Paper Citing NAMD - Abstract
Mathew, Damien C.; Luthey-Schulten, Zaida
Influence of Montmorillonite on Nucleotide Oligomerization Reactions: A Molecular Dynamics Study
ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES, 40:303-317, JUN 2010
We investigate a proposed origins of life scenario involving the clay montmorillonite and its catalytic role in forming oligonucleotides from activated mononucleotides. Clay and mineral surfaces are important for concentrating the reactants and for promoting nucleotide polymerization reactions. Using classical molecular dynamics methods we provide atomic details of reactant conformations prior to polynucleotide formation, lending insight into previously reported experimental observations of this phenomenon. The simulations clarify the catalytic role of metal ions, demonstrate that reactions leading to correct linkages take place primarily in the interlayer, and explain the observed sequence selectivity in the elongation of the chain. The study comparing reaction probabilities involving L- and D-chiral forms of the reactants has found enhancement of homochiral over heterochiral products when catalyzed by montmorillonite.
