Koda S - Search Results

1

Initial-value semiclassical propagators for the Wigner phase space representation: Formulation based on the interpretation of the Moyal equation as a Schrödinger equation.

Koda S. Koda S. J Chem Phys. 2015 Dec 28;143(24):244110. doi: 10.1063/1.4938235. J Chem Phys. 2015. PMID: 26723654

2

Equivalence between a generalized dendritic network and a set of one-dimensional networks as a ground of linear dynamics.

Koda S. Koda S. J Chem Phys. 2015 May 28;142(20):204112. doi: 10.1063/1.4921730. J Chem Phys. 2015. PMID: 26026439

3

A theoretical investigation of symmetry-origin unidirectional energy gradient in light-harvesting dendrimers.

Koda S. Koda S. J Chem Phys. 2016 Mar 21;144(11):114101. doi: 10.1063/1.4943510. J Chem Phys. 2016. PMID: 27004856

The present analysis and proposition are based on the theory of the linear chain (LC) decomposition [S. Koda, J. Chem. Phys. 142, 204112 (2015)], which equivalently transforms the model system into a set of one-dimensional systems on the basis of the symmetry of den …

The present analysis and proposition are based on the theory of the linear chain (LC) decomposition [S. Koda, J. Chem. Phys. 1 …

4

Mixed semiclassical-classical propagators for the Wigner phase space representation.

Koda S. Koda S. J Chem Phys. 2016 Apr 21;144(15):154108. doi: 10.1063/1.4947041. J Chem Phys. 2016. PMID: 27389210

We formulate mixed semiclassical-classical (SC-Cl) propagators by adding a further approximation to the phase-space SC propagators, which have been formulated in our previous paper [S. Koda, J. Chem. Phys. 143, 244110 (2015)]. We first show that the stationary phase …

We formulate mixed semiclassical-classical (SC-Cl) propagators by adding a further approximation to the phase-space SC propagators, which ha …

5

Locating Transition States by Variational Reaction Path Optimization with an Energy-Derivative-Free Objective Function.

Koda SI, Saito S. Koda SI, et al. J Chem Theory Comput. 2024 Apr 9;20(7):2798-2811. doi: 10.1021/acs.jctc.3c01246. Epub 2024 Mar 21. J Chem Theory Comput. 2024. PMID: 38513192

6

Flat-Bottom Elastic Network Model for Generating Improved Plausible Reaction Paths.

Koda SI, Saito S. Koda SI, et al. J Chem Theory Comput. 2024 Aug 16. doi: 10.1021/acs.jctc.4c00792. Online ahead of print. J Chem Theory Comput. 2024. PMID: 39150850

7

An alternative interpretation of the slow KaiB-KaiC binding of the cyanobacterial clock proteins.

Koda SI, Saito S. Koda SI, et al. Sci Rep. 2020 Jun 26;10(1):10439. doi: 10.1038/s41598-020-67298-7. Sci Rep. 2020. PMID: 32591637 Free PMC article.

8

Molecular Mechanism of Acceleration and Retardation of Collective Orientation Relaxation of Water Molecules in Aqueous Solutions.

Moritsugu N, Nara T, Koda SI, Tominaga K, Saito S. Moritsugu N, et al. Among authors: koda si. J Phys Chem B. 2020 Dec 24;124(51):11730-11737. doi: 10.1021/acs.jpcb.0c10036. Epub 2020 Dec 15. J Phys Chem B. 2020. PMID: 33320675

9

Multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by ADP/ATP exchange inhibition.

Koda SI, Saito S. Koda SI, et al. PLoS Comput Biol. 2022 Mar 7;18(3):e1009243. doi: 10.1371/journal.pcbi.1009243. eCollection 2022 Mar. PLoS Comput Biol. 2022. PMID: 35255087 Free PMC article.

10

Conformational rearrangements of the C1 ring in KaiC measure the timing of assembly with KaiB.

Mukaiyama A, Furuike Y, Abe J, Koda SI, Yamashita E, Kondo T, Akiyama S. Mukaiyama A, et al. Among authors: koda si. Sci Rep. 2018 Jun 11;8(1):8803. doi: 10.1038/s41598-018-27131-8. Sci Rep. 2018. PMID: 29892030 Free PMC article.

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