1. Tomoyuki Hayashi, and Alexei Stuchebrukhov, "Electron Tunnelingnext Pathways in Respiratory Complex I: The Role of the Internal Water between the Enzyme Subunits", J. Electroanal. Chem. (in press)
2. Tomoyuki Hayashi, and Alexei Stuchebrukhov, "Quantum Electron Tunneling in Respiratory Complex I", J. Phys. Chem. B,  115, 5354 (2011) [pdf]
3. Tomoyuki Hayashi, and Alexei Stuchebrukhov, "Electron Tunneling in Respiratory Complex I", Proc. Natl. Acad. Sci. USA,  107, 19157 (2010) [pdf]
4. Shihai Yan, Sunwoo Kang, Tomoyuki Hayashi, Shaul Mukamel, and Jin Yong Lee, “Computational Studies on Electron and Proton Transfer in Phenol-Imidazole-Base Triads”, J. Comp. Chem. 31, 393 (2010) [pdf]
5. Wei Zhuang, Tomoyuki Hayashi, and Shaul Mukamel, "Coherent Multidimensional Vibrational Spectroscopy of Biomolecules; Concepts, Simulations and Challenges," Angew. Chem. 48, 3750 (2009) [pdf]
6. Alex Paarmann, Tomoyuki Hayashi, Shaul Mukamel and R. J. Dwayne Miller, “Nonlinear response of vibrational excitons: Simulating the two-dimensional infrared spectrum of liquid water”, J. Chem. Phys. 130, 204110 (2009) [pdf]
7. Tomoyuki Hayashi, and Shaul Mukamel, “Two-Dimensional Vibrational Lineshapes of All Amide Bands in a Helical Peptide”, J. Mol. Liq. 141, 149 (2008) [pdf]
8. Alex Paarmann, Tomoyuki Hayashi, Shaul Mukamel and R. J. D. Miller, “Probing Intermolecular Couplings in Liquid Water with 2DIR Photon Echo Spectroscopy”,J. Chem. Phys. 128, 191103 (2008) [pdf]
9. Sayuri Yamaguchi, Motohiro Banno, Kaoru Ohta, Keisuke Tominagaa, and Tomoyuki Hayashi, “Vibrational dynamics of benzoic acid in nonpolar solvents studied by subpicosecond infrared pump–probe spectroscopy”, Chem. Phys. Lett. 462, 238-242 (2008) [pdf]
10. Cyril Falvo, Tomoyuki Hayashi, Wei Zhuang, and Shaul Mukamel, "Coherent 2D Spectroscopy of a Cyclic Decapeptide Antamanide: A Simulation Study of the Amide-I and Amide-A Bands," , J. Phys. Chem. B 112, 12479 (2008) [pdf]
11. Tomoyuki Hayashi, and Shaul Mukamel, “Vibraion-exciton Couplings for the  Amide I, II, III and A Modes of Peptides”, J. Phys. Chem. B 111, 11032-11046 (2007) (A Figure selected for Cover Art) [pdf]
12. Wei Zhuang, Darius. Abramavicius, Tomoyuki Hayashi, Shaul Mukamel, "Simulation Protocols for Coherent Femtosecond Vibrational Spectra of Peptides", J. Phys. Chem. B 110, 3362-3374 (2006)
13. Tomoyuki Hayashi, and Shaul Mukamel, "Correlated Hydrogen Bonding Fluctuations and Vibrational Cross Peaks in NMA: Simulation Based on a Complete Electrostatic DFT Map", J. Chem. Phys. 125, 194510-194520 (2006) (Selected for December 1, 2006 issue of Virtual Journal of Biological Physics Research) [pdf]
14. Tomoyuki Hayashi, Thomas la Cour Jansen, Wei Zhuang, Shaul Mukamel, "Collective Solvent Coordinates for the Infrared Spectrum of HOD in D2O Based on an Ab Initio Electrostatic Map", J. Phys. Chem. A, 109 64-82 (2005). [pdf]
15. Thomas la Cour Jansen, Tomoyuki Hayashi, Wei Zhuang and Shaul Mukamel, "Stochastic Liouville Equations for Hydrogen-Bonding Fluctuations and their Signatures in Two Dimensional Vibrational Spectroscopy of Water", J. Chem. Phys. 123, 114504-114514 (2005)
16. Tomoyuki Hayashi, Wei Zhuang and Shaul Mukamel, "Electrostatic DFT Map for the Complete Vibrational Amide Band of NMA", J. Phys. Chem. A109, 9747-9759 (2005) [pdf]
17. Tomoyuki Hayashi and Shaul Mukamel, "Arnoldi Algorithm for the Simulation of Multidimensional Infrared Spectroscopy", Bull. Kor. Chem. Soc. 24, 1107-1110 (2003).
