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The Hybrid Idea of Optimization Methods Applied to the Energy Minimization of (Prion) Protein Structures

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Title: The Hybrid Idea of Optimization Methods Applied to the Energy Minimization of (Prion) Protein Structures


1
The Hybrid Idea of Optimization Methods Applied
to the Energy Minimization of (Prion) Protein
Structures
  • Jiapu
  • Zhang

2
We will minimize
i.e.
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  • Details of algorithms to solve the above two
    problems can be seen from website
  • http//arxiv.org/abs/1504.03614
  • In the below, we just want to through graphs
    illuminate how to understand these two problems.

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potential energy
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potential energy
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Mathematical properties of LJ potential(Xue G.L.
(1997) J Glob Optim 11 83-90 Barron-Romero C.
(2005) arXiv0504030v5) - e.g. the most simple
ones
Mathematical Programming Society of USA specially
edited one Newsletter (OPTIMA No. 76, March 2008)
to talk about LJ problem and Global Optimization.
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Lennard-Jones clusters ofUniversity of
Cambridgehttp//doye.chem.ox.ac.uk/jon/structures
/LJ.html
  • Tables of Global minima
  • N3-150
  • N310-561
  • N562-1000
  • LJ151-309
  • LJ1001-1610
  • For me, I got N30,40,42,48,55,75,76,97 (see J
    Theor Biol 279(1) 17-28 (2011)).

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(This figure is seen in websitehttp//people.mbi
.ucla.edu/david/)
For min Evan-der-Waals , , e.g. see papers
1 Journal of Molecular Modelling 17(1) 173-9
(2011). 2 J Theor Biol 279(1) 17-28 (2011). 3
J Theor Biol 284(1) 149-57 (2011). 4 Natural
Science 4 (12A) 1097-108 (2012). 5 book ISBN
978-3-8465-2139-7. The hybrid idea of
optimization methods is used.
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  • For this problem and its follower MD (molecular
    dynamics),
  • The hybrid idea of optimization methods is
    firstly used for optimizing protein structures.
  • The impacts of my works
  • One CSIRO award in 2006 (with Jose Varghese and
    Vidana Epa)
  • World impact in 2011

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Computer results of the CSIRO Award of Year 2006
were confirmed in 2010 by X-ray laboratory
results of Uni of Toronto (see PNAS 107
19808-13).
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At the back of the poser, there is a Story with
Alex
  • My last contact/email with Alex.

25
I heard bad news from website http//constructiveo
ptimisation.com/vfd/ on Professor Vladimir
Demyanov - I hope it is not true, I am also in
memory of Professor Vladimir Demyanov
All the pictures in this presentation
are gotten from google search. I do not own any
copyright.
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