Coauthored Publications
Below are a number publications where the involvement of ICHEC staff members has lead to their inclusion as coauthors.
| Title: | Transitioning a message passing interface wavefront sensor model to a graphics processor environment |
| Authors: | Michael T. Browne, Renato Miceli, 2011 |
| Abstract: | Previous work produced a parallel and moderately scalable wavefront sensor model as part of a larger integrated telescope model. This relied on traditional high performance computing (HPC) techniques using optimised C and MPI based parallelism to marry maximum performance with the productive high-level modelling environment of MATLAB. In the intervening period the computational power and flexibility offered by graphics processors (GPUs) has increased dramatically. This presents both new options in terms of the level of hardware required to perform simulations and also new capabilities in terms of the scope of such simulations. We present a discussion of the currently available approaches and test case performance results based on a port to a GPU platform. |
| ICHEC Project: | |
| Publication: | Integrated Modeling of Complex Optomechanical Systems, Proceedings Vol. 8336, DOI: 10.1117/12.915921 |
| URL: | http://dx.doi.org/10.1117/12.915921 |
| Keywords: | GPU MATLAB Wavefront sensor |
| Status: | Published |
| Title: | The Eyjafjallajökull ash plume – Part 2: Simulating ash cloud dispersion with REMOTE |
| Authors: | C. O'Dowd, S. Varghese, D. Martin, R. Flanagan, A. McKinstry, D. Ceburnis, J. Ovadnevaite, G. Martucci, J. Bialek, C. Monahan, H. Berresheim, A. Vaishya, T. Grigas, Z. McGraw, S.G. Jennings, B. Langmann, T. Semmler, R. McGrath, 2011 |
| Abstract: | The recent eruption of Iceland's Eyjafjallajökull volcano caused extensive disruption across Europe. In this paper, we describe the volcanic ash parameterisation incorporated in the regional climate model (REMOTE) for forecasting volcanic ash dispersion. We investigate model sensitivity to emission parameters including eruption column height and vertical release distribution. Model results over a number of key ash incursion events are assessed in terms of agreement with both ground based measurements and retrieved LIDAR data at a number of European sites. |
| ICHEC Project: | |
| Publication: | DOI:10.1016/j.atmosenv.2011.10.037 |
| URL: | http://www.sciencedirect.com/science/article/pii/S1352231011011113 |
| Keywords: | Volcano, Ash, REMOTE, Eyjafjallajokull; Volcanic ash; Dispersion; Modelling |
| Status: | Published |
| Title: | The impact of Arctic sea ice on the Arctic energy budget and on the climate of the Northern mid- latitudes |
| Authors: | Tido Semmler, Raymond McGrath, Shiyu Wang, 2012 |
| Abstract: | The atmospheric general circulation model EC-EARTH-IFS has been applied to investigate the influence of both a reduced and a removed Arctic sea ice cover and therefore a reduced meridional temperature gradient on the climate of the Northern mid-latitudes. Three 40-year simulations driven by original and modified ERA-40 sea surface temperatures and sea ice distributions have been performed at T255L62 resolution, corresponding to about 50 km horizontal resolution. Simulated changes between sensitivity and reference experiments are most pronounced over the Arctic itself where the reduced or removed sea ice leads to strongly increased upward heat and longwave radiation fluxes and precipitation in winter. In summer, the most pronounced change is the stronger absorption of shortwave radiation which is enhanced by optically thinner clouds. Averaged over the year and over the area north of 70° N, the negative energy imbalance at the top of the atmosphere decreases by about 10 W/m2 in both sensitivity experiments. The energy transport across 70° N is reduced as a result of the decreased temperature gradient. Changes are not restricted to the Arctic. A weaker pressure gradient, less extreme cold events and less precipitation are simulated in sub-Arctic and Northern mid- latitude regions in winter |
| ICHEC Project: | Simulating the Global Climate with the EC-EARTH Coupled Atmosphere-Ocean-Ice Model |
| URL: | http://ecearth.knmi.nl/Semmleretal.pdf |
| Keywords: | climate, EC-EARTH |
| Status: | Submitted |
| Title: | EC-EARTH: A seamless earth system prediction approach in action |
| Authors: | Hazeleger, W., Severijns, C., Semmler, T., Stefanescu, S., Yang, S., Wang, X., Wyser, K., Baldasano, J. M., Bintanja, R., Bougeault, P., Caballero, R., Dutra, E., Ekman, A. M. L., Christensen, J. H., van den Hurk, B., Jimenez, P., Jones, C., Kallberg, P., Koenigk, T., McGrath, R., Miranda, P., van Noije, T., Parodi, J. A., Schmith, T., Selten, F., Storelvmo, T., Sterl, A., Tapamo, H., Vancoppenolle, M., Viterbo, P., and Willen, U., 2010 |
| ICHEC Project: | Simulating the Global Climate with the EC-EARTH Coupled Atmosphere-Ocean-Ice Model |
| Publication: | Bulletin of the American Meteorological Society, |
| URL: | http://www.ametsoc.org/PUBS/bams/ |
| Status: | Published |
| Title: | A prediction of cell differentiation and proliferation within a collagen-glycosaminoglycan scaffold subjected to mechanical strain and perfusive fluid flow |
| Authors: | AJF Stops, KB Heraty, M Browne, FJ O’Brien, PE McHugh, 2010 |
