Nonequilibrium Work Fluctuations in Force-induced Melting of a Short B-DNA
Fuente:
arXiv
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1866915438001127424 |
|---|---|
| author | Chari, S. Siva Nasarayya Maiti, Prabal K. |
| author_facet | Chari, S. Siva Nasarayya Maiti, Prabal K. |
| contents | A system of a solvated canonical B-DNA of 12 base pairs with the specified sequence is initially equilibrated in a state of zero external force $f$ acting on it. After equilibration, a switching experiment is performed over the system by pulling one end of the DNA while restraining its other end. The finite time pulling process is performed at a constant rate of the applied force until a maximum value of 400 pN. The associated nonequilibrium work done $(W)$ during this process is determined by numerically integrating the force-extension curve as a function of the applied force. An ensemble of the work values, $P(W)$, is obtained by repeating the pulling experiment a large number of times. We determine the free energy difference $(ΔF)$ between the equilibrium and force-induced melted states of the DNA by employing the Jarzynski equality. The value of $ΔF$ is found to be in close agreement with the conventional equilibrium methods. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2508_07354 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Nonequilibrium Work Fluctuations in Force-induced Melting of a Short B-DNA Chari, S. Siva Nasarayya Maiti, Prabal K. Soft Condensed Matter Biological Physics A system of a solvated canonical B-DNA of 12 base pairs with the specified sequence is initially equilibrated in a state of zero external force $f$ acting on it. After equilibration, a switching experiment is performed over the system by pulling one end of the DNA while restraining its other end. The finite time pulling process is performed at a constant rate of the applied force until a maximum value of 400 pN. The associated nonequilibrium work done $(W)$ during this process is determined by numerically integrating the force-extension curve as a function of the applied force. An ensemble of the work values, $P(W)$, is obtained by repeating the pulling experiment a large number of times. We determine the free energy difference $(ΔF)$ between the equilibrium and force-induced melted states of the DNA by employing the Jarzynski equality. The value of $ΔF$ is found to be in close agreement with the conventional equilibrium methods. |
| title | Nonequilibrium Work Fluctuations in Force-induced Melting of a Short B-DNA |
| topic | Soft Condensed Matter Biological Physics |
| url | https://arxiv.org/abs/2508.07354 |