PhD and Postdoctoral Opportunities

Postdoctoral opportunities in the UCD School of Physics 

Continuous Reel to Reel Manufacturing of Nanoscale Patterned Aligned Carbon Nanotube Arrays - CORE- VANTA

Supervisor: Associate Prof. Dominic Zerulla

Applications are invited for the position of Postdoctoral Fellow in the Plasmonics and Ultrafast Nanooptics group. This is a two year, fixed term contract based at the School of Physics, UCD. 

PhD opportunities in the UCD School of Physics (for further details contact the PI).

  1. Observational Astrophysics (Morgan Fraser)
  2. Star Formation (Deirdre Coffey) 
  3. Single Quantum Dot imaging (James Rice)
  4. Plasmon enhanced bio-imaging (James Rice)
  5. Transferable coarse-grained potentials for studies of proteins, nucleic acids and their interactions (Vio Buchete)
  6. Methods for multiscale biomolecular simulations (Vio Buchete)
  7. Molecular studies of amyloid fibrils and aggregation (Vio Buchete)
  8. Very High Energy Gamma-Ray Astronomy of Galactic and Extragalactic Gamma-Sources (John Quinn)
  9. Ultrafast Plasmonics (Dominic Zerulla)
  10. Spin-Plasmonics (Dominic Zerulla)
  11. Novel Solar Cell Concepts (Dominic Zerulla)
  12. Social Physics: Modelling collective behaviour (Vladimir Lobaskin)
  13. Multiscale modelling of biointerfaces (Vladimir Lobaskin)
  14. Advanced optical imaging and biophysical applications (Brian Vohnsen)


Observational Astrophysics

SupervisorDr. Morgan Fraser

Applications are invited for PhD positions in observational astrophysics, working on supernovae and massive stars. Projects will entail using observational data from world-class observatories to understand the final stages in the life of a massive star. Stars above about 8 solar masses will end their lives with a spectacular explosion, as a core-collapse supernovae. These supernovae inject heavy elements and energy into galaxies, trigger star formation, and provide the building blocks of future stars and planets. However, many aspects of supernovae remain uncertain -  including what type of stars explode, whether some collapse to form a black hole without a bright optical transient . Students will use data from a range of telescope facilities obtained through the PESSTO and NUTS collaborations to understand these fascinating events. Funding opportunities are available through IRC and other grants. For further details, please contact Dr. Morgan Fraser (morgan.fraser@ucd.ie)


Star Formation

SupervisorDr. Deirdre Coffey 
Applications are invited for PhD and postdoctoral positions in the area of Star Formation. Young stars are born via the gravitational collapse of a cloud of dust and gas into a stellar core where fusion begins. Any initial rotation of the cloud causes a circumstellar disk to form which becomes the building site for planets. Meanwhile, bizarrely, astronomers also observe high velocity bipolar jets being ejected from these young stars. The complex mechanisms involved in star and planet formation remain a mystery. Applications are invited to work on the interpretation of observations from world-class telescopes of young stellar objects, their disks and jets/outflows. PhD and postdoctoral opportunities are available continuously through self-funding IRC grants.

Single Quantum Dot Imaging 

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. 

Novel optical near-field imaging methodology

SupervisorDr. 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.

Transferable coarse-grained potentials for studies of proteins, nucleic acids and their interactions

SupervisorDr. 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. 

Methods for multiscale biomolecular simulations

SupervisorDr. 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. 

Molecular studies of amyloid fibrils and aggregation

SupervisorDr. 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. 

Very High Energy Gamma-Ray Astronomy of Galactic and Extragalactic Gamma-Sources

SupervisorDr. 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 bursts, 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/ 

Ultrafast Plasmonics

SupervisorDr. 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. 


SupervisorDr. 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. 

Novel Solar Cell Concepts

SupervisorDr. 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. 

Social Physics: Modelling Collective Behaviour

SupervisorDr. Vladimir Lobaskin 
Since two decades scientists have been successfully using physical models for describing collective behaviour of living organisms. Such was the theory of flocking by Tamas Vicsek that explored the analogy between alignment of magnetic dipoles and flying birds. The success of social physics is based on the fact that many macroscopic properties of large groups are independent of the microscopic, individual details of the active agents. This allows us to develop generic models of collective behaviour that imitate an enormous range of phenomena from collective cell migration to human opinion dynamics or car traffic. The degree of collectivity is then analysed by methods of none-equilibrium and equilibrium statistical physics. This PhD project is theoretical and will involve developing theory and computer simulations of social systems to study interactions, polarisation, and opinion dynamics.

Multiscale modeling of biointerfaces

SupervisorDr. Vladimir Lobaskin 
Modern biotechnology and medicine have been developing fast and exploiting novel advanced materials. Personalised medicine involving lab-on-a-chip devices, medical imaging and diagnostics using nanoparticles, sensors, implants and food processing units involve sophisticated surface modification and depend on our understanding of the bionano interface – the nanoscale layer where engineered materials and biomolecules come in contact. Moreover, understanding of the bionano interface is required for assessment of toxicity of industrial nanomaterials like carbon nanotubes. In our lab, we develop computational methods for modelling bionano interface and prediction of interactions between biomolecules and foreign materials. We lead a European consortium SmartNanoTox working on nanomaterial toxicity assessment and collaborate with biologists, medics and chemists across Europe. The PhD researcher working on this project will join a team developing multiscale modelling techniques based on statistical physics, bioinformatics and biophysics to predict the safety of biomaterials. 

Advanced optical imaging and biophysical applications

SupervisorDr. 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. For more information please contact Dr Brian Vohnsen.