Diffusion-equation method

Piela L, Kostrowicki J and Scheraga H A 1989 The multiple-minima problem in the conformational analysis of molecules. Deformation of the potential energy hypersurface by the diffusion equation method J. Phys. Chem. 93 3339... 

J. Kostrowicki and H.A. Scheraga, Application of the diffusion equation method for global optimization to oligopeptides, J. Phys. Chem. 96 (1992), 7442-7449. M. Levitt, A simplified representation of protein confomations for rapid simulation of protein folding, J. Mol. Biol. 104 (1976), 59-107. 

L. Piela, J. Kostrowicki, and H. A. Scheraga,/. Phys. Chem., 93,3339 (1989). The Multiple-Minima Problem in Conformational Analysis of Molecules. Deformation of the Potential Energy Hypersurface by the Diffusion Equation Method. 

The conformational spaces of clusters of Lennard-Jones atoms were searched by application of the diffusion equation method for clusters of various sizes m from m = 5 to 55. For example, for m = 55, with 3m - 6 = 159 degrees of freedom, there are about 1045 local minima, and the global minimum (a MacKay icosahedron) was found in about 400 s on an IBM 3090 computer.205... 

Performance of the Diffusion Equation Method in Searches for Optimum Structures of Clusters of Lennard-Jones Atoms. 

J. Kostrowicki, L. Piela, B.J. Cherayil, H.A. Scheraga, Performance of the diffusion equation method in searches for optimum structures of clusters of Lennard-Jones clusters, J. Phys. Chem. 95 (1991), 4113. 

T. Huber, A.E. Torda, W.F. van Gunsteren, Structure optimization combining soft-core interaction functions, the diffusion equation method and molecular dynamics, J. Phys. Chem. AlOl (1997), 5926. 

Related Approaches Target Function Minimization, the Diffusion Equation Method, and the Ellipsoid Algorithm... 

Figure 17 The diffusion equation method schematic representation of how the energy surface is transformed until only one minimum is obtained.

Kostrowicki J, Scheraga HA (1992) Application of the diffusion equation method for global optimization to oligopeptides. J Phys Chem-Us 96 7442-7449... 

CBMC = configurational bias Monte Carlo DEM = diffusion equation method LES = locally enhanced sampling QMA = quantum mechanical annealing. 

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