Molecular Dynamics Simulations for Complexation of DNA with 2 kDa PEI Reveal Profound Effect of PEI Architecture on Complexation
Bibliographic record
Abstract
A series of all-atom molecular dynamics (MD) simulations of the complexation between DNA and 2 kDa branched and linear polyethylenimines (PEIs) are reported in this study. The simulations revealed distinct binding modes of branched and linear PEIs to DNA, with branched PEIs adhering to the DNA surface like beads and linear PEIs adhering to the DNA surface like cords. The dynamics of each PEI's binding state to the DNA during the simulations and how the PEIs neutralize the DNA were quantified. For both branched and linear PEIs, the addition of salt ions similar to physiological conditions were found to have only a small effect on DNA/PEI complexation compared to salt-free conditions. The simulation results reported here will be helpful to understand the mechanism of action for the PEI-based gene carriers.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 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".