Molecular Dynamics Simulation Study of Adsorption and Patterning of DNA Bases on the Au(111) Surface
Bibliographic record
Abstract
To understand of the mechanism of self-assembly of DNA base molecules on the Au(111) surface, molecular dynamics simulations of different surface coverage of guanine, adenine, cytosine, and thymine molecules at 300 and 400 K are performed. At low coverage, guanine, adenine, and thymine form hydrogen bonded chains on the surface, while cytosine molecules cluster into islands. At larger coverage, simulations indicate that adenine molecules form ordered two-dimensional hexagonal structures, while guanine, cytosine, and thymine molecules aggregate into small random clusters. These observations agree with scanning tunneling microscopy (STM) experiments of the DNA bases on gold surfaces. The simulations show that arrangement of the molecules on the gold surface is controlled by base–base interactions. The hydrogen bond interactions and stability of base–base homopairs, which are the smallest components of the self-assembled structures on the Au(111) surface, are calculated and compared with calculations of the homopairs in the gas phase and with values available in the literature. The binding energies per base on the surface initially decrease in magnitude with increasing surface coverage and then reach a constant plateau at large coverages. The mechanisms of molecular mobility for the bases with one and two molecule coverage on the surface are analyzed at two temperatures.
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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".