| Yuriko Aoki | Last modified date：2024.04.26 |
Professor /
Material Science /
Department of Advanced Materials Science and Engineering /
Faculty of Engineering Sciences
Presentations
| 1. | Yuriko Aoki, Yuuichi Orimoto, Order-N Elongation method toward multiscale calculations, TACC2023, 2023.09. |
| 2. | ＠イヴォニナ マリア、＠折本裕一、＠青木百合子, Mutagenesis in methylated DNA: a quantum chemical insight via Through-space/bond orbital interaction analysis, 第17回分子科学討論会, 2023.09. |
| 3. | Y. Aoki, Y. Orimoto, Order-N Elongation method for highly accurate bio/material design, The 10th edition of the conference of The Asia Pacific Association of Theoretical and Computational Chemists (APATCC-10), 2023.02, [URL]. |
| 4. | X. Huang, Y. Orimoto, and Y. Aoki, Novel Polycarbonate Material Design of Light-Resistance: a Theoretical Investigation, The 10th edition of the conference of The Asia Pacific Association of Theoretical and Computational Chemists (APATCC-10), 2023.02, [URL]. |
| 5. | M. Ivonina, Y. Orimoto, and Y. Aoki, Through-space/Through-bond method for analyzing molecular orbital interactions and its application to DNA mutations (Physical Chemistry Chemical Physics poster award), The 10th edition of the conference of The Asia Pacific Association of Theoretical and Computational Chemists (APATCC-10), 2023.02, [URL], Being able to quantify molecular orbital interactions is helpful for studying properties of molecular systems such as stability, reactivity, chemical bonds pattern, etc. For this purpose, we developed an ab initio approach for analyzing various molecular orbital interactions that occur through space and through bond, the so-called “Through-space/Through-bond” (TS/TB) method. The proposed approach is based on the idea of extremely increasing the absolute value of exponent for interacting orbitals and, thus, cutting off the corresponding one- and two-electron integrals. Within two rounds of SCF calculation (i.e., one before and one after cutting off integrals) it is possible to estimate the contribution of target interaction into system stability through the difference in the resulting total energies. In this presentation, we will discuss the concept of TS/TB method and some relevant features: (1) using natural orbitals instead of Gaussian-type orbitals to investigate charge transfer or conjugation effects, (2) taking solvent effect into account via PCM integrals, and (3) including electron correlation via MP2 correction. As an application example, we will demonstrate how TS/TB method was used to evaluate the inter- and intra-molecular interactions (i.e. hydrogen bonds, π-conjugation, stacking) in a DNA fragment that includes O6-methylated guanine lesion, which causes transition mutation G···C→A···T.. |
| 6. | Yuuichi Orimoto, Keisuke Hisama, Yuriko Aoki, Computational analysis of local electronic structures in block sequence DNA/RNA via elongation method and neural networks, ISNAC2022, 2022.11, The ab initio elongation method provides “local” electronic structures in a target system with high-throughput efficiency. The method was applied to acquire local site information such as local HOMO/LUMO levels in various block sequence nucleic acids. Neural network was adopted to analyze the acquired huge data to recognize patterns and detect singular electronic structure site. This approach can be useful to elucidate DNA/RNA related diseases from electronic structure viewpoints.. |
| 7. | M. Ivonina, Y. Orimoto，and Y. Aoki, Exploring the mutagenesis mechanism in DNA damaged by O6-methylguanine via through-space/bond orbital interaction analysis, 第16回分子科学討論会, 2022.09. |
| 8. | D. Mashkovtsev, Y. Orimoto，and Y. Aoki, Modified Local Excitation Approximation for fast and accurate TDDFT calculations in photoactive center of macromolecules, 第16回分子科学討論会, 2022.09. |
| 9. | X. Huang，Y. Orimoto，and Y. Aoki, Theoretical exploitation of novel light-resistant polycarbonate material design, 第16回分子科学討論会, 2022.09. |
| 10. | Yuuichi Orimoto, Keisuke Hisama, Anna Pomogaeva, Kazuhiko Nakatani, Yuriko Aoki, Computational ligand design for DNA bulge recognition by a combination of multi-level layered elongation method and machine learning, ISNAC2021, 2021.10. |
