BioSimGrid: towards a worldwide repository for biomolecular simulations.

BioSimGrid is a database for biomolecular simulations, or, a "Protein Data Bank extended in time" for molecular dynamics trajectories. We describe the implementation details: architecture, data schema, deposition, and analysis modules. We encourage the simulation community to explore BioSimGrid and work towards a common trajectory exchange format.

A lotka-volterra model of coexistence between a sexual population and multiple asexual clones.

At carrying capacity, small advantages in competitive ability can compensate a sexual population for its two-fold disadvantage in growth capacity when facing invasion by asexual mutants. In this paper, we develop a generic analytical model to consider the ecology of a sexual population comprising equal numbers of males and females, competing for shared prey resources with multiple female-only clones. We assume that the clones arise from the sexual population and are distinguished from it only by having narrower resource niches and twice the growth capacity.

Comparison of algorithms for non-linear inverse 3D electrical tomography reconstruction.

Non-linear electrical impedance tomography reconstruction algorithms usually employ the Newton-Raphson iteration scheme to image the conductivity distribution inside the body. For complex 3D problems, the application of this method is not feasible any more due to the large matrices involved and their high storage requirements. In this paper we demonstrate the suitability of an alternative conjugate gradient reconstruction algorithm for 3D tomographic imaging incorporating adaptive mesh refinement and requiring less storage space than the Newton-Raphson scheme.

Optimal imaging with adaptive mesh refinement in electrical impedance tomography.

In non-linear electrical impedance tomography the goodness of fit of the trial images is assessed by the well-established statistical chi2 criterion applied to the measured and predicted datasets. Further selection from the range of images that fit the data is effected by imposing an explicit constraint on the form of the image, such as the minimization of the image gradients. In particular, the logarithm of the image gradients is chosen so that conductive and resistive deviations are treated in the same way.