Publication

    2024
  1. S-i. Koda and S. Saito,
    Locating transition states by a variational reaction path optimization with an energy-derivative-free objective function J. Chem. Theory Comput 20, 2798-2811 (2024).
  2. J. Ono, Y. Matsumura, T. Mori, and S. Saito,
    Conformational dynamics in proteins: Entangled slow fluctuations and nonequilibrium reaction events (Perspective), J. Phys. Chem. B 128, 20-32 (2024).

    2023
  3. T. Inagaki, M. Hatanaka, and S. Saito,
    Anisotropic and finite effects on intermolecular vibration and relaxation dynamics: Low-frequency Raman spectroscopy of water film and droplet on graphene by molecular dynamics simulations, J. Phys. Chem. B 127, 5869-5880 (2023).
  4. T. Kato and S. Saito,
    Kohn-Sham potentials by an inverse Kohn-Sham equation and accuracy assessment by virial theorem, J. Chin. Chem. Soc. 70, 554-569 (2023).

    2022
  5. T. Mori and S. Saito,
    Molecular insights into the intrinsic dynamics and their roles during catalysis in Pin1 peptidyl-prolyl isomerase, J. Phys. Chem. B 126, 5185-5193 (2022).
  6. Y. Furuike, A. Mukaiyama, S.-i. Koda, D. Dimon, D. Ouyang, K. Ito-Miwa, S. Saito, E. Yamashita, T. Nishikawa-Ohkawa, K. Terauchi, T. Kondo, and S. Akiyama,
    Regulation mechanisms of the dual ATPase in KaiC, Proc. Nat. Acad. Sci. USA 119, e2119627119 (10 pages) (2022).
  7. Z. Zhu, M. Higashi, and S. Saito,
    Excited states of chlorophyll a and b in solution by time-dependent density fun ctional theory, J. Chem. Phys. (Special Topic on Photosynthetic Light-Harvesting and Energy Conversion) 156, 124111 (13 pages) (2022).
  8. S.-i. Koda and S. Saito,
    Multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by ADP/ATP exchange inhibition, PLoS Comput. Biol. 18, e1009243 (24 pages) (2022).
  9. T. Inagaki and S. Saito,
    Hybrid Monte Carlo method with potential scaling for sampling from the canonical multimodal distribution and imitating the relaxation process, J. Chem. Phys. 156, 104111 (12 pages) (2022).

    2021
  10. M. Kalathingal, T. Sumikama, S. Oiki, and S. Saito,
    Vectorial insertion of a β-helical peptide into membrane: A theoretical study on polytheonamide B, Biophys. J. 120, 4786 (2021).
  11. I. Ohmine and S. Saito,
    Dynamical behavior of water; Fluctuation, reactions and phase transitions, Bull. Chem. Soc. Jpn. 94, 2575-2601 (2021).
  12. Y.-W. Kuo, P.-H. Tang, H. Wang, T.-M. Wu, and S. Saito,
    Tetrahedral structure of supercooled water at ambient pressure and its influence on dynamic relaxation: Comparative study of water models, J. Mol. Liquids 341, 117269 (2021).
  13. Y. Matsumura and S. Saito,
    Microscopic insights into dynamic disorder in the isomerization dynamics of the protein BPTI, J. Chem. Phys. 154, 224113 (2021).
  14. M. Maurya, A. K. Metya, J. K. Singh, and S. Saito,
    Effects of interfaces on structure and dynamics of water droplets on a graphene surface: A molecular dynamics study, J. Chem. Phys. 154, 164704 (2021).