| 11. | D. Mashkovtsev，Y. Orimoto，Y. Aoki, Fast calculation of electron excitations based on Regional Localized Molecular Orbitals, 第15回分子科学討論会, 2021.09, [URL]. |
| 12. | M. Ivonina，Y. Orimoto，Y. Aoki, Quantum chemistry-machine learning combined approach for computational design of functional polymers for nonlinear optics application., 第15回分子科学討論会, 2021.09. |
| 13. | , [URL]. |
| 14. | , [URL]. |
| 15. | M. V. Ivonina, Y. Orimoto, and Y. Aoki, Nonlinear optical properties of push-pull π-conjugated molecules via elongation-FF method, The 2nd R-CCS international symposium, 2020.03, [URL]. |
| 16. | Y. Aoki, Y. Orimoto, and A. Pomogaeva, A linear scaling approach for efficient geometry optimization in perturbed DNAs, The Ninth Conference of the Asia-Pacific Association of Theoretical and Computational Chemists (APATCC2019), 2019.10. |
| 17. | Y. Orimoto, A. Pomogaeva, K. Hisama, A. Yano, K. Miyagawa, K. Nakatani, and Y. Aoki, Computer-aided molecular design for DNA bulge recognition ligands by order-N elongation method, The 46th International Symposium on Nucleic Acids Chemistry(ISNAC2019), 2019.10. |
| 18. | Yuuichi Orimoto, Anna Pomogaeva, Keisuke Hisama, Ayaka Yano, Koichi Miyagawa, Kazuhiko Nakatani, Yuriko Aoki, Computer-aided molecular design for DNA bulge recognition ligands by order-N elongation method, ISNAC2019, 2019.10. |
| 19. | Y. Aoki, Y. Orimoto, and A. Pomogaeva, Linear-scaling two-ways elongation method for local perturbation on nanotubes/DNA, Current Trends in Theoretical Chemistry VIII(CTTC 8), 2019.09, We have been developing “elongation method” to calculate electronic states of one-dimensional polymers as well as three-dimensional materials efficiently and accurately for last 30 years [for examples, 1-6]. The main point of this method is to create the region localized molecular orbitals (RLMOs) [2] in the process of the system elongation, namely during adding interacting molecules to the original cluster. To treat local perturbation of large systems more efficiently, we extended the one-way elongation method to the two-ways elongation method. This treatment targets the systems in which local perturbations like defects, interactions, or structural deformations occur on a special region in a polymer, surface, or solid. By this treatment one can perform the electronic states calculations from the important perturbed region (PR) to the other environment region (ER) and vice-versa. The advantage of this treatment is that different levels of calculations can be applied to the PR and ER easily and automatically, according to the importance of the occurring phenomenon. For examples, if a special site on a nanotube interacts with anion dopants, one can calculate the PR by MP2/6-311+G(d,p) [4] and the ER by HF/3-21G basis set, or if some defect occurs, one can treat the PR as open-shell [3], while the ER far from the defect as closed-shell as the ER electronic states might remain unchanged. Such kind of different levels of calculations on different regions can be combined seamlessly under the RLMOs created during system elongation. We call this method as Central (C) to Terminal (T) [C2T] or Terminal (T) to Central (C) [T2C] elongation method and it will be a useful tool for the efficient analysis/prediction of the phenomena in large-scale complex systems for which conventional method cannot handle. In this talk, we explain the basic concept of this method and show some examples that were applied to nanotubes and DNA. [1] A. Imamura, Y. Aoki, K. Maekawa, J. Chem. Phys., 95 (1991) 5419. [2] F. L. Gu, Y. Aoki, J. Korchowiec, A. Imamura, B. Kirtman, J. Chem. Phys., 121 (2004) 10385. [3] J. Korchowiec, F. L. Gu, Y. Aoki, Int. J. Quantum Chem., 105, (2005) 875. [4] M. Makowski, J. Korchowiec, F. L. Gu, Y. Aoki, J. Comput. Chem., 31 (2010) 1733. [5] Y. Aoki, F. L. Gu, Phys. Chem. Chem. Phys., 14 (2012) 7640. [6] K. Liu, Y. Yan, F. L. Gu, Y. Aoki, Chem. Phys. Lett., 565 (2013) 143.. |
| 20. | 青木 百合子, 高分子における量子化学計算, 2018東海シンポジウム, 2019.01. |
| 21. | Y. Orimoto, A. Pomogaeva, A. Yano, K. Nakatani, and Y. Aoki, High throughput molecular design/exploration for DNA bulge/mismatch recognition: computational approach by elongation method, The 45th International Symposium on Nucleic Acids Chemistry(ISNAC2018), 2018.11. |
