Development of a direct kinetic Monte Carlo method for the investigation of nanostructure formation processes

• Project/Area Number: 26410013
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Physical chemistry
• Research Institution: Nagoya University
• Principal Investigator: Irle Stephan 名古屋大学, トランスフォーマティブトランスフォーマティブ生命分子研究所, 教授 (00432336)
• Project Period (FY): 2014-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2016: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2015: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2014: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
• Keywords: kinetic Monte Carlo / nanostructure formation / extended timescale / molecular dynamics / nanotubes / DFTB/MD / rare events / KMC / 量子化学分子動力学 / 分子動力学 / Monte Carlo

Outline of Final Research Achievements

We have successfully connected the global reaction route mapping (GRRM) method for use with the density-functional tight-binding (DFTB) quantum chemical potential. Since DFTB is 3 orders of magnitude faster than conventional DFT methods, it became possible to use the GRRM-DFTB combination in on-the-fly kinetic Monte Carlo simulations. "flyKMC" achieved good agreement with the 1st order kinetics of carbon atom migration on an iron nanoparticle observed during independent quantum chemical molecular dynamics simulations using the DFTB potential.

Research Products

• [Int'l Joint Research] Newcastle University(Australia)
• [Int'l Joint Research] Dr. Alister J. Page/Newcastle University/Newcastle, NSW, Australia(Australia)
• [Int'l Joint Research]
• [Journal Article] A Global Reaction Route Mapping-based Kinetic Monte Carlo Algorithm (2016)
  • Author(s): Izaac Mitchel, Stephan Irle, Alister J. Page
  • Journal Title: J. Chem. Phys. Volume: 145 Issue: 2
  • DOI: 10.1063/1.4954660
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Spanning the “Parameter Space” of Chemical Vapor Deposition Graphene Growth with Quantum Chemical Simulations (2016)
  • Author(s): A. J. Page, I. Mitchell, H.-B. Li, M.-G. Jiao, Y. Wang, S. Irle, K. Morokuma
  • Journal Title: J. Phys. Chem. C Volume: 120 Issue: 26 Pages: 13851-13864
  • DOI: 10.1021/acs.jpcc.6b02673
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Cycloparaphenylene as molecular porous carbon solid with uniform pores exhibiting adsorption-induced softness (2016)
  • Author(s): H. Sakamoto, T. Fujimori, X. Li, K. Kaneko, K. Kan, N. Ozaki, Y. Hijikata, S. Irle, K. Itami
  • Journal Title: Chem. Sci. Volume: Just accepted Issue: 7 Pages: 4204-4210
  • DOI: 10.1039/c6sc00092d
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Molecular dynamical modelling of endohedral fullerenes formation in plasma (2016)
  • Author(s): A. S. Fedorov, E. A. Kovaleva, T. A. Lubkova, Z. I. Popov, A. A. Kuzubov, M. A. Visotin, S. Irle
  • Journal Title: IOP Conf. Series: Materials Science and Engineering Volume: 110 Pages: 012078-012078
  • DOI: 10.1088/1757-899x/110/1/012078
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Implementation of replica-exchange umbrella sampling to DFTB+ simulation package (2016)
  • Author(s): S. Ito, S. Irle, Y. Okamoto
  • Journal Title: Comp. Phys. Commun. Volume: accepted Pages: 1-10
  • DOI: 10.1016/j.cpc.2016.02.010
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Self-assembly of endohedral metallofullerenes: a decisive role of cooling gas and metal–carbon bonding (2016)
  • Author(s): Q. Deng, Th. Heine, S. Irle, A. A. Popov
  • Journal Title: Nanoscale Volume: 8(6) Issue: 6 Pages: 3796-3808
  • DOI: 10.1039/c5nr08645k
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Diversity in electronic structure and vibrational properties of fullerene isomers correlates with cage curvature (2016)
  • Author(s): H. A. Witek, S. Irle
  • Journal Title: Carbon Volume: 100 Pages: 484-494
  • DOI: 10.1016/j.carbon.2016.01.015
