Molecular Dynamics Study of Oxidized Lipid Bilayers in NaCl Solution
Bibliographic record
Abstract
Polyunsaturated lipids are major targets of free radicals forming oxidized lipids through the lipid peroxidation process. Thus, oxidized lipids play a significant role in cell membrane damage. Using atomistic molecular dynamics (MD) simulations to investigate the dynamics of oxidized lipid bilayers, we examined the effects of NaCl on them. Lipid bilayer systems of 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphatidylcholine (PLPC) and 4 oxidation products, namely, 9-tc-hydroperoxide linoleic acid, 13-tc-hydroperoxide linoleic acid, 9-oxononanoic acid, and 12-oxo-9-didecadienoic acid in 0, 0.06, and 1 M NaCl solution were studied. These 51 systems, combined over 15 μs of total simulation time, show Cl(-) anions remaining in the water phase and Na(+) cations permeating into the headgroup region of the bilayer leading to membrane packing. The effects of NaCl on thickness and area per molecule were found to be independent of the concentration of oxidized lipids. NaCl disturbed the bilayers with aldehyde lipids more than those with peroxide lipids. The key finding is that oxidized lipids bend their polar tails toward the water interface. This behavior was monitored by following the time evolution of hydrogen bonds between the oxidized functional groups of different lipids, and the concomitant increase of hydrogen bonds between oxidized functional groups and water molecules. Our results also show that the number of hydrogen bonds should be considered as an equilibration parameter: Very long simulations are needed to equilibrate systems with high NaCl concentrations.
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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 | 0.000 |
| 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".