copper delafossites have been studied extensively as p-type TCOs, but have been hampered by activated conductivity and indirect band gaps. In this study we use first principles methods to understand extrinsic and intrinsic conductivity limits in delafossite materials, attempt to use these insights to predict novel p-type materials
  • Chemistry
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    Prof. Graeme Watson
    Trinity College Dublin
    CdTe has historically been used in solar cells, infrared optical windows, and in radiation dectectors for x-rays, gamma-rays, beta particles and alpha particles. Doping of CdTe to make it n-type has been achieved, but is often limited by the well known phenomenon of “self-compensation”. The exact mechanisms for these effects are unknown, but are thought to be a synergistic effect between DX and AX defects. In this study we use first principles methods to pinpoint the doping limits of CdTe, and to understand the origins of these doping limits
  • Life Sciences
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    Dr. Adrian Bracken
    Trinity College Dublin
    The Bracken lab is focused on understanding the signaling pathways which regulate cellular senescence. Recently the lab identified a senescence signature of 300 genes that are expressed in young but not in senescent cells of both breast and stromal lineages. Significantly, these genes are highly expressed in breast cancer and correlate with poor prognosis, in keeping with the fact that advanced stage cancers must overcome the cellular senescence checkpoint (Narita and Lowe, Nature Medicine, 2005). However, lost amongst this information are the master transcriptional regulators (MTRs) which drive the expression of these genes and are candidate therapeutic targets for breast cancer. We will employ recently developed reverse engineering algorithms (ARACNE) to infer these MTRs from multiple published microarrays of breast cancer. We anticipate that this strategy will identify the ~10 MTRs which will then be further evaluated for their role as potential breast cancer therapeutic targets.
  • Physics
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    Prof. Stefano Sanvito
    Trinity College Dublin
    Si(100) is a technologically important substrate for electronic device fabrication and has been the subject of intense study over the last forty years. Despite this big effort, many aspects are still open to debate. The details of the mechanism related to the surface reconstruction, for example, are still unclear as well as the chemisorption of H and P atoms on the surface. In addition, there has been growing interest in the properties of chemically passivated Si(100), particularly the use of hydrogen, since its small size and similar electronegativity minimizes stress and charge separation at the interface. H-passivated Si(100) surfaces are relatively air stable, allowing processing and functionalization with a wide range of chemical agents that has in turn led to sensor and device applications. The aim of this project is to perform computer simulations to clarify these unclear aspects by making use of density functional theory (DFT) techniques. We will make use of codes such as OpenMx, VASP and Smeagol to calculate electronic and transport properties.
  • Life Sciences
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    Dr. Arun Bokde
    Trinity College Dublin
    Cognition requires a high level of coordination among regions of a brain network. The structural integrity of the brain will affect the function of the brain networks and thus cognitive performance. Working memory, the capacity to hold information in mind, is affected by increasing age and genes. We will investigate how brain structure changes due to age and different genes alter the functioning of the brain network supporting working memory. The results will lead to greater understanding of how age and genes alter brain function, and will aid in understanding how diseases alter normal function in healthy subjects.
  • Physics
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    Prof. Stefano Sanvito
    Trinity College Dublin
    In a close collaboration with experimentalists in the EU FP-7 framework, we approach the problem of interfacing nanoscopic molecules with macroscopic electrodes by using nanoscale intermediates. Our multiple-scale architecture, based on two-dimensional arrays of nanoparticles and metallic nanowires, provides reliable and robust access to electrical, optical and mechanical properties of molecular systems. Such system will be investigated theoretically by means of the density functional theory, as implemted in SIESTA code. In particular, we use various strongly correlated methods developed our group, including the atomic self-interaction scheme, the fully self-consistent self-interaction corrections method and the exact exchange scheme. Electron transport in molecular junctions will be investigated with our state of the art quantum transport code Smeagol (www.smeagol.tcd.ie). Smeagol combines density functional theory with the non-equilibrium Green’s function method for quantum transport and is capable of evaluating the I-V curves and inelastic spectra without the need of adjustable parameters.
  • Life Sciences
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    Prof Hugh Garavan
    Trinity College Dublin
    University of Melbourne, Australia
    ADHD is thought to have a strong genetic component and executive function measures such as response inhibition might index susceptibility to ADHD. The DAT1 gene codes for the dopamine transporter, which clears dopamine from the synaptic cleft, and a variant of this gene has previously been associated with compromised response inhibition in individuals with ADHD. In the present study, we used fMRI to investigate how activation associated with successful and unsuccessful inhibitions differs based on ADHD-diagnosis and DAT1-genotype in adolescents performing a go/nogo task. The results identify regional specificity concerning which functional differences can be attributed to the clinical condition, the possession of the HR DAT1 genotype or an interaction between the two. During response inhibition, individuals with two copies of the 10-repeat allele showed increased activation in frontal, medial, and parietal regions, which may indicate that inhibition is more effortful for this group. Conversely, this group displayed a reduced error response in the parahippocampal gyrus, suggestive of reduced learning from errors. There were also a number of frontal, parietal, medial and occipital regions, where the relationship between genotype and fMRI-activation differed between the ADHD group and typically developing adolescents. Finally, the ADHD group displayed decreased activation in parietal and (pre)frontal regions during response inhibition, and in frontal and medial brain regions on error trials.
  • Life Sciences
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    Prof Hugh Garavan
    Trinity College Dublin
    In the current phase of the Velocardiofacial projectongoing in TCIN and in conjunction with Prof. Hugh Garavan (TCD),Prof. Kieran Murphy (RCSI) and Prof. Colm McDonald (NUIG), MR imaging is being used to explore functional and structural aspects of the 22q11.DS syndrome. This project involves detailed structural,functional and DTI image analyses of a patient population with the 22q11.DSsyndrome, a chromosome deletion disorder affecting 1 in 5000 live births approximately. Analysis will consist of fMRI using AFNI, structural MRI usingFreesurfer and FSL_VBM, and DTI using FSL_TBSS to probe the anatomical and cognitive characteristics of the condition. This will require running data analyses on the HPC clusters based at TCIN and all associated support fromthe TCHPC experts where necessary.

Last updated 19 Dec 2014Contact TCHPC: info | support.