Add comprehensive Programming Framework content and cross-disciplinary examples

CHAT_AGENT_NOTE.md

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+# Note for Programming Framework Space Chat Agent
+
+## **Project Context:**
+You are working in the **Programming Framework Space** directory (`/home/gdubs/progframe/programming_framework/`). This is a **separate project** from the GLMP (Genome Logic Modeling Project) that focuses specifically on the **Programming Framework methodology** for analyzing complex systems across multiple disciplines.
+
+## **Key Files You'll Be Working With:**
+- `README.md` - The main Programming Framework Space README (with Hugging Face Space configuration)
+- `index.html` - Main Space interface with tabbed navigation
+- `style.css` - Modern styling for the Space interface
+- `programming_framework_article.html` - The comprehensive academic article about the Programming Framework
+- `computer_science_processes.html` - Computer science examples and processes
+- `chemistry_examples.html` - Chemistry examples and processes
+- `physics_processes.html` - Physics examples and processes
+- `mathematics_processes.html` - Mathematics examples and processes
+
+## **Project Purpose:**
+The Programming Framework is a **systematic visualization methodology** that translates complex systems (biology, chemistry, physics, computer science, mathematics) into standardized computational representations using:
+- **Mermaid Markdown syntax**
+- **Universal color coding system** (Red/Yellow/Green/Blue/Violet)
+- **LLM processing** for automated analysis
+- **Cross-disciplinary pattern recognition**
+
+## **Important Distinction:**
+- **GLMP Project** (`/home/gdubs/glmp/`) = Biological systems analysis with 297+ processes
+- **Programming Framework Space** (`/home/gdubs/progframe/programming_framework/`) = Cross-disciplinary methodology and framework
+
+## **Your Role:**
+Help develop and enhance the Programming Framework Space, including:
+- Improving the Space interface and documentation
+- Creating additional examples across disciplines
+- Enhancing the methodology documentation
+- Developing tools and resources for framework application
+- Integrating the cross-disciplinary HTML files into the main interface
+
+## **Key Methodology:**
+The framework uses a **5-category color system**:
+- 🔴 **Red**: Triggers & Inputs
+- 🟡 **Yellow**: Structures & Objects  
+- 🟢 **Green**: Processing & Operations
+- 🔵 **Blue**: Intermediates & States
+- 🟣 **Violet**: Products & Outputs
+
+## **Current Space Structure:**
+The Hugging Face Space is configured as a **static site** with:
+- **Overview Tab**: Introduction to the Programming Framework concept
+- **Methodology Tab**: 4-step framework methodology (Foundation → Analysis → Implementation → Optimization)
+- **Examples Tab**: Practical examples showing how to apply the framework to real problems
+- **Resources Tab**: Curated learning resources for programming education
+
+## **Integration Opportunities:**
+Consider integrating the cross-disciplinary HTML files into the main interface:
+- Add links to the discipline-specific examples in the Examples tab
+- Create a new "Cross-Disciplinary Applications" tab
+- Enhance the methodology section with real examples from the HTML files
+- Add interactive elements to demonstrate the framework in action
+
+## **Reference:**
+The complete biological dataset (297+ processes) is available in the separate GLMP project, but your focus is on the **universal framework methodology** that can be applied across all disciplines.
+
+## **Next Steps:**
+1. Review the existing HTML files to understand the framework applications
+2. Consider how to integrate them into the main Space interface
+3. Enhance the methodology documentation with real examples
+4. Develop additional interactive features or examples
+5. Ensure the Space effectively communicates the cross-disciplinary nature of the framework
+
+---
+
+**Remember**: This is a **methodology framework** project, not a biological analysis project. Focus on the universal principles and cross-disciplinary applications.

README.md

@@ -1,12 +1,12 @@
 ---
 title: Programming Framework
-emoji: 🐢
+emoji: 🚀
 colorFrom: blue
-colorTo: gray
+colorTo: purple
 sdk: static
 pinned: false
-license: cc-by-nc-sa-4.0
-short_description: The Programming Framework is a process analysis methodology
+license: mit
+short_description: A comprehensive framework for programming education and practice
 ---
 
 Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference

chemistry_examples.html

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+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+    <title>Chemistry Examples - Programming Framework Analysis</title>
+    <style>
+        body { 
+            font-family: 'Times New Roman', Times, serif, 'Arial Unicode MS'; 
+            margin: 0; 
+            background: #ffffff; 
+            color: #000000; 
+            line-height: 1.6; 
+            font-size: 12pt; 
+        }
+        .container { 
+            max-width: 1000px; 
+            margin: 0 auto; 
+            padding: 1.5rem; 
+        }
+        h1, h2, h3 { 
+            color: #000000; 
+            margin-top: 1.5rem; 
+            margin-bottom: 0.75rem; 
+        }
+        h1 { 
+            font-size: 18pt; 
+            text-align: center; 
+        }
+        h2 { 
+            font-size: 16pt; 
+            border-bottom: 2px solid #000; 
+            padding-bottom: 0.5rem; 
+        }
+        h3 { 
+            font-size: 14pt; 
+        }
+        p { 
+            margin-bottom: 1rem; 
+            text-align: justify; 
+        }
+        .figure { 
+            margin: 1rem 0; 
+            text-align: center; 
+            border: 1px solid #ccc; 
+            padding: 1rem; 
+            background: #f9f9f9; 
+        }
+        .figure-caption { 
+            margin-top: 1rem; 
+            font-style: italic; 
+            text-align: left; 
+        }
+        .mermaid { 
+            background: white; 
+            padding: 1rem; 
+            border-radius: 4px; 
+        }
+    </style>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
+    <script>
+        mermaid.initialize({ 
+            startOnLoad: true, 
+            theme: 'default', 
+            flowchart: { 
+                useMaxWidth: false, 
+                htmlLabels: true,
+                curve: 'linear',
+                nodeSpacing: 50,
+                rankSpacing