Computer Simulation of In Vitro Formation of PHB Granules: Particulate Polymerization
Bibliographic record
Abstract
The kinetics of poly(3-hydroxybutyrate) granules formed in vitro from [R]-(–)-3-hydroxybutyryl–Coenzyme A (CoA) monomer in the presence of PHA synthase were followed using transmission electron microscopy (TEM) and Cryo-TEM. Round granules were formed rapidly at the beginning of the experiment, growing from the initially observed diameter of 0.1 μm to about 1 μm within a few minutes. In contrast to the rapid granule growth, the initial conversion (polymerization) rate was slow. After a lag phase lasting several minutes, the conversion rate reached its maximum value while the total number of granules steadily declined. We account for these observations as follows: • The initial granules are vesicle-like, being stabilized by a monomolecular enzyme layer on their surface. • The initial granules are microporous, i.e., contain some polymer but are mainly filled with water. • The granules collide due to Brownian motion and coalescence occurs accounting for most of the diameter growth. • The polymerization is topotactic and is hindered by the surface energy required to extrude the hydrophobic polymer into the largely aqueous environment inside the granules. • As the granules accumulate PHB, polymerization is increasingly favored and its rate reaches a maximum. A computer program was written to test the model. The dynamic display simulates the in vitro growth of the granules in three-dimensional space. The simulation mimics granule formation, monomer conversion, Brownian motion, and coalescence. The sizes and compositions of all particles are recorded and simulated data are plotted and compared with experimental observations. The computer simulation approximated the experimental data and validated the mechanistic hypotheses.
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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".