358 research outputs found
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, in which
not temperatures but the van der Waals radius parameter is exchanged. By
decreasing the van der Waals radii that control spatial sizes of atoms, this
Hamiltonian replica-exchange method overcomes the steric restrictions and
energy barriers. Furthermore, the simulation based on this method escapes from
the local-minimum free-energy states and realizes effective sampling in the
conformational space. We applied this method to an alanine dipeptide in aqueous
solution and showed the effectiveness of the method by comparing the results
with those obtained from the conventional canonical method.Comment: 14 pages, (Revtex4), 11 figure
Practice supporting system with related problem set generator based on targeted educational effects
Effective Sampling in the Configurational Space by the Multicanonical-Multioverlap Algorithm
We propose a new generalized-ensemble algorithm, which we refer to as the
multicanonical-multioverlap algorithm. By utilizing a non-Boltzmann weight
factor, this method realizes a random walk in the multi-dimensional,
energy-overlap space and explores widely in the configurational space including
specific configurations, where the overlap of a configuration with respect to a
reference state is a measure for structural similarity. We apply the
multicanonical-multioverlap molecular dynamics method to a penta peptide,
Met-enkephalin, in vacuum as a test system. We also apply the multicanonical
and multioverlap molecular dynamics methods to this system for the purpose of
comparisons. We see that the multicanonical-multioverlap molecular dynamics
method realizes effective sampling in the configurational space including
specific configurations more than the other two methods. From the results of
the multicanonical-multioverlap molecular dynamics simulation, furthermore, we
obtain a new local-minimum state of the Met-enkephalin system.Comment: 15 pages, (Revtex4), 9 figure
都市の時空間構造に関する地理学的研究
金沢大学教育学部研究課題/領域番号:62780265, 研究期間(年度):1987出典:研究課題「都市の時空間構造に関する地理学的研究」課題番号62780265(KAKEN:科学研究費助成事業データベース(国立情報学研究所)) (https://kaken.nii.ac.jp/ja/grant/KAKENHI-PROJECT-62780265/)を加工して作
非物理空間における都市の内部構造の研究
金沢大学教育学部研究課題/領域番号:01780275, 研究期間(年度):1989出典:研究課題「非物理空間における都市の内部構造の研究」課題番号01780275(KAKEN:科学研究費助成事業データベース(国立情報学研究所)) (https://kaken.nii.ac.jp/ja/grant/KAKENHI-PROJECT-01780275/)を加工して作
- …