| 22. | Y. Aoki, Elongation method for efficient material design by quantum chemical calculations, 16-th V.A. Fock Meeting on Theoretical, Quantum and Computational Chemistry, 2018.10. |
| 23. | Y. Orimoto, S. Shirane, and Y. Aoki, Ab initio MO study of propylene polymerization by zirconocene/borate catalyst, 16-th V.A. Fock Meeting on Theoretical, Quantum and Computational Chemistry, 2018.10. |
| 24. | D. Mashkovtsev, W. Mizukami, J. Korchowiec, A. Stachowicz-kuśnierz, and Y. Aoki, Improving the elongation method: intermediate electrostatic field for DNA and proteins via genetic algorithms, 第12回分子科学討論会, 2018.09. |
| 25. | Y. Aoki, Efficient electronic states calculations by elongation method and its application to DNA, Nanotubes, and functional polymer design, St. Petersburg State University, 2018.09. |
| 26. | Y. Aoki, A. Pomogaeva, and Y. Orimoto, Development of efficient elongation method toward locally perturbed aperiodic nano/bio systems, 7th JCS SYMPOSIUM, 2018.05. |
| 27. | D. Mashkovtsev, W. Mizukami, and Y. Aoki, Accelerating modeling of polymers: atomic charges via genetic algorithms, 三者連携シンポジウム 100年後の科学と社会を考える “数理・AI が解く未来 ～計算科学の展開と期待～”, 2018.05. |
| 28. | H. Teramae and Y. Aoki, Ab Initio Electronic Structure Calculation of Polymononucleotide, a Model of B‐type DNA, 14th International Conference of Computational Methods in Sciences and Engineering(ICCMSE 2018), 2018.03, [URL]. |
| 29. | 青木 百合子, 水上 渉, 大川 育子, 折本 裕一, Elongation method for efficient quantum chemistry calculations toward functional designs of bio/nano materials, 第1回 九州大学女性研究者ダイバーシティシンポジウム ―理工系分野―, 2018.03. |
| 30. | Y. Orimoto, S. Shirane, and Y. Aoki, Mechanism of Highly Selective Olefin Polymerization by Metallocene Catalyst: Computational Approach, IRCCS-JST CREST Joint Symposium, 2018.01, [URL]. |
| 31. | S. Shirane, Y. Orimoto, and Y. Aoki, Selectivity of olefin polymerization with metallocene catalyst and the effects of producted polymers on its mechanism, The 19th Cross Straits Symposium on Energy and Environmental Science and Technology(CSS-EEST19), 2017.11, [URL]. |
| 32. | Y. Orimoto and Y. Aoki, Computational design of DNAs: property control via elongation method, The 44th International Symposium on Nucleic Acids Chemistry(ISNAC 2017), 2017.11, [URL]. |
| 33. | H. Teramae and Y. Aoki, Ab Initio Calculations on Polymononucleotide and Polydinucleotides as Model of B-type DNA Polymers, 11th European Conference on Theoretical and Computational Chemistry(EUCO-TCC 2017), 2017.09, [URL]. |
| 34. | H. Teramae and Y. Aoki, Ab Initio Crystal Orbital Calculation of Electronic Structure of B-type model-DNA, 11th Triennial Congress of the World Association of Theoretical and Computational Chemists(WATOC 2017), 2017.08, [URL]. |
| 35. | Y. Aoki, Efficient quantum chemical method for functional material design, The 10th International Conference on Computational Physics(ICCP10), 2017.01, [URL]. |
| 36. | Y. Aoki and Y. Orimoto, An efficient NLO functional optimization by elongation method for nanotubes and DNA, Stereodynamics 2016, 2016.11, [URL]. |
| 37. | , [URL]. |
| 38. | , [URL]. |
| 39. | Y. Aoki and Y. Orimoto, Linear-scaling elongation method for efficient search of the best functional polymers-applications to DNA, Current Trends in Theoretical Chemistry VII, 2016.09, [URL]. |
| 40. | Y. Aoki, HPC approaches in Materials Science, International HPC Summer School 2016, 2016.06. |
| 41. | H. Teramae and Y. Aoki, An Attempt at Ab Initio Crystal Orbital Calculation of Electronic Structure of B-type model-DNA, International Conference of Computational Methods in Sciences and Engineering, 2016.04. |
| 42. | Y. Aoki, Linear Scaling Method for Large Systems and its Applications to Nano-Bio Systems, The 6th JCS International Symposium on Theoretical Chemistry (JCS-2015), 2015.10, [URL]. |
| 43. | Y. Orimoto and Y. Aoki, Computational functional design of artificial DNAs: application of elongation method and through-space/bond interaction analysis, ISNAC 2015 The 42nd International Symposium on Nucleic Acids Chemistry, 2015.09, [URL]. |
