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A new publication by PhD student Nicolas Jaccard
- CoMPLEX PhD student Nicolas Jaccard has recently published an article on the journal Biotechnology and Bioengineering
CoMPLEX Deputy Director in Bloomsbury Festival and Lunch Hour lecture
Dr. David Fallaize
In my PhD thesis, I presented a linearised PBE solver called the “Boundary Element Electrostatics Program” (BEEP). BEEP is based on the Boundary Element Method (BEM), in combination with a recently developed O(N) Fast Multipole Method (FMM) algorithm which approximates the far-field integrals within the BEM, yielding a method which scales linearly with the number of particles. BEEP improves on existing methods by parallelising the underlying algorithms for use on modern cluster architectures, as well as taking advantage of recent progress in the field of GPGPU (General Purpose GPU) Programming, to exploit the highly parallel nature of graphics cards.
We found the stability and numerical accuracy of the BEM/FMM method to be highly dependent on the choice of surface representation and integration method. For real proteins we demonstrate the critical level of surface detail required to produce converged electrostatic solvation energies, and introduce a curved surface representation based on Point-Normal G1-continuous triangles which we find generally improves numerical stability compared to a simpler surface constructed from planar triangles. Despite our improvements upon existing BEM methods, we find that it is not possible to directly integrate BEM surface solutions to obtain intermolecular electrostatic forces. It is, however, practicable to use the total electrostatic solvation energy calculated by BEEP to drive a Monte-Carlo simulation.
Current Employment: Software Developer at Gloucester Research, London.
Page last modified on 19 nov 12 13:52