    2020
  15. N. Moritsugu, T. Nara, S.-i. Koda, K. Tominaga, and S. Saito,
    Molecular mechanism of acceleration and retardation of collective orientation relaxation of water molecules in aqueous solutions, J. Phys. Chem. B 124, 11730-11737 (2020).
  16. Y. Nam, M. Kalathingal, S. Saito, and J. Y. Lee,
    Tautomeric effect of histidine on β-sheet formation of amyloid beta 1−40: 2D-IR simulations, Biophys. J. 119, 831-842 (2020).
  17. C. R. Baiz , B. Błasiak, J. Bredenbeck, M. Cho, J.-H Choi, S. A. Corcelli, A. G. Dijkstra, C.-J. Feng, S. Garrett-Roe, N.-H. Ge, M. W. D. Hanson-Heine, J. D. Hirst, T. L. C. Jansen, K. Kwac, K. J. Kubarych, C. H. Londergan, H. Maekawa, M. Reppert, S. Saito, S. Roy, J. L. Skinner, G. Stock, J. E. Straub, M. C. Thielges, K. Tominaga, A. Tokmakoff, H. Torii, L. Wang, L. J. Webb, and M. T. Zanni,
    Vibrational frequency map, vibrational spectroscopy, and intermolecular interaction, Chem. Rev. 120, 7152-7218 (2020).
  18. S.-i. Koda and S. Saito,
    An alternative interpretation of the slow KaiB-KaiC binding of the cyanobacterial clock proteins, Sci. Rep. 10, 10439 (2020).
  19. T. Mori and S. Saito,
    Dissecting the dynamics during enzyme catalysis: A case study of Pin1 peptidyl-prolyl isomerase, J. Chem. Theory Comput. 16, 3396-3407 (2020).
  20. T. Kato, K. Nobusada, and S. Saito,
    Inverse Kohn-Sham equations derived from the density equation theory, J. Phys. Soc. Jpn 89, 024301 (2020).

    2019
  21. S. Saito, M. Higashi, and G. R. Fleming,
    Site-dependent fluctuations optimize electronic energy transfer in the Fenna-Matthews-Olson protein, J. Phys. Chem. B 123, 9762-9772 (2019).
  22. T. L. C. Jansen, S. Saito, J. Jeon, and M. Cho,
    Theory of coherent two-dimensional vibrational spectroscopy, J. Chem. Phys. (Perspective) 150, 100901 (17 pages) (2019).
  23. S. Saito and B. Bagchi,
    Thermodynamic picture of vitrification of water through complex specific heat and entropy: A journey through "No Man's Land", J. Chem. Phys. 150, 054502 (14 pages) (2019).
    Selected as the Featured Article and the best in the Liquids, Glasses, and Crystals section in the last two years (2018-2020).
  24. T. Mori and S. Saito,
    Conformational excitation and non-equilibrium transition facilitate enzymatic reactions: Application to Pin1 peptidyl-prolyl isomerase, J. Phys. Chem. Lett. 10, 474-480 (2019).
    Selected as the supplementary journal cover.

    2018
  25. K. Shiraga, K. Tanaka, T. Arikawa, S. Saito, and Y. Ogawa,
    Reconsideration of the relaxational and vibrational line shapes of liquid water based on ultrabroadband dielectric spectroscopy, Phys. Chem. Chem. Phys. 20 26200-26209 (2018). This article is selected as a 2018 PCCP HOT Articles.
  26. S. Saito, B. Bagchi, and I. Ohmine,
    Crucial role of fragmented and isolated defects in persistent relaxation of deeply supercooled water, J. Chem. Phys. 149, 124504 (8 pages) (2018)
    Selected as the best in the Liquids, Glasses, and Crystals section in the last two years (2018-2020).
  27. M. Okuda, M. Higashi, K. Ohta, S. Saito, and K. Tominaga,
    Theoretical investigation on vibrational frequency fluctuations of SCN-derivatized vibrational probe molecule in water, Chem. Phys. 512, 82-87 (2018).
  28. M. Kalathingal, T. Sumikama, T. Mori, S. Oiki, and S. Saito,
    Structure and dynamics of solvent molecules inside Polytheonamide B channel in different environments: A molecular dynamics study, Phys. Chem. Chem. Phys. 20, 3334-3348 (2018).
  29. P. Pongprayoon and T. Mori,
    Critical role of dimer formation in monosaccharide binding to human serum albumin, Phys. Chem. Chem. Phys. 20, 3249-3257 (2018).

    30. 2017
  30. M. Okuda, M. Higashi, K. Ohta, S. Saito, and K. Tominaga,
    Vibrational frequency fluctuations of ionic vibrational probe in water: theoretical study with molecular dynamics simulation, Chem. Phys. Lett. 683, 547-552 (2017).

