UCD Search

Supervisor: Dr. James Rice
Optical microscopy is an important and widely used method for studying (soft) condensed matter. The resolution of optical microscopy is however limited by diffraction to imaging in the visible region of the electromagnetic spectrum to length scales >100 nm. As a consequence, present optical microscopy technology cannot image the many structures and (quantum) processes that occur on the nanoscale, which requires an image resolution of one hundred nanometres or less. Metamaterial based optics enables imaging without a theoretically unlimited resolution in the far-field. Metamaterial optics restore evanescent waves and project sub-diffraction-limited images in wide-field. The application of this metamaterial-based technology to demonstrate optical imaging is a current research goal.
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Supervisor: Dr. James Rice
Scanning near-field microscopy provides an optical resolution beyond the diffraction limit of conventional microscopy. Scanning near-field optical absorption imaging is based on the collection of scattered electromagnetic radiation via the near-field positioned aperture. Due to the elastic light scattering mechanism and the complex dielectric value of the sample recovery of precise absorption information is challenging. Combining atomic force microscopy and optical mythology is an alternative method to performing sub-wavelength absorption imaging. To date this approach has enabled a resolution of lambda/150. Developing and applying such mythology will enable detailed information of nanoscale optical processes and structure to be performed.
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Supervisor: Dr. John Quinn
Applications are invited for an SFI-funded Ph.D. position in gamma-ray astronomy with the High Energy Astrophysics group. The group has a long history in ground-based gamma-ray astronomy and pioneered the imaging atmospheric Cherenkov technique with the Whipple collaboration. The group is a founding member of the Very Energetic Radiation Imaging Telescope Array System (VERITAS) collaboration, which currently operates an array of four 12m telescope for TeV gamma-ray astronomy in southern Arizona. The project will be to utilise data from NASA’s Fermi Gamma-ray Space Telescope, which operates in the 100 MeV to 300 GeV energy range, and VERITAS, which operates in the 100 GeV to 50 TeV energy range, to study the blazar class of Active Galactic Nuclei. Combined with observations at other wavelengths, the broadband spectra of these objects will be measured and compared to theoretical models. Through searching for evidence of energy-dependent absorption in the gamma-ray spectra of blazars at different redshifts, constraints will be placed on the intensity of the extragalactic background radiation field in the infra-red regime. The Ph.D. position is funded for four years with an annual stipend of EUR16,000 and annual fees of EUR5,500. Travel to the site of the VERITAS observatory in Arizona to participate in the observing and telescope maintenance/calibration programs, possibly for extended periods, is mandatory. The candidate is expected to have a good (upper second-class honours or first-class honours) primary degree in Physics or a cognate subject, and to have strong problem-solving, analytic, and computer skills. Applicants should submit a CV including details of academic history and the contact details of two referees to Dr. John Quinn.
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Supervisor: Dr. Vio Buchete
The development of coarse-grained interaction potentials is an active area of research in computational molecular biology and structural bioinformatics. Accurate coarse-grained modeling methods will likely lead to simulations that can go beyond the studies of fast and local events, enabling the study of slow, non-local conformational rearrangements in biomolecules. Such approaches will enable large-scale, genomic-wide studies of biomolecular structure, dynamics and interactions. Coarse-grained modeling efforts of proteins and protein-protein interactions have included system-specific information(e.g., native state information in a Go-like manner). Physics-based, transferable models have recently been developed, yet they are relatively complex and their efficiency is still under testing. Alternatively, statistical analysis methods were used to derive parameters for new distance and orientation-dependent potentials from protein structural databases, a major advance over earlier approaches that included only inter-residue distances. This project will systematically advance the development of coarse-grained potentials by comparing and combining the complementary information offered by these two approaches. The project can be funded under Simulation Science structured PhD programme (see above).
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Supervisor: Dr. Vio Buchete
Key to the success of a multiscale approach in molecular simulations is that information is exchanged accurately and efficiently between the layers of resolution. Preliminary results from large sets of molecular dynamics (MD) trajectories that sample exhaustively the conformational space of short peptides provided a quantitative measure of the limits imposed by the intrinsic information loss that occurs when switching from an atomistic to a coarse-grained representation. Even for a simple two-state mapping of the conformational space of a single residue in a peptide (e.g., helix-coil), various types of transition paths can occur. Therefore, even for short peptides, the dimensionality and complexity of the simplest nearest-neighbor kinetic model can be large, and the full, accurate structure of even a coarse-grained transition rate matrix can be very difficult to estimate. This project will advance the recently developed master equation-based methods for analysis of molecular simulations for finding the simplest yet accurate coarse-grained representation of a system, and the corresponding kinetic pathways. Methodologically, these studies are important because the knowledge of the accurate coarse-grained kinetic pathways can be used to drive atomic-level MD algorithms, leading to faster, larger scale simulations and to more accurate kinetic analysis methods. The project can be funded under Simulation Science structured PhD programme (see above).
