Self-avoiding walk between two fixed points as a tool to calculate reaction paths in large molecular systems

1990/03/17 by Ryszard Czerminski, Ryszard Czermiński, Ron Elber · 130 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · Mathematics · #Chain (unit) #Chemistry #Classical mechanics #Computational chemistry #Computer science #Dipeptide #Gaussian #Interpolation (computer graphics) #Mass Spectrometry Techniques and Applications #Mathematics #Path (computing) #Physics #Protein Structure and Dynamics #Quantum mechanics #RNA and protein synthesis mechanisms #Statistical physics

paper · doi:10.1002/qua.560382419

published in International Journal of Quantum Chemistry 38(S24), 167-185 (Wiley)

openalex publication_date 1990/03/17 · openalex created_date 2025/10/10 · openalex updated_date 2026/06/26

Abstract

A new computational technique is presented to calculate approximate reaction paths in complex molecules. The method is based on the Gaussian chain approach proposed by Elber and Karplus [1] but avoids some computational difficulties of this technique. It is also more than 10 times faster. The new formulation is quite general and enables empirical interpolation between two types of motions which differ considerably: trapped and ballistic (see also “Note Added in Proof”). We present test results for two model molecules: alanine dipeptide (AD) and isobutyryl-(ala)3-NH-methyl (IAN). The optimization of the chain is very stable and provides an approximate continuous path even if the initial guess is poor.

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