Molecular dynamics simulation studies on the aggregation of amyloid-β peptides and their disaggregation by ultrasonic wave and infrared laser irradiation
Alzheimer's disease is understood to be caused by amyloid fibrils and oligomers formed by
aggregated amyloid-β (Aβ) peptides. This review article presents molecular dynamics (MD) …
aggregated amyloid-β (Aβ) peptides. This review article presents molecular dynamics (MD) …
Temperature and pressure denaturation of chignolin: Folding and unfolding simulation by multibaric‐multithermal molecular dynamics method
H Okumura - Proteins: Structure, Function, and Bioinformatics, 2012 - Wiley Online Library
A multibaric‐multithermal molecular dynamics (MD) simulation of a 10‐residue protein,
chignolin, was performed. All‐atom model with the Amber parm99SB force field was used for …
chignolin, was performed. All‐atom model with the Amber parm99SB force field was used for …
Replica-permutation method with the Suwa–Todo algorithm beyond the replica-exchange method
We propose a new method for molecular dynamics and Monte Carlo simulations, which is
referred to as the replica-permutation method (RPM), to realize more efficient sampling than …
referred to as the replica-permutation method (RPM), to realize more efficient sampling than …
Enhanced sampling algorithms
In biomolecular systems (especially all-atom models) with many degrees of freedom such as
proteins and nucleic acids, there exist an astronomically large number of local-minimum …
proteins and nucleic acids, there exist an astronomically large number of local-minimum …
Temperature and pressure dependence of alanine dipeptide studied by multibaric− multithermal molecular dynamics simulations
We applied the multibaric− multithermal (MUBATH) molecular dynamics (MD) algorithm to
an alanine dipeptide in explicit water. The MUBATH MD simulation covered a wide range of …
an alanine dipeptide in explicit water. The MUBATH MD simulation covered a wide range of …
Multidimensional generalized-ensemble algorithms for complex systems
A Mitsutake, Y Okamoto - The Journal of Chemical Physics, 2009 - pubs.aip.org
We give general formulations of the multidimensional multicanonical algorithm, simulated
tempering, and replica-exchange method. We generalize the original potential energy …
tempering, and replica-exchange method. We generalize the original potential energy …
Multibaric–multithermal ensemble molecular dynamics simulations
We present new generalized‐ensemble molecular dynamics simulation algorithms, which
we refer to as the multibaric–multithermal molecular dynamics. We describe three algorithms …
we refer to as the multibaric–multithermal molecular dynamics. We describe three algorithms …
Replica-exchange method in van der Waals radius space: Overcoming steric restrictions for biomolecules
We present a new type of the Hamiltonian replica-exchange method, where the van der
Waals radius parameter and not the temperature is exchanged. By decreasing the van der …
Waals radius parameter and not the temperature is exchanged. By decreasing the van der …
Generalized-ensemble algorithms for the isobaric–isothermal ensemble
We present generalized-ensemble algorithms for isobaric–isothermal molecular simulations.
In addition to the multibaric–multithermal algorithm and replica-exchange method for the …
In addition to the multibaric–multithermal algorithm and replica-exchange method for the …
Transformation of a design peptide between the α-helix and β-hairpin structures using a helix-strand replica-exchange molecular dynamics simulation
We investigated the transformation between the α-helix and β-hairpin structures of an 18-
residue design peptide, whose sequence is INYWLAHAKAGYIVHWTA. This peptide has …
residue design peptide, whose sequence is INYWLAHAKAGYIVHWTA. This peptide has …