Hori N - Search Results

1

Competition between Stacking and Divalent Cation-Mediated Electrostatic Interactions Determines the Conformations of Short DNA Sequences.

Mondal B, Chakraborty D, Hori N, Nguyen HT, Thirumalai D. Mondal B, et al. Among authors: hori n. J Chem Theory Comput. 2024 Apr 9;20(7):2934-2946. doi: 10.1021/acs.jctc.3c01193. Epub 2024 Mar 18. J Chem Theory Comput. 2024. PMID: 38498914

2

Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension.

Hori N, Denesyuk NA, Thirumalai D. Hori N, et al. J Mol Biol. 2016 Jul 17;428(14):2847-59. doi: 10.1016/j.jmb.2016.06.002. Epub 2016 Jun 15. J Mol Biol. 2016. PMID: 27315694 Free PMC article.

3

Protein collapse is encoded in the folded state architecture.

Samanta HS, Zhuravlev PI, Hinczewski M, Hori N, Chakrabarti S, Thirumalai D. Samanta HS, et al. Among authors: hori n. Soft Matter. 2017 May 21;13(19):3622-3638. doi: 10.1039/c7sm00074j. Epub 2017 Apr 27. Soft Matter. 2017. PMID: 28447708

4

Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA.

Chakraborty D, Hori N, Thirumalai D. Chakraborty D, et al. Among authors: hori n. J Chem Theory Comput. 2018 Jul 10;14(7):3763-3779. doi: 10.1021/acs.jctc.8b00091. Epub 2018 Jun 26. J Chem Theory Comput. 2018. PMID: 29870236 Free PMC article.

5

Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot.

Roca J, Hori N, Baral S, Velmurugu Y, Narayanan R, Narayanan P, Thirumalai D, Ansari A. Roca J, et al. Among authors: hori n. Proc Natl Acad Sci U S A. 2018 Jul 31;115(31):E7313-E7322. doi: 10.1073/pnas.1717582115. Epub 2018 Jul 16. Proc Natl Acad Sci U S A. 2018. PMID: 30012621 Free PMC article.

6

Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover.

Hori N, Denesyuk NA, Thirumalai D. Hori N, et al. J Phys Chem B. 2018 Dec 13;122(49):11279-11288. doi: 10.1021/acs.jpcb.8b07129. Epub 2018 Sep 18. J Phys Chem B. 2018. PMID: 30179471

7

Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding.

Denesyuk NA, Hori N, Thirumalai D. Denesyuk NA, et al. Among authors: hori n. J Phys Chem B. 2018 Dec 20;122(50):11860-11867. doi: 10.1021/acs.jpcb.8b08142. Epub 2018 Dec 5. J Phys Chem B. 2018. PMID: 30468380

8

Ion Condensation onto Ribozyme Is Site Specific and Fold Dependent.

Hori N, Denesyuk NA, Thirumalai D. Hori N, et al. Biophys J. 2019 Jun 18;116(12):2400-2410. doi: 10.1016/j.bpj.2019.04.037. Epub 2019 May 11. Biophys J. 2019. PMID: 31130233 Free PMC article.

9

Theory and simulations for RNA folding in mixtures of monovalent and divalent cations.

Nguyen HT, Hori N, Thirumalai D. Nguyen HT, et al. Among authors: hori n. Proc Natl Acad Sci U S A. 2019 Oct 15;116(42):21022-21030. doi: 10.1073/pnas.1911632116. Epub 2019 Sep 30. Proc Natl Acad Sci U S A. 2019. PMID: 31570624 Free PMC article.

10

Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA.

Hori N, Denesyuk NA, Thirumalai D. Hori N, et al. Proc Natl Acad Sci U S A. 2021 Mar 9;118(10):e2020837118. doi: 10.1073/pnas.2020837118. Proc Natl Acad Sci U S A. 2021. PMID: 33658370 Free PMC article.

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