The effective diffusion coefficient of a small molecule in a two-phase gel medium.

Using simple theoretical arguments and exact numerical lattice calculations, Hickey et al. [J. Chem. Phys. 124, 204903 (2006)] derived and tested an expression for the effective diffusion coefficient of a probe molecule in a two-phase medium consisting of a hydrogel with large gel-free inclusions. Although providing accurate predictions, this expression neglects important characteristics that such two-phase systems can present. In this article, we extend the previously derived expression in order to include local interactions between the gel and the analyte, interfacial effects between the main phase and the inclusions, and finally a possible incomplete separation between the two phases. We test our new, generalized expressions using exact numerical calculations. These generalized equations should be a useful tool for the development of novel multiphase systems for specific applications, such as drug-delivery platforms.

Modeling the separation of macromolecules: a review of current computer simulation methods.

Theory and numerical simulations play a major role in the development of improved and novel separation methods. In some cases, computer simulations predict counterintuitive effects that must be taken into account in order to properly optimize a device. In other cases, simulations allow the scientist to focus on a subset of important system parameters. Occasionally, simulations even generate entirely new separation ideas! In this article, we review the main simulation methods that are currently being used to model separation techniques of interest to the readers of Electrophoresis. In the first part of the article, we provide a brief description of the numerical models themselves, starting with molecular methods and then moving towards more efficient coarse-grained approaches. In the second part, we briefly examine nine separation problems and some of the methods used to model them. We conclude with a short discussion of some notoriously hard-to-model separation problems and a description of some of the available simulation software packages.

Quantitative predictions for DNA two-dimensional display according to size and nucleotide sequence composition.

2-D DNA display is a simple separation method that provides a fast and economical way of visualizing polymorphism and comparing genomes. The DNA fragments are separated first according to their size by standard gel electrophoresis and then according to their sequence composition using denaturing gradient gel electrophoresis. First developed by Fischer and Lerman (Cell 1979, 16, 191-200), this method has recently been used to distinguish strains within a bacterial species. The genomic restriction fragments are displayed as spots on a 2-D surface. Although most of the relevant physical mechanisms are understood, this technique is mostly empirical and remains essentially qualitative. In view of optimizing this procedure, we combine our understanding of the different physical mechanisms at play to develop a complete numerical model to predict the relative coordinates of the spots as a function of the corresponding DNA sequence and of the experimental conditions. We experimentally validate our model by predicting the outcome of a 2-D display of the lambda phage genome. It thus becomes possible to optimize in silico the experimental parameters, to predict whether specific mutations as well as yet undescribed genetic polymorphisms can be resolved, and to assist in interpreting the experimental data.