I have joined  Ph.D. Program in Biomedical Artificial Intelligence (BAI), at National Tsin Hua University (NTHU), Taiwan, since August 2023 as an assistant professor.
I've embarked on learning Chinese and am relishing the dual roles of both a teacher and a student.
As an application of AI, I utilized AI assistance in crafting this personal website. 

EDUCATION
Ph.D, Organic and Polymeric Materials, Tokyo Institute of Technology, 2006
Concentrations: polymer chemistry and physics
Dissertation: Studies on Relaxation Processes and Dynamic Correlation in Glass-forming Polymer
Dissertation Advisor: Hidemine Furuya (associate professor)

B.A., Polymer Chemistry at Tokyo Institute of Technology, 2001

EMPLOYMENT
2006.4 – 2008.3 postdoc, IMCB, Univ. of Tokyo
2008.4 – 2011.3 postdoc, Institute for Molecular Science
2011.4 – 2018.3 postdoc, IMCB, Univ. of Tokyo
2018.4 – 2019.3 postdoc, TokyoTech
2019.4 – 2020.3 Specially Appointed Lecturer, TokyoTech
2020.4 – 2023.3 Specially Appointed Associate Professor, TokyoTech

2023.4 –  Specially Appointed Researcher, TokyoTech

 2023.8 –  Assitant Professor, BAI, NTHU

PUBLICATIONS

1.      Dependence of Vibrational Energy Transfer on Distance in a Four-Helix Bundle Protein: Equidistant Increments with the Periodicity of α Helices, S. Yamashita, M. Mizuno, K. Takemura, A. Kitao, Y. Mizutani, J. Phys. Chem. B, 126, 3283-3290 (2022).
2.      Regulatory Switching by Concerted Motions on the Microsecond Time Scale of the Oxygen Sensor Protein FixL, T. Yamawaki, M. Mizuno, H. Ishikawa, K. Takemura, A. Kitao, Y. Shiro and Y. Mizutani, J. Phys. Chem. B 125, 6847-6856 (2021).
3.      Regulation of caveolae through cholesterol-depletion-dependent tubulation mediated by PACSIN2, A. Gusmira, K. Takemura, S.Y. Lee, T. Inaba, K. Hanawa-Suetsugu, K. Oono-Yakura, K. Yasuhara, A. Kitao and S. Suetsugu, J. Cell. Sci. 133 (2020).
4.      An Efficient Timer and Sizer of Biomacromolecular Motions, J. Chan, K. Takemura, H.R. Lin, K.C. Chang, Y.Y. Chang, Y. Joti, A. Kitao and L.W. Yang, Structure 28, 259-269 e258 (2020).
5.      Impact of key residues within chloroplast thioredoxin-f on recognition for reduction and oxidation of target proteins, Y. Yokochi, K. Sugiura, K. Takemura, K. Yoshida, S. Hara, K. I. Wakabayashi, A. Kitao, and T. Hisabori, J. Biol. Chem., 294, 17437-17450 (2019).
6.      Everdock bai: Machine-learning-guided selection of protein-protein complex structure, K. Terayama, A. Shinobu, K. Tsuda, K. Takemura, and A. Kitao, J. Chem. Phys., 151, 215104 (2019).
7.      More efficient screening of protein-protein complex model structures for reducing the number of candidates, K. Takemura and A. Kitao, Biophys. Physicobiol., 16, 295 (2019).
8.      Enhancing Biomolecular Sampling with Reinforcement Learning: A Tree Search Molecular Dynamics Simulation Method, K. Shin, D.P. Tran, K. Takemura, A. Kitao, K. Terayama, and K. Tsuda, ACS Omega, 4, 13853-13862 (2019).
9.      Phagocytosis is mediated by two-dimensional assemblies of the f-bar protein gas7, K. Hanawa-Suetsugu, Y. Itoh, M. Ab Fatah, T. Nishimura, K. Takemura, K. Takeshita, S. Kubota, N. Miyazaki, W. N. I. Wan Mohamad Noor, T. Inaba, N. T. H. Nguyen, S. Hamada-Nakahara, K. Oono-Yakura, M. Tachikawa, K. Iwasaki, D. Kohda, M. Yamamoto, A. Kitao, A. Shimada and S. Suetsugu, Nat Commun, 10, 4763 (2019).
10.   Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations, A. Shinobu, K. Takemura, N. Matubayasi, and A. Kitao, J. Chem. Phys., 149, 195101 (2018).
