Methods
Cell processor: the case study of molecular dynamics
The Cell broadband engine is a new processor architecture created by Sony-Toshiba-IBM\cite{ibmcellsite} which allows for high computational performance and low production costs removing, by design, many important bottlenecks of standard processors. In the present version, it comprises one simplified power PC core (PPE) which runs the operating system and acts as a standard processor and 8 independent synergetic processing elements (SPEs). Main memory can be accessed only by the PPE core while each SPE can use its limited in-chip local memory (local store) accessed directly without any intermediate caching. This architectural design removes the memory bottleneck which is afflicting modern processors and furnishes a direct way to improve performance by adding more SPEs without having to rely only on clock frequency. Each core (PPE or SPEs) features a single instruction multiple data (SIMD) vector unit which gives a combined peak performance of around 230 Gflops at 3.2Ghz. I have looked at the important application case of molecular dynamics. G. De Fabritiis, Performance of the Cell processor for bio-molecular simulations, preprint (2006). pdf
Hybrid molecular dynamics (MD) - fluctuating hydrodynamics (FH)
Hybrid MD is a multiphysics (multiscale) coupled model between molecular dynamics (MD) and a continuum representation of a mesoscale fluid resolved by fluctuating hydrodynamics (FH). This very power technique allow simulation of large time and length scales keeping the molecular specificy in a sub-domain of the entire system (for instance a boundary condition). The two models MD and FH are separate executables which can be deploied on different computational resources but interface on-the-fly by exchanging momentum and mass. The coupling protocol requires to mantain a open MD system which is made possible by new algorithms of molecule insertion. G. De Fabritiis, R. Delgado-Buscalioni and P. V. Coveney, Modelling the mesoscale with molecular specificity, in press Phys. Rev. Lett. (2006). pdf
Insertion of polar molecules in dense liquids
Insertion of a water molecule in the hydrogen bond network of bulk water. The local structure of liquid water at equilibrium presents a hydrogen bond network formed by oxygen and hydrogen atoms of neighbouring water molecules. This configuration makes it very hard for an incoming water molecule to find low energy configurations. We demonstrate a novel method to insert efficiently water molecules in aqueous environment.
G. De Fabritiis, R. Delgado-Buscalioni and P. V. Coveney, Energy controlled insertion of polar molecules in dense fluids, J. Chem. Phys. 121, 12139 (2004). Selected for the Virtual Journal of Biological Physics Research, December 15, 2004 Volume 8, Issue 12. pdf
Stochastic integration methods for mesocopic models
- The efficient simulation of models defined in terms of stochastic differential equations (SDEs) depends critically on an efficient integration scheme. We investigated under which conditions the integration schemes for general SDEs can be derived using the Trotter expansion. It follows that, in the stochastic case, some care is required in splitting the stochastic generator. We also derive a new numerical scheme for dissipative particle dynamics and furnish the DPD code for it.
Applications
A model of membrane channels: Gramicidin A
Gramicidin A channel solvated in a DMPC lipid membrane (not shown).
- The permeation of ions in protein channels is important to control cell activity. However, a direct measurement of the conductivity via molecular simulations is not possible because the time scales involved are too long (micro-milli seconds). Rather, the potential of mean force (PMF) of the crossing is computed and the conductance estimated from it. We are currently looking at a simple non-equilibrium method to compute the PMF which is based on the Crooks non-equilibrium relation [Phys. Rev. E 61 2361 (2000)] over the Gramicidin A membrane protein. The equilibrium PMF is reconstructed from a set of controlled non-equilibrium pullings of ions trough the channel. This procedure also allows to compute the position dependent diffusion coefficient.
Computing
I make use of supercomputing facilities in UK, US and Spain. Some of the Grid middleware used is provided by the RealityGrid project (http://www.realitygrid.org) in particular the computational steering framework and the application hosting environment (AHE). I am part of the infrastructure group of the Integrative Biology project (http://www.integrativebiology.ox.ac.uk) and a coordinator of the ICT panel of the STEP EU project: A road map towards the Europhysiome (http://www.europhysiome.org).
Coupled models on distributed resources
I have previously participated to this e-science grid computing project in UK http://www.integrativebiology.ox.ac.uk.
Multi-scale modeling of physical systems is often employed to enable an accurate but computationally expensive model to be applied to regions of a system where it is required while a less accurate model can be used elsewhere. This enables far larger systems/longer timescales to be modeled than can be tackled using the accurate model alone. A coupled model could be written as a single executable code, but for flexibility, scalability and ultimately, performance reasons, we consider the case of a coupled model constructed from independent components which are interfaced to allow them to exchange information. These components are then free to be deployed in such a way as to make the best use of available resources; particularly important in a Grid environment. Hybrid molecular dynamics is a very good candidate for this kind of deployment. (Presentation [PDF])