HexaGene is a parameter-free physics engine for biological systems — derived from a single integer, validated on IBM quantum hardware, and demonstrated across four unrelated application domains using one identical architecture.
ibm_fez jobsThe HexaGene architecture has been executed on IBM's ibm_fez 156-qubit Heron r2 processor across more than two hundred production jobs, spanning four unrelated application domains. Only the domain inputs and the bond topology change between domains; the circuit, the gauge diagnostic, and the energy extraction are identical.
DNA is not just information — it is a physical polymer with measurable mechanical properties. Base-pair stacking energies, hydrogen-bond strengths, and local flexibility are governed by well-understood thermodynamics. HexaGene formalises these principles into a deterministic scoring framework.
DNA stability depends on stacking interactions between adjacent base pairs — the same principle used in RNA folding models and PCR primer design.
A mutation's impact depends on its neighbours. CpG dinucleotides, trinucleotide contexts, and codon position all modulate local physical stability.
Mutations that disrupt local stiffness, introduce torsional strain, or break symmetric patterns create measurable structural dissonance.
Every score returned by HexaGene is a function of these seven deterministic features. None of them are learned. None of them are tuned. Each emerges from the structural physics of the sequence.
Every claim in HexaGene is tied to an independently published dataset. The numbers below are reproducible end-to-end from the validation scripts on GitHub.
38,000 genetic variants from NCBI ClinVar in the original
blind study. The engine was blind to clinical labels.
Physics-based risk calculation separated benign from
pathogenic with mathematical certainty.
Production formula LP-S14.01
now extends this to 198,494 variants with
zero tuned parameters.
2,000 ClinVar missense variants benchmarked against the REVEL ensemble predictor. HexaGene maintains discrimination where conservation-based tools fail — proving statistical independence and complementary signal in the grey zone where REVEL scores fall between 0.4 and 0.6.
Routine biomarkers from the CDC national survey, mapped into structural state without genetic data. The same equations that map sequence to structure can be inverted to map blood panels to structure. Lead time of 6–18 months over standard risk tools (which typically achieve 1.5–2σ separation; HexaGene reaches 4.62σ on the original cohort).
IPNS enzymes across fifteen organisms. Structural conflict rate predicts expression stability with near-perfect correlation. In a parallel GLP-1 peptide validation, structural conflict rate at junction regions correlated with aggregation propensity (ρ = 0.67, p = 0.002), with failed constructs showing 14% higher junction conflict.
HexaCore is the deterministic physics engine at the foundation. Each application below is a validated configuration of the same underlying physics — not a separate model.
Identify structural-stress patterns in DNA sequences that lead to expression failure, independent of codon adaptation. Flag aggregation-prone candidates before formulation.
Quantify silent-risk variants and structurally robust therapeutic sequences early in development. Ab-initio drug–drug interaction detection on quantum hardware.
Assess functional risk of genetic variants — including synonymous and ultra-rare ones — through mechanistic, explainable physics.
Quantify system-level resilience from routine biomarkers. Structural decay rises before biomarkers cross diagnostic thresholds.
Validation datasets, reproducible scripts, and the gauge-symmetry manuscript are publicly available. The internal mathematical construction of the engine is patent-protected.
Built-in error detection on IBM ibm_fez. 230+ production jobs. Cross-domain validation. Per-cell reliability diagnostic at zero qubit overhead.
academia.edu →Centralised profile linking competition entries, research submissions, and ongoing quantum-software work in the quantum-research community.
aqora.io/sharadbachani →Reproducible analysis pipelines for the published validation studies. Benchmark datasets and end-to-end scripts. The internal engine remains protected.
github.com/sharadbachani-oss/hexagene →Complete dataset from the reverse-imputation study: 7,939 subjects, 10-marker panels, outcome validation. Citable DOI for downstream use.
zenodo.org/records/18141545 →Metabolic-risk demonstration on 3,097 NHANES subjects. Enter biomarkers and see the structural state computed in real time.
Try the clinical demo →Active deployments span pharmaceutical R&D, genomic diagnostics, biomanufacturing, and precision health, alongside quantum-hardware research with the IBM Quantum Network.
See engagement modes →HexaGene is in active commercial deployment. Engagement modes include API access, embedded integrations into client pipelines, custom validation studies, and patent licensing. Each engagement begins with a scoping conversation to match capability to use case.
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Patent and proprietary information. The internal structure of the cell Hamiltonian, the bond-term construction, the dose-encoding maps, the gate decomposition of each Trotter step, the explicit forms of the energy terms, and the application-specific input mappings for each demonstrated domain are proprietary subject matter covered by U.S. provisional patent applications PPA-1 through PPA-10 (including but not limited to US 64/027,290) and corresponding non-provisional filings, owned by Merlin Digital. The gauge-symmetry mechanism is disclosed in the published manuscript for the purpose of scientific review; no other implementation details are released. Use of any of the foregoing proprietary subject matter for commercial purposes requires a license.