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] QM/MD studies on graphene growth from small islands on the Ni(111) surface (2016)
  • Author(s): M. Jiao, W. Song, H.-J. Qian, Y. Wang, Z. Wu, S. Irle, Keiji Morokuma
  • Journal Title: Nanoscale Volume: 8(5) Pages: 3067-3074
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Automatized Parameterization of DFTB using Particle Swarm Optimization (2016)
  • Author(s): C.-P. Chou, Y. Nishimura, C.-C. Fan, G. Mazur, S. Irle, H. A. Witek
  • Journal Title: J. Chem. Theory Comput. Volume: 12(1) Issue: 1 Pages: 53-64
  • DOI: 10.1021/acs.jctc.5b00673
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Automatized Parameterization of the Density-functional Tight-binding Method. II. Two-center Integrals (2016)
  • Author(s): H. A. Witek, C.-P. Chou, G. Mazur, Y. Nishimura, S. Irle, Th. Frauenheim, K. Morokuma
  • Journal Title: J. Chin. Chem. Soc. Volume: 63(1) Issue: 1 Pages: 57-68
  • DOI: 10.1002/jccs.201500066
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Large-Scale Quantum-Mechanical Molecular Dynamics Simulations Using Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method (2015)
  • Author(s): Y. Nishimoto, H. Nakata, D. G. Fedorov, S. Irle
  • Journal Title: J. Chem. Phys. Lett. Volume: 6(24) Issue: 18 Pages: 5034-5039
  • DOI: 10.1021/jz4015647
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Third-order density-functional tight-binding combined with the fragment molecular orbital method (2015)
  • Author(s): Y. Nishimoto, D. G. Fedorov, S. Irle
  • Journal Title: Chem. Phys. Lett. Volume: 636 Pages: 90-96
  • DOI: 10.1016/j.cplett.2015.07.022
  • NAID: 120005674619
• [Journal Article] Fabrication and Optical Probing of Highly Extended, Ultrathin Graphene Nanoribbons in Carbon Nanotubes (2015)
  • Author(s): H.E. Lim, Y. Miyata, M. Fujihara, S. Okada, Z. Liu, Arifin, K. Sato, H. Omachi, R. Kitaura, S. Irle, K. Suenaga, H. Shinohara
  • Journal Title: ACS nano Volume: 未確定 Issue: 5 Pages: 5034-5040
  • DOI: 10.1021/nn507408m
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Locking Covalent Organic Frameworks with Hydrogen Bonds: General and Remarkable Effects on Crystalline Structure, Physical Properties, and Photochemical Activities (2015)
  • Author(s): X. Chen, M. Addicoat, E. Jin, L. Zhai, H. Xu, N. Huang, Z. Guo, L. Liu, S. Irle, D. Jiang
  • Journal Title: J. Am. Chem. Soc. (Communication) Volume: 137 Issue: 9 Pages: 3241-3247
  • DOI: 10.1021/ja509602c
  • Peer Reviewed
• [Journal Article] Insights into carbon nanotube and graphene formation mechanisms from molecular simulations (2015)
  • Author(s): A. J. Page, F. Ding, S. Irle, K. Morokuma
  • Journal Title: Rep. Prog. Phys. Volume: 78 Issue: 3 Pages: 036501-036501
  • DOI: 10.1088/0034-4885/78/3/036501
  • Peer Reviewed
• [Journal Article] Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method (2014)
  • Author(s): Yoshio Nishimoto, Dmitri G. Fedorov, and Stephan Irle
  • Journal Title: Journal of Chemical Theory and Computation Volume: 10 Issue: 11 Pages: 4801-4812
  • DOI: 10.1021/ct500489d
  • Peer Reviewed
• [Journal Article] Direct evidence of active and inactive phases of Fe catalyst nanoparticles for carbon nanotube formation (2014)
  • Author(s): S. Mazzucco, Y. Wang, M. Tanase, M. Picher, K. Li, Z. Wu, S. Irle, R. Sharma
  • Journal Title: J. Catalysis Volume: 319 Pages: 54-60
  • DOI: 10.1016/j.jcat.2014.07.023
  • Peer Reviewed
• [Journal Article] Quantum dynamics simulations reveal vibronic effects on the optical properties of [n]cycloparaphenylenes (2014)
  • Author(s): V. S. Reddy, C. Camacho, J. Xia, R. Jasti, S. Irle
  • Journal Title: J. Chem. Theory Comput. Volume: 10 Issue: 9 Pages: 4025-4036
  • DOI: 10.1021/ct500524y
  • Peer Reviewed
• [Journal Article] Super-Reduced Polyoxometalates: Excellent Molecular Cluster Battery Components and Semipermeable Molecular Capacitors (2014)
