With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly
ordered three-dimensional structures that define their functions. The key to folding of a …

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Molecular dynamics simulations have strongly matured as a method to study biomolecular
processes. Their validity, however, is determined by the accuracy of the underlying force …

Type V CRISPR-Cas interference proteins use a single RuvC active site to make RNA-
guided breaks in double-stranded DNA substrates, an activity essential for both bacterial …

We report the folding thermodynamics of ccUUCGgg and ccGAGAgg RNA tetraloops using
atomistic molecular dynamics simulations. We obtain a previously unreported estimation of …

Determination of RNA structural-dynamic properties is challenging for experimental
methods. Thus, atomistic molecular dynamics (MD) simulations represent a helpful …

Hybridization of short nucleic acid segments (< 4 nt) to single-strand templates occurs as a
critical intermediate in processes such as nonenzymatic nucleic acid replication and toehold …

We develop a robust coarse-grained model for single-and double-stranded DNA by
representing each nucleotide by three interaction sites (TIS) located at the centers of mass of …

In the past two decades, our understanding of how the genome of mammalian cells is
spatially organized in the three-dimensional (3D) space of the nucleus and how key nuclear …