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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
    Compute
    C
    Prof. Graeme Watson
    Trinity College Dublin
    Discovering new candidate p-type transparent conducting oxides has become a major goal for material scientists. Combining the native p-type conductivity of Cu2O with the larger band gaps of other binary oxides, ternary Cu-based delafossite materials have attracted much attention since Hosono and co-workers first reported the optical and electrical properties of copper aluminate (CuAlO2). The Cu(I)-based delafossite structure, Cu(I)M(III)O2, can accommodate a wide range of rare earth and transition metal cations on the M(III) site. These ternary semiconductors exhibit more flexible properties arising from their enhanced chemical and structural freedoms. [2-5]In this poster we report a density functional theory investigation of Cu(I)M(III)O2 (where M(III) represents a range of trivalent metal ions), examining the stability and electronic structure using GGA corrected for on-site Coulomb interactions in strongly correlated systems (GGA U). From analysis of the calculated formation energies, band structure and density of states, we present predictions of new compounds in the family of delafossites. 1 H. Kawazoe, H. Yasakuwa, H. Hyodo, M. Kurita, H. Yanagi, and H. Hosono, Nature London 389, 939 (1997).2 J. E. Jaffe and A. Zunger, Phys. Rev. B 28, 5822 (1983).3 Y. Meng, X. Yang, H. Chen, J. Shen, Y. Jiang, Z. Zhang and Z. Hua, Thin Solid Films 394, 219 (2001).4 S. Chen, X. G. Gong, and S.-H. Wei, Phys. Rev. B 75, 205209 (2007).5 D.O. Scanlon, K.G. Godinho, et al, The Journal of Chemical Physics 132, 024707 (2010)
  • Physics
    Storage
    Compute
    B
    Prof. Stefano Sanvito
    Trinity College Dublin
    In this project we shall investigate the electronic structure of transition metal (TM) doped ZnO grain boundaries (GBs) in order to better understand the role of extended defect structures in stabilizing long range magnetic order in this material. Recent experimental work has shown that grain boundaries and defects associated to them possibly play a fundamental role in the observed ferromagnetism of TM doped ZnO [1]. This observed correlation between the presence of GBs and ferromagnetism will be investigated in this work with the help of ab-initio electronic structure calculations. Identifying qualitative as well as quantitative differences between the electronic structures of TM dopants in the bulk material and at the grain boundary is key to understanding this phenomenon. To this end we shall be employing self-interaction corrected density functional theory (DFT) methods incorporated into the SIESTA platform.[1]. Phys Rev B 79, 205206 (2009)
  • Life Sciences
    Storage
    A
    Prof. Fional Newell
    Trinity College Dublin
    The aim of our research programme is to elucidate the neural processes underpinning multisensory perception in the human brain. To that end, we have engaged in a series of studies, using fMRI, DTI and VBM measures, that are associated with behavioural performance in cross-modal perceptual tasks ranging from Tactile-Visual texture discrimination (Simoes-Franklin and Whitaker), haptic object perception (Chan) to synaesthesia (O\'Hanlon). We have also tried to assess the role of sensory deprivation on processing in the intact senses (Noone). Our research stems from a multidisciplinary approach to the study of human perceptual processing, involving a range of disciplines from psychology and neuroscience to engineering and genetics. These MRI studies are essential to improve our understanding of how perception is achieved by the human brain.
  • Chemistry
    Compute
    C
    Prof. Mathias Senge
    Trinity College Dublin
    The effects of protein induced conformational distortion of porphyrinoid cofactors have long been believed to be a modulator of their numerous biological functions. However, explicit descriptions of the precise functional roles of particular conformations in specific proteins, beyond their citation as important, are available for only a minority subset of tetrapyrrole proteins (e.g. ferrochelatease). With this in mind, systematic investigation of the structure, effects and biological consequences of these nonplanar distortions in different biological systems is warranted. To follow from our previous work on photosynthetic reaction centers, we are investigating the possible role of conformational modulation in the control of electron transfer in the cytochrome subunit of the reaction center from Blastochloris viridis. This problem requires delineation of the various structural features that contribute to the large range of redox potentials exhibited by the chemically identical cofactors in this tetraheme cytochrome (-60 to 370mv) since other binding-site interactions (dielectric, H-bonding and steric) and substituent effects (e.g. propionate orientation and protonation state) are known to greatly influence the potentials. For our own investigations, we are primarily interested in whether the physicochemical contributions of the intrinsic structural influences (e.g. cofactor conformation) are significantly affected by the macrocycle\'s nonplanarity. This can be achieved by calculating their relative reduction potentials via high-level single-point calculations on the various conformations of each cofactor from the cytochrome subunit (taken from published crystal structures) in an isolated state. In aid of this, incremental addition of the normal-mode distortions that make-up the observed cofactor conformations to planar models of haem will show the effect and importance of each component of the conformation as well as their combined effect.\n
  • Engineering
    Compute
    C
    Dr. Niall English
    University College Dublin
    Molecular dynamics simulations of a variety of processes will be carried out, focussing, inter alia, on the interactions of solvents and molecules with nanostructured metal and metal oxide surfaces and also of dynamical and structural characteristics of molecular liquids and solids.
  • Computer Science
    Compute
    C
    Dr. Saturnino Luz
    Trinity College Dublin
    The protein folding problem has long been a preoccupation of the biological sciences. While the amino acid sequence of the protein can be determined it appears that the biological effects of the protein are determined substantially by its surface appearance and this by its fold conformation. Prediction of the fold conformation from the amino acid sequence has been described as one of the biggest unsolved problems in science [1]. During the 1980\'s a view emerged that the hydrophobic interaction dominated the fold structure that emerged and one approach has been to look at simplified models based around this perspective.
  • Life Sciences
    Compute
    C
    Ian Robertson
    Trinity College Dublin
    Cognitive decline has emerged as one of the greatest health threats of senescence. The prevalence of cognitive impairment with advancing age, together with rapid demographic ageing makes increasing understanding of the ageing brain and cognitive decline an imperative. However, there is considerable variability with regard to both the nature and the severity of cognitive disturbances observed. We have previously combined neuropsychological and electrophysiological techniques to distinguish between age groups (young, old) and/or cognitive performance groups (old high performers, old low performers). The overall approach taken was to capture cognitive variability through the identification of cognitive performance sub-groups and then ascertain whether neurphysiological differences support these classifications. Old participants were sub-divided on the basis of their performance on a memory test relative to an estimate of their pre-morbid IQ. Significant EEG markers could also distinguish between these groups (resting EEG alpha power, ERP components such as the N1, and late positivity). We now endeavor to source the anatomical substrates of these neurophysiological effects using structural MRI. Two measures of interest are anatomical volumetrics, and cortical thinning. Both of these approaches have been previously used to highlight structural abnormalities in Alzheimers disease, Mild cognitive impairment and the onset of Alzheimers disease (Teipel et al, 2007; Dickinson et al., 2011). Understanding the anatomical underpinnings of this cognitive marker is key to the development of future cognitive and pharmacological interventions.
  • Life Sciences
    Compute
    C
    Dr. Gary Donohoe
    Trinity College Dublin
    Cognitive deficits associated with schizophrenia are not thought to be localised to a single part of the brain, but rather to represent more widespread cognitive dysfunction. As such, the study of this disorder may benefit from research focussing on the interactions between different brain regions. The proposed project will examine the effects of psychosis risk gene variants on functional and effective connectivity between neuronal populations. Functional neuroimaging will be conducted and samples for genotyping will be acquired from an Irish sample of schizophrenia patients and healthy controls. It is hoped that this research will help elucidate the mechanisms by which certain genes confer increased risk for schizophrenia. A clearer understanding of these mechanisms will help in the development of novel therapies for the disorder.
  • Life Sciences
    Storage
    Compute
    C
    Prof. Marina Lynch
    Trinity College Dublin
    Alzheimer\'s disease (AD) is an incurable form of dementia, affecting more than 26 million people worldwide. The APP/PS1 line of double transgenic mice is a mouse model of AD, that has been shown to correlate with the behavioural and cognitive deficits associated with the human form of the disease. In this study, high resolution magnetic resonance imaging (MRI) was carried out on mice expressing both transgenes, and their wildtype littermates, to assess for any volumetric differences in the brains of the transgenic mice. These differences can then be correlate with neurobiological changes, including cell stress and neuronal atrophy.
  • Life Sciences
    Storage
    Compute
    C
    Dr. Jan de Vries
    Trinity College Dublin
    The aim of this study is to investigate the neural response to cognitive dissonance (CD) using functional magnetic resonance imaging (fMRI). The objective is to identify how common everyday events that could generate dissonance are processed in the brain. On the basis of present neurological evidence it is hypothesised that the anterior cingulate cortex (ACC) and parts of the prefrontal cortex are implicated. Most of the research is based on relatively contrived lab tasks. This study attempts to establish whether the hypothesis still holds when CD induction takes place in a more naturalistic way presenting participants with day to day situations that generate dissonance. The study is part of a wider effort to bridge the gap between research on social cognition and neuroscience.Background Cognitive Dissonance (CD) (Festinger, 1957) is the result of simultaneously holding two or more inconsistent cognitions, or exhibiting behaviour that is inconsistent with beliefs or values. This is experienced as an uncomfortable tension motivating efforts to reduce dissonance and therefore discomfort. This is commonly done by changing cognitions or behaviours, but also by trivialising or seeking distraction. Evidence from neurological studies suggests that dissonance discomfort is detected in various brain structures, notably the anterior cingulate cortex (ACC), while efforts to resolve it take place in the prefrontal cortex (Amodio et al, 2004; Harmon-Jones et al., 2008). Research Approach and Design Main Study: The study will make use of a within-subject 2 x 2 design baseline condition. Participants will all undergo the same procedure. They will be presented with a series of questions while undergoing an fMRI scan. In the experimental condition, the stimulus consists of (1) a primer which presents a common value; followed by (2) a memory prompt to think of personal violations of this value. Dissonance is expected to occur as a result. Three control conditions will provide necessary contrasts for fMRI analysis, while an added control condition serves as a baseline comparison. They use the same format with contrasting primers and memory prompts. Pilot Study: To select the items for inclusion in the fMRI study, a pilot study will take place in which the memory prompts will be tested. Those that are recalled most consistently will form the pool of items to be used in the experimental condition of the study. Data Collection Methods Main Study: The study will use fMRI scanning. Biographical data and intervention checks will make use of yes/no questions, 4-point Likert scales, and a dissonance questionnaire (Elliot and Devine, 1994). Responses to the stimuli during the scan will be given by pushing buttons on a panel in the scanner. Pilot Study: The pilot will make use of questionnaire which participants can complete on-line in Survey Monkey.

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