Shuichi Miyamoto

TL;DR: In this article, an analytical algorithm called SETTLE for resetting the positions and velocities to satisfy the holonomic constraints on the rigid water model is presented, which is based on the Cartesian coordinate system and can be used in place of SHAKE and RATTLE.

TL;DR: These results are consistent with the interpretation that the entropy increase to be expected from hydrophobic interactions from desolvation of biotin is counterbalanced by a decrease in entropy accompanying the formation of buried hydrogen bonds, which have been derived from the apparentlyconflicting experimental data.

TL;DR: Free energy perturbation methods using molecular dynamics have been used and reproduce the significantly more negative free energy of association of biotin to streptavidin, compared to N-L-acetyltryptophanamide/alpha-chymotrypsin.

TL;DR: In this article, the relative free energies of calixspherand complexation with alkali metal cations were determined using a thermodynamic free energy perturbation method, using two sets of van der Waals parameters, two methods of describing 1-4 nonbonded interactions and two extreme models of solvation for the calix spherand andalkali ion complex.

TL;DR: In this paper , a simple and convenient experimental system with agar-gel was constructed to measure the diffusion coefficients of sugars, which is a spontaneous process and one of the physicochemical phenomena responsible for molecular transport, the rate of which is governed mainly by the diffusion coefficient.