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Dynamically induced conformation depending on excited normal modes of fast oscillation
Yoshiyuki Y Yamaguchi1, Tatsuo Yanagita2, Tetsuro Konishi3
1Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University, Kyoto 606-8501, Japan.
Physical Review. E
|July 20, 2022
Summary
Dynamical effects influence molecular conformation by creating an effective potential. This study reveals how spring motion and energy shape these dynamically induced conformations.
Area of Science:
- Computational physics
- Molecular dynamics
- Statistical mechanics
Background:
- Molecular conformation is typically defined by potential energy functions.
- Fast internal motions can significantly alter a system's effective potential and stable states.
Purpose of the Study:
- To investigate how dynamical effects influence molecular conformation in a simplified model.
- To develop a theoretical framework for understanding dynamically induced conformations.
Main Methods:
- Utilized a bead-spring model with three beads and two stiff springs.
- Employed multiple-scale analysis and the averaging method to derive the effective potential.
- Performed numerical simulations to verify the theory's efficiency.
Main Results:
- The effective potential is influenced by the excited normal modes of the springs.
- The amount of spring energy plays a crucial role in determining the effective potential.
- Dynamical effects lead to 'dynamically induced conformations' not solely predicted by static potentials.
Conclusions:
- Fast spring motions construct an effective potential that governs molecular conformation.
- The developed theory accurately describes how dynamics induce conformational changes.
- This work provides insights into the interplay between dynamics and structure in molecular systems.
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