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Protein dimerization in 2D vs 3D: Geometric allostery enhances binding affinity
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The Journal of Chemical Physics
J. Chem. Phys. 163, 034116 (2025)
Published: July 2025
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Characterizing the embedded states of a fluorescent probe within a lipid bilayer using molecular dynamics simulations
Available to PurchaseRyo Okabe, Natsuumi Ito, Yuya Matsubara, Nozomi Morishita Watanabe, Hiroshi Umakoshi, Kento Kasahara, Nobuyuki Matubayasi
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The Journal of Chemical Physics
J. Chem. Phys. 163, 034708 (2025)
Published: July 2025
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AutoSIM: Redesigning and automating umbrella sampling for biomolecular conformational transitions
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The Journal of Chemical Physics
J. Chem. Phys. 163, 014111 (2025)
Published: July 2025
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Exploring minimum free-energy pathway of GB1 dimerization in dilute and crowded solution
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The Journal of Chemical Physics
J. Chem. Phys. 162, 225101 (2025)
Published: June 2025
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Additive strategy for nucleation pathway control based on the understanding of molecular size effect on crystallization
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The Journal of Chemical Physics
J. Chem. Phys. 162, 214503 (2025)
Published: June 2025
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You reap what you sow: On the impact of nuclei morphology on seeded molecular dynamics simulations
Open Access
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The Journal of Chemical Physics
J. Chem. Phys. 162, 184503 (2025)
Published: May 2025
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Considerations in the use of machine learning force fields for free energy calculations
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The Journal of Chemical Physics
J. Chem. Phys. 162, 174119 (2025)
Published: May 2025
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An iterative and automatic collective variable optimization scheme via unsupervised feature selection with CUR matrix decomposition
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The Journal of Chemical Physics
J. Chem. Phys. 162, 174101 (2025)
Published: May 2025
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Data efficient learning of molecular slow modes from nonequilibrium metadynamics
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The Journal of Chemical Physics
J. Chem. Phys. 162, 164101 (2025)
Published: April 2025
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Solvation enhances folding cooperativity and the topology dependence of folding rates in a lattice protein model
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The Journal of Chemical Physics
J. Chem. Phys. 162, 145104 (2025)
Published: April 2025
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Learning transition path and membrane topological signatures in the folding pathway of bacteriorhodopsin (BR) fragment with artificial intelligence
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The Journal of Chemical Physics
J. Chem. Phys. 162, 104110 (2025)
Published: March 2025
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Unveiling nucleosome dynamics: A comparative study using all-atom and coarse-grained simulations enhanced by principal component analysis
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The Journal of Chemical Physics
J. Chem. Phys. 162, 065101 (2025)
Published: February 2025
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Evaluating multi-state free energy profiles from splitting probability
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The Journal of Chemical Physics
J. Chem. Phys. 162, 055102 (2025)
Published: February 2025
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