Stress-induced shape transitions in polymers using a new approach to steered molecular dynamics
Bibliographic record
Abstract
Tertiary folds are structurally stable, yet present a notable degree of plasticity. This duality is a key feature to understanding biological function and activity. Recent experiments using atomic force microscopy allow one to assess folding stability by directly measuring conformational changes in a single biomolecule. Experimental data can be complemented by the microscopic detail provided by computer simulations of mechanical unfolding. In this work, we present a simple computational alternative to study stress-induced transitions in chain molecules. In our approach to steered molecular dynamics, a soft perturbation is introduced by performing regular “pull/push” events localized on two bonds at the chain's ends, followed by constrained dynamics with two anchored atoms. We test the procedure on a hydrocarbon chain, and then illustrate its potential by studying the stretching of an α-helix. Shape transitions are monitored in terms of molecular size and chain entanglements. We find that extensive distorsions of the helix can proceed at essentially constant molecular size. The results highlight the importance of using complementary shape descriptors to understand the behaviour of stressed chain molecules.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 teacher head, 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".