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Molecular Dynamics Simulations of Water/Mucus Partition Coefficients for Feeding Stimulants in Fish and the Implications for Olfaction

Evidence and attribution

Authority of statements

Prose sections below (Summary, Methods, Findings, etc.) are curated summaries of the publication identified by doi, title, and pdf_path in the front matter above. They are not new primary claims by this wiki.

For definitive numerical values, reaction schemes, and interpretations, use the peer-reviewed article (and optional records under normalized/papers/ when present)—not this page alone.

Summary

All-atom molecular dynamics on a simplified mucus model estimates water/mucus partition coefficients for amino-acid feeding stimulants (alanine, glycine, cysteine, valine) in fresh versus salt water. Fresh water favors mucus partitioning for all four acids with ordering linked to hydrophobicity; salt reverses preference (except glycine) through ion-mediated interactions. Partition coefficient variation stays ~one order of magnitude, much narrower than air/mucus spans in mammals, arguing against strong spatial chromatography for fish olfaction (abstract; introduction, extract pages 1–2).

Methods

Grounding: papers/Rygg_PLOSone_2013.pdf; normalized/extracts/2013rygg-venue-pone_p1-2.txt (abstract + start of Methods / model description).

1 — MD application (all-atom MD; simplified mucus model)

  • Engine / code: Molecular dynamics simulations are used (abstract). The MD package is not named on the indexed excerpt pages (normalized/extracts/2013rygg-venue-pone_p1-2.txt).
  • System size & composition: The study uses a simplified molecular model of olfactory mucus to compute water/mucus partition coefficients for alanine, glycine, cysteine, and valine feeding stimulants (abstract). Atom counts are not stated on p1–2.
  • Electrolyte / environment: Both fresh water and salt water environments are considered (abstract). The introduction discusses ion-mediated interactions between salt ions, odorants, and mucin as part of the partitioning story (extract).
  • Boundaries / periodicity: N/A — PBC details are not stated on the indexed excerpt pages.
  • Ensemble: NVT equilibration at 300 K followed by NPT equilibration at 1 bar and 300 K, then production NPT at 1 bar and 300 K (papers/Rygg_PLOSone_2013.pdf, Methods excerpt extracted from PDF text).
  • Timestep: N/A — not stated on the indexed excerpt pages.
  • Duration / stages: N/A — not stated on the indexed excerpt pages.
  • Thermostat / barostat: N/A — not stated on the indexed excerpt pages.
  • Temperature: N/A — explicit simulation temperature(s) are not stated on the indexed excerpt pages.
  • Pressure: N/A.
  • Electric field: N/A.
  • Replica / enhanced sampling: N/A.

2 — Force-field training

N/A — classical all-atom MD with a reduced mucus model (not a ReaxFF parametrization paper).

Findings

  • Outcomes & mechanisms: In fresh water, all four amino acids prefer mucus over bulk water, with partition coefficient trends linked to hydrophobicity (abstract). In salt water, partitioning reverses so stimulants (except glycine) prefer water over mucus, attributed to ion–odorant and ion–mucin interactions (abstract).
  • Comparisons: Contrasts water/mucus partitioning spreads (~one order of magnitude) with air/mucus spans that can reach ~six orders of magnitude in mammalian discussions (abstract).
  • Sensitivity / design levers: Fresh vs salt solvent environment is the primary comparative axis in the abstract framing.
  • Limitations & outlook: The abstract argues this argues against strong spatial chromatography for fish olfaction versus terrestrial nasal chromatography narratives, consistent with reported lack of spatial ORN organization in fish epithelium (abstract).
  • Corpus honesty: Indexed excerpt includes model formulation start but not full force field, thermostat, or run-length tables; read pdf_path Methods for reproducibility.

Limitations

Mucus chemistry is simplified; receptor-level biology and fluid advection (CFD) are outside the MD core reported in the opening pages.

Relevance to group

van Duin coauthorship connects biomolecular MD modeling traditions at Penn State alongside reactive materials work.

Citations and evidence anchors

  • PLoS ONE 8(9): e72271; DOI 10.1371/journal.pone.0072271 (abstract metadata in extract).
  • Abstract partition-coefficient narrative (extract page 1).