175 citations · 415 across the 10 of their papers we have counts for
10 papers
Ion Condensation onto Ribozyme is Site-Specific and Fold-Dependent
Naoto Hori, Natalia A. Denesyuk, D. Thirumalai
The highly charged RNA molecules, with each phosphate carrying a single negative charge, cannot fold into well-defined architectures with tertiary interactions, in the absence of i…
Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover
Naoto Hori, Natalia A. Denesyuk, D. Thirumalai
We investigated frictional effects on the folding rates of a human telomerase hairpin (hTR HP) and H-type pseudoknot from the Beet Western Yellow Virus (BWYV PK) using simulations…
Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension
Naoto Hori, Natalia A. Denesyuk, D. Thirumalai
Because of the potential link between -1 programmed ribosomal frameshifting and response of a pseudoknot (PK) RNA to force, a number of single molecule pulling experiments have bee…
Development and applications of Coarse Grained models for RNA
Changbong Hyeon, Natalia A. Denesyuk, D. Thirumalai
In contrast to proteins much less attention has been focused on development of computational models for describing RNA molecules, which are being recognized as playing key roles in…
Entropic stabilization of the folded states of RNA due to macromolecular crowding
Natalia A. Denesyuk, D. Thirumalai
We review the effects of macromolecular crowding on the folding of RNA by considering the simplest scenario when excluded volume interactions between crowding particles and RNA dom…
A Coarse-Grained Model for Predicting RNA Folding Thermodynamics
Natalia A. Denesyuk, D. Thirumalai
We present a thermodynamically robust coarse-grained model to simulate folding of RNA in monovalent salt solutions. The model includes stacking, hydrogen bond and electrostatic int…