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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
    Dr Isabel Rozas
    Trinity College Dublin
    CSIC (Spain)
    An experimental and theoretical study of the Intramolecular Hydrogen Bond (IHB) in 5-substituted 2-guanidinium-pyridines in order to verify the influence of thid IHB in the relative conformation of the guanidinium system.
  • Physics
    Compute
    C
    Dr Paul Eastham
    Trinity College Dublin
    Imperial College London
    Semiconductor nanostructures, such as quantum Hall bilayers and semiconductor microcavities, are transistor-like devices in which many exotic ordered electronic states have been observed. In particular, recent experiments have shown the existence of Bose-Einstein condensates of excitons in quantum Hall bilayers, and a Bose-Einstein condensate of polaritons in microcavities. These phenomena will dramatically modify the electrical or optical transport properties of the structures, leading for example to dissipationless electrical transport in the quantum Hall bilayer. This project aims to predict and analyse the results of transport experiments on these systems, using a combination of numerical simulations and analytical studies. Since these transport properties are largely controlled by disorder this requires a significant numerical effort, to obtain good statistics over the random disorder potential.
  • Life Sciences
    Storage
    C
    Prof. Joseph Keane
    Trinity College Dublin
    Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is a major global disease burden. It most commonly infects the lungs, where it infects and replicates within macrophages and dendritic cells. These phagocytic antigen presenting cells (APCs) form part of the innate immune response, which is vital to host immunity during tuberculosis infection. My project examines the viability and function of both macrophages and dendritic cells during infection with Mtb.
  • Physics
    Compute
    A
    Dr. Sinead Ryan
    Trinity College Dublin
    The spectrum of charmonium will be determined from lattice QCD, including disconnected diagrams and threshold effects. The calculation uses distillation technology for quark propagators, recently developed at TCD.
  • Life Sciences
    Compute
    C
    Prof. Louise Gallagher
    Trinity College Dublin

    People with high functioning autism (HFA) have difficulties in social interaction, communication and behaviour, but normal intelligence. In spite of the enormous impact associated with autism, no effective treatment has yet been developed. To devise a therapy for any disorder, knowledge of the basic underlying problems is essential. Unfortunately, in autism, these are not yet fully understood. It has been suggested that a multidisciplinary approach is essential in furthering our understanding of the cause of autism (e.g. Dawson et al, 2002). This study is strongly interdisciplinary, seeking to investigate links between neuropsychological and neuroimaging abnormalities in autism. Scientific research shows that individuals with HFA have trouble orienting attention. Abnormalities in brain structure and function and unusual connections between brain regions may underpin this problems but are not yet fully understood. Such an understanding is essential for the development of rational treatments for this disorder.

    Theory: That people with HFA have difficulties orienting attention and that this problem is associated with underlying structural and functional brain abnormalities.

    Objectives: To investigate brain activity and connections between brain regions in HFA during performance of psychological tasks. To relate brain activity and connectivity to brain structure.

    Methods: Computer-based psychological tasks will be administered to a group with HFA and controls. Neuroimaging techniques will detect differences in brain activation and brain structure between the groups during these tasks.

    Likely outcomes: During the psychological tasks, we expect children with HFA to have performance difficulties and abnormal brain activity. We anticipate that abnormal brain activity will occur in areas of the brain that are structurally abnormal.

  • Computer Science
    Compute
    C
    Prof. Vincent Wade
    Trinity College Dublin
    Latent Dirichlet Allocation (LDA) is a generative probabilistic model for uncovering the underlying semantic structure of a text corpus. Topic models work off the assumption that documents are made up from mixtures of topics, where each topic is defined as a distribution over words. The problem is modeled using a three-level hierarchical Bayesian approach and is solved using Gibbs sampling methods as exact inference is intractable. In the Author-Topic model, authorship information is also taken into account; where each author is associated with a multinomial distribution over words in the vocabulary. Authorship information is neatly incorporated into the standard topic model by using some additional inference (the additional computational overhead being low). Experiments were conducted on message forum data from a well-known website which consisted of ~50,000 authors and ~60 million words. All calculations are optimised for parallel CPU execution on facilities provided by TCHPC.Eamonn is also involved in the application of deep belief networks to large text corpora and accelerating the training time of such networks using GPUs.
  • Physics
    Dedicated human Support
    C
    Prof. Stefano Sanvito
    Trinity College Dublin
    The design, implementation and hosting of a group website to assist in the presentation of data and work. This is helpful in the distribution of data and software to interested parties, including the SFI review team.
  • Mathematics
    Compute
    C
    Dr. Mike Peardon
    Trinity College Dublin
    This project is concerned with Linear Algebra on GPU with CUDA, and forms part of Lattice QCD research at TCD. 3D Lattice data is supplied, including periodic boundary conditions, producing Hermitian Matrices with sizes in the 10,000s (24x24x24). The goal is to use the GPU to efficiently calculate the lowest modes of the matrices and their corresponding eigenvectors (100s).This will involve implementing the Lanzcos algorithm for sparse matrices in CUDA.
  • Life Sciences
    Compute
    C
    Dr. Jan de Vries
    Trinity College Dublin
    This is an fMRI project on Cognitive Dissonance. The objective of the programme is to identify the neural substrate of cognitive dissonance. In a 2x2 baseline design dissonance will be induced in participants in the experimental condition. The control conditions should not generate dissonance It is hypothesised that only the experimental condition will lead to combined activation of anterior cingulated cortex and pre frontal lobe.
  • Chemistry
    Dedicated human Support
    B
    Dr. Mark Brown
    Trinity College Dublin
    University of Edinburgh
    Host-parasite interactions are among the most dynamic interactions in the biological world. This project will utilise both parasitological and molecular techniques to examine the natural host-parasite interaction of the bumblebee, Bombus terrestris Linnaeus (Apidae) and the nematode, Sphaerularia bombi Dufour (Tylenchida), at the gene expression level. S. bombi is unique in that it infects overwintering queens, with one of its main pathological effects being the castration of the host. In addition, the parasite manipulates the immune system and behaviour of the host. Using molecular and transcriptomic techniques, the main aim of this study is to identify genes, both in the host and parasite, that have an altered gene expression during a host-parasite interaction. In addition, reference transcriptomes for the life stages of both the bumblbee and nematode will be generated to provide genetic support for the analysis of the host-parasite interaction. The results of the study will provide a novel insight into the interaction at the genetic level of both the host and parasite, as well as improving our knowledge of the two organisms as a whole.

Last updated 01 Sep 2014Contact TCHPC: info | support.