Molecular Dynamics Simulation of Water and Ions in Nanopores of Lysozyme Protein Crystal
Bibliographic record
Abstract
Highly porous cross-linked protein crystals are a novel class of nanoporous materials with vast applications in biocatalysis and selective separation membranes. Long time equilibrium molecular dynamics (MD) simulations were performed to study the behavior of water and ions in the nanopores of lysozyme protein crystals. Pore size profile along different axes showed that the main pores lie along the z-axis consisting of an anisotropic structure. The morphology of pore network and pore sizes, influence water dynamics in protein crystals. Transport properties of water molecules were investigated under two diffusion regimes around protein surface, i.e. surface and core zone. Results showed that water molecules near the surface zone had the anomalous diffusion behavior while the behavior in the core zone was diffusive. Moreover, an anisotropic diffusion behavior was occurred along different axes in accordance to experimental predictions. Simulations demonstrated that nearly 16 percent of water molecules have the residence time above 100 ps at the first hydration layer around the protein crystal, while 3.3 percent of those remain in the cavities over a longer time of about 1400 ps. The behavior of chloride counter ions in the first hydration layer around the protein crystal or on the specific residues of the crystal was investigated as well. The simulation results were in a good agreement with the previous theoretical studies and experimental data. This study provides valuable insights into understanding the transport phenomena in the protein crystals in view of the nature of solvent-protein and ion-protein interactions.
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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 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 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".