Preprints 　(*Corresponding author)

  1. K. Nakajima*, T. Yoshikawa, Y. Suzuki, S. Nakatani, K. Adachi, N. Nakamura, S. Murayama, H. Sakuta, N. Yangisawa, N. A. Erkamp, T. Sneideris, M. Fukuyama, M. Taniguchi, M. Yanagisawa, H. Ogi, T.P.J. Knowles "Tracer-free Contactless Acoustic Microrheometry Quantifies Viscoelastic Spectrum of Phase-separated Condensates", arXiv (2026).
  2. N. Fujiwara, H. Okita, M. Uno, K. Adachi, K. Nakajima, N. Nakamura, M.-H. Kim, M. Kino-oka, K. Ogawa, K. Ikenaka, and H. Ogi* "Focused acoustic-radiation-force microscopy for live-cell selective nucleus deformation and nucleus viscoelasticity measurement", bioRxiv (2025).
  3. N.A Erkamp*, I. Sanchez-Burgos, A. Zhou, T.J. Krug, S. Qamar, T. Sneideris, E. Zhang, K. Nakajima, A. Chen, R. Collepardo-Guevara, J.V. Hest, P. St George-Hyslop, D.A. Weitz, J.R. Espinosa, T.P.J. Knowles* "Dynamically arrested condensate fusion creates complex structures with varying material properties", bioRxiv (2024).



Papers (First or Corresponding Author) 　(*Corresponding author / †Equally Contributed)

  1. K. Nakajima*, T. Sneideris, L.L. Good, N.A. Erkamp, Y. Hideshima, H. Ogi, and T.P.J. Knowles* "Mechanical profiling of biopolymer condensates through acoustic trapping", PRX Life (2026) in Press.
  2. T. Ota, K. Nakajima*, K. Nakandakari, T. Kondo, K. Yamaguchi, H. Matsuda, Y. Goto, and H. Ogi*, "Quantitative analysis of amyloid-fibril nucleation by linking folding and nucleation pathways using robust ultrasonic assay", ACS Omega, Vol. 11, 13855-13864 (2026).
  3. K. Nakajima†,*, K. Hanada†, M. So, K. Yamaguchi, Y. Goto, and H. Ogi, "Ultrasonic frequency and intensity dependence in β2-microglobulin amyloid seed detection: Balancing cavitation-induced nucleation, fragmentation, and radical formation", Ultrason. Sonochem., Vol. 123, 107694 (2025).
  4. T. Ota, K. Nakajima*, K. Yamaguchi, Y. Goto, and H. Ogi, "Ultrasonic detection of α-synuclein amyloid seeds from a highly crowded environment", Biophys. J., Vol. 124, 1-11 (2025).
  5. K. Nakajima†,*, T. Ota†, H. Toda, K. Yamaguchi, Y. Goto, and H. Ogi, "Surface Modification of Ultrasonic Cavitation by Surfactants Improves Detection Sensitivity of α-synuclein Amyloid Seeds", ACS Chem. Neurosci., Vol. 15, 1643-1651 (2024).
  6. K. Nakajima†, K. Yamaguchi†, M. Noji†, C. Aguirre, K. Ikenaka, H. Mochizuki, L. Zhou, H. Ogi, T. Ito, I. Narita, F. Gejyo, H. Naiki, S. Yamamoto*, and Y. Goto*, "Macromolecular crowding and supersaturation protect hemodialysis patients from the onset of dialysis-related amyloidosis", Nat. Commun., Vol. 13, 5689 (2022). (Press Release)
  7. K. Nakajima, T. Tsujimura, K. Doi, and S. Kawano*, "Visualization of optical vortex forces acting on Au nanoparticles transported in nanofluidic channels", ACS Omega, Vol. 7, 2638-2648 (2022).
  8. K. Nakajima†, H. Toda†, K. Yamaguchi, M. So, K. Ikenaka, H. Mochizuki, Y. Goto, and H. Ogi*, "Half-time heat map reveals ultrasonic effects on morphology and kinetics of amyloidogenic aggregation reaction", ACS Chem. Neurosci., Vol. 12, 3456-3466 (2021).
  9. K. Nakajima, K. Noi, K. Yamaguchi, M. So, K. Ikenaka, H. Mochizuki, H. Ogi, and Y. Goto*, “Optimized sonoreactor for accelerative amyloid-fibril assays through enhancement of primary nucleation and fragmentation”, Ultrason. Sonochem., Vol. 73, 105508 (2021).
  10. K. Nakajima, R. Nakatsuka, T. Tsuji, K. Doi, and S. Kawano*, "Synchronized resistive-pulse analysis with flow visualization for single micro- and nanoscale objects driven by optical vortex in double orifice", Sci. Rep., Vol. 11, 9323 (2021).
  11. K. Nakajima, T. Yamazaki, Y. Kimura, M. So, Y. Goto, and H. Ogi*, "Time-resolved observation of evolution of amyloid-β oligomer with temporary salt crystals", J. Phys. Chem. Lett., Vol. 11, 6176-6184 (2020). (Press Release)
  12. K. Nakajima, D. Nishioka, M. Hirao, M. So, Y. Goto, and H. Ogi*, "Drastic acceleration of fibrillation of insulin by transient cavitation bubble", Ultrason. Sonochem., Vol. 36, 206-211 (2017).
  13. K. Nakajima, M. So, K. Takahashi, Y. Tagawa, M. Hirao, Y. Goto, and H. Ogi*, "Optimized ultrasonic irradiation finds out ultrastable Aβ1-40 oligomers", J. Phys. Chem. B, Vol. 121, 2603-2613 (2017).
  14. K. Nakajima, H. Ogi*, K. Adachi, K. Noi, M. Hirao, H. Yagi, and Y. Goto, "Nucleus factory on cavitation bubble for amyloid β fibril", Sci. Rep., Vol. 6, 22015 (2016). (Press Release)

