Molecular Simulations of RNA 2′-O-Transesterification Reaction Models in Solution

Molecular simulations of RNA 2'-O-transesterification reaction models in solution.

We employ quantum mechanical/molecular mechanical umbrella sampling simulations to probe the free energy surfaces of a series of increasingly complex reaction models of RNA 2'-O-transesterification in aqueous solution under alkaline conditions. Such models are valuable for understanding the uncatalyzed processes underlying catalytic cleavage of the phosphodiester backbone of RNA, a reaction of ...

Crossed molecular beam studies on the reaction dynamics of O ( D 1 ) + N 2 O

Molecular Dynamics Simulations of RNA Molecules

a Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic; Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, Olomouc, Tr. 17. Listopadu 12, 771 46 Olomouc, Czech Republic; Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 N...

Molecular dynamics simulations of papilloma virus E2 DNA sequences: dynamical models for oligonucleotide structures in solution.

The specificity of papilloma virus E2 protein-DNA binding depends critically upon the sequence of a region of the DNA not in direct contact with the protein, and represents one of the simplest known examples of indirect readout. A detailed characterization of this system in solution is important to the further investigation hypothesis of a structural code for DNA recognition by regulatory prote...

Parallel Solution of Cardiac Reaction-Diffusion Models

We present and study a parallel iterative solver for reaction-diffusion systems in three dimensions arising in computational electrocardiology, such as the Bidomain and Monodomain models. The models include intramural fiber rotation and anisotropic conductivity coefficients that can be fully orthotropic or axially symmetric around the fiber direction. These cardiac models are coupled with a mem...