11.   ColDock: Concentrated Ligand Docking with All-Atom Molecular Dynamics Simulation, K. Takemura, C. Sato, and A. Kitao, J. Phys. Chem. B, 122, 7191−7200, (2018).
12.   Binding free energy analysis of protein-protein docking model structures by evERdock, K. Takemura, N. Matubayasi, and A. Kitao*, J. Chem. Phys., 148, 105101-1-10, (2018).
13.   Protein–Ligand Dissociation Simulated by Parallel Cascade Selection Molecular Dynamics, DP Tran, K Takemura, K Kuwata, A Kitao, J. chem. theory computation 14, 404-417 (2017).
14.   Salt bridge formation between the I-BAR domain and lipids increases lipid density and membrane curvature, K Takemura, K Hanawa-Suetsugu, S Suetsugu, A Kitao, Scientific reports 7, 6808 (2017).
15.   High anisotropy and frustration: the keys to regulating protein function efficiently in crowded environments, A Kitao, K Takemura, curr. Opin. Struct. Biol., 42, 50-58 (2017)
16.   Eritoran inhibits S100A8-mediated TLR4/MD-2 activation and tumor growth by changing the immune microenvironment. A. Deguchi, T. Tomita, U. Ohto, K Takemura, A. Kitao, S. Akashi-Takamura, K. Miyake, Y. Maru, Oncogene,35, 1445-1456 (2016).
17.   Drug Targeting Based on a New Concept-Targeting Against TLR4 as an Example
Y. Maru, T. Tomita, A. Deguchi, K. Ieguchi, M. Takita, F. Tsukahara, K. Takemura, A. Kitao, F. Gusovsky, Endocrine, Metabolic & Immune Disorders-Drug Targets 15, 83-87(2015).
18.   TRPV4 channel activity is modulated by direct interaction of the ankyrin domain to PI(4,5)P2. N. Takahashi*, S. Hamada-Nakahara*, Y. Itoh*, K. Takemura*, A. Shimada, Y. Ueda, M. Kitamata, R. Matsuoka, K. Hanawa-Suetsugu, Y. Senju, M. X. Mori, S. Kiyonaka, D. Kohda, A. Kitao, Y. Mori and S. Suetsugu,
Nature Comm. 5, 4994 (2014). *equal contribution
19.   Mechanism of Deep-Sea Fish α-Actin Pressure Tolerance Investigated by Molecular Dynamics Simulations. N. Wakai, K. Takemura, T. Morita, and A. Kitao
PLoS One 9, e85852 (2014).
20.   Free-energy analysis of lysozyme-triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representation. K. Takemura, R.R. Burri, T. Ishikawa, T. Ishikura, S. Sakuraba, N. Matubayasi, K. Kuwata, A. Kitao Chem. Phys. Lett. 559, 94-98 (2013).
21.   Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation. K. Takemura, H. Guo, S. Sakuraba, N. Matubayasi, and A. Kitao,
J. Chem. Phys. 137, 215105-1 ~ 215105-10 (2012).
22.   Water Model Tuning for Improved Reproduction of Rotational Diffusion and NMR Spectral DensityK. Takemura and A. KitaoJ. Phys. Chem. B 116, 6279 (2012).
23.   Effects of Water Model and Simulation Box Size on Protein Diffusional Motions
K. Takemura and A. KitaoJ. Phys. Chem. B, ACS Publications, 111, 11870-11872 (2007).
24.   Motional Coherency in Chain Dynamics of Glass-Forming Polymers
H. Furuya, K. Takemura, and T. Kanaya Macromol. Symp, 249 - 250, 498 – 501, (2007).
25.   Motional coherency in chain dynamics of polybutadiene studied by molecular dynamics simulations K. Takemura, H. Furuya, and T. KanayaPolymer, 47, 5973 – 5978 (2006).
26.   Thermal Neutron Spin-Echo Studies on Dynamics of a Glass-Forming Polymer in a High Q Range T. Kanaya, K. Kakurai, I. Tsukushi, R. Inoue, H. Watanabe, M. Nishi, K. Nakajima, K. Takemura, and H. FuruyaJ. Phys. Soc. Jpn, 74, 3236-3240 (2005).
27.   Molecular dynamics simulation of short dynamics in polymer glass: chain dynamics and fast process H. Furuya, O. Okada, K. Takemura, and T. Kanaya
Polym. Mater. Sci. Eng, 85, 238 (2001).
 
 
BOOK
1.      “Plasma Membrane Shaping” (Chapter 25 “Molecular Dynamics), Elsevier, 2022