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ABSTRACT

The task of finding saddle points on potential energy surfaces plays a crucial role in understanding the dynamics of a micro-molecule as well as in studying the folding pathways of macro-molecules like proteins. This paper primarily focusses on computing saddle points on potential energy surfaces. A stability boundary based approach that explores the dynamic and geometric characteristics of stability boundaries of a nonlinear dynamical system has been used to compute saddle points. A novel ray-adjustment procedure is used to trace the stability boundary. A simpler version of the algorithm has also been used to find the saddle points of symmetric systems. Our approach was also successful in finding saddle points on higher dimensional energy surfaces.

REFERENCES

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INDEX TERMS

Keywords:
bioinformatics, potential energy surfaces, saddle points, stability boundaries, stability regions