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Smoothing techniques for macromolecular global optimization

Description: We study global optimization problems that arise in macromolecular modeling, and the solution of these problems via continuation and smoothing. Our results unify and extend the theory associated with the use of the Gaussian transform for smoothing. We show that the, Gaussian transform can be viewed as a special case of a generalized transform and that these generalized transforms share many of the properties of the Gaussian transform. We also show that the smoothing behavior of the generalized transform can be studied in terms of the Fourier transform and that these results indicate that the Gaussian transform has superior smoothing properties.
Date: September 1, 1995
Creator: More, J.J. & Wu, Zhijun
Partner: UNT Libraries Government Documents Department

Global smoothing and continuation for large-scale molecular optimization

Description: We discuss the formulation of optimization problems that arise in the study of distance geometry, ionic systems, and molecular clusters. We show that continuation techniques based on global smoothing are applicable to these molecular optimization problems, and we outline the issues that must be resolved in the solution of large-scale molecular optimization problems.
Date: October 1995
Creator: More, J. J. & Wu, Zhijun
Partner: UNT Libraries Government Documents Department

Global continuation for distance geometry problems

Description: Distance geometry problems arise in the interpretation of NMR data and in the determination of protein structure. The authors formulate the distance geometry problem as a global minimization problem with special structure, and show the global smoothing techniques and a continuation approach for global optimization can be used to determine solutions of distance geometry problems with a nearly 100% probability of success.
Date: March 1, 1995
Creator: More, J.J. & Wu, Zhijun
Partner: UNT Libraries Government Documents Department

The effective energy transformation scheme as a special continuation approach to global optimization with application to molecular conformation

Description: This paper discusses a generalization of the function transformation scheme for global energy minimization applied to the molecular conformation problem. A mathematical theory for the method as a special continuation approach to global optimization is established. We show that the method can transform a nonlinear objective function into a class of gradually deformed, but {open_quote}smoother{close_quote} or {open_quotes}easier{close_quote} functions. An optimization procedure can then be applied to the new functions successively, to trace their solutions back to the original function. Two types of transformation are defined: isotropic and anisotropic. We show that both transformations can be applied to a large class of nonlinear partially separable functions including energy functions for molecular conformation. Methods to compute the transformation for these functions are given.
Date: November 1, 1996
Creator: Wu, Zhijun
Partner: UNT Libraries Government Documents Department