Localization for a Family of One-dimensional Quasiperiodic Operators of Magnetic Origin

We show strong dynamical localization for a family of one-dimensional quasiperiodic Jacobi operators of magnetic origin, throughout the regime of positive Lyapunov exponents.The authors were supported in part by BSF grant 2002068 and NSF grant DMS-0300974.submitted 7/07/04, accepted 22/07/04     

Centred TVD schemes for hyperbolic conservation laws

New first- and high-order centred methods for conservation lawsare presented. Convenient TVD conditions for constructing centredTVD schemes are then formulated and some useful results areproved. Two families of centred TVD schemes are constructedand extended to nonlinear systems. Some numerical results arealso presented.     

Geometry optimization for peptides and proteins: comparison of Cartesian and internal coordinates

We present the results of several benchmarks comparing the relative efficiency of different coordinate systems in optimizing polypeptide geometries. Cartesian, natural internal, and primitive internal coordinates are employed in quasi-Newton minimization for a variety of biomolecules. The peptides and proteins used in these benchmarks range in size from 16 to 999 residues. They vary in complexity from polyalanine helices to a beta-barrel enzyme. We find that the relative performance of the different coordinate systems depends on the parameters of the optimization method, the starting point for the optimization, and the size of the system studied. In general, internal coordinates were found to be advantageous for small peptides. For larger structures, Cartesians appear to be more efficient for empirical potentials where the energy and gradient can be evaluated relatively quickly compared to the cost of the coordinate transformations.     

Comparison of double-ended transition state search methods

While a variety of double-ended transition state search methods have been developed, their relative performance in characterizing complex multistep pathways between structurally disparate molecular conformations remains unclear. Three such methods (doubly-nudged elastic band, a string method, and a growing string method) are compared for a series of benchmarks ranging from permutational isomerizations of the seven-atom Lennard-Jones cluster (LJ(7)) to highly cooperative LJ(38) and LJ(75) rearrangements, and the folding pathways of two peptides. A database of short paths between LJ(13) local minima is used to explore the effects of parameters and suggest reasonable default values. Each double-ended method was employed within the framework of a missing connection network flow algorithm to construct more complicated multistep pathways. We find that in our implementation none of the three methods definitively outperforms the others, and that their relative effectiveness is strongly system and parameter dependent.