We construct a base-stacking model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four- or six-letter alphabets. With only two kinds of bases, most sequences have many alternative folding configurations and are consequently thermally unstable. Stable ground states are found only fo...

Stability of the π-π stacking interactions in the Ben||N-substituted-coronene complexes was studied using the computational quantum chemistry methods (where Ben is benzene and || denotes π-π stacking interaction, and N-substituted-coronene is coronene molecule which substituted with different number of N atoms). The results reveal simultaneous effects of structure and number of Heteroatom on th...

Submitted for the MAR08 Meeting of The American Physical Society Single stranded DNA hairpin loop kinetics: A Brownian dynamics study MARTIN KENWARD, KEVIN DORFMAN, University of Minnesota — The dynamics of single stranded DNA (ssDNA) molecules play a role in a number of biological functions and have a found uses in several microfluidic applications. In particular, ssDNA having complementary se...

High level ab initio methods have been used to study stacking interactions in ten unique base pair steps both in A-RNA and in B-DNA duplexes. The protocol for selection of geometries based on molecular dynamics (MD) simulations is proposed, and its suitability is demonstrated by comparison with stacking in steps at fiber diffraction geometries. It is shown that fiber diffraction geometries are ...

low stacking fault energy face centered cubic (fcc) materials contain characteristic defect structures. stackingfault tetrahedral are one of those rare structures that occur under special experimental conditions. for the first time,stacking fault tetrahedral were observed in fe-30mn-3al-3si twinning induced plasticity (twip) steel. theirpresence resulted from a quenching heat treatment.

stability of the π-π stacking interactions in the ben||n-substituted-coronene complexes was studied using the computational quantum chemistry methods (where ben is benzene and || denotes π-π stacking interaction, and n-substituted-coronene is coronene molecule which substituted with different number of n atoms). the results reveal simultaneous effects of structure and number of heteroatom on th...

In this web appendix we demonstrate the construction of a regular type. The idea is to construct hierarchies out of “stacking” finite truncations of other hierarchies on top of each other. We illustrate with a simple example with 2 players. Let p̄ = (p1, p2, . . .) be an infinite sequence of numbers pn ∈ [0, 1] . Consider a hierarchy u p̄ according to which player i believes that the state of nat...

stability of the ;-; stacking interactions in the substituted-coronene||cyclooctatetraene complexes wasstudied using the computational quantum chemistry methods (where || denotes ;–; stackinginteraction, and substituted-coronene is coronene which substituted with four similar x groups; x =oh, sh, h, f, cn, and no). there are meaningful correlations between changes of geometricalparameters and t...