    31. 2016
  31. T. Mori and S. Saito,
    Molecular Mechanism Behind the Fast Folding/Unfolding Transitions of Villin Headpiece Subdomain: Hierarchy and Heterogeneity, J. Phys. Chem. B 120, 11683-11691 (2016).
  32. M. Higashi and S. Saito,
    Quantitative Evaluation of Site Energies and Their Fluctuations of Pigments in the Fenna-Matthews-Olson Complex with an Efficient Method for Generating a Potential Energy Surface, J. Chem. Theor. Comput. 12, 4128-4137 (2016).

    33. 2015
  33. J. Abe, T. Hiyama, A. Mukaiyama, S. Son, T. Mori, S. Saito, M. Osako, J. Wolanin, E. Yamashita, T. Kondo, and S. Akiyama,
    Atomic-Scale Origins of Slowness in the Cyanobacterial Circadian Clock, Science 349, 312 (2015).
  34. S. Imoto, S. S. Xantheas, and S. Saito,
    Ultrafast Dynamics of Liquid Water: Energy Relaxation and Transfer Processes of the OH Stretch and the HOH Bend, J. Phys. Chem. B 119, 11068-11078 (2015).
  35. J. Ono, S. Takada, and S. Saito,
    Couplings between Hierarchical Conformational Dynamics from Multi-Time Correlation Functions and Two-Dimensional Lifetime Spectra: Application to Adenylate Kinase, J. Chem. Phys. (Special Topic on Multidimensional Spectroscopy) 142, 212404 (13 pages) (2015).
  36. T. Mori and S. Saito,
    Dynamic Heterogeneity in the Folding/Unfolding Transitions of FiP35, J. Chem. Phys. 142, 135101 (7 pages) (2015). Selected as "the 2015's most read papers in J. Chem. Phys."

    37. 2014
  37. M. Higashi, T. Kosugi, S. Hayashi, and S. Saito,
    Theoretical Study on Excited States of Bacteriochlorophyll a in Solutions with Density Functional Assesment, J. Phys. Chem. B, 118, 10906-10918 (2014).

    38. 2013
  38. T. Sumikama, S. Saito, and I. Ohmine,
    Mechanism of ion permeation through a model channel: Roles of energetic and entropic contributions, J. Chem. Phys. 139, 165106 (8 pages) (2013).
  39. K. Kim, S. Saito, K. Miyazaki, G. Biroli, and D. R. Reichman,
    Dynamic Length Scales in Glass-Forming Liquids: An Inhomogeneous Molecular Dynamics Simulation Approach, J. Phys. Chem. B 117 , 13259–13267 (2013).
  40. S. Imoto, S. Xantheas, and S. Saito,
    Ultrafast dynamics of liquid water: Frequency fluctuations of the OH stretch and the HOH bend, J. Chem. Phys. 139, 044503 (2013).
    Selected as "the most-accessed articles in Liquids, Glasses, and Crystals in J. Chem. Phys. in 2013"
  41. S. Saito, I. Ohmine, and B. Bagchi,
    Frequency Dependence of Specific Heat in Supercooled Liquid Water and Emergence of Correlated Dynamics, J. Chem. Phys. 138, 094503 (7 pages) (2013).
    Selected as "the most-accessed articles in Liquids, Glasses, and Crystals in J. Chem. Phys. in 2013"
  42. S. Imoto, S. Xantheas, and S. Saito,
    Molecular Origin of the Difference in the HOH Bend of the IR Spectra between Liquid Water and Ice, J. Chem. Phys. 138, 054506 (8 pages) (2013).
  43. M. Higashi, S. Hirai, M. Banno, K. Ohta, S. Saito, and K. Tominaga,
    Theoretical and Experimental Studies on Vibrational Energy Relaxation of the CO Stretching Mode of Acetone in Alcohol Solutions, J. Phys. Chem. B 117, 4723-4731 (2013) (invited).
  44. K. Kim and S. Saito,
    Multiple Length and Time Scales of Dynamic Heterogeneities in Model Glass-Forming Liquids: A Systematic Analysis of Multi-Point and Multi-Time Correlations, J. Chem. Phys. (Special Topic on Glass Transition) 138, 12A506 (12 pages) (2013) (invited).
    Selected as "the most-accessed articles from Q1 2013" and "the most-accessed articles in 2014".
  45. T. Yagasaki and S. Saito,
    Fluctuations and Relaxation Dynamics of Liquid Water Revealed by Linear and Nonlinear Spectroscopy, Annu. Rev. Phys. Chem. 64, 55-75 (2013) (invited).
  46. K. Ohta, J. Tayama, S. Saito, and K. Tominaga,
    Solvation Dynamics of Vibrational State in Hydrogen-bonding Solvents Vibrational Frequency Fluctuation Studied by Three-Pulse Infrared Photon Echo Method, 'Ultrafast Infrared Vibrational Spectroscopy' edited by M. D. Fayer, (CRC Press).

