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A model to describe the mechanism of conformational dynamics in secondary protein based on matter interactions is proposed. The approach deploys the lagrangian method by imposing certain symmetry breaking. The protein backbone is initially assumed to be nonlinear and represented by the Sine-Gordon equation, while the nonlinear external bosonic sources is represented by $phi^4$ interaction. It is argued that the nonlinear source induces the folding pathway in a different way than the previous work with initially linear backbone. Also, the nonlinearity of protein backbone decreases the folding speed.
A model to describe the mechanism of conformational dynamics in protein based on matter interactions using lagrangian approach and imposing certain symmetry breaking is proposed. Both conformation changes of proteins and the injected non-linear sourc
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with the solven
Processes that proceed reliably from a variety of initial conditions to a unique final form, regardless of moderately changing conditions, are of obvious importance in biophysics. Protein folding is a case in point. We show that the action principle
Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in coevolutio
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as variables as op