Computer simulation of DNA interacting electrostatically with phosphatidylcholine and trimethylammoniumpropane interfaces
Bibliographic record
Abstract
The region of a lipid membrane, with all hydrocarbon chains equal, embedded in an aqueous solution and interacting with a single DNA molecule, has been modelled. The lattice model used assigned an area characteristic of a lipid molecule in a gel phase to each lattice site. In a fluid phase two lipid molecules occupy three sites. We studied a membrane composed of lipids with phosphatidylcholine (PC) and trimethylammoniumpropane (TAP) headgroups. Lipid headgroup states were enumerated as described elsewhere (Pink et al., Biochim. Biophys. Acta, 1988, 1368, 289). Here charged lipid moieties were represented by point charges inside an excluded volume. The aqueous solution was modelled as a linearized Poisson–Boltzmann system characterized by a Debye screening length, κ−1. We employed standard Monte Carlo computer simulation techniques. We came to the following conclusions. (a) In the absence of DNA, PC and TAP headgroup pairs formed dynamic bound states in a gel phase. These did not occur if the PC was represented as an object carrying no charges. Accordingly, although PC carries zero net charge, it is important to represent the charged moieties explicitly. The gel–fluid phase transition in a 1:1 PC–TAP membrane (with equal hydrocarbon chain lengths) might thus involve not only hydrocarbon chain disordering but also the break-up of the dynamical PC–TAP bound pairs. (b) Increasing TAP concentration resulted in changing the orientation of the PC dipole. (c) DNA binding is a complex process and can involve weak binding even to a pure PC interface (which could, however, be disrupted by membrane undulations not modelled here) and tighter binding when TAP is present. The minimum concentration for the latter depends upon κ. DNA binding at low TAP concentrations would be changed if the PC was represented by a chargeless object. (d) A bound DNA changes the headgroup orientation in its proximity and also results in increased headgroup lateral packing in the immediate neighbourhood of the DNA. The latter could result in denser lateral hydrocarbon chain packing in the neighbourhood of the DNA. Both of these phenomena exhibited a dependence upon the TAP concentration. (e) The average lipid–DNA binding energies per DNA PO2− group can be as large as 2kBT or more depending upon the TAP concentration. (f ) DNA can be unbound by changing the ionic concentration. We compare our results with experimental data and other simulations.
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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) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 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".