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Use this search facility to find out more about the profile of our HPC-Europa2 visitors, the type of work they have been doing, and their project achievements.
To develop models useful in many-body physics. While the model for solid HD is still under construction (a model including phonons, rotations, and their couplings is under way), here the question of polarized insulation in strongly correlated models was addressed via variational methods.
This project achieved the simple description of a metal-insulator transition (and metal-metal transitions away from half-filling) in which bound excitons play a key role. The metal-insulator transition in strongly correlated systems is in many ways still an open question. Variational wavefunctions (Baeriswyl and Baeriswyl-Gutzwiller projected wavefunctions) were studied via the well-known Gutzwiller ansatz applied in reciprocal space. The phase diagram was calculated resulting in a metal-insulator transition in which exciton binding plays the key role both in the metal-insulator transition at half-filling and the metal-metal transition away from half-filling. For the Baeriswyl-Gutzwiller projected wavefunction the transition occurs between a correlated metallic state of the Gutzwiller type and an insulator with bound excitons.
The main objective of the project was to develop an easy to use standalone C program capable of solving the bi-domain reaction-diffusion partial differential equations that describe electrical activity in the heart: where the Vm and Fe are the transmembrane and the extra-cellular potentials respectively, Iion is the current density flowing through the cell at location x, Iapp(x,t) is an applied stimulus current per unit area, b is a geometrical constant, Cm is the capacitance of the cell membrane, Di and De are conductivity tensors which is used to describe the anisotropic nature of the cardiac microstructure, x is the spatial position. The purpose of developing such a simple to use computational code was to facilitate in silico experimentation into the effects of electrolytes on human ventricular activity. The electrical activity cell models were proposed to be The recent Grandi et al. (GPB model) cell model along with a a novel variant of the GPB model to accurately simulate APs in mid-myocardial cells of the ventricular wall. The computational code was expected to be able to reproduce pseudo-ECG from first principles at run time as the volume integral. The complete model was aimed at large scale parameter sweep simulations where the effects of altered potassium concentration ([K+]o) on the ECG would be quantified. The simulations were expected to be in simplified 1D as well as whole ventricle simulations.
The achievements as a direct result of HPC Europa2 support can be enumerated as follows: a) completed and ongoing scientific studies; b) collaborative grant applications; c) novel software development.
a. Scientific studies: The code developed during the project was successfully used to elicit the effects of extracellular potassium on pseudo-ECG. As shown in Figure 1, the computational model can conclusively correlate extracellular potassium to the ECG. A compound measure, called TA, was defined and depends on ECG T wave amplitude and repolarisation slope. The simulations show that it is correlated to the [K+]o values. A relationship can potentially assist clinicians in eliciting information about plasma [K+]o levels in dialysis patients by means of a non-invasive ECG.
The applicant as well as the host are actively extending the 1D results to the 3D whole heart. As expected, the whole heart simulations are complex and require considerably more complex algorithms for efficient solvers and data management. The HPC Europa2 project allowed the applicant and host to form a collaboration with members of Bioengineering Group, KIT, Germany. Their ongoing efforts are to extend the above study to the whole heart. This study is ongoing and is expected to be complete in late 2013.
b. Collaborative grant application: In view of career development for the applicant, a collaborative grant application in the form of a 2 year personal fellowship (Inter-European Fellowship) is being prepared for submission in April-May 2013. The pilot data from this IEF application was obtained during and as a direct result of the HPC2 Europa project.
c. Novel software development: The knowledge gained during the visit has allowed the applicant to successfully contribute to ongoing efforts of developing an easy to use cardiac simulation environment. He has used his expertise in code development as well as demonstrating the efficacy as well as extensive applicability of the new codes. Indeed, the idea of developing a simple to use program is aligned with the ongoing software development project.
We planned to extend our previous work, in which we constructed 3D hydrodynamical and non-ideal magnetohydrodynamical (MHD) simulations of supernova driven turbulence in the interstellar medium. We have investigated the effect of radiative cooling and differential rotation on the hydrodynamics of galactic disks. We had begun production runs for a Grand Challenge project through CSC to investigate the properties of the galactic dynamo through SN driven turbulence and rotational shear.Arising from our MHD simulations, we have established additional collaboration with overseas members of LOFAR (European radio telescopic array) to simulate line of sight synchroton emissions for comparison with observations. Newcastle is a member of the UK LOFAR consortium ( http://lofar-uk.org/ ). Realistically motivated 3D simulations of the interstellar medium are of direct interest to many involved in the astronomical and astrophysical community. The primary objective of this visit was to analyse and visualise the data produced from our MHD production runs and to write up our results. Additional production runs were planned to further probe interesting parameters, which might include different levels of resistivity, density fluctuations typical of spiral arms or other galaxies or a range of rotation parameters. Our model consists of a local 3D model of the stratified, rotating ISM in the shearing box approximation. The system is driven by localised injection of thermal energy, modelling supernovae star (SNe) explosions. The expanding blast waves compress and heat the gas, resulting in a highly inhomogeneous, multiphase medium with temperature ranging from 1e2 to 1e8 Kelvin and density ranging from 1e-4 to 1e2 particles per cubic cm. Our standard grid separation is 4 parsecs (pc) a maximum permissible to adequately represent small scale effects. Our standard domain is 1x1x2 kpc a minimum requirement to model large scale structures. Our computing mesh is therefore about 256x256x512 or larger. The resources needed to conduct these simulations are typically 25000 cpu hrs per 100 Myr and we typically require over 250 Myr for each run. Our temporary data stored at present on louhi (CSC) is in excess of 2 Tb. These require 256 to 1024 parallel processors to execute. I for runs investigating the dynamo we anticipate needing to exceed 1Gyr for at least one run so runs will need to be of order 2 weeks+ duration.
Our reference run has extended to over 1Gyr and we have used this to start several other comparison runs. We have succeeded in finding a dynamo, with conditions which are marginally critical. (i.e. the conditions are only just sufficient to drive the dynamo) Although the growth of the dynamo is found to be sensitive to rates of rotation, shear and SNe all variants are producing growth in the magnetic field. From theory we expect the growth to end and the magnetic field strength to become quasi stable when the magnetic energy matches the kinetic energy density. At current growth rates we would expect this to require at least anoth 0.5Gyr.
To understand the dynamo we need to understand the velocity field. Due to the complexity of the results we are still analysing the data from the original non-magnetic runs. However we anticipate the submission of the first paper on the three phase structure of the interstellar medium, followed shortly by a paper on the vortical and helical structure of the ISM, which should give some insight into the structure of the dynamo from our latest simulations.
Previous simulations of the interstellar medium have either not included magnetic fields or have been unable to identify a dynamo with parameters typical of the ISM in the solar neighbourhood, despite compelling evidence from observations that the strength of the magnetic field is hard to explain in the absence of such a dynamo. Understanding the process by which this dynamo is effective may be a significant step in understanding the dynamo in general astrophysical structures.