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            <span class="tag">Technical Documentation</span>
            <h1>HAWRA-PQPE Architecture</h1>
            <p style="margin-bottom: 2rem; color: #a0a0a0;">Reference documentation for the Phyto-synthetic Quantum Processing Entity (PQPE).</p>

            <div class="card" style="margin-bottom: 3rem; border-left: 4px solid var(--secondary-color);">
                <h3>Project Overview</h3>
                <p>HAWRA (Hardware-Agnostic Wetware-Reliant Architecture) is a living computing infrastructure. It repurposes the energy transport mechanisms of photosynthesis to perform quantum logic operations at room temperature, within genetically modified cells of <i>Ficus elastica</i>.</p>
            </div>

            <div class="card" style="margin-bottom: 3rem;">
                <h3>1. PQPE Formal Model</h3>
                <p>The system is based on harnessing the P700 reaction center. The evolution of the quantum state is described by the Lindblad equation for open quantum systems:</p>
                <div class="code-block">
                    dρ/dt = -i[H, ρ] + Σ [ L_i ρ L_i† - 1/2 {L_i† L_i, ρ} ]
                </div>
                <p>Where the Hamiltonian <i>H</i> models the excitonic interaction induced by light pulses programmed by the BioOS.</p>
            </div>

            <div class="card" style="margin-bottom: 3rem;">
                <h3>2. Arbol Language & Full Compilation Loop</h3>
                <p>Arbol is the first DSL (Domain Specific Language) for programming living matter. The BioOS compiler translates Arbol code into BSIM (Biological Instruction Set Architecture) instructions, which are then natively executed by the Multiphysics Engine.</p>
                <div class="code-block">
// Arbol circuit definition: "First Bloom"
genes {
    gene "psaA" with basal_rate = 0.1, light_sensitivity = 0.8;
}

run { step(100.0); } // Wait for P700 accumulation
H(q1);               // Apply Hadamard gate
measure q1;          // Probabilistic readout
                </div>
                <p style="margin-top: 1rem; font-size: 0.85rem;">
                    🔗 <a href="https://github.com/selectess/HAWRA/blob/main/04_validation_benchmarks/first_bloom.arbol" style="color: var(--primary-color);">View Source: first_bloom.arbol</a> |
                    ⚙️ <a href="https://github.com/selectess/HAWRA/blob/main/arbol/compiler/compiler.py" style="color: var(--primary-color);">Compiler Source</a>
                </p>
            </div>

            <div class="card" style="margin-bottom: 3rem;">
                <h3>3. Numerical Validation (Digital Twin) ✅</h3>
                <p>The multiphysics simulator unifies three synchronized computing engines to validate the architecture before biological synthesis. As of 2026-01-01, the <strong>First Bloom</strong> benchmark has been fully validated.</p>
                <ul>
                    <li><strong>Environmental Engine:</strong> Manages photonic (800 µmol/m²/s) and thermal fluxes.</li>
                    <li><strong>Biological Engine:</strong> Resolves P700 accumulation dynamics (Steady state reached at t=150s).</li>
                    <li><strong>Quantum Engine:</strong> Simulates T2 coherence (200ps) and Hadamard gate fidelity (100%).</li>
                </ul>
                <p style="margin-top: 1rem; font-size: 0.85rem;">
                    📂 <a href="https://github.com/selectess/HAWRA/tree/main/02_bioos_engine/simulations/multiphysics_simulator" style="color: var(--primary-color);">Access Multiphysics Engine Source</a> |
                    📜 <a href="04_validation_benchmarks/CERTIFICATION_REPORT.md" style="color: var(--primary-color);">View Latest Certification Report</a> |
                     📚 <a href="00_docs/scientific/HAWRA_MEGA_REPORT_2026.md" style="color: var(--primary-color);">HAWRA Mega-Report (v4.0): Full Technical Compendium</a>
                </p>
            </div>

            <div class="card" style="margin-bottom: 3rem;">
                <h3>4. Biological Synthesis Readiness 🧬</h3>
                <p>The validated plasmid sequence (18.1 kb) has been processed for large-scale DNA synthesis. We have moved from digital twin validation to physical manufacturing preparation.</p>
                <ul>
                    <li><strong>Fragmentation:</strong> Sequence divided into 7 blocks of ~3kb with 40bp Gibson overlaps.</li>
                    <li><strong>Complexity Check:</strong> High GC content (76%) identified in Glycine-rich linkers.</li>
                    <li><strong>Assembly Strategy:</strong> <em>Gibson Assembly Ultra</em> protocol selected for 18kb reconstruction.</li>
                </ul>
                <p style="margin-top: 1rem; font-size: 0.85rem;">
                    <a href="genomics/processed_sequences/synthesis_order/SYNTHESIS_PREP_REPORT.md" class="btn" style="padding: 0.3rem 0.8rem;">View Synthesis Report</a>
                    <a href="genomics/processed_sequences/synthesis_order/GIBSON_ASSEMBLY_PROTOCOL.md" class="btn" style="padding: 0.3rem 0.8rem; background: var(--secondary-color); color: white;">Gibson Assembly Protocol</a>
                </p>
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            <div class="card" style="margin-bottom: 3rem;">
                <h3>4. Genetic Architecture</h3>
                <p>The PQPE is enabled by the <strong>pHAWRA v5.8</strong> cassette, including Lsi1 for silica biomineralization and modified PSAA/PSAB genes.</p>
                <p style="margin-top: 1rem; font-size: 0.85rem;">
                    🧬 <a href="https://github.com/selectess/HAWRA/blob/main/01_genomics/plasmids/validated/HAWRA_FINAL_VALIDATED.gb" style="color: var(--primary-color);">Download Validated GenBank (.gb)</a>
                </p>
            </div>

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                <h2 style="font-size: 1.5rem; margin-bottom: 2rem;">Roadmap & Perspectives</h2>
                <div class="grid">
                    <div class="card" style="padding: 1rem;">
                        <span class="roadmap-date">2026</span>
                        <p>Genetic cassette synthesis and <i>in vitro</i> validation of the Silica Shield.</p>
                    </div>
                    <div class="card" style="padding: 1rem;">
                        <span class="roadmap-date">2027</span>
                        <p>Photonic interconnection between plant tissues for distributed computing.</p>
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