| Budget Amount *help |
¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000)
Fiscal Year 2014: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2013: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2012: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2011: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
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| Outline of Final Research Achievements |
Biomolecules such as proteins have complicated free energy surfaces with many local minima. Conventional molecular dynamics simulations tend to get trapped in these local-minimum states. One of the powerful techniques to avoid this difficulty is the replica-exchange method.
We proposed a new type of the replica-exchange method, which is referred to as helix-strand replica-exchange molecular dynamics method. In this method umbrella potential which enhances alpha-helix or beta-strand conformation is exchanged. We applied this method to a design peptide and compared the results with those obtained by usual replica-exchange method.
We also proposed a better alternative to the replica-exchange method, which we refer to as the replica-permutation method. In replica-permutation method, not only exchanges between two replicas but also permutations among more than two replicas are performed.
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