David Fallaize Email & Phone Number

United Kingdom

London

London, England, United Kingdom

London, United Kingdom

All life is based on the interactions between biological molecules (e.g. proteins, nucleic acids), which in human cells coexist in a complicated and crowded mixture. It is extremely difficult to directly measure the interactions between individual biomolecules in the lab because of the very small length-scale and short time-scale over which these processes occur. Computer simulations which model these interactions can improve our understanding and suggest avenues for further experiment. With increased knowledge of how biomolecules interact comes better understanding of what happens in illnesses where biomolecules misbehave, and ultimately leads to progress in medical science and the treatment of disease.In order to carry out large-scale simulations, we need to be able to calculate the electrostatic force between proteins (like that between a positive and negative charge). This can be found by solving the Poisson-Boltzmann Equation (PBE), but unfortunately the process is generally non-trivial.I have written a program which solves the linearised PBE using the "boundary element method" (BEM) with a linearly-scaling fast multipole method (FMM) . I improved and parallelised these highly complex algorithms, using a number of open source tools and libraries along the way (e.g. Boost, OpenCL, OpenMP). My PBE solver now runs on both desktop computers and HPC clusters, and uses GPUs to accelerate the near-field integration terms of the BEM.Our results of running my solver on proteins show that the stability and numerical accuracy of the combined BEM/FMM method is extremely sensitive to the choice of surface representation and integration method. I used a curved triangulated surface to improve numerical stability and accuracy, and conclude that it is practicable to use the total electrostatic solvation energy to drive a Monte-Carlo simulation of protein-protein interactions.

Worked as part of the IT team on diverse projects including: website development and maintenance; database design; integration of our systems with those of our clients and partners; CMS/document management using VB/VBA; automatic document classification using latent semantic analysis.

Cambridge, United Kingdom

I worked as a Summer intern on firmware/USB driver for an embedded system (electronic roulette).

Enfield, United Kingdom

As a Summer intern I implemented a test suite for the BGP network protocol (written in C).

Doctor Of Philosophy (Ph.D.), Computational Biophysics

Mres, Modelling Biological Complexity

Meng, Engineering

Activities and Societies: Rowing in the men's 4th boat - obtained two sets of spoons!Downing College