All Outputs (4)

Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding (2018)
Journal Article
Denesyuk, N. A., Hori, N., & Thirumalai, D. (2018). Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding. Journal of Physical Chemistry B, 122(50), 11860-11867. https://doi.org/10.1021/acs.jpcb.8b08142

How ions affect RNA folding thermodynamics and kinetics is an important but a vexing problem that remains unsolved. Experiments have shown that the free-energy change, δG(c), of RNA upon folding varies with the salt concentration (c) as, δG(c) = k c... Read More about Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding.

Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover (2018)
Journal Article
Hori, N., Denesyuk, N. A., & Thirumalai, D. (2018). Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover. Journal of Physical Chemistry B, 122(49), 11279-11288. https://doi.org/10.1021/acs.jpcb.8b07129

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 of the Three Interaction Site (TIS) model for RNA. The heat capacity f... Read More about Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover.

Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot (2018)
Journal Article
Roca, J., Hori, N., Baral, S., Velmurugu, Y., Narayanan, R., Narayanan, P., …Ansari, A. (2018). Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot. Proceedings of the National Academy of Sciences, 115(31), E7313-E7322. https://doi.org/10.1073/pnas.1717582115

The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability, and dynamics. Therefore, it is important to... Read More about Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot.

Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA (2018)
Journal Article
Chakraborty, D., Hori, N., & Thirumalai, D. (2018). Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA. Journal of Chemical Theory and Computation, 14(7), 3763-3779. https://doi.org/10.1021/acs.jctc.8b00091

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 sugar, phosphate, and base. The resulting TIS model includes base-stacking... Read More about Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA.