69 citations · 150 across the 5 of their papers we have counts for
5 papers
Sequential replica exchange with solute tempering for atomistic modeling of supramolecular polymer structures
Hadi H. Arefi, Takeshi Yamamoto
Predicting detailed atomistic structures of self-assembling systems remains a challenge for all-atom molecular dynamics simulations. Replica exchange with solute tempering (REST) h…
Self-assembly of a model supramolecular polymer studied by replica exchange with solute tempering
Hadi H. Arefi, Takeshi Yamamoto
Conventional molecular-dynamics (cMD) simulation has a well-known limitation in accessible time and length scales, and thus various enhanced sampling techniques have been proposed…
Variational and perturbative formulations of QM/MM free energy with mean-field embedding and its analytical gradients
Takeshi Yamamoto
Conventional quantum chemical solvation theories are based on the mean-field embedding approximation. That is, the electronic wavefunction is calculated in the presence of the mean…
Path-integral virial estimator for reaction rate calculation based on the quantum instanton approximation
Sandy Yang, Takeshi Yamamoto, William H. Miller
The quantum instanton approximation is a type of quantum transition state theory that calculates the chemical reaction rate using the reactive flux correlation function and its low…
Path integral virial estimator based on the scaling of fluctuation coordinates: Application to quantum clusters with fourth-order propagators
Takeshi M. Yamamoto
We first show that a simple scaling of fluctuation coordinates defined in terms of a given reference point gives the conventional virial estimator in discretized path integral, whe…