  • Author(s): Yoshio Nishimoto, Daisuke Yokogawa, Hirofumi Yoshikawa, Kunio Awaga, and Stephan Irle
  • Journal Title: Journal of the American Society Volume: 136 Issue: 25 Pages: 9042-9052
  • DOI: 10.1021/ja5032369
  • Peer Reviewed
• [Presentation] Molecular Dynamics in Computational Materials Sciences: From the Study of Nanostructure Formation to the Design of Fluorescent Dyes (2016)
  • Author(s): S. Irle
  • Organizer: Computational Chemistry (CC) symposium, International Conference on Computational Methods in Science and Engineering (ICCMSE) 2016
  • Place of Presentation: Metropolitan Hotel, Athens, Greece
  • Year and Date: 2016-03-17
  • Invited
• [Presentation] A priori prediction of chemical reaction mechanisms in complex systems based on quantum chemical molecular dynamics (2015)
  • Author(s): S. Irle
  • Organizer: Pacifichem 2015
  • Place of Presentation: Honolulu, HI, U.S.A.
  • Year and Date: 2015-12-15
  • Int'l Joint Research / Invited
• [Presentation] Calculation of Charge Carrier Mobility in Covalent Organic Frameworks (2015)
  • Author(s): S. Irle
  • Organizer: Pacifichem 2015
  • Place of Presentation: Honolulu, HI, U.S.A.
  • Year and Date: 2015-12-15
  • Int'l Joint Research / Invited
• [Presentation] Simulations of dynamic C60-Ih self-assembly cut the Gordian Knot: Coexistence of bottom-up and top-down mechanisms (2015)
  • Author(s): S. Irle
  • Organizer: Molecular Designs for Advance Materials: Workshop and Conference
  • Place of Presentation: Chiang Mai University, Thailand
  • Year and Date: 2015-11-24
  • Invited
• [Presentation] Fun with graphenes: Quantum chemical simulations of synthesis and hydrogenation dynamics (2015)
  • Author(s): S. Irle
  • Organizer: Satellite meeting of the 15th International Congress of Quantum Chemistry (ICQC)
  • Place of Presentation: Hefei, China
  • Year and Date: 2015-06-14
  • Int'l Joint Research / Invited
• [Presentation] Calculation of Charge Carrier Mobility in Covalent Organic Frameworks (2014)
  • Author(s): Stephan Irle
  • Organizer: XIXth International Workshop on Quantum Systems in Chemistry, Physics and Biology (QSCP XIX)
  • Place of Presentation: Taipei, Taiwan
  • Year and Date: 2014-11-11 – 2014-11-17
  • Invited
• [Presentation] CPP fluorescence and seeded SWCNT growth mechanisms probed in quantum chemical simulations (2014)
  • Author(s): Stephan Irle
  • Organizer: Fusion Conference “From Carbon-Rich Molecules to Carbon-Based Materials”
  • Place of Presentation: El Jadida, Morocco
  • Year and Date: 2014-09-22 – 2014-09-25
  • Invited
• [Presentation] Recent developments for the quantum chemical investigation of systems with high structural complexity (2014)
  • Author(s): Stephan Irle
  • Organizer: Satellite Meeting “Japan-Russia Joint Symposium - Chemical Theory for Complex Systems” of the International Conference “Molecular Complexity in Modern Chemistry [MCMC-2014]
  • Place of Presentation: Moscow, Russia
  • Year and Date: 2014-09-13 – 2014-09-19
  • Invited
• [Presentation] Simulations of dynamic C60-Ih self-assembly cut the Gordian Knot: Coexistence of bottom-up and top-down mechanisms (2014)
  • Author(s): Stephan Irle
  • Organizer: 47th Fullerene-Nanotubes-Graphene General Symposium
  • Place of Presentation: Nagoya University, Nagoya
  • Year and Date: 2014-09-03 – 2014-09-05
• [Presentation] Unusual fluorescence from lanthanide-containing endohedral metallofullerenes and metal carbide fullerenes (2014)
  • Author(s): S. Irle, J. Wang, T. Kowalczyk
  • Organizer: XI GIRONA SEMINAR on Carbon, Metal, and Carbon-Metal Clusters: From Theory to Applications
  • Place of Presentation: Girona, Spain
  • Year and Date: 2014-06-30 – 2014-07-03
  • Invited
• [Remarks] Irle Group Webpage
  • URL: http://qc.chem.nagoya-u.ac.jp
• [Remarks] "Carbon nanotubes grown in combustion flames"
  • URL: http://www.researchsea.com/2015.pdf