Okumura H - Search Results

1

Single-Molecule Kinetic Observation of Antibody Interactions with Growing Amyloid β Fibrils.

Yagi-Utsumi M, Kanaoka Y, Miyajima S, Itoh SG, Yanagisawa K, Okumura H, Uchihashi T, Kato K. Yagi-Utsumi M, et al. Among authors: okumura h. J Am Chem Soc. 2024 Nov 20;146(46):31518-31528. doi: 10.1021/jacs.4c08841. Epub 2024 Oct 24. J Am Chem Soc. 2024. PMID: 39445702 Free PMC article.

2

Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles.

Okumura H, Itoh SG, Okamoto Y. Okumura H, et al. J Chem Phys. 2007 Feb 28;126(8):084103. doi: 10.1063/1.2434972. J Chem Phys. 2007. PMID: 17343436

3

Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules.

Itoh SG, Okumura H, Okamoto Y. Itoh SG, et al. Among authors: okumura h. J Chem Phys. 2010 Apr 7;132(13):134105. doi: 10.1063/1.3372767. J Chem Phys. 2010. PMID: 20387919

4

Free-energy calculation via mean-force dynamics using a logarithmic energy landscape.

Morishita T, Itoh SG, Okumura H, Mikami M. Morishita T, et al. Among authors: okumura h. Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Jun;85(6 Pt 2):066702. doi: 10.1103/PhysRevE.85.066702. Epub 2012 Jun 11. Phys Rev E Stat Nonlin Soft Matter Phys. 2012. PMID: 23005238

5

Coulomb replica-exchange method: handling electrostatic attractive and repulsive forces for biomolecules.

Itoh SG, Okumura H. Itoh SG, et al. Among authors: okumura h. J Comput Chem. 2013 Mar 30;34(8):622-39. doi: 10.1002/jcc.23167. Epub 2012 Nov 29. J Comput Chem. 2013. PMID: 23197415

6

On-the-fly reconstruction of free-energy profiles using logarithmic mean-force dynamics.

Morishita T, Itoh SG, Okumura H, Mikami M. Morishita T, et al. Among authors: okumura h. J Comput Chem. 2013 Jun 15;34(16):1375-84. doi: 10.1002/jcc.23267. Epub 2013 Mar 5. J Comput Chem. 2013. PMID: 23460528

7

Transformation of a design peptide between the α-helix and β-hairpin structures using a helix-strand replica-exchange molecular dynamics simulation.

Okumura H, Itoh SG. Okumura H, et al. Phys Chem Chem Phys. 2013 Sep 7;15(33):13852-61. doi: 10.1039/c3cp44443k. Epub 2013 Jul 10. Phys Chem Chem Phys. 2013. PMID: 23839056

8

Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides.

Itoh SG, Okumura H. Itoh SG, et al. Among authors: okumura h. J Comput Chem. 2013 Nov 5;34(29):2493-7. doi: 10.1002/jcc.23402. Epub 2013 Aug 7. J Comput Chem. 2013. PMID: 23925979

9

Decomposition-order effects of time integrator on ensemble averages for the Nosé-Hoover thermostat.

Itoh SG, Morishita T, Okumura H. Itoh SG, et al. Among authors: okumura h. J Chem Phys. 2013 Aug 14;139(6):064103. doi: 10.1063/1.4817194. J Chem Phys. 2013. PMID: 23947839

10

Amyloid fibril disruption by ultrasonic cavitation: nonequilibrium molecular dynamics simulations.

Okumura H, Itoh SG. Okumura H, et al. J Am Chem Soc. 2014 Jul 30;136(30):10549-52. doi: 10.1021/ja502749f. Epub 2014 Jul 9. J Am Chem Soc. 2014. PMID: 24987794

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