| 44. | W. Mizukami, K. Matsubara, and Y. Aoki, Analysis and modeling of molecular interactions in halogen-bonded cocrystal, 51st Symposium on Theoretical Chemistry(STC2015), 2015.09, [URL]. |
| 45. | K. Kato, Y. Orimoto, and Y. Aoki, 光電変換ワイヤの効率的理論設計法と応⽤, 第９回分子科学討論会, 2015.09, [URL]. |
| 46. | Y. Orimoto and Y. Aoki, 機能性人工核酸の理論的分子設計～導電性・強磁性・非線形光学特性～, 第９回分子科学討論会, 2015.09, [URL]. |
| 47. | K. Matsubara, W. Mizukami, and Y. Aoki, 相互作⽤解析によるハロゲン結合をベースとした共結晶⽣成過程の理解, 第９回分子科学討論会, 2015.09, [URL]. |
| 48. | Y. Aoki, K. Liu, W. Mizukami, and Y. Orimoto, ⼤規模原⼦分⼦系に向けた効率的Elongation法の展開と応⽤, 第９回分子科学討論会, 2015.09, [URL]. |
| 49. | X. Zhu, and Y. Aoki, 開殻⾼分⼦安定スピン状態予測のための⾮結合性最⼩Mixing(NB-MM)MO-ELG法, 第９回分子科学討論会, 2015.09, [URL]. |
| 50. | Y. Aoki, An efficient quantum chemical approach for material design, 2015 International Symposium for Advanced Materials Research (ISAMR 2015), 2015.08, [URL]. |
| 51. | Y. Aoki, Theoretical design for NLO polymers, 2015 International Symposium for Advanced Materials Research (ISAMR 2015), 2015.08, [URL]. |
| 52. | Y. Orimoto and Y. Aoki, Highly efficient electronic structure calculations of biomaterials for their functional design, 2015 International Symposium for Advanced Materials Research (ISAMR 2015), 2015.08, [URL]. |
| 53. | L. Jin and Y. Aoki, Interaction of OH- with Xylan and Its Hydrated Complexes: Structures and Molecular Dynamics Study Using Elongation Method, 2015 International Symposium for Advanced Materials Research (ISAMR 2015), 2015.08, [URL]. |
| 54. | Y. Aoki, Elongation Method for Functional Design of Nano-Bio Systems, The 15th International Congress of Quantum Chemistry (ICQC), 2015.06, [URL], Although quantum chemistry to precisely calculate molecular properties was accomplished and developed rapidly with the remarkable progress of the computers, the problem left is for the application to large-scale systems. Because the functional property of materials is based on the microscopic electronic states, quantum chemistry that reflects the property of the individual atom and molecule precisely must be effective. However, the computational time required is N^3~4 (N: number of the bases functions) at Hartree-Fock (HF) level, and it becomes N^5~7 at post HF level, and then applications to cohesion systems and materials are difficult even if we use a super parallel computers. Therefore, we developed Elongation (ELG) method [1] as a tool for the large-scale complex system for which conventional method cannot handle. The original idea of the ELG method mimics experimental polymerization/ copolymerization procedures. Contrast to some other approximation methods for large systems, the elongation is fully variational. It has been already demonstrated that the total energy obtained by the ELG method is in excellent agreement to those by the conventional method. The error of the elongation method is within 10-9 a.u./atom, showing its high accuracy compared to other methodologies. The main idea of the ELG method and its applications to various complex systems has been presented in Perspective [2]. It was generalized to two- and even three-dimensional systems with high speed calculations while giving results almost identical to those by conventional method. We show the efficiency and accuracy of our treatment by applying it for large systems like nanotubes, DNA, and some complicated proteins like enzymes [3, 4]. In this talk, 3D-ELG method for three-dimenstional systems and some new progresses will be reported for one to three dimensional systems. Some benchmark test calculations are presented to show the reliability and applicability of the 3D-ELG method. [1] A. Imamura, Y. Aoki, K. Maekawa, J. Chem. Phys., 95 (1991) 5419. [2] Y. Aoki, F. L. Gu, Phys. Chem. Chem. Phys., 14 (2012) 7640. [3] Orimoto, F. L. Gu, A. Imamura, and Y. Aoki, J. Chem. Phys., 126 (2007) 215104. [4] K. Liu, L. Peng, F. L. Gu, and Y. Aoki, Chem. Phys. Lett., 560 (2013) 66.. |
| 55. | Y. Aoki, Efficient NLO Calculations by Elongation Method, The 15th International Congress of Quantum Chemistry (ICQC) Satellite Meeting, 2015.06, [URL]. |
