Macoto Kikuchi web site

Publications

Recent Papers, Preprints and Selected Old Papers

• Macoto Kikuchi: Phenotype selection due to mutational robustness, arXiv:2310.15729 (to be published in PLOS ONE, 2024)
• 菊池誠: 遺伝子制御ネットワークの変異に対する頑健性と双安定性の進化の定量評価：レアイベントサンプリングの手法 (in Japanese), 生物物理62(2022) 360-364
• Tadamune Kaneko and Macoto Kikuchi: Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution, PLoS Comput Biol 18 (2022): e1009796
• Shintaro Nagata and Macoto Kikuchi: Emergence of cooperative bistability and robustness of gene regulatory networks, PLoS Comput Biol 16 (2020) e1007969
• Shin-ichi Tadaki, Macoto Kikuchi, Akihiro Nakayama, Akihiro Shibata, Yuki Sugiyama and Satoshi Yukawa: Characterizing and distinguishing free and jammed traffic flows from the distribution and correlation of experimental speed data , New J. Phys., vol.18 083022 (2016)
• Akihiro Nakayama, Macoto Kikuchi, Akihiro Shibata, Yuki Sugiyama, Shin-ichi Tadaki, Satoshi Yukawa: Quantitative explanation of circuit experiments and real traffic using the optimal velocity model , New J. Phys., vol.18 043040 (2016)
• Nobu C. Shirai and Macoto Kikuchi: The interplay of intrinsic disorder and macromolecular crowding on alpha-synuclein fibril formation , J. Chem. Phys. Vol.144 (2016) 055101
• Ryo Kanada, Fumiko Takagi and Macoto Kikuchi: Nucleotide-dependent structural fluctuations and regulation of microtubule-binding affinity of KIF1A, Proteins: Structure, Function, and Bioinformatics Vol.83 (2015) p.809-819
• Akimasa Kitajima and Macoto Kikuchi: Numerous but Rare: An Exploration of Magic Squares, PLOS ONE, vol.10 (2015) e0125062
• Shin-ichi Tadaki, Macoto Kikuchi, Minoru Fukui, Akihiro Nakayama, Katsuhiro Nishinari, Akihiro Shibata, Yuki Sugiyama, Taturu Yosida and Satoshi Yukawa: Phase transition in traffic jam experiment on a circuit, New J. Phys. Vol.15 (2013) 103034.
• Nen Saito and Macoto Kikuchi: Robustness leads close to the edge of chaos in coupled map networks: toward the understanding of biological networks, New J. Phys. Vol.15 (2013) 053037
• Nobu C. Shirai, and Macoto Kikuchi: Structural flexibility of intrinsically disordered proteins induces stepwise target recognition, J.Chem.Phys. Vol.139 (2013) 225103
• Katsuyoshi Matsushita and Macoto Kikuchi: Frustration-induced protein intrinsic disorder, J.Chem.Phys. Vol.130 (2013) 105101
• Atsunari Katsuki and Macoto Kikuchi: Simulation of barchan dynamics with inter-dune sand streams, New J. Phys. Vol.13 (2011) 063049
• A.Katsuki, M.Kikuchi, H.Nishimori, N.Endo, and K.Taniguchi: Cellular model for sand dunes with saltation, avalanche and strong erosion: collisional simulation of barchans, Earth Surface Processes and Landforms Vol.36 (2011) 372
• Hiroo Kenzaki and Macoto Kikuchi: Free-energy landscape of kinesin by a realistic lattice model, Proteins: Structure, Function, and Bioinformatics Vol.71 (2008) p.389-395
• Yuki Sugiyama, Minoru Fukui, Macoto Kikuchi, Katsuya Hasebe, Akihiro Nakayama, Katsuhiro Nishinari, Shin-ichi Tadaki and Satoshi Yukawa: Traffic jam without bottleneck - Experimental evidence for the physical mechanism of forming a jam, New J. Phys. Vol.10 (2008) 033001
• Fumiko Takagi and Macoto Kikuchi: Structural Change and Nucleotide Dissociation of Myosin Motor Domain: Dual Go Model Simulation, Biophys.J. Vol.93 (2007) p.3820-3827
• Hiroo Kenzaki and Macoto Kikuchi: Diversity in free energy landscape and folding pathway of proteins with the same native topology, Chem.Phys.Lett. Vol.427 (2006) p.414-417
• Kazuki Nakanishi and Macoto Kikuchi: Thermodynamics of Aggregation of Two Proteins, J.Phys.Soc.Jpn. Vol.75 (2006) 064803
• Atsunari Katsuki, Macoto Kikuchi, and Noritaka Endo: Emergence of a Barchan Belt in a Unidirectional Flow: Experiment and Numerical Simulation, J.Phys.Soc.Jpn. Vol.74 (2005) p.878-881
• George Chikenji and Macoto Kikuchi: What is the role of non-native intermediates of beta-lactoglobulin in protein folding? , Proc.Natl.Acad.Sci. Vol.97 (2000) p.14273-14277
• George Chikenji, Macoto Kikuchi, and Yukito Iba: Multi-Self-Overlap Ensemble for protein folding: ground state search and thermodynamics, Phys.Rev.Lett. Vol.83 (1999) p.1886-1889
• Yukito Iba, George Chikenji, and Macoto Kikuchi: Simulation of Lattice Polymers with Multi-Self-Overlap Ensemble, J.Phys.Soc.Jpn. Vol.67 (1998) p.3327-3330
• Shin-ichi Tadaki, Macoto Kikuchi, Yuki Sugiyama, and Satoshi Yukawa: Coupled map traffic flow simulator Based on Optimal Velocity Functions, J.Phys.Soc.Jpn. Vol.67 (1998) p.2270-2276
• Gen Tatara, Macoto Kikuchi, Satoshi Yukawa, and Hiroshi Matsukawa: Dissipation Enhanced Asymmetric Transport in Quantum Ratchets, J.Phys.Soc.Jpn. Vol.67 (1998) p.1090-1093
• Tomotoshi Nishino, Koichi Okunishi, and Macoto Kikuchi: Numerical Renormalization Group at Criticality, Phys. Lett. A213 (1996) p.69-72
• Satoshi Yukawa and Macoto Kikuchi: Coupled-Map Modeling of One-Dimensional Traffic Flow, J.Phys.Soc.Jpn. Vol.64 (1995) p.35-38
• Macoto Kikuchi and Yutaka Okabe: Multispin Coding of the Monte Carlo Simulation of the Three-State Random Potts Model and the Block-Spin Transformation, Intntl.J.Mod.Phys. C6 (1995) p.747-763
• Macoto Kikuchi and Kurt Binder: Microphase separation in Thin Films of the Symmetric Diblock-Copolymer Melt, J.Chem.Phys. Vol.101 (1994) p.3367-3377
• Satoshi Yukawa, Macoto Kikuchi, and Shin-ichi Tadake: Dynamical Phase Transition in One Dimensional Traffic Flow Model with Blockage, J.Phys.Soc.Jpn. Vol.63 (1994) p.3609-3618
• Macoto Kikuchi and Nobuyasu Ito: Statistical Dependence Time and Its Application to the Dynamical Critical Exponent, J.Phys.Soc.Jpn. Vol.62 (1993) p.3052-3061
• Hikaru Kawamura and Macoto Kikuchi: Free-vortex formation and topological phase transitions of two-dimensionsal spin systems, Phys.Rev. B47 (1993) p.1134-1137
• Macoto Kikuchi, Yutaka Okabe, and Seiji Miyashita: On the Ground-State Phase Transition of the Spin 1/2 $XXZ$ Model on the Square Lattice, J.Phys.Soc.Jpn. Vol.59 (1990) p.492-496
• Yutaka Okabe and Macoto Kikuchi: Quantum Monte Carlo Simulation of the Spin 1/2 $XXZ$ Model on the Square Lattice, J.Phys.Soc.Jpn. Vol.57 (1988) p.4351-4358
• >Macoto Kikuchi and Yutaka Okabe: A Scaling Approach to Monte Carlo Renormalization Group, Prog.Theor.Phys. Vol.78 (1987) 540-551
• Macoto Kikuchi and Yutaka Okabe: Renormalization, Self-Similarity, and Relaxation of Order-Parameter Structure in Critical Phenomena, Phys.Rev. B35 (1987) p.5382-5384
• Macoto Kikuchi and Yutaka Okabe: Critical Relaxation of Three-Dimensional Kinetic Ising Model, J.Phys.Soc.Jpn. Vol.55 (1986) p.1359-1363
• Macoto Kikuchi and Yutaka Okabe: Monte Carlo Study of the Surface Critical Phenomena of the Ising Model, Prog.Theor.Phys. Vol.73 (1985) p.32-40
• Macoto Kikuchi and Yutaka Okabe: Monte Carlo Study of Critical Relaxation Near a Surface, Phys.Rev.Lett. Vol.55 (1985) p.1220-1222

