153 citations · 457 across the 12 of their papers we have counts for
12 papers
Estimating relaxation times from a single trajectory
Takuma Akimoto, Eiji Yamamoto, Takashi Uneyama
Complex systems such as protein conformational fluctuations and supercooled liquids exhibit a long relaxation time and are considered to posses multiple relaxation times. We analyt…
Heterogeneous biological membranes regulate protein partitioning via fluctuating diffusivity
Ken Sakamoto, Takuma Akimoto, Mayu Muramatsu +3
Cell membranes phase separate into ordered and disordered domains depending on their compositions. This membrane compartmentalization is heterogeneous and r…
Wetting hysteresis induces effective unidirectional water transport through a fluctuating nanochannel
Noriyoshi Arai, Eiji Yamamoto, Takahiro Koishi +3
We propose a water pump that actively transports water molecules through nanochannels. Spatially asymmetric thermal fluctuations imposed on the channel radius cause unidirectional…
Ligand-induced protein dynamics differences correlate with protein-ligand binding affinities: An unsupervised deep learning approach
Ikki Yasuda, Katsuhiro Endo, Eiji Yamamoto +2
Prediction of protein-ligand binding affinity is a major goal in drug discovery. Generally, free energy gap is calculated between two states (e.g., ligand binding and unbinding). T…
Universal relation between instantaneous diffusivity and radius of gyration of proteins in aqueous solution
Eiji Yamamoto, Takuma Akimoto, Ayori Mitsutake +1
Protein conformational fluctuations are highly complex and exhibit long-term correlations. Here, molecular dynamics simulations of small proteins demonstrate that these conformatio…
Local reservoir model for choice-based learning
Makoto Naruse, Eiji Yamamoto, Takashi Nakao +6
Decision making based on behavioral and neural observations of living systems has been extensively studied in brain science, psychology, and other disciplines. Decision-making mech…