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 as the trust verdict. 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. The GTI verdict is on the COMPUTATION, never on 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.