Publications

Recent highlights

(For a full list of publications see below or go to Google Scholar)

Watching ion-driven kinetics of folding and misfolding caused by energetic and topological frustration one molecule at a time

We show how RNA folding and misfolding are driven by divalent cations. The movie above is an example of the folding ribozyme. Watch a misfolding ribozyme here on YouTube.

N Hori, D Thirumalai
Nucleic Acids Res. (2023) 51(19) 10737 10.1093/nar/gkad755

Condensates in RNA Repeat Sequences are Heterogeneously Organized and Exhibit Reptation Dynamics

We simulated phase separation of repeat RNA sequences. This highlight the mechanism of liquid-liquid phase separation

HT Nguyen, N Hori, D Thirumalai
Nat. Chem. (2022) 14, 775–785
Preprint bioRxiv:2021.02.20.432119

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

From simulations of ribosomal RNA folding, we revealed the coupling of folding and Mg2+ associations, and how the ions interact with RNA segments in a coordinated manner.

N Hori, NA Denesyuk, D Thirumalai
Proc. Natl. Acad. Sci. U.S.A. (2021) 118 e2020837118
Preprint bioRxiv:2020.04.08.032474

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

Based on the theory of polyatomic liquids, we invented a new simulation model for RNA enables us to simulate large RNA folding with interactions to Mg2+ and Ca2+ accurately.

HT Nguyen, N Hori, D Thirumalai
Proc. Natl. Acad. Sci. U.S.A. (2019) 116(42) 21022-21030
Preprint bioRxiv:732917

Ion Condensation onto Ribozyme is Site-Specific and Fold-Dependent

This study demonstrated that, unlike what previously suggested, ion condensation of divalent cations is highly specific and depends on the architecture of RNAs, even at very low ionic concentrations.

N Hori, NA Denesyuk, D Thirumalai
Biophys. J. (2019) 116(12) 2400
Featured in New and Notable

Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover

We showed that there is an optimal solvent viscosity for RNA folding kinetics, and that Kramers’ theory holds in RNA folding.

N Hori, NA Denesyuk, D Thirumalai
J. Phys. Chem. B (2018) 122(49) 11279
Preprint arXiv

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

Together with experimentalists (Ansari’s group), we revealed the folding pathway of a viral RNA pseudoknot can be modulated by K+ ions.

J Roca, N Hori, S Baral, Y Velmurugu, R Narayanan, P Narayanan, D Thirumalai, A Ansari
Proc. Natl. Acad. Sci. U.S.A. (2018) 115(31) E7313

 

Full list of publications

  1. Salt-dependent self-association of trinucleotide repeat RNA sequences
    H Maity, HT Nguyen, N Hori, D Thirumalai
    J. Phys. Chem. Lett. (2024) 15: 3820 10.1021/acs.jpclett.3c03553    bioRxiv:2023.11.26.568751
  2. Competition between stacking and divalent cation-mediated electrostatic interactions determines the conformations of short DNA sequences
    B Mondal, D Chakraborty, N Hori, HT Nguyen, D Thirumalai
    J. Chem. Theory Comput. (2024) 10.1021/acs.jctc.3c01193    bioRxiv:2023.10.05.561104
  3. Watching ion-driven kinetics of folding and misfolding caused by energetic and topological frustration one molecule at a time
    N Hori, D Thirumalai
    Nucleic Acids Res. (2023) 51(19) 10737 10.1093/nar/gkad755
  4. Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation
    H Maity, HT Nguyen, N Hori, D Thirumalai
    Proc. Natl. Acad. Sci. U.S.A. (2023) 120(24) e2301409120    bioRxiv:2023.01.09.523227
  5. Condensates in RNA Repeat Sequences are Heterogeneously Organized and Exhibit Reptation Dynamics
    HT Nguyen, N Hori, D Thirumalai
    Nat. Chem. (2022) 14, 775–785    bioRxiv:2021.02.20.432119
  6. Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA
    N Hori, NA Denesyuk, D Thirumalai
    Proc. Natl. Acad. Sci. U.S.A. (2021) 118 e2020837118
  7. Theory and simulations for RNA folding in mixtures of monovalent and divalent cations
    HT Nguyen, N Hori, D Thirumalai
    Proc. Natl. Acad. Sci. U.S.A. (2019) 116(42) 21022-21030
  8. Ion Condensation onto Ribozyme is Site-Specific and Fold-Dependent
    N Hori, NA Denesyuk, D Thirumalai
    Biophys. J. (2019) 116(12) 2400
  9. Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding
    NA Denesyuk, N Hori, D Thirumalai
    J. Phys. Chem. B (2018) 122(50) 11860
  10. Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover
    N Hori, NA Denesyuk, D Thirumalai
    J. Phys. Chem. B (2018) 122(49) 11279
  11. Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA
    D Chakraborty, N Hori, D Thirumalai
    J. Chem. Theory Comput. (2018) 14(7) 3763
  12. Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot
    J Roca, N Hori, S Baral, Y Velmurugu, R Narayanan, P Narayanan, D Thirumalai, A Ansari
    Proc. Natl. Acad. Sci. U.S.A. (2018) 115(31) E7313
  13. Protein Collapse is Encoded in the Folded State Architecture
    HS Samanta, PI Zhuravlev, M Hinczewski, N Hori, S Chakrabarti, D Thirumalai D
    Soft Matter (2017) 13(19) 3622
  14. Recognize Online Handwritten Bangla Characters Using Hausdorff Distance-Based Feature
    S Sen, R Sarkar, K Roy, N Hori
    Proceedings of the 5th International Conference on Frontiers in Intelligent Computing (2017) 515 541-549 Springer
  15. Handwritten Devanagari numerals recognition using grid based Hausdorff distance
    S Bhowmik, S Sen, N Hori, R Sarkar, M Nasipuri
    Computer, Communication and Electrical Technology (2017) 15-18 CRC Press
  16. Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension
    N Hori, NA Denesyuk, D Thirumalai
    J. Mol. Biol. (2016) 428(14) 2847
  17. How co-translational folding of multi-domain protein is affected by elongation schedule: Molecular simulations
    T Tanaka, N Hori, S Takada
    PLOS Comput. Biol. (2015) 11(7) e1004356
  18. Coarse-grained structure-based model for RNA-protein complexes developed by fluctuation matching
    N Hori, S Takada
    J. Chem. Theory Comput. (2012) 8(9) 3384
  19. CafeMol: A coarse-grained biomolecular simulator for simulating proteins at work
    H Kenzaki, N Koga, N Hori, R Kanada, W Li, K Okazaki, XQ Yao, S Takada
    J. Chem. Theory Comput. (2011) 7(6) 1979
  20. Multiscale methods for protein folding simulations
    W Li, H Yoshii, N Hori, T Kameda, S Takada
    Methods (2010) 52: 106
  21. Folding energy landscape and network dynamics of small globular proteins
    N Hori, G Chikenji, RS Berry, S Takada
    Proc. Natl. Acad. Sci. U.S.A. (2009) 106(1) 73