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Naoto Hori

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Nottingham Research Fellow at School of Pharamacy, University of Nottingham

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Research interests


  1. Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics
    Nguyen HT ; Hori N ; Thirumalai D
    Nat. Chem. (2022) 10.1038/s41557-022-00934-z    [bioRxiv]
  2. Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA
    Hori N ; Denesyuk NA ; Thirumalai D
    Proc. Natl. Acad. Sci. U.S.A. (2021) 118: e2020837118 10.1073/pnas.2020837118    [bioRxiv]
    Mg-induced Folding of the central domain of 16S rRNA
  3. Theory and simulations for RNA folding in mixtures of monovalent and divalent cations
    Nguyen HT ; Hori N ; Thirumalai D
    Proc. Natl. Acad. Sci. U.S.A. (2019) 116(42): 21022-21030 10.1073/pnas.1911632116    [PDF]
  4. Ion Condensation onto Ribozyme is Site-Specific and Fold-Dependent
    Hori N ; Denesyuk NA ; Thirumalai D
    Biophys. J. (2019) 116(12): 2400-2410 10.1016/j.bpj.2019.04.037    [PDF]
    ---> Featured in New and Notable: "Site-Specific Binding of Non-Site-Specific Ions"
  5. Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding
    Denesyuk NA ; Hori N ; Thirumalai D
    J. Phys. Chem. B (2018) 122(50): 11860-11867 10.1021/acs.jpcb.8b08142   
  6. Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover
    Hori N ; Denesyuk NA ; Thirumalai D
    J. Phys. Chem. B (2018) 122(49): 11279-11288 10.1021/acs.jpcb.8b07129    [arXiv]
  7. Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA
    Chakraborty D ; Hori N ; Thirumalai D
    J. Chem. Theory Comput. (2018) 14(7): 3763-3779 10.1021/acs.jctc.8b00091    [bioRxiv] [arXiv]
  8. 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
    Proc. Natl. Acad. Sci. U.S.A. (2018) 115(31) E7313-E7322 10.1073/pnas.1717582115    [PDF]
  9. VPK pathways depending on ion concentrations
  10. Protein Collapse is Encoded in the Folded State Architecture
    Samanta HS ; Zhuravlev PI ; Hinczewski M ; Hori N ; Chakrabarti S ; Thirumalai D
    Soft Matter (2017) 13(19): 3622-3638 10.1039/C7SM00074J    [arXiv]
  11. Recognize Online Handwritten Bangla Characters Using Hausdorff Distance-Based Feature
    Sen S ; Sarkar R ; Roy K ; Hori N
    Proceedings of the 5th International Conference on Frontiers in Intelligent Computing (2017) 515: 541-549 Springer 10.1007/978-981-10-3153-3_54
  12. Handwritten Devanagari numerals recognition using grid based Hausdorff distance
    Bhowmik S ; Sen S ; Hori N ; Sarkar R ; Nasipuri M
    Computer, Communication and Electrical Technology (2017) 15-18 CRC Press ISBN 9781315400624
  13. Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension
    Hori N ; Denesyuk NA ; Thirumalai D
    J. Mol. Biol. (2016) 428(14): 2847-2859 10.1016/j.jmb.2016.06.002    [arXiv]
  14. How co-translational folding of multi-domain protein is affected by elongation schedule: Molecular simulations
    Tanaka T ; Hori N ; Takada S
    PLOS Comput. Biol. (2015) 11(7): e1004356 10.1371/journal.pcbi.1004356    [PDF]
  15. Coarse-grained structure-based model for RNA-protein complexes developed by fluctuation matching
    Hori N ; Takada S
    J. Chem. Theory Comput. (2012) 8(9): 3384-3394 10.1021/ct300361j
  16. CafeMol: A coarse-grained biomolecular simulator for simulating proteins at work
    Kenzaki H ; Koga N ; Hori N ; Kanada R ; Li W ; Okazaki K ; Yao XQ ; Takada S
    J. Chem. Theory Comput. (2011) 7(6): 1979-1989 10.1021/ct2001045
  17. Multiscale methods for protein folding simulations
    Li W ; Yoshii H ; Hori N ; Kameda T ; Takada S
    Methods (2010) 52: 106-114 10.1016/j.ymeth.2010.04.014
  18. Folding energy landscape and network dynamics of small globular proteins
    Hori N ; Chikenji G ; Berry RS ; Takada S
    Proc. Natl. Acad. Sci. U.S.A. (2009) 106(1): 73-78 10.1073/pnas.0811560106     [PDF]


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