Pith Number

pith:EMDA5BHD

pith:2026:EMDA5BHDYYW6O355DLSVHVAHOB

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An Efficient Approach for Calculating Free Energy in Molecular Dynamics: Demineralization of Hydroxyapatite as a Case Study

Alexander M. Korsunsky, Jin-Chong Tan, Mahdi Tavakol

An adaptive method mixes expensive high-quality free energy runs with cheap low-quality ones to profile hydroxyapatite demineralization at far lower total cost.

arxiv:2605.16957 v1 · 2026-05-16 · cond-mat.mtrl-sci

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Claims

C1strongest claim

We designed a new adaptive free energy calculation methodology which combines high quality, high computational cost free energy values with lower quality, lower cost values to build up the entire free energy profile. In the best case scenario this method lowers manifold the computational cost required for the non-equilibrium work free energy calculations compared to both the regular method and the reversible simulation.

C2weakest assumption

The assumption that a small number of high-quality reversible pulling simulations (each taking 75 days) provide an accurate ground-truth free energy profile against which the adaptive combination of mixed-quality runs can be reliably validated, and that differences in initial structure equilibration dominate over the number of independent trajectories.

C3one line summary

The authors propose an adaptive non-equilibrium work method for free energy profiles in MD that combines high- and low-quality simulations to cut computational cost while matching results from long reversible reference runs, shown on hydroxyapatite demineralization.

References

4 extracted · 4 resolved · 1 Pith anchors

[1] Because such rare events underlie critical molecular phenomena, the ability to compute accurate free energy differences and profiles is of vital importance. At the conceptual level, the importance of 1997

[2] University of Oxford Advanced Research Computing Facility · doi:10.5281/zenodo.22558

[3] References (1) Alder, B. J.; Wainwright, T. E. Phase Transition for a Hard Sphere System. J. Chem. Phys. 1957, 27 (5), 1208–1209. 17 (2) Mi, F.; He, Z.; Jiang, G.; Ning, F. Effect of Glucose on CH4 Hy 1957

[4] Uncovering the role of ionic doping in hydroxyapatite: The building blocks of tooth enamel and bones 2016 · arXiv:2604.13339

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Receipt and verification

First computed	2026-05-20T00:03:32.848616Z
Builder	pith-number-builder-2026-05-17-v1
Signature	Pith Ed25519 (`pith-v1-2026-05`) · public key
Schema	pith-number/v1.0

Canonical hash

23060e84e3c62de76fbd1ae553d4077077487280e1c03ae9588685b7fa385bca

Aliases

arxiv: 2605.16957 · arxiv_version: 2605.16957v1 · doi: 10.48550/arxiv.2605.16957 · pith_short_12: EMDA5BHDYYW6 · pith_short_16: EMDA5BHDYYW6O355 · pith_short_8: EMDA5BHD

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Verify this Pith Number yourself

curl -sH 'Accept: application/ld+json' https://pith.science/pith/EMDA5BHDYYW6O355DLSVHVAHOB \
  | jq -c '.canonical_record' \
  | python3 -c "import sys,json,hashlib; b=json.dumps(json.loads(sys.stdin.read()), sort_keys=True, separators=(',',':'), ensure_ascii=False).encode(); print(hashlib.sha256(b).hexdigest())"
# expect: 23060e84e3c62de76fbd1ae553d4077077487280e1c03ae9588685b7fa385bca

Canonical record JSON

{
  "metadata": {
    "abstract_canon_sha256": "6f81223fd4de3151046569e05a03a2d89fbdaab77edb63b6a73b0a815ce322b1",
    "cross_cats_sorted": [],
    "license": "http://creativecommons.org/licenses/by-nc-nd/4.0/",
    "primary_cat": "cond-mat.mtrl-sci",
    "submitted_at": "2026-05-16T12:18:08Z",
    "title_canon_sha256": "29c76b40908c6440a61a3375a38e9bbcc956509d87c2c67837a89f57af5342dd"
  },
  "schema_version": "1.0",
  "source": {
    "id": "2605.16957",
    "kind": "arxiv",
    "version": 1
  }
}