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TU Dresden » Faculty of Mechanical Science and Engineering » Institute for Materials Science » Chair of Materials Science and Nanotechnology



Thursday, 09 June 2011
(at 13:00 in room 115, Hallwachsstr. 3)
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Large-scale ab initio simulations for biomolecular systems

Shigenori Tanaka

Graduate School of System Informatics
Kobe University
  Japan  






We have developed an ab initio methodology to calculate the electronic states of biomolecules on the basis of fragment molecular orbital (FMO) method. For instance, we have recently performed large-scale electron-correlated (MP2 and MP3) calculations for influenza virus hemagglutinin (HA) complexes up to the size of about 36,000 atoms [1]. These calculated results have been used for the analyses of specific molecular interactions associated with HA and for their applications to mutation prediction and drug design for influenza viruses. In addition, we have also carried out the FMO calculations for excited states of biomolecules such as red fluorescent protein and firefly luciferase-oxyluciferin complex [2] to investigate their absorption and emission spectra. Since these FMO calculations are completed in relatively short computational time, we could perform the molecular orbital calculations for many snapshots generated through molecular dynamics simulations in near future. Then, combining the dynamical information about nuclear motion with that associated with the electronic coupling between donor and acceptor, we can analyze the charge and energy transfer dynamics in an ab initio way even for large biomolecules [3,4]. In this talk, I will also touch upon some topics related to aqueous solvent surrounding biomolecules: Solvation energies can be efficiently evaluated with the aid of the implicit solvent model in the framework of the FMO method [5]. The periodic boundary condition has also been incorporated into the FMO calculations to appropriately perform molecular simulations in aqueous solution [6]. Nuclear quantum effect associated with hydrogen atoms can be taken into account by employing the path integral method based on the FMO scheme [7].
References
[1] Y. Mochizuki, K. Yamashita, K. Fukuzawa, K. Takematsu, H. Watanabe, N. Taguchi, Y. Okiyama, M. Tsuboi, T. Nakano and S. Tanaka, Chem. Phys. Lett. 493 (2010) 346.
[2] A. Tagami, N. Ishibashi, D. Kato, N. Taguchi, Y. Mochizuki, H. Watanabe, M. Ito and S. Tanaka, Chem. Phys. Lett. 472 (2009) 118.
[3] S. Tanaka and E.B. Starikov, Phys. Rev. E 81 (2010) 027101.
[4] S. Tanaka, Chem. Phys. Lett. 508 (2011) 139.
[5] H. Watanabe, Y. Okiyama, T. Nakano and S. Tanaka, Chem. Phys. Lett. 500 (2010) 116.
[6] T. Fujita, T. Nakano and S. Tanaka, Chem. Phys. Lett. 506 (2011) 112.
[7] T. Fujita, H. Watanabe and S. Tanaka, J. Phys. Soc. Jpn. 78 (2009) 104723.

Brief Bio:

Ph.D. (physics), University of Tokyo, 1986; JSPS Fellow, 1986-1987; Research Associate, University of Tokyo, 1987-1989; Researcher, Toshiba Research and Development Center, 1989-2004; Visiting Associate, California Institute of Technology, 1995-1996; Project Leader, ACT-JST, 2001-2004; Project Leader, JST-CREST, 2004-2010; Professor (Computational Biology), Kobe University, 2004-today



slides (pdf)

Invited by G. Cuniberti

Within the nanoSeminar

last modified: 2018.10.24 Mi
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