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Hysteresis and nonequilibrium work theorem for DNA unzipping
1Indian Institute of Science Education and Research Mohali, Knowledge City, Sector 81, SAS Nagar - 140 306, Punjab India. rkapri@iisermohali.ac.in
Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|December 11, 2012
Summary
This study simulates DNA unzipping and rezipping hysteresis using Monte Carlo methods. Hysteresis was observed, and a method was developed to extract equilibrium DNA isotherms from nonequilibrium measurements.
Area of Science:
- Biophysics
- Computational Biology
- Statistical Mechanics
Background:
- Studying DNA mechanics is crucial for understanding genetic processes.
- Hysteresis in DNA duplexes provides insights into their thermodynamic properties.
Purpose of the Study:
- To investigate hysteresis during DNA unzipping and rezipping using Monte Carlo simulations.
- To develop a method for extracting equilibrium DNA isotherms from nonequilibrium force measurements.
Main Methods:
- Monte Carlo simulations in a fixed force ensemble.
- Applying the work theorem to nonequilibrium force measurements.
- Varying pulling rates to observe their effect on hysteresis.
Main Results:
- Observed significant hysteresis during complete cycles of double-stranded DNA (dsDNA) unzipping and rezipping.
- Probability distributions of work performed showed the mean closely approximated the hysteresis loop area.
- Successfully extracted equilibrium and nonequilibrium force-separation isotherms for dsDNA.
Conclusions:
- Nonequilibrium force measurements can accurately reproduce equilibrium DNA isotherms.
- The developed simulation method is effective for studying DNA mechanical properties and hysteresis.
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