Molecular Design Studio - GPU-bound provable sampler + exact cited verification (no AI)

What it is

The research-grade composing surface of the verifiable molecular-design engine. It builds a REAL materials/polymer (or small-molecule aromatic) combinatorial chemical space from a cited scaffold plus a monomer/linker/side-group fragment library, brute-force enumerates the whole index space on the GPU (one thread per combinatorial index) for a property vector, a CITED energy V and a Gibbs log-weight, re-reduces the log-partition function on a 16-limb GeoNum GPU tree, and runs a symmetric single-site Metropolis-Hastings walker that PROVABLY targets the Gibbs measure exp(-beta V) toward the user property targets - the exact detailed-balance residual of the kernel is measured and reported under its own sampler-correctness band. Every returned candidate is RE-VERIFIED exactly on its explicit atom-bond graph: MW from IUPAC 2021 standard atomic masses, logP by Hansch-Leo 1979, TPSA by Ertl 2000, pKa by Hammett where applicable, HBD/HBA/rotatable-bonds/rings by their standard definitions, with Lipinski 2001 and Veber 2002 as derived flags, plus an integer-exact validity report and its deterministic seed provenance. There is NO learned model, no training, and no tuning of the energy to the target. GeoNum trust reads UNTRACKED with a reason (the pipeline routes no kernel drift); the reported bands describe the COMPUTATION, never whether a molecule is good, novel, or synthesizable, and no claim is made that the geometric substrate is chemically special (mesh57/HVP benchmarked information-equivalent to Weisfeiler-Leman). This is the pre-cluster design and triage step that runs BEFORE expensive HPC docking and FEP, not a substitute for them.

Honest scope

Authorities cited

• Hansch & Leo 1979, Substituent Constants for Correlation Analysis in Chemistry and Biology (Wiley), Table 4-7. Additive logP; logP(benzene) = 2.13.
• Ertl, Rohde & Selzer 2000, J. Med. Chem. 43, 3714. Topological polar surface area (TPSA) from atom-type contributions.
• Lipinski, Lombardo, Dominy & Feeney 2001, Adv. Drug Deliv. Rev. 46, 3. Rule of Five; HBD/HBA definitions.
• Veber, Johnson, Cheng, Smith, Ward & Kopple 2002, J. Med. Chem. 45, 2615. Rotatable-bond and TPSA rules.
• IUPAC 2021 standard atomic weights (molecular weight from exact standard atomic masses).
• Metropolis et al. 1953, J. Chem. Phys. 21, 1087; Hastings 1970, Biometrika 57, 97. A symmetric proposal targets exp(-beta V) by detailed balance.
• Odian, Principles of Polymerization, 4th ed., Wiley 2004 (polymer repeat-unit scaffolds + monomer/linker chemistry).
• Standard main-group valences (Greenwood & Earnshaw 1997; IUPAC 2005) define validity; cyclomatic formula defines ring count. Defined chemistry, not fit.