    47. 2012
  47. K. Ohta, J. Tayama, S. Saito, and K. Tominaga,
    Vibrational Frequency Fluctuation of Ions in Aqueous Solutions Studied by Three-Pulse Infrared Photon Echo Method, Acc. Chem. Res. 45, 1982 (2012) (invited).
  48. N. Yamamoto, O. Kambara, K. Yamamoto, A. Tamura, S. Saito, and K. Tominaga,
    Temperature and Hydration Dependence of Low-Frequency Spectra of Poly-L-Glutamic Acid with Different Secondary Structures Studied by Terahertz Time-Domain Spectroscopy, Soft Matter, 8, 1997-2006 (2012).

    49. 2011
  49. T. Yagasaki and S. Saito,
    Energy Relaxation of Intermolecular Motions in Supercooled Water and Ice: A Molecular Dynamics Study, J. Chem. Phys. 135, 244511 (2011).
  50. J. Liu, W. H. Miller, G. S. Fanourgakis, S. S. Xantheas, S. Imoto, and S. Saito,
    Insights in Quantum Dynamical Effects in the Infrared Spectroscopy of Liquid Water from a Semiclassical Study with an Ab Initio-Based Flexible and Polarizable Force Field, J. Chem. Phys. 135, 244503 (14 pages)(2011).
  51. M. Higashi and S. Saito,
    Direct Simulation of Excited-State Intramolecular Proton Transfer and Vibrational Coherence of 10-Hydroxybenzo[h]quinoline in Solution, J. Phys. Chem. Letters 2, 2366-2371 (2011).
  52. S. Yamaguchi, K. Tominaga, and S. Saito,
    Intermolecular Vibrational Mode of the Benzoic Acid Dimer in Solution Observed by Terahertz Time-Domain Spectroscopy, Phys. Chem. Chem. Phys. 13, 14742-14749 (2011).
  53. T. Yagasaki and S. Saito,
    A Novel Method for Analyzing Energy Relaxation in Condensed Phases Using Nonequilibrium Molecular Dynamics Simulations: Application to the Energy Relaxation of Intermolecular Motions in Liquid Water, J. Chem. Phys. 134, 184503 (9 pages) (2011).
    This paper was selected in "Virtual Journal of Biological Physics Research" 21 (10) (2011).

    54. 2010
  54. K. Kim and S. Saito,
    Hidden Slow Time Scale of Crrelated Motions in Supercooled Liquids: Multi-Time Correlation Function Approach, J. Non-Crystalline. Solids 357, 371-375 (2010).
  55. T. Yagasaki, S. Saito, and I. Ohmine,
    Effects of Nonadditive Interactions on Ion Solvation at the Water/Vapor Interface: A Molecular Dynamics Study,J. Phys. Chem. A 114, 12573-12584 (2010).(invited)
  56. C. Kobayashi and S. Saito,
    Relation between conformational heterogeneity and reaction cycle of Ras: Molecular simulation of Ras, Biophys. J., 99, 3726-3734 (2010).
  57. K. Kim, K. Miyazaki, and S. Saito,
    Molecular dynamics studies of slow dynamics in random media: Type A-B and reentrant transitions, Eur. Phys. J. Special Topics., 189, 135-139 (2010).
  58. K. Kim and S. Saito,
    Role of the Lifetime of Dynamic Heterogeneity in the Frequency Dependent Stokes-Einstein Relation of Supercooled Liquids, J. Phy. Soc. Jpn., 79, 093601 (4 pages) (2010).
  59. K. Kim and S. Saito,
    Multi-Time Density Correlation Functions in Glass-Forming Liquids: Probing Dynamical Heterogeneity and its Lifetime, J. Chem. Phys. 133, 044511 (10 pages) (2010).
  60. J. Tayama, A. Ishihara, M. Banno, K. Ohta, S. Saito, and K. Tominaga,
    Temperature Dependence of Vibrational Frequency Fluctuation of N3- in D2O, J. Chem. Phys. 133, 014505 (11 pages) (2010).

