Quantifying the Properties of Nonproductive Attempts at Thermally Activated Energy-Barrier Crossing through Direct Observation
Thermally activated energy-barrier crossing is ubiquitous in physical, chemical, and biological processes. Most barrier-crossing attempts have insufficient energy to overcome the barrier; hence, productive transition paths that successfully cross the barrier are very rare compared to nonproductive f...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
American Physical Society
2024-02-01
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| Series: | Physical Review X |
| Online Access: | http://doi.org/10.1103/PhysRevX.14.011017 |
| _version_ | 1797308543758499840 |
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| author | Aaron Lyons Anita Devi Noel Q. Hoffer Michael T. Woodside |
| author_facet | Aaron Lyons Anita Devi Noel Q. Hoffer Michael T. Woodside |
| author_sort | Aaron Lyons |
| collection | DOAJ |
| description | Thermally activated energy-barrier crossing is ubiquitous in physical, chemical, and biological processes. Most barrier-crossing attempts have insufficient energy to overcome the barrier; hence, productive transition paths that successfully cross the barrier are very rare compared to nonproductive fluctuations that enter the barrier region but return without crossing it. Recent experimental advances have yielded important insights into transition paths, but nonproductive attempts remain little studied experimentally or theoretically, even though they can reveal information about parts of the reaction energy landscape not visited during transition paths. Observing the diffusive dynamics of a bead hopping between bistable optical traps as a model system, we measured the duration, maximum position along the reaction coordinate, and occupancy statistics of unsuccessful crossing attempts. Experimental results agreed quantitatively with expectations of an analytical framework we derived from committor theory. Applying these analyses to a more complex example, DNA hairpin folding under tension, we found that some properties differed from those of transition paths, such as the asymmetric occupancies for folding and unfolding attempts, whereas others were similar, such as the diffusion coefficient reflecting landscape roughness. These results show how nonproductive crossing attempts can be detected and analyzed rigorously, enabling characterization of the full dynamics within the transition region. |
| first_indexed | 2024-03-08T01:13:15Z |
| format | Article |
| id | doaj.art-5e235e003e604492abc927b13ce2fd04 |
| institution | Directory Open Access Journal |
| issn | 2160-3308 |
| language | English |
| last_indexed | 2024-03-08T01:13:15Z |
| publishDate | 2024-02-01 |
| publisher | American Physical Society |
| record_format | Article |
| series | Physical Review X |
| spelling | doaj.art-5e235e003e604492abc927b13ce2fd042024-02-14T15:03:53ZengAmerican Physical SocietyPhysical Review X2160-33082024-02-0114101101710.1103/PhysRevX.14.011017Quantifying the Properties of Nonproductive Attempts at Thermally Activated Energy-Barrier Crossing through Direct ObservationAaron LyonsAnita DeviNoel Q. HofferMichael T. WoodsideThermally activated energy-barrier crossing is ubiquitous in physical, chemical, and biological processes. Most barrier-crossing attempts have insufficient energy to overcome the barrier; hence, productive transition paths that successfully cross the barrier are very rare compared to nonproductive fluctuations that enter the barrier region but return without crossing it. Recent experimental advances have yielded important insights into transition paths, but nonproductive attempts remain little studied experimentally or theoretically, even though they can reveal information about parts of the reaction energy landscape not visited during transition paths. Observing the diffusive dynamics of a bead hopping between bistable optical traps as a model system, we measured the duration, maximum position along the reaction coordinate, and occupancy statistics of unsuccessful crossing attempts. Experimental results agreed quantitatively with expectations of an analytical framework we derived from committor theory. Applying these analyses to a more complex example, DNA hairpin folding under tension, we found that some properties differed from those of transition paths, such as the asymmetric occupancies for folding and unfolding attempts, whereas others were similar, such as the diffusion coefficient reflecting landscape roughness. These results show how nonproductive crossing attempts can be detected and analyzed rigorously, enabling characterization of the full dynamics within the transition region.http://doi.org/10.1103/PhysRevX.14.011017 |
| spellingShingle | Aaron Lyons Anita Devi Noel Q. Hoffer Michael T. Woodside Quantifying the Properties of Nonproductive Attempts at Thermally Activated Energy-Barrier Crossing through Direct Observation Physical Review X |
| title | Quantifying the Properties of Nonproductive Attempts at Thermally Activated Energy-Barrier Crossing through Direct Observation |
| title_full | Quantifying the Properties of Nonproductive Attempts at Thermally Activated Energy-Barrier Crossing through Direct Observation |
| title_fullStr | Quantifying the Properties of Nonproductive Attempts at Thermally Activated Energy-Barrier Crossing through Direct Observation |
| title_full_unstemmed | Quantifying the Properties of Nonproductive Attempts at Thermally Activated Energy-Barrier Crossing through Direct Observation |
| title_short | Quantifying the Properties of Nonproductive Attempts at Thermally Activated Energy-Barrier Crossing through Direct Observation |
| title_sort | quantifying the properties of nonproductive attempts at thermally activated energy barrier crossing through direct observation |
| url | http://doi.org/10.1103/PhysRevX.14.011017 |
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