Large Scale Lattice Boltzmann for Biocolloidal Systems


Grant number: EP/I034661/1
Grant duration: 01-OCT-2011 to 30-SEP-2014
Funding agency: EPSRC
Monetary value: £519,283
CCS members: Rupert Nash

Many of the most important structural components of biological materials exist on length scales of nanometres to microns. Examples include long polymers (such as DNA or flexible proteins), compact objects such as globular proteins (either in isolation or in structured assemblies such as the body of a virus); and lipid bilayer membranes (such as the walls that enclose the cells in our bodies). This range of length-scales is known as the colloidal domain. It is one where physical processes can be at least as important as biochemical ones; for instance, inside every cell, there are 'regulatory' proteins which have to search the genome (DNA) seeking preferential places of attachment (from which they then control the production of other proteins). To find these places, the regulatory proteins depend, at least in part, on the completely random motion, called Brownian motion, that occurs when particles on the colloidal scale are bombarded by the thermal energy of the surrounding solvent (water) molecules. This diffusive process is considerably complicated by the fact that motion of one colloidal object sets the surrounding solvent into motion, which causes all nearby objects also to move. This is referred to as a hydrodynamic interaction. Similarly, if one designs a drug delivery system in which drug molecules are encapsulated, the capsules are again on the colloidal scale but their motion in the bloodstream is dominated by their being swept along by the flow of blood, which is another form of hydrodynamic effect. In some modern therapies, magnetic colloids are steered with or against this flow by an external field; in such cases it is important to understand the effect of hydrodynamics on the response to a force.

The physical consequences of hydrodynamic couplings in bio-colloidal systems are thus wide ranging. However, it is currently very difficult to predict any of these important effects, even using simplified models in which the biochemical detail of the colloidal objects is omitted. Fortunately, such problems can increasingly be addressed using very large scale computer simulation on some of the world's most powerful computers. The so-called lattice Boltzmann algorithm (LB) offers a specific technical solution to the challenges of hydrodynamics, by using a discrete lattice to model the flow of fluid from place to place. Unlike some other methods it can include the random forces responsible for Brownian motion. Also, as well as modelling colloids and polymers surrounded by simple solvents such as water, LB can also address solvents comprising complex fluids. The latter include the so-called 'amphiphilic mesophases' in which small molecules (with a water-loving head and water-hating tail) self-assemble into a labyrinth within which proteins or nanocolloids can reside.

We aim to develop LB algorithms in the bio-colloidal context, and apply these to create new scientific knowledge that has been out of reach until now. Indeed we plan very large simulations of a range of hydrodynamic problems that lie at the interface between physics and the life sciences. These problems include: the flow of magnetic colloids in the blood stream as a model for 'Magnetic Drug Targetting' (MDT) on real patients; the motion of nanocolloids within amphiphilic mesophases suitable for drug delivery applications; the ejection of DNA from the body of a virus as it infects a cell; the dynamical behaviour of the highly confined DNA that is found within the bacterial and other cells; and the interaction between colloidal particles and DNA within the cellular environment. The last of these topics is crucial to understanding the problem of genome exploration by regulatory proteins as mentioned earlier, which we also plan to address. In all these areas, large-scale computer simulation has the potential to change the way science is done. We hope to establish a world lead for the UK in this emerging field.