Centered tethers and circles share a conditional Twinkle encounter law

**Result:** A centered reflecting DNA tether and an equal-length circle have identical conditional fork-encounter-time distributions under uniform non-fork attachment and homogeneous diffusion. This exact null comparison, applied to purified human TWNK/Twinkle, shows why a centered-linear versus circular encounter fraction cannot isolate a topology effect under those premises. **Methods:** A source-grounded theoretical calculation used the reported rounded 18-kb substrate and diffusion coefficient 0.787 ± 0.065 kb²/s. The approximately 120-s fork observation/bleaching time supplied an illustrative horizon, not a molecular lifetime. A continuous fork-position survival mixture was evaluated at 101 positions for each of three diffusion scenarios and checked with a separately implemented finite-volume diffusion solver. Scenarios are deterministic calculations, not biological replicates or confidence intervals. **Findings:** At 120 s, the conditional encounter probability was 0.6049993 for an end target and 0.9543534 for both the centered tether and the equal-length circle. Changing the diffusion coefficient by one reported standard error gave end-target probabilities 0.5807354–0.6278288 and centered probabilities 0.9421107–0.9640069. Refinement reduced all nine numerical discrepancies; the largest refined absolute discrepancy was 0.00008570. The increment beyond published diffusion and fork arrest is a reproducible geometry-comparison diagnostic, not discovery of sliding or new first-passage mathematics. **Consequence and limit:** An end-versus-center comparison changes the conditional geometric prediction; the centered-tether/circle comparison is an informative null. A counterexample to their equality under the exact premises would defeat the calculation. Preferential direct fork attachment is already observed, and non-fork start density, end behavior, physical loss and observation censoring remain unresolved. The result does not estimate biological capture, unwinding, mitochondrial replication or clinical benefit.

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Publication Details

Journal
Zenodo (CERN European Organization for Nuclear Research)
Published
2026-11-02
DOI
https://doi.org/10.5281/zenodo.23890834
Primary Topic
Diffusion and Search Dynamics
Type
article
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article

Centered tethers and circles share a conditional Twinkle encounter law

Andrew Friedl
1 links
Zenodo (CERN European Organization for Nuclear Research)
Diffusion and Search Dynamics
article

Centered tethers and circles share a conditional Twinkle encounter law

Andrew Friedl
article en

Abstract

**Result:** A centered reflecting DNA tether and an equal-length circle have identical conditional fork-encounter-time distributions under uniform non-fork attachment and homogeneous diffusion. This exact null comparison, applied to purified human TWNK/Twinkle, shows why a centered-linear versus circular encounter fraction cannot isolate a topology effect under those premises. **Methods:** A source-grounded theoretical calculation used the reported rounded 18-kb substrate and diffusion coefficient 0.787 ± 0.065 kb²/s. The approximately 120-s fork observation/bleaching time supplied an illustrative horizon, not a molecular lifetime. A continuous fork-position survival mixture was evaluated at 101 positions for each of three diffusion scenarios and checked with a separately implemented finite-volume diffusion solver. Scenarios are deterministic calculations, not biological replicates or confidence intervals. **Findings:** At 120 s, the conditional encounter probability was 0.6049993 for an end target and 0.9543534 for both the centered tether and the equal-length circle. Changing the diffusion coefficient by one reported standard error gave end-target probabilities 0.5807354–0.6278288 and centered probabilities 0.9421107–0.9640069. Refinement reduced all nine numerical discrepancies; the largest refined absolute discrepancy was 0.00008570. The increment beyond published diffusion and fork arrest is a reproducible geometry-comparison diagnostic, not discovery of sliding or new first-passage mathematics. **Consequence and limit:** An end-versus-center comparison changes the conditional geometric prediction; the centered-tether/circle comparison is an informative null. A counterexample to their equality under the exact premises would defeat the calculation. Preferential direct fork attachment is already observed, and non-fork start density, end behavior, physical loss and observation censoring remain unresolved. The result does not estimate biological capture, unwinding, mitochondrial replication or clinical benefit.

Zenodo (CERN European Organization for Nuclear Research)
Openalex Percentile: Top 25%
Diffusion and Search Dynamics
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Centered tethers and circles share a conditional Twinkle encounter law — Andrew Friedl · Zenodo (CERN European Organization for Nuclear Research) (2026) | TGRS Research Map | TGRS