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Papers

Preprint

  1. “Universal Negative Energetic Elasticity in Polymer Chains: Crossovers among Random, Self-Avoiding, and Neighbor-Avoiding Walks”
    Nobu C. Shirai, Naoyuki Sakumichi, arXiv:2408.14992 (2024)
    https://doi.org/10.48550/arXiv.2408.14992

Journal Articles

  1. “Solvent-Induced Negative Energetic Elasticity in a Lattice Polymer Chain”
    Nobu C. Shirai, Naoyuki Sakumichi, Phys. Rev. Lett. 130, 148101 (2023)
    doi:10.1103/PhysRevLett.130.148101
  2. “The interplay of intrinsic disorder and macromolecular crowding on α-synuclein fibril formation”
    Nobu C. Shirai, Macoto Kikuchi, J. Chem. Phys. 144 055101 (2016)
    doi:10.1063/1.4941054 arXiv:1411.3383
  3. “Structural flexibility of intrinsically disordered proteins induces stepwise target recognition”
    Nobu C. Shirai, Macoto Kikuchi, J. Chem. Phys. 139 225103 (2013)
    doi:10.1063/1.4838476 arXiv:1310.0889

Proceedings

  1. “How to estimate the number of self-avoiding walks over 10^100? Use random walks.”
    Nobu C. Shirai, Macoto Kikuchi, Interdisciplinary Information Sciences 19 79 (2013)
    doi:10.4036/iis.2013.79 arXiv:1304.7352
  2. “Multicanonical simulation of the Domb-Joyce model and the Go model: new enumeration methods for self-avoiding walks”
    Nobu C. Shirai, Macoto Kikuchi, J. Phys.: Conf. Ser. 454 012039 (2013)
    doi:10.1088/1742-6596/454/1/012039 arXiv:1212.2181

International Conferences

  1. “Negative Energetic Elasticity in Gels: Insights from a Lattice Polymer Chain”
    Nobu C. Shirai, Naoyuki Sakumichi, APS March Meeting 2024, Minneapolis, Z31.00007 (Oral), Mar. 8, 2024.


  2. “Scaling in Gel Mechanics: Crossover between Self- and Neighbor-Avoiding Walks”
    Nobu C. Shirai, Naoyuki Sakumichi, APS March Meeting 2024, Minneapolis, N00.00115 (Poster), Mar. 6, 2024.


  3. Negative Energetic Elasticity in Gels: Insights from a Lattice Polymer Chain
    Nobu C. Shirai, MRSEC Seminar, Feb. 29, 2024

  4. “Microscopic origin of negative energetic elasticity in polymer gels: effective intra-chain repulsive interaction”
    Nobu C. Shirai, Naoyuki Sakumichi, ISMC2023, Osaka, 1a-F-a4, Sep. 4, 2023.


  5. “Scaling relation in a lattice polymer chain with negative energetic elasticity”
    Nobu C. Shirai, Naoyuki Sakumichi, StatPhys28, Tokyo, PSb-94, Aug. 8, 2023.

  6. “Disordered tail of linker histone H1 in chromatin compaction dynamics studied by coarse-grained simulations”
    Nobu C. Shirai, 5th International Symposium of the Mathematics on Chromatin Live Dynamics, Invited talk, Hiroshima, Mar. 8, 2017.

  7. “Disordered tail of the linker histone H1 in chromatin compaction dynamics studied by coarse-grained simulations”
    Nobu C. Shirai and Shoji Takada, Protein Society 30th Anniversary Symposium, Baltimore, Maryland, PE-027, Jul. 17, 2016.

  8. “THE INTERPLAY OF INTRINSIC DISORDER AND MACROMOLECULAR CROWDING ON α-SYNUCLEIN FIBRIL FORMATION.”
    Nobu C. Shirai and Macoto Kikuchi, Biophysical Society 60th Annual Meeting, Los Angeles, California, 2723-Pos, Mar. 2, 2016.

  9. “Statistical enumeration of self-avoiding polygons on a torus”
    Nobu C. Shirai, Quantum Information via Statistical Mechanics – Counting Steps toward Realization -, Kyoto, Jan. 2013

  10. “Multicanonical simulation of the Domb-Joyce model and the Go model: new enumeration methods of self-avoiding walks”
    Nobu C. Shirai and Macoto Kikuchi, CCP2012, Kobe, Oct. 2012

  11. “A lattice model of Intrinsically Disordered Proteins”
    Nobu Shirai, 2010 NCTS September Workshop on Critical Phenomena and Complex Systems, Academia Sinica, Taiwan, Sep. 2010

The Physical Society of Japan

  1. “Macromolecular crowding effect on fibril formation of α-synuclein”
    Nobu C. Shirai and Macoto Kikuchi, 27aAB-6 (2013).

