Elastic Bag Model of One-Dimensional Pulsed-Field Gel Electrophoresis (ODPFGE)
Bibliographic record
Abstract
Gel electrophoresis is one of the most common techniques used in molecular biology for the separation of DNA molecules. Conventional gel electrophoresis (using a static electric field) does not permit separation of DNA fragments larger than 30-50 kbp (1) as shown in Fig. 1A of Chapter 7 . This is a surprising result as one would think that larger molecules would suffer a larger retardation, and separation over any size range would be possible. The inability to separate is related to the molecular conformation of a polyelectrolyte, such as DNA, migrating in a disordered medium, such as a gel, under the influence of a static electric field. During continuous field electrophoresis, the larger DNA fragments tend to orient and stretch in the field direction because they migrate in a one-dimensional fashion between the gel fibers (2-4). When this orientation is negligible, e.g., for smaller molecules or for very low field intensities, they maintain a three-dimensional random-walk conformation intertwined with the gel fibers during migration, and experience a retardation that is proportional to the mol size. However, when the orientation becomes large, the molecules become stretched and migrate essentially linearly along the field direction (5). The electrophoretic mobility then becomes independent of the mol size and no separation of molecules of different sizes is possible (Fig. 1A of Chapter 7 ). Physically, this is a consequence of the fact that for long molecules stretched and oriented in the field direction, both the electrical force on the molecule and the average friction opposing the forward motion are proportional to the length. It follows that the velocity, which is the ratio of these two quantities, depends only on the force per unit length and is independent of the actual mol length. This explains why a plateau of length-independent mobility is reached in a continuous electric field (Fig. 2 of Chapter 7 ).
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.003 |
| Open science | 0.004 | 0.001 |
| Research integrity | 0.003 | 0.002 |
| Insufficient payload (model declined to judge) | 0.018 | 0.007 |
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".