Presentations

• 計算統計力学で生命の進化について何が言えるか: 統計力学の手法で稀なものを探す (物理学会新潟支部例会特別講演, 2023, in Japanese)
• Phenotype selection due to mutational robustness in gene regulatory networks (ICBP2023, Seoul, 2023)
• Non-equilibrity of evolution revealed by multicanonical ensemble method: Phenotype selection due to mutational robustness in gene regulatory networks (STATPHYS28, Tokyo, 2023)
• Phenotype Selection Due To Mutational Robustness: A Computational Study (Biophysical Society Meeting 2023)
• Evolution enhances the mutational robustness and suppresses emergence of a new phenotype (Kikuchi Lab. seminar, 2021)
• Evolution enhances the mutational robustness and suppresses emergence of a new phenotype (Fujimoto Lab. seminar, 2020)
• Function and Robustness of Gene Regulatory Network: Toward the Landscape Picture of Evolution (Kaneko Lab. seminar, 2019)
• 遺伝子制御ネットワークの機能と頑健性をレアイベントサンプリングで考える: 進化のランドスケープ的な理解に向けて (統計物理学懇談会2019, in Japanese)
• Fitness Landscape and Emergence of Robustness in Gene Regulatory Networks" (JPS fall meeting 2018)
• 生命進化へのレアイベントサンプリングの応用 (学祭計算物理学研究会2018, in Japanese)
• Simultaneous Emergence of Cooperative Response and Mutational Robustness in Gene Regulatory Networks (Conference on Complex Systems 2018)
• Robustness against Fluctuations and Mutation in Gene Regulatory Network (APEF2018, Poster)
• Exploring the Fitness Landscape and Emergence of Mutational Robustness in Gene Regulatory Network (ALIFE2018, Poster)
• Funnel Gas Model for Protein Many-Body Systems under the Crowded Environment (Biophysical Society Meeting 2018)
• Finding Protein Folding Funnels in Random Networks (Conference on Computationsl Physics 2017)
• Finding Protein Folding Funnels in Random Networks (Dynamic Days Asia-Pacific 2016)
• Allosterically Regulated Structural Fluctuation and Microtubule-Binding Affinity of KIF1A – A Simulation Study of Coarse-Grained Model – (Biophysical Society Meeting 2016, Poster)