Dynamics of curved DNA molecules: prediction and experiment

We have developed a quantitative predictive model capable of describing the dynamics of migration of intrinsically curved DNA fragments on polyacrylamide gels. The model takes into account structural features of DNA, end-to-end distance, screening of hydrodynamic interactions, ionic strength of buffer, electrostatic persistence length, structural fluctuations of the macromolecule, counter condensation, and variation of dielectric constant and viscosity of water with MPD. In doing so, we have also addressed a decade old issue on the effect of the organic solvent 2-methyl-2,4-pentanediol on gel migration of phased A-tracts. We show here that A-tract-solvent interactions are less favored compared with A-tract-A-tract and solvent-solvent interactions.     

CAROTENE and CYTOCHROME C DEPENDENT SURVIVAL KINETICS IN RESPONSE TO HIGH INTENSITY VISIBLE LIGHT IN THE SMUT FUNGUS Ustilago violacea

Abstract— Exposure of variously pigmented strains of Ustilago violacea to high intensity incandescent radiation resulted in the generation of three types of survival curves. High carotene, low cytochrome c containing strains of U. violacea were generally characterized by linear type I survival curves with slopes approximately equal to zero. Strains which lacked carotenes were characterized by exponential decay type II survival curves. A third survival curve, type III was observed with carotene accumulating strains which also contained large amounts of cytochrome c. The type III curves are characterized by an initial loss of viability, similar to the type II curves, followed by a recovery period, with eventual stability in survival. The survival curve type appears to be dependent on the relative mg quantities of cytochrome c and carotenes in the cells. Strains with carotene/cytochromec ratios of0–1 × 10^-1,3–15× 10^-1 and l6 × 10^-1 and above had type II, type III and type I survival curves, respectively.     

Generating M-Indeterminate Probability Densities by Way of Quantum Mechanics

Probability densities that are not uniquely determined by their moments are said to be “moment-indeterminate,” or “M-indeterminate.” Determining whether or not a density is M-indeterminate, or how to generate an M-indeterminate density, is a challenging problem with a long history. Quantum mechanics is inherently probabilistic, yet the way in which probability densities are obtained is dramatically different in comparison with standard probability theory, involving complex wave functions and operators, among other aspects. Nevertheless, the end results are standard probabilistic quantities, such as expectation values, moments and probability density functions. We show that the quantum mechanics procedure to obtain densities leads to a simple method to generate an infinite number of M-indeterminate densities. Different self-adjoint operators can lead to new classes of M-indeterminate densities. Depending on the operator, the method can produce densities that are of the Stieltjes class or new formulations that are not of the Stieltjes class. As such, the method complements and extends existing approaches and opens up new avenues for further development. The method applies to continuous and discrete probability densities. A number of examples are given.

     

Correction to: Preface

Foundations of Computational Mathematics -     

New results for diffusion in Lorentz lattice gas cellular automata

New calculations to over ten million time steps have revealed a more complex diffusive behavior than previously reported of a point particle on a square and triangular lattice randomly occupied by mirror or rotator scatterers. For the square lattice fully occupied by mirrors where extended closed particle orbits occur, anomalous diffusion was still found. However, for a not fully occupied lattice the superdiffusion, first noticed by Owczarek and Prellberg for a particular concentration, obtains for all concentrations. For the square lattice occupied by rotators and the triangular lattice occupied by mirrors or rotators, an absence of diffusion (trapping) was found for all concentrations, except on critical lines, where anomalous diffusion (extended closed orbits) occurs and hyperscaling holds for all closed orbits withuniversal exponentsd _f =7/4 and =15/7. Only one point on these critical lines can be related to a corresponding percolation problem. The questions arise therefore whether the other critical points can be mapped onto a new percolation-like problem and of the dynamical significance of hyperscaling.