  2. “The possible advantage of structural disorder of intrinsically disordered proteins in the new type of signaling mechanism II”
    Nobu Shirai and Macoto Kikuchi, 28aPS-108 (2013).

  3. “The statistical enumeration method for self-avoiding walks using the extended ensemble method”
    Nobu Shirai and Macoto Kikuchi, 26pXR-5 (2013).

  4. “The possible advantage of structural disorder of intrinsically disordered proteins in the new type of signaling mechanism”
    Nobu Shirai and Macoto Kikuchi, 20pAB-7 (2012).

  5. “A Lattice Gas Model of Protein Binding Process II”
    Nobu Shirai and Macoto Kikuchi, 27aPS-33 (2012).

  6. “Thermodynamic analysis of a lattice model of Intrinsically Disordered Proteins II”
    Nobu Shirai and Macoto Kikuchi, 24aPS-25 (2011).

  7. “A Lattice Gas Model of Protein Binding Process”
    Nobu Shirai and Macoto Kikuchi, 28aGV-9 (2011).

  8. “Thermodynamic analysis of a lattice model of Intrinsically Disordered Proteins”
    Nobu Shirai and Macoto Kikuchi, 23aTG-7 (2010).

  9. “A lattice model of intrinsically disordered proteins”
    Nobu Shirai and Macoto Kikuchi, 21aEF-11 (2010).

The Biophyiscal Society of Japan

  1. “Effect of bending energy on negative energetic elasticity in a lattice polymer chain”
    Nobu C. Shirai and Sakumichi Naoyuki, 1Pos198, Nagoya, Nov. 17 (2023).

  2. “Cooperativity of protein folding tells us about topology selectivity in genome”
    Nobu C. Shirai and Minami Shintaro, 1Pos075, Okayama, Sep. 15 (2018).

  3. “Relation between cooperative protein folding and loop connections: comprehensive analysis over 2α-4β protein topologies”
    Nobu C. Shirai and Minami Shintaro, 3Pos034, Kumamoto, Sep. 21 (2017).

  4. “Relation between cooperative protein folding and loop connections”
    Nobu C. Shirai and Minami Shintaro, 3Pos053, Tsukuba, Nov. 27 (2016).

  5. “Disordered tail of the linker histone H1 in chromatin compaction dynamics studied by coarse-grained simulations”
    Nobu C. Shirai and Shoji Takada, 1O1600, Kanazawa, Sep. 13 (2015).

  6. “Intrinsic disorder under crowded environment: thermodynamic simulation of α-synuclein amyloid fibril formation”
    Nobu C. Shirai, 3SEA-06, Sapporo, Sep. 27 (2014).

  7. “Coarse-grained simulation of chromatosome: H1-mediated dynamic compaction of nucleosome structure”
    Nobu C. Shirai and Shoji Takada, 3P118, Sapporo, Sep. 27 (2014).

  8. “Macromolecular crowding effect on fibril formation of α-synuclein”
    Nobu C. Shirai and Macoto Kikuchi, 2P074, Kyoto, Oct. 29 (2013).

  9. “The possible advantage of structural disorder of intrinsically disordered proteins in the new type of signaling mechanism”
    Nobu C. Shirai and Macoto Kikuchi, 1B1534, Nagoya, Sep. 22 (2012).

  10. “Binding Process of Intrinsically Disordered Protein Studied by a Lattice Model of Protein”
    Nobu Shirai and Macoto Kikuchi, 1F1648, Kobe, Sep. 16 (2011).

  11. “A Lattice Model of Intrinsically Disordered Proteins”
    Nobu Shirai and Macoto Kikuchi, 2P056, Sendai, Sep. 21 (2010).

Protein Science Society of Japan

  1. Computer simulations of intrinsically disordered protein to search for a functional advantage of structural disorder
    Nobu Shirai and Macoto Kikuchi, 2WC-3 (2013).
  2. The possible advantage of structural disorder of intrinsically disordered proteins in the new type of signaling mechanism
    Nobu Shirai and Macoto Kikuchi, 1P-060 (2012).