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Yuko Okamoto

Publications and source records attributed to Yuko Okamoto.

45 records · Page 3Linked to original sources
arXiv1997

Generalized-ensemble Monte carlo method for systems with rough energy landscape

We present a novel Monte Carlo algorithm which enhances equilibrization of low-temperature simulations and allows sampling of configurations over a large range of energies. The method is based on a non-Boltzmann probability weight factor and is another version of the so-called generalized-ensemble techniques. The effectiveness of the new approach is demonstrated for the system of a small peptide, an example of the frustrated system with a rugged energy landscape.

cond-mat↗
arXiv1997

Molecular dynamics, Langevin, and hybrid Monte Carlo simulations in multicanonical ensemble

We demonstrate that the multicanonical approach is not restricted to Monte Carlo simulations, but can also be applied to simulation techniques such as molecular dynamics, Langevin, and hybrid Monte Carlo algorithms. The effectiveness of the methods are tested with an energy function for the protein folding problem. Simulations in the multicanonical ensemble by the three methods are performed for a penta peptide, Met-enkephalin. For each algorithm, it is shown that from only one simulation run one can not only find the global-minimum-energy conformation but also obtain probability distributions in canonical ensemble at any temperature, which allows the calculation of any thermodynamic quantity as a function of temperature.

physics.chem-ph↗
arXiv1997

Numerical Comparisons of Three Recently Proposed Algorithms in the Protein Folding Problem

We compare numerically the effectiveness of three recently proposed algorithms, multicanonical simulations, simulations in a 1/k-ensemble, and simulated tempering for the protein folding problem. For this we perform simulations with high statistics for one of the simplest peptides, Met-enkephalin. While the performances of all three approaches is much better than traditional methods, we find that the differences among the three are only marginal.

physics.chem-ph↗
arXiv1995

Thermodynamics of helix-coil transitions studied by multicanonical algorithms

Thermodynamics of helix-coil transitions in amino-acid homo-oligomers are studied by the recently proposed multicanonical algorithms. Homo-oligomers of length 10 are considered for three characteristic amino acids, alanine (helix former), valine (helix indifferent), and glycine (helix breaker). For alanine other lengths (15 and 20) are also considered in order to examine the length dependence. From one multicanonical production run with completely random initial conformations, we have obtained the lowest-energy conformations and various thermodynamic quantities (average helicity, Zimm-Bragg $s$ and $σ$ parameters, free energy differences between helix and coil states, etc.) as functions of temperature. The results confirm the fact that alanine is helix-forming, valine is helix-indifferent, and glycine is helix-breaking.

chem-ph↗
arXiv1994

Comparative Study of Multicanonical and Simulated Annealing Algorithms in the Protein Folding Problem

We compare a few variants of the recently proposed multicanonical method with the well known simulated annealing for the effectiveness in search of the energy global minimum of a biomolecular system. For this we study in detail Met-enkephalin, one of the simplest peptides. We show that the new method not only outperforms simulated annealing in the search of the energy groundstate but also provides more statistical-mechanical information about the system.

chem-ph↗
arXiv1993

Prediction of Peptide Conformation by the Multicanonical Algorithm

We test the effectiveness of the multicanonical algorithm for the tertiary structure prediction of peptides and proteins. As a simple example we study Met-enkephalin. The lowest-energy conformation obtained agrees with that determined by other methods such as Monte Carlo simulated annealing. But unlike to simulated annealing the relationship to the canonical ensemble remains exactly controlled. Thermodynamic quantities at various temperature can be calculated from one run.

cond-mat↗
arXiv1993

Prediction of Peptide Conformation by Multicanonical Algorithm: A New Approach to the Multiple-Minima Problem

We apply a recently developed method, multicanonical algorithm, to the problem of tertiary structure prediction of peptides and proteins. As a simple example to test the effectiveness of the algorithm, Met-enkephalin is studied and the ergodicity problem, or multiple-minima problem, is shown to be overcome by this algorithm. The lowest-energy conformation obtained agrees with that determined by other efficient methods such as Monte Carlo simulated annealing. The superiority of the present method to simulated annealing lies in the fact that the relationship to the canonical ensemble remains exactly controlled. Once the multicanonical parameters are determined, only one simulation run is necessary to obtain the lowest-energy conformation and furthermore the results of this one run can be used to calculate various thermodynamic quantities at any temperature. The latter point is demonstrated by the calculation of the average potential energy and specific heat as functions of temperature.

hep-lat↗
arXiv1992

Generalized Einstein Theory on Solar and Galactic Scales

We study a generalized Einstein theory with the following two criteria:{\it i}) on the solar scale, it must be consistent with the classical tests of general relativity, {\it ii}) on the galactic scale, the gravitational potential is a sum of Newtonian and Yukawa potentials so that it may explain the flat rotation curves of spiral galaxies. Under these criteria, we find that such a generalized Einstein action must include at least one scalar field and one vector field as well as the quadratic term of the scalar curvature.

astro-ph↗