Papers (Co-author) 　(*Corresponding author / †Equally Contributed)

  1. Yuji Goto, Keiichi Yamaguchi, K. Nakajima, Ikuko Yumen, Ruiming He, Hirokazu Matsuda, Tetsushi Wazawa, Takeharu Nagai, Nobuhiro Tsukada, Suguru Yamamoto, Johannes Buchner, and Hirotsugu Ogi, Constrictions and shear stress are key determinants of AL amyloidosis", FEBS J. (2026) in Press.
  2. J. Kawakami, T. Ozawa, Y. Maruyama, H. Ishikawa, K. Yamauchi, K. Kobayashi, S. Kajimoto, T. Nakabayashi, S. Tomita, T. Agarwal, T. Sneideris, K. Nakajima, K. Shiraki, H. Taguchi, A. Hibara, T.P.J. Knowles, E. Chatani, Y. Mizuno, Y. Ohhashi, M. Fukuyama*, "Size of Biomolecular Condensates Dictates Fate in Liquid-Solid Phase Transitions through Amorphous-Amyloid Competition", J. Am. Chem. Soc. (2026) Vol. 148, 23837–23849 (2026). (Press Release)
  3. K. Yamaguchi*, M. Sawada, K. Nakajima, H. Ogi, Y. Kawata, and Y. Goto "Adenosine triphosphate promotes amyloid formation of α-synuclein in a concentration-dependent manner", Langmuir, Vol. 42, 1106-1115 (2026).
  4. K. Nakandakari, T. Ota, K. Nakajima, K. Yamaguchi, Y. Goto, J. Kardos, and H. Ogi* "Deep-learning prediction of protein secondary structure from circular dichroism spectrum using three-layer image recognition", Anal. Chem., Vol. 97, 26342-26348 (2025).
  5. Y. Oishi*, M. Kitatani, K. Nakajima, H. Ogi, and K. Kusakabe "Computational study of conformational interconversion of an amyloid β double layer system", RSC Adv., Vol. 5, 42395-42401 (2025).
  6. C. Aguirre, Y. Miyanoiri, M. So, H. Tamaki, T. Maruno, J. Doi, N. Wang, K. Yamaguchi, K. Nakajima, Y. Yamamori, H. Inoura, C.-J. Choong, K. Kakuda, T. Ajiki, Y. Kimura, T. Ozono, K. Baba, S. Nagano, Y. Nagai, H. Ogi, S. Uchiyama, Y. Matsuki, K. Tomii, Y. Goto, K. Ikenaka*, H. Mochizuki* "Conformational Switch in the Alpha-Synuclein C-Terminal Domain Directs Its Fibril Polymorphs", Chem. Eur. J., Vol. 31, e202500650 (2025).
  7. K. Yamaguchi*, K. Nakajima, H. Ogi, and Y. Goto "Mechanism of amyloid formation triggered by breakdown of supersaturation", npj Biosensing, Vol. 2, 7 (2025).
  8. K. Yamaguchi*, J. Mima, K. Nakajima, H. Sakuta, K. Yoshikawa, and Y. Goto* "Accelerated amyloid fibril formation at the interface of liquid–liquid phase‐separated droplets by depletion interactions", Protein Sci., Vol. 34, e5163 (2025).
  9. S. Yamamoto*, K. Yamamoto, Y. Hirao, K. Yamaguchi, K. Nakajima, M. Sato, M. Kawachi, M. Domon, K. Goto, K. Omori, N. Iino, H. Shimada, R. Aoyagi, I. Ei, S. Goto, Y. Goto, F. Gejyo, T. Yamamoto, and I. Narita* "Mass spectrometry-based proteomic analysis of proteins adsorbed by hexadecyl-immobilized cellulose bead column for the treatment of dialysis-related amyloidosis", Amyloid, 1-11 (2024).
