Applying the TPS method to modeling and simulation of biological systems
Bibliographic record
Abstract
Deformable biological structures are typically modeled with the finite element method, but we have designed a much simpler impulse-based method called the "tethered particle system " (TPS). The TPS involves the use of discrete-event simulation to track the positions of a large number of particles. Two of these particles approaching to each other may collide and rebound off. The difference is that, provided they are "tethered", two separating particles may also collide and retract inwards. This constrains the distances between pairs of particles, allowing various deformable structures to be represented. In this article, we present the application of the TPS method to the simulation of different biological structures found in nerve cells: actin filaments, cell membranes and synapsin protein that bind with actin, mitochondria, and water particles which influence the motion of other structures. This includes advanced visualization methods. 1.
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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".