Chaire d'Analyse Appliquée

Overview of DNA Research

General Research Description

The group's work in modelling DNA involves the application of techniques of continuum mechanics, particularly of the theory of elastic rods, to the development of computational codes and analytical techniques for describing the basic mechanical properties of DNA. The objective of the modelling is to produce quantitative predictions that can be compared with experimental data. To this end we collaborate with various experimental groups--both biochemists in Jason Kahn's lab, Maryland, and electron microscopists in Jacques Dubochet's group at University of Lausanne LAU. The motif of DNA mini-circles, i.e. closed loops of a few hundred base pairs (check some cryo-em stereo pairs of micrographs), is currently the centre of our attention. The codes being developed include energy minimization, or statics, and various dynamic models.

Our current research in statics is focussed on two areas:

More detailed descriptions of completed research focused on rod mechanics per se and applications to DNA are available.

For dynamics the research on constitutive relations is just as important as for statics, but for dynamics the computational methods required are considerably more intensive, and the mathematical models are less well-developed. DNA dynamics involves motion that is both damped and stochastically driven by the solvent, so the primary question is to understand the properties of the long-time equilibrium distribution (if there is one) of the dynamics of the stochastic partial differential equations arising in the models. Research areas of interest include the investigation and comparison  to cryo-EM experimental data of equilibrium distributions computed via models involving Monte Carlo, Langevin and Brownian approximations, the development of statistical mechanics theories appropriate for continuum rod models, and the development of appropriate continuum level approximations for damping and driving effects of the solvent.

Return to the homepage of "Chaire d'Analyse Appliquée"