Conceptual Framework for Developing a Stable, Ultra-Powerful, and Precise Hadronic Quantum Computer Based on Protons.

Quantum computing holds transformative potential for simulating complex quantum systems, yet current platforms suffer from short coherence times and scalability limitations. This manuscript introduces a comprehensive conceptual framework for a hadronic quantum computer (HQC) utilizing protons as robust, spin-1/2 qubits, harnessing their intrinsic QCD confinement for exceptional stability ($\tau_2 > 100$ s) and room-temperature operation. We derive the effective Rabi Hamiltonian for single-qubit control, one-pion-exchange potentials for entanglement, and coherence timescales via perturbative QCD and chiral effective field theory, projecting gate fidelities exceeding 99.9%.Central to the architecture is a face-centered cubic proton lattice in a Paul trap, enabling variational quantum eigensolver (VQE) state preparation with an augmented, hardware-efficient ansatz incorporating additional ZZ-interaction layers to mitigate barren plateaus and achieve sub-MeV precision in hadron spectra simulations. Topological error correction employs SU(3) color codes with detailed syndrome extraction protocols, yielding thresholds $p_{th} \approx 0.7%$. Extensions to neutron and deuteron qubits are explored, revealing enhanced neutrality for neutrons and qutrit encoding for deuterons.Reproducible QuTiP simulations validate Rabi oscillations and VQE convergence on Ising proxies, demonstrating relative energy errors below 2.3%. Applications span QCD lattice simulations, real-time LHC event reconstruction, and novel drug discovery via QCD-mapped protein folding, projecting 10-fold acceleration in biomolecular virtual screening. Challenges, including fm-scale trapping and scalability, are addressed alongside a phased roadmap to fault-tolerant $10^6$-qubit systems by 2035.This self-contained theoretical model bridges particle physics and quantum information, paving the way for ultra-precise, stable quantum supremacy in high-energy and biomolecular sciences.Keywords: Hadronic quantum computing, Proton qubits, Lattice QCD, Variational quantum eigensolver, Topological error correction