    61. 2009
  61. K. Kim, K. Miyasaki, and S. Saito,
    Slow Dynamics in Random Media: Crossover from Glass to Localization Transition, Europhys. Lett. 88, 36002 (5 pages) (2009).
  62. T. Yagasaki, J. Ono, and S. Saito,
    Ultrafast Energy Relaxation and Anisotropy Decay of the Librational Motion in Liquid Water: A Molecular dynamics Study, J. Chem. Phys. 131, 164511 (11 pages) (2009).
    This paper was selected in "Virtual Journal of Biological Physics Research" 18 (9) (2009).
    This paper was selected in "Virtual Journal of Ultrafast Science" 8 (11) (2009).
  63. K. Kim and S. Saito,
    Multiple Time Scales Hidden in Heterogeneous Dynamics of Glass-Forming Liquids, Phys. Rev. E 79, 060501(R) (4 pages) (2009).
  64. T. Yagasaki and S. Saito,
    Molecular Dynamics Simulation of Nonlinear Spectroscopies of Intermolecular Motions in Liquid Water, Acc. Chem. Res. 42, 1250-1258 (2009).(invited)
  65. A. Furukawa, K. Kim, S. Saito, and H. Tanaka,
    Anisotropic Cooperative Structural Rearrangements in Sheared Supercooled Liquids, Phys. Rev. Lett. 102, 016001 (4 pages) (2009).

    66. 2008
  66. T. Yagasaki and S. Saito,
    Ultrafast Intermolecular Dynamics of Liquid Water: A Theoretical Study on Two-dimensional Infrared spectroscopy, J. Chem. Phys. 128, 154521 (7 pages) (2008)
    This paper was selected in "Virtual Journal of Biological Physics Research" 15 (9) 2008.
    This paper was selected in "Virtual Journal of Ultrafast Science" 7 (5) 2008.

    67. 2007
  67. M. Kamiya, S. Saito and I. Ohmine,
    Proton Transfer and Associated Molecular Rearrangements in Photocycle of Photoactive Yellow Protein; Role of Water Molecular Migration on Proton Transfer Reaction, J. Phys. Chem. B 111, 2948-2956 (2007)

    68. 2006
  68. T. Sumikama, S. Saito, and I. Ohmine,
    Mechanism of Ion Permeation in Model Channel; Free Energy Surface and Dynamics of K+ Ion Transport in Anion-Doped Carbon Nanotube, J. Phys. Chem. B 110, 20671-20677 (2006)
  69. S. Saito and I. Ohmine,
    Fifth-Order Two-Dimensional Raman Spectroscopy of Liquid Water, Crystalline Ice Ih and Amorphous Ices: Sensitivity to Anharmonic Dynamics and Local Hydrogen Bond Network Structure, J. Chem. Phys. 125, 084506 (12 pages) (2006).
    This paper was selected in "Virtual Journal of Biological Physics Research" 12 (5) 2006.
    This paper was selected in "Virtual Journal of Ultrafast Science" 5 (9) 2006.
  70. A. Shudo, K. Ichiki, and S. Saito,
    Origin of slow relaxation in liquid water dynamics: A possible scenario for the presence of bottleneck in phase space, Europhys. Lett. 73, 826-832 (2006).

    71. 2005
  71. T. Yagasaki, K. Iwahashi, S. Saito, and I. Ohmine,
    A Theoretical Study on Anomalous Temperature Dependence of pKw of Water, J. Chem. Phys. 122, 144504 (9 pages) (2005).
  73. T. Uemura, S. Saito, Y. Mizutani, and K. Tominaga,
    Isotope Dilution Effects on the Hydroxyl Strech Bands of Alchols, Mol. Phys. 103(1), 37-44 (2005).
  74. A. Shudo and S. Saito,
    Slow Relaxation in Hamiltonian Systems with Internal Degrees of Freedom, Adv. Chem. Phys. 130, 375-421, (2005).

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