18. Tomoyuki Hayashi and Shaul Mukamel, "Multidimensional Infrared Signatures of Intramolecular Hydrogen-Bonding in Malonaldehyde", J. Phys. Chem. A 107, 9113-9131 (2003) [pdf].
19. Tomoyuki Hayashi, and Shaul Mukamel, "Infrared Signatures of Proton Transfer in G.C and A.T Base Pairs: DFT Study", Israel J. Chem. 44, 185-191 (2003).
20. Tomoyuki Hayashi, and Hiro-o Hamaguchi, "Solvent Induced Dynamic Polarization, Vibrational Dephasing, and Infrared Band Shape of the C=O Stretch Mode of Acetone in Acetonitrile: a New Theoretical Approach", Chem. Phys. Lett. 326, 115-122 (1998) [pdf]

Unrefereed Journal Publications and Conference Papers

1. Tomoyuki Hayashi, “Simulational Approach to Vibrational Dyanmics in Solution and Its Application to 2-Dimensional Infrared Spectrosocpy" (in Japanese), The Bulletin of the Molecular Simulation Society of Japan, 11, 37-42 (2009)
2. Tomoyuki Hayashi, “Guide to Carrying out Postodoctoral Research in the USA” (in Japanese), Molecular Science, Vol. 1, No.1, A0014(2007)
3. Alex Paarmann, Tomoyuki Hayashi, Shaul Mukamel and R. J. Dwayne Miller,"Nonlinear Vibrational Response of Coupled Anharmonic System-Towards the 2DIR Spectrums of H2O," TRVS Proceedings (2007)
4. Tomoyuki Hayashi, Wei Zhuang, Shaul Mukamel, "Nonlinear Vibrational Response of the Amide I, II, III and A Bands of NMA: Simulation Study Based on an Electrostatic DFT Map", TRVS XII Conference Proceeding, (2006)
5. Frantisek Sanda, Wei Zhuang, Thomas La Cour Jansen, Tomoyuki Hayashi and Shaul Mukamel "Signatures of Chemical Exchange in 2D Vibrational Spectroscopy; Simulation Based on the Stochastic Liouville Equations", In Ultrafast Phenomena XV, R.J.D. Miller, A.M. Weiner, P. Cornum and D.M. Jonas (editors) Springer Verlag (2006)
6. Tomoyuki Hayashi, Wei Zhuang and Shaul Mukamel, "Lineshapes and Correlations in Two Dimensional Vibrational Signals of NMA", In Ultrafast Phenomena XV, R.J.D. Miller, A.M. Weiner, P. Cornum and D.M. Jonas (editors) Springer Verlag (2006)
7. Tomoyuki Hayashi and Shaul Mukamel, "Multidimensional Nonlinear Spectroscopy of Conformational Relaxation in Azobenzene", R. Venkatramani, in Ultrafast Phenomena XIII, R.J.Miller, M.M. Murnane, N.F. Scherer, and A.M. Wiener, Editors (Springer-Verlag, Berlin) 619-621 (2002)