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Published on: November 21, 2017
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Nonlinear irreversible thermodynamics of single-molecule experiments
I Santamaría-Holek1, N J López-Alamilla1, M Hidalgo-Soria1
1UMDI-Facultad de Ciencias, Universidad Nacional Autónoma de México Campus Juriquilla, Querétaro 76230, México.
Summary
This study presents irreversible thermodynamics for single-molecule experiments under mechanical forces. It explains RNA stretching oscillations and resonant phenomena, aligning calculations with experimental observations.
Area of Science:
- Thermodynamics
- Single-molecule biophysics
- Nonlinear dynamics
Background:
- Single-molecule experiments often involve external mechanical forces.
- Understanding systems under nonequilibrium constraints is crucial.
- Existing thermodynamic formalisms may not fully capture nonlinear behaviors.
Purpose of the Study:
- To extend irreversible thermodynamics to nonlinear single-molecule systems under external forces.
- To calculate entropy production and kinetic equations for such systems.
- To analyze phenomena like RNA stretching and resonance.
Main Methods:
- Extension of Onsager's formalism to nonlinear, nonequilibrium systems.
- Calculation of entropy production and general nonlinear kinetic equations.
- Application of Kramer's approach to determine hopping rates.
Main Results:
- Developed a theoretical framework for irreversible thermodynamics in constrained single-molecule experiments.
- Predicted and explained critical oscillations in RNA stretching protocols.
- Calculated entropy production during configurational state changes.
- Observed resonant phenomena in single RNA stretching experiments.
- Hopping rates calculated via Kramer's approach showed good agreement with experimental data.
Conclusions:
- The extended thermodynamic formalism accurately describes nonlinear phenomena in single-molecule experiments.
- The study provides a theoretical basis for understanding resonance and oscillations in biophysical stretching experiments.
- The findings offer insights into the behavior of molecules like RNA under external mechanical stress.
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