| 56. | 青木 百合子, Elongation Method for Efficient Quantum Chemical Calculations of Large Systems towards Material Design, The First Joint Symposium of Kyushu University and Yonsei University on Materials Science and Chemical Engineering(SKY-1), 2015.02. |
| 57. | Y. Furutani and Y. Aoki, A Quantum Chemical Study on Cathode Active Materials of Organic Radical-Molecules in Secondary Battery, 16th Cross Straits Symposium on Energy, Environmental Science and Technology (CSS-EEST 16), 2014.11. |
| 58. | Y. Aoki, Recent development of highly accurate linear scaling elongation method and its applications to large systems, 2014 International Workshop on Frontiers of Theoretical and Computational Physics and Chemistry (WFTCPC 2014), 2014.08. |
| 59. | Y. Orimoto, K. Liu, and Y. Aoki, Functional design of natural and artificial nucleic acids via ab initio order-N elongation method: computational approaches, The 40th International Symposium on Nudeic Acids Chemistry, 2013.11. |
| 60. | Y. Orimoto, K. Liu, and Y. Aoki, Highly effcient O(N) calculations of natural and artificial DNAs by elongation method, 第７回分子科学討論会, 2013.09. |
| 61. | Y. Aoki, K. Liu, P. Xie, and Y. Orimoto, An efficient searching of optimized geometries for proteins and DNA by ELG-OPT method, 第７回分子科学討論会, 2013.09. |
| 62. | L. Jiang, Y. Orimoto, and Y. Aoki, Through-space/bond interaction analysis on NLO properties enhancement of molecular switches, 第７回分子科学討論会, 2013.09. |
| 63. | X. Zhu, K. Liu, Y. Orimoto, and Y. Aoki, Development of open-shell elongation method and its application to ferromagnetic material design, 第７回分子科学討論会, 2013.09. |
| 64. | K. Liu, Y. Orimoto, and Y. Aoki, Highly efficient analyses of I-M-I transition in quasi-1D metal complexes by elongation method, 第７回分子科学討論会, 2013.09. |
| 65. | R. Tsutsui, K. Liu, Y. Orimoto, H. Honda, and Y. Aoki, Functional properties and electronic states of metal included BN/C heteronanotubes by Elongation method, 第７回分子科学討論会, 2013.09. |
| 66. | Y. Aoki, Elongation method for efficient and accurate calculations of large systems and applications to DNA, proteins, and nanotubes towards material design, Current Trends in Theoretical Chemistry VI, 2013.09. |
| 67. | P. Kuźniarowicz, Y. Aoki, A. Stachowicz, and J. Korchowiec, Intermediate field for the elongation method, Current Trends in Theoretical Chemistry VI, 2013.09. |
| 68. | L. Jiang, Y. Orimoto, and Y. Aoki, Insights into substituents and solvent effects on SN2 reaction by through space/bond interaction analysis, 14th Cross Straits Symposium on Energy and Environmental Science and Technology (CSS-EEST 14), 2013.02. |
| 69. | Y. Orimoto, P. Xie, K. Liu, and Y. Aoki, Highly efficient quantum chemistry calculations of DNA for designing biomaterials, 14th Cross Straits Symposium on Energy and Environmental Science and Technology (CSS-EEST 14), 2013.02. |
| 70. | R. Tsutsui, K. Liu, Y. Orimoto, and Y. Aoki, Functional properties of BN nanotubes by highly efficient Geometry optimization method, 14th Cross Straits Symposium on Energy and Environmental Science and Technology (CSS-EEST 14), 2013.02. |
| 71. | Y. Furutani, Y. Orimoto, and Y. Aoki, A quantum chemical study on cathode active materials of organc radical-molecules in secondary battery, 14th Cross Straits Symposium on Energy and Environmental Science and Technology (CSS-EEST 14), 2013.02. |
| 72. | Y. Aoki, Highly accurate and efficient quantum chemical method for nano-bio functional designs, The 2nd International Symposium on Large-scale Computional Science and Engineering, 2012.11. |
| 73. | P. Xie, Y. Orimoto, K. Liu, Y. Yan, F. L. Gu, and Y. Aoki, Elongation dynamics and local transition state search on reaction site, 第６回分子科学討論会, 2012.09. |
| 74. | Y. Aoki, K. Liu, and F. L. Gu, Highly accurate linear scaling method -elongation method- and its applications to large systems, 7th Congress of the International Society for Theoretical Chemical Physics(ISTCP‐Ⅶ), 2011.09. |
| 75. | A. Imamura and Y. Aoki, Electric structures and molecular structures of polyynes, 7th Congress of the International Society for Theoretical Chemical Physics(ISTCP‐Ⅶ), 2011.09. |
| 76. | Y. Aoki, Highly accurate O(N) method for Nano-Bio systems, ICCMSE 2010, 2010.10. |
| 77. | 愛媛. |
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