  10. Y. Goto*, K. Nakajima, S. Yamamoto, and K. Yamaguchi, "Supersaturation, a critical factor underlying proteostasis of amyloid fibril formation", J. Mol. Biol. Vol. 436, 168475 (2024).
  11. L. Zhou, T. Hajiri, K. Nakajima, C. Aguirre, K. Ikenaka, H. Mochizuki, K. Yamaguchi, Y. Goto, and H. Ogi*, "Ultra-stiff amyloid-fibril network of α-synuclein formed by surface seeding reaction confirmed by multichannel electrodeless quartz-crystal-microbalance biosensor", ACS Sens., Vol. 8, 2598-2608 (2023).
  12. C. J. Choong †, C. Aguirre †, K. Kakuda, G. Beck, H. Nakanishi, Y. Kimura, S. Shimma, K. Nabekura, M. Hideshima, J. Doi, K. Yamaguchi, K. Nakajima, T. Wadayama, H. Hayakawa, K. Baba, K. Ogawa T. Takeuchi, S. M. M. Badawy, S. Murayama, S. Nagano, Y. Goto, Y. Miyanoiri, Y. Nagai, H. Mochizuki*, and K. Ikenaka*, "Phosphatidylinositol-3,4,5-trisphosphate interacts with alpha-synuclein and initiates its aggregation and formation of Parkinson’s disease-related fibril polymorphism", Acta Neuropathol., Vol. 145, 573-595 (2023) (Press Release)
  13. K. Yamaguchi*, K. Nakajima, and Y. Goto, "Mechanisms of polyphosphate-induced amyloid fibril formation triggered by breakdown of supersaturation", Biophys. Physicobiol., e200013 (2023).
  14. Y. Goto*, M. Noji, K. Nakajima, and K. Yamaguchi, "Supersaturation-dependent formation of amyloid fibrils", Molecules, Vol. 27, 4588 (2022).
  15. K. Noi, K. Nakajima, K. Yamaguchi, M. So, K. Ikenaka, H. Mochizuki, Y. Goto, and H. Ogi*, "Acceleration of amyloid fibril formation by multichannel sonochemical reactor", Jpn. J. Appl. Phys., Vol. 61, SG1002 (2022).
  16. M. Hideshima, Y. Kimura, C. Aguirre, K. Kakuda, T. Takeuchi, C.-J. Choong, K. Nabekura, K. Yamaguchi, K. Nakajima, K. Baba, S. Nagano, Y. Goto, Y. Nagai, H. Mochizuki, and K. Ikenaka*, "Two-step screening method to identify α-synuclein aggregation inhibitors for Parkinson's disease", Sci. Rep., Vol. 12, 351 (2022).
  17. Y. Goto*, K. Nakajima, K. Yamaguchi, M. So, K. Ikenaka, H. Mochizuki, and H. Ogi, "Development of HANABI, an ultrasonication-forced amyloid fibril inducer", Neurochem. Int., Vol. 153, 105270 (2022).
  18. R. Nakatsuka, S. Yanai, K. Nakajima, K. Doi, and S. Kawano, "Electrical sensing of Au Nanoparticles manipulated by an optical vortex", J. Phys. Chem. C, Vol. 125, 9507-9515 (2021).
  19. T. Tsuji, R. Nakatsuka, K. Nakajima, K. Doi, and S. Kawano, "Effect of hydrodynamic inter-particle interaction on the orbital motion of dielectric nanoparticles driven by an optical vortex", Nanoscale, Vol. 12, 6673-6690 (2020).