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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.
  • Chemistry
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    Prof. John Boland
    Trinity College Dublin
    We consider the reaction of 1,3-cyclohexadiene (1,3-CHD) on Si(100) and show that the observed reactivity and stereoselectivity cannot be explained on the basis of thermodynamics. We postulate the existence of secondary orbital interactions (SOIs) and introduce a simple algorithm that examines all possible secondary interactions between the frontier orbitals of the molecule and the surface. In this manner, we demonstrate that SOIs favor a particular molecular configuration, consistent with the experimental observations.
  • Life Sciences
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    Prof Hugh Garavan
    Trinity College Dublin
    Drugs of abuse produce widespread effects on the structure and function of neurons throughout the brain's reward circuitry, and these changes are believed to underlie the long-lasting phenotypes that characterize addiction. Ecstasy (3,4-methylenedioxymethamphetamine) is a drug often in the headlines owing to concerns about its contribution to the death of young people and also to whether its widespread use will result in an ‘epidemic’ of people with cognitive problems later in life. To date, most studies have investigated the effects of Ecstasy on adult animals. Although loss of serotonergic neurons in non-human primates has had a powerful impact on how the danger of ecstasy is perceived, whether it occurs in humans remains controversial. This thesis focuses on microstructures of specific cognitive subcomponents as they may be more likely to reveal deficits than using standard batteries of complex executive tasks. More specifically, the research presented in this thesis uses cognitive functional magnetic resonance imaging (fMRI) in chronic ecstasy users to investigate differences in neural activity related to response inhibition, learning and memory functioning, processing of drug-related cues, and emotion regulation. Given that the literature is suggestive that females may be more susceptible to the chronic effects of ecstasy sex is included as an independent variable, and menstrual cycle phase and contraception usage is controlled for between ecstasy and control groups.Using fMRI this thesis has provided strong evidence for alterations in the executive components of cognitive and emotional neuronal processing in ecstasy users. Dysregulations were observed in ecstasy users with respect to response inhibition, learning and memory functioning, processing of drug-related cues, and emotion regulation. Furthermore, these results were independent of sex, promoting future studies to take menstrual cycle in to consideration and reducing the rationale for excluding women from pharmacological studies.
  • Life Sciences
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    Dr. Aine Kelly
    Trinity College Dublin
    Environmental enrichment has been shown to upregulate neurotrophins and neurogenesis in animals and also improve hippocampal-dependent cognition. Hippocampal volume, levels of neurogenesis and cognitive ability all decline with age and this analysis will assess whether environmental enrichment can protect against any age-related grey matter volume reduction using voxel-based morphometry (VBM). Young rats (3mo) were scanned in 7T MR scanner to obtain a baseline high resolution whole brain scan. Following this, rats were randomly assigned to control or enriched conditions for a period of 21 months, during which rats were scanned again at middle age (17mo) and old age (24mo). VBM will be used to analyse any changes within and between the groups
  • Life Sciences
    Economics
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    Dr. Pedro Vicente
    Trinity College Dublin
    The paper investigates whether positive network effects may have existed between large-scale commercial farmers and small-scale communal farmers prior to the recent land redistribution in Zimbabwe. A difference-in-difference approach is used where measurement is carried out using several data sources including farm level, geographic and survey information for cotton farmers in Mashonaland Central. It tests whether the removal of large-scale farmers has resulted in a decline in productivity for those small-scale farmers close to redistributed land when compared to those with more distant farms. A significant negative productivity effect is found in addition to a country-wide negative redistribution effect in general (due mainly to wider economic and political instability over the last 10 years).
  • Life Sciences
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    Prof. John O'Docherty
    Trinity College Dublin
    Multivariate fMRI studies is an emerging trend in cognitive neuroscience. Standard practice in neuroimaging is to analyses data on a voxel-by-voxel basis. Voxel responses are independently examined for significant increases in activity using general linear models (GLMs). Unfortunately, this approach is fundamentally limited in what it can achieve since researchers are restricted to inferring whether a particular region of the brain is significantly active or not during a particular cognitive process. In recent years, these limitations have begun to be overcome by the use of multivariate methods which make use of distributed patterns of neural activity. That is, these techniques elicit combinatorial codes of voxel values which can represent cognitive functions. Whereas univariate GLM analyses can highlight where in the brain significant neural activity occurs, multivariate methods can go beyond this to determine what information is being processed and begin to investigate how. The goal of the current project is to apply multivariate pattern analysis to fMRI data from studies on reward learning and decision making.
  • Physics
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    Dr. Charles Patterson
    Trinity College Dublin
    Computer simulations of nanostructures frequently require positions of atoms to be relaxed toan equilibrium configuration. Structure relaxations using quantum mechanical methods suchas density functional theory are relatively expensive compared to methods which use classicalforce fields (short range interactions parameterised by e.g. exponential functions and longrange coulomb interactions). This project will be to derive force field parameters from densityfunctional theory calculations on systems with small unit cells and to use them for structurerelaxation of nanostructures with many atoms. The project will use the Quantum Espressoand GULP codes. It will allow you to become acquainted with density functional theory, methods for performing Ewald lattice sums and will require some coding in a compiled language.
  • Mathematics
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    Dr. Konstantinos Drakakis
    University College Dublin
    Costas arrays are square arrays of 1s/dots and 0s/blanks, such that there is exactly one dot per row and column, and such that any two linear segments connecting pairs of dots have either different length or different slope. The latter property is equivalent to the following three conditions: a) no four non-collinear dots form a parallelogram; b) no four collinear dots form two equidistant pairs; and c) no three collinear dots are equidistant. Though they originated as time-frequency waveform descriptions in SONAR systems, they soon became objects of mathematical study, due to the many and interesting problems they give rise to in combinatorics, algebra, and number theory.Two algebraic construction techniques exist, based on the theory of finite fields, which successfully construct nxn Costas arrays for infinitely many, though not all, orders n. However, even in the orders where these methods are applicable, they fail to yield all existing Costas arrays there. Until today, the only available method guaranteed to yield all Costas arrays in a certain order is enumeration through exhaustive search, whereby each of the n! permutation arrays of order n is tested for the Costas property. Until today, enumeration has covered orders n<29. The aim of this project is to enumerate all Costas arrays of order 29.
  • Physics
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    Dr. Charles Patterson
    Trinity College Dublin
    Functional oxides which are proposed for study include copper oxide transparent conducting oxides, magnetite, doped magnetite and ferromagnetic thin films of non-magnetic oxides such as ZnO for spintronics applications and oxides with the pyrochlore structure, which have ultra-high-k values. In each case we will simulate vibrational, electron paramagnetic resonance or optical spectroscopies with the aim of understanding how these oxides acquire their properties. We propose to use the Crystal code, with which we have more than 10 years’ experience, and we will acquire experience in using the Quantum-Espresso code. We will also continue development of the Exciton code. We will use methods with which we have extensive experience and we will acquire experience in calculating EPR spectra of paramagnetic defects and Raman scattering cross-sections of ultra-high-k oxides.
  • Life Sciences
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    Dedicated human Support
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    Dr. Juan Pablo Labrador
    Trinity College Dublin
    In this project the aim is to apply a method developed in the laboratory to identify protein-protein interactions using in silico approaches only. The method is under experimental trial and its success will open new research avenues in the understanding of interaction dynamics between proteins. In the pot-genomic era the amount of available information at the genome and proteome levels is overwhelming. It becomes urgent to deal with this information at a large scale by designing programs powerful enough to comprehensively undertake challenging analyses with these data. At the moment such programs are rather lacking and therefore progress in this area is crucial. Here we would like to try a novel software to identify in silico interactions and to complement experimental analyses aimed at achieving such an objective.The trial of this program will be based upon the analysis of the coevolutionary relationships--which is a measure of covariation of two proteins across evolutionarily ralted organisms--among all possible pairs of proteins for which we have genome information. This project will take exhaustive computational resources that will be difficult to get unless supported by TCHPC facilities.
  • Mathematics
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    Dr. Mike Peardon
    Trinity College Dublin
    The standard model of particle physics describes interactions of the fundamental constituents of matter up to all energies so far explored in particle accelerators. It includes quantum chromodynamics, the theory that describes the strong nuclear force. The strength of interactions in this theory means the only way to make direct predictions from the theory is to perform numerical investigations of the theory represented on a four-dimensional space-time lattice (lattice QCD). This project will use lattice QCD to measure the masses of particles built from a charm and an anti-charm quark. These heavy states have been the subject of intense experimental scrutiny recently as new measurements do not fit neatly into model predictions. The project will determine the masses of radial and orbital excitations of these particles, as well as the so-called hybrid states that include intrinsic excitations

Last updated 15 Apr 2014Contact TCHPC: info | support.