| Abstract: | scaffold strain magnitudes and inlet fluid velocities to specific cell responses are thus far underdeveloped. This investigation attempted to simulate cell responses in a collagen–glycosaminoglycan (CG) scaffold within a bioreactor. CG scaffold deformation was simulated using μ-computed tomography (CT) and an in-house finite element solver (FEEBE/linear). Similarly, the internal fluid velocities were simulated using the afore-mentioned μCT dataset with a computational fluid dynamics solver (ANSYS/CFX). From the ensuing cell-level mechanics, albeit octahedral shear strain or fluid velocity, the proliferation and differentiation of the representative cells were predicted from deterministic functions. Cell proliferation patterns concurred with previous experiments. MSC differentiation was dependent on the level of CG scaffold strain and the inlet fluid velocity. Furthermore, MSC differentiation patterns indicated that specific combinations of scaffold strains and inlet fluid flows cause phenotype assemblies dominated by single cell types. Further to typical laboratory procedures, this predictive methodology demonstrated loading-specific differentiation lineages and proliferation patterns. It is hoped these results will enhance in-vitro tissue engineering procedures by providing a platform from which the scaffold loading applications can be tailored to suit the desired tissue. |
| ICHEC Project: | A FINITE ELEMENT ANALYSIS OF THE MICROSCALE FORCES THAT DRIVE CELL-DERIVED TISSUE FORMATION: A TISSUE ENGINEERING SOLUTION |
| Publication: | Journal of Biomechanics, vol. 43, pp. 618-626, DOI: 10.1016/j.jbiomech.2009.10.037 |
| URL: | http://www.jbiomech.com/ |
| Keywords: | Collagen–glycosaminoglycan scaffold, Perfusion bioreactor, Tissue engineering |
| Status: | Published |
| Title: | Dispersion analysis and computational efficiency of elastic lattice methods for seismic wave propagation |
| Authors: | O'Brien G.S., Bean C.J. and Tapamo H., 2009 |
| Abstract: | Discrete particle methods or elastic lattice methods represent a 3D elastic solid by a series of interconnected springs arranged on a regular lattice. Generally, these methods only consider nearest neighbour interactions, i.e. they are first-order in space. These interconnected springs interacted through a force term (Hooke's Law for an elastic body), which when viewed on a macroscopic scale provide a numerical solution for the elastodynamic wave equations. Along with solving the elastodynamic wave equations these schemes are capable of simulating elastic static deformation. However, as these methods rely on nearest neighbour interactions they suffer from more pronounced numerical dispersion than traditional continuum methods. By including a new force term, the numerical dispersion can be reduced while keeping the flexibility of the nearest neighbour interaction rule. We present results of simulations where the additional force term reduces the numerical dispersion and increases the accuracy of the elastic lattice method solution. The computational efficiency and parallel scaling of this method on multiple processors is compared with a finite-difference solution to assess the computational cost of using this approach for simulating seismic wave propagation. We also show the applicability of this method to modelling seismic propagation in a complex Earth model. |
| ICHEC Project: | Seismic source modelling and wave propagation in volcanoes |
| Publication: | Computers & Geosciences (2009) 35:1768-1775 |
| URL: | http://dx.doi.org/10.1016/j.cageo.2008.12.004 |
| Keywords: | Computational seismic wave propagation; Discrete particle method; Elastic lattice method; Numerical seismic dispersion |
| Status: | Published |
| Title: | Spectrum of the non-abelian phase in Kitaev’s honeycomb lattice model |
| Authors: | Lahtinen V., Kells G., Carollo A., Stitt T., Vala J. and Pachos J.K., 2008 |
| Abstract: | The spectral properties of Kitaev's honeycomb lattice model are investigated both analytically and numerically with the focus on the non-abelian phase of the model. After summarizing the fermionization technique which maps spins into free Majorana fermions, we evaluate the spectrum of sparse vortex configurations and derive the interaction between two vortices as a function of their separation. We consider the effect vortices can have on the fermionic spectrum as well as on the phase transition between the abelian and non-abelian phases. We explicitly demonstrate the 2n-fold ground state degeneracy in the presence of 2n well separated vortices and the lifting of the degeneracy due to their short-range interactions. The calculations are performed on an infinite lattice. In addition to the analytic treatment, a numerical study of finite size systems is performed which is in exact agreement with the theoretical considerations. The general spectral properties of the non-abelian phase are considered for various finite toroidal systems. |
| ICHEC Project: | Topological phases in quantum lattice systems |
| Publication: | Annals of Physics (2008) 323:2286-2310 |
| URL: | http://dx.doi.org/10.1016/j.aop.2007.12.009 |
| Keywords: | Topological models; Non-abelian vortices; Kitaev's model |
| Status: | Published |
| Title: | Shoreline approximation for unstructured mesh generation |
| Authors: | G.J. Gorman, D. Piggott, and C.C. Pain, 2007 |
| Abstract: | A new method for approximating shorelines (polygons and polylines) is presented. The algorithm differs from commonly used Douglas-Peucker type algorithms as the method can approximate to some feature error given the constraint that edge lengths must satisfy some minimum edge length criteria. This constraint is necessary for the shoreline approximation to be useful for unstructured mesh generation for ocean modelling. In addition the method applies local optimisations to iteratively improve the shoreline approximation. Applications of the method are presented. |
| ICHEC Project: | Parallel unstructured adaptive mesh method for three-dimensional range-of-scale ocean modelling |
| Publication: | Computers & Geosciences, to appear |
| Keywords: | simplification; shoreline; mesh generation; ocean modelling |
| Status: | Accepted |