Effect of the intermediate state on the loop-to-coil transition of a telechelic chain
Bibliographic record
Abstract
The kinetics of conformational fluctuations of a telechelic chain with two binding sites at both ends is studied by Monte Carlo simulations. The site-to-site binding energy is −ε. An example of the telechelic biopolymer is RNA or ssDNA made of a homogeneous sequence such as poly(T) with complementary bases at both ends. The conformation of such a chain fluctuate from loop (closed) to coil (open) state and the probability of the coil state depends on the temperature. An all-or-none transition between open and closed states is often adopted to depict the melting curves. It is found that the two-state model fails due to the existence of the intermediate state. A three-state model including open, intermediate, and closed states is proposed. The melting curves obtained from such a scenario agree quite well with the simulation results and there are two characteristic temperatures. The rate constants from closed to intermediate states kc,i and from intermediate to open states ki,o are independent of chain length but proportional to e−ε/kT. In contrast, the rate constants from open to intermediate states ko,i is independent of temperature and that from intermediate to closed states ki,c is essentially constant.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".