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Supervisor: Dr. Vio Buchete
Amyloid fibrils are of outstanding interest as they are associated with a wide variety of diseases, including Alzheimer's, Parkinson's, Huntington's, prion diseases, and diabetes, and also with new types of nano-materials. The detailed structural characterization of these self-assembled structures is a central step toward the understanding of the mechanism leading to the formation and stability of ordered, fibrillar aggregates. This project will study the effect of the environment (e.g., hydrophobic/ hydrophilic interfaces or molecular crowding agents) on the kinetic and thermodynamic properties of peptide folding and aggregation. Based on atomically detailed, explicit solvent, MD simulation of Alzheimer's amyloid fibrils, we will perform coarse-grained simulations of fibrils that would permit the study of more realistic, larger fibril segments. The new residue-level models would incorporate structural details revealed by all-atom simulations and by experiments (e.g., solid state NMR). Applications range from the study of fibril nucleation/growth inhibitors (i.e., potential drugs) to the control of amyloid formation and to the design and development of new types of nanomaterials. The project can be funded under Simulation Science structured PhD programme (see above).
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Supervisor: Dr. John Quinn
The High Energy Astrophysics group is involved in the study of the extreme universe; gamma-ray astronomy allows us to probe sites of particle acceleration in nature at energies well beyond those achievable in accelerators on the Earth. The group in a founder member of the VERITAS collaboration, which has constructed, and is now operating, an array of four 12m telescopes, located in the Arizona desert, for gamma-ray astronomy above 100 GeV. By combining the VERITAS data with data from satellites at X-ray and MeV-GeV gamma- ray energies,we can learn much about the acceleration and emission mechanisms in objects such as supernova remnants, binary systems, gamma-ray busts, and the jets from active galactic nuclei. Upcoming PhD opportunities in the group include the observational study of both galactic and extragalactic objects with VERITAS, the analysis of multiwavelength data from other observatories/satellites, and the modelling and interpretation of the results. For more information see http://ferdia.ucd.ie/
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Supervisor: Dr. Dominic Zerulla
Since 2001, there has been an explosive growth of scientific interest in the role of plasmons in optical phenomena, including guided-wave propagation and imaging at the subwavelength scale, nonlinear spectroscopy and negative index metamaterials. Building on our extensive experience in the field of plasmonics, in this project we are extending our research to the direction of ultrafast plasmonics. Tailor designed RUNs (Resonant Ultrafast Structures) will be developed using a combination of PVD (Physical Vapour Deposition) and FIB (Field Ion Beam) technologies, available in house. In this project, in combination with a state of the art ultrafast laser source (10 fs), measurement and imaging techniques such as, PEEM (Photo-Emission Electron Microscopy), FROG (Frequency Resolved Optical Gating), SPIDER (Spectral Phase Interferometry for Direct Electric-field Reconstruction), s-SNOM (scattering Scanning Near-Field Optical Microscopy), will be employed to investigate Surface Plasmon dynamics on the RUNs at femtosecond timescales and nanometer spatial resolutions. In addition to the experimental characterisation, computational analysis will be carried out using Greens functions and finite element methods.
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Supervisor: Dr. Dominic Zerulla
Currently, plasmonics is a cutting edge, enthusiastic and quickly growing field of research that offers seemingly endless research opportunities [e.g. Science, 189, 311, 2006, Phys. Rev. Lett. 98, 133901, 2007]. It has already presented important influences in varied fields of research, from bio-analysis and sensors to magneto-optics and nano-manipulation. At the very heart of this field is fundamental research on Surface Plasmon Polaritons (SPPs) - mixed states of photons and electron density waves which propagate along the surface of a conductor. This project introduces a new degree of freedom into the field of plasmonics: the electron spin. We will initiate a novel opto-electronic technology platform for information processing and data storage based on Plasmonic and Spintronic (Spin Electronic) concepts. This new hybrid field is referred to as Spin-Plasmonics. Techniques including, MPMS (Magnetic Property Measurement System), high magnetic field cryogenic temperature spectroscopy, MFM (Magnetic Force Microscopy), PEEM (Photo-Emission Electron Microscopy), will be employed to investigate the Surface Plasmon dynamics on Multilayer magneto-active structures.
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Supervisor: Dr. Dominic Zerulla
Two PhD positions are available in the advanced photovoltaic fields of dye sensitised solar cells and II-VI nanorod solar cells. Excitonic solar cells - including organic, hybrid organic-inorganic and dye-sensitized cells (DSCs) - are promising devices for inexpensive, large-scale solar energy conversion [e.g. Nature Materials 4, 455 - 459 (2005)]. DSCs are currently the most efficient and stable excitonic photocells. Central to this device is a thick nanoparticle film that provides a large surface area for the adsorption of light-harvesting molecules. Nanorod solar cells generate new degrees of freedoms in the design of photovoltaic devices. By controlling nanorod parameters, the distance over which electrons are transported directly through the thin film device can be modified. Tuning the band gap by altering the nanorod radius enables optimization of the overlap between the absorption spectrum of the cell and the solar emission spectrum. The PhD students will have the responsibility of designing new cell types, and to optimise their efficiency using (e.g.) laser spectroscopy and a variety of imaging techniques (SEM, PEEM, AFM) in order to control the cell development progress. The candidate must be self motivated, willing and capable to work both independently and as part of a team. The candidate must have received (or anticipate receiving) a 1st or upper 2nd class honours degree in Physics, Material Science or a suitable Engineering discipline.
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Supervisor: Dr. Vladimir Lobaskin
In medicine, simulations of particle motion near nanostructured surfaces are stimulated by studies of blood clotting, thrombosis, or in-stent restenosis phenomena. In particular, one of the serious issues caused by introduction of vascular devices is an inflammatory response determined and mediated by platelet attachment, aggregation, signalling and the recruitment of leucocytes. The coagulation cascade leading to the thrombus or clot formation is extremely complex and occurring on long timescales (seconds or minutes). At the same time, in a number of numerical studies it has been shown that the reactions have threshold character in terms of concentration of binding agent and flow rates, and the initiation of the cascade strongly depends on the early stages of the platelet attachment process. This project will address the attachment kinetics of nanoscale bodies at various interfaces under flow and have implications for design of biomimetic coatings for medical implants. The project can be funded under Simulation Science structured PhD programme (see above).
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Supervisor: Dr. Vladimir Lobaskin
A number of challenges in modern bio-nanotechnology and medicine require a quantitative modeling of dynamics of nanostructured surfaces (the most prominent example being the blood flow past endothelium). The typical questions arising there are development of nanoparticle or virus-based high-precisicion drug delivery techniques and gene therapy, estimation of biological risks related to nanoparticles, etc. Theoretical progress on these directions requires understanding of systemic transport of nanoobjects including natural or synthetic nanoparticles and viruses as well as transfection mechanisms of various antibodies into a cell. The minimal setup for quantifying the nanoparticle transport past the cell membrane includes the blood, the particle and the endothelial interface themselves. The main task for the PhD researcher in this project will be to prepare a coarse-grained simulation model for studying dynamics of biointerfaces such as endothelial glycocalix or cell membrane and their protective function, based on the results of MD simulation of relevant biomolecules. The project can be funded under Simulation Science structured PhD programme (see above).
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Supervisor: Dr. Brian Vohnsen
The Advanced Optical Imaging group at UCD invites applications for PhD in optics and optical imaging down to the nanoscale. The opportunities will be available continuously through self-funding, ircset grants or DGPP (see above). For more information please contact Dr Brian Vohnsen.
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Supervisor: Prof. David.Coker
Theoretical and computational methods and models will be developed and applied to study excitation energy transfer in photosynthetic light harvesting chromophore arrays. In these systems excitons apparently move in coherent multichromophore quantum superposition states, and with essentially no energy loss over large distances to efficiently deposit their energy into reaction centres where transformation and storage are initiated. Experiments suggest that this lossless energy transmission is due to correlated motions of the nanostructured protein scaffolding in which the chromophores are embedded. Large-scale classical simulations of these systems will be carried out to parameterize multistate quantum system - bath models whose coherent quantum dynamics can be studied with recently developed mixed quantum-classical methods. The project can be funded under Simulation Science structured PhD programme (see above).
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