43 citations · 58 across the 5 of their papers we have counts for
5 papers
Exact electrostatic energy calculation for charged systems neutralized by uniformly distributed background charge using fast multipole method and its application to efficient free energy calculation
Ryo Urano, Wataru Shinoda, Noriyuki Yoshii +1
In the molecular dynamics calculations for the free energy of ions and ionic molecules, we often encounter wet charged molecular systems where electrical neutrality condition is br…
Aerosol-OT surfactant forms stable reverse micelles in aploar solvent in the absence of water
Ryo Urano, George A. Pantelopulos, John E. Straub
Normal micelle aggregates of amphiphilic surfactant in aqueous solvent are formed by a process of entropically driven self-assembly. The self-assembly of reverse micelles from amph…
Designed-walk replica-exchange method for simulations of complex systems
Ryo Urano, Yuko Okamoto
We propose a new implementation of the replica-exchange method (REM) in which replicas follow a pre-planned route in temperature space instead of a random walk. Our method satisfie…
Deterministic replica-exchange method without pseudo random numbers for simulations of complex systems
Ryo Urano, Yuko Okamoto
We propose a replica-exchange method (REM) which does not use pseudo random numbers. For this purpose, we first give a conditional probability for Gibbs sampling replica-exchange m…
Predictions of tertiary stuctures of -helical membrane proteins by replica-exchange method with consideration of helix deformations
Ryo Urano, Hironori Kokubo, Yuko Okamoto
We propose an improved prediction method of the tertiary structures of -helical membrane proteins based on the replica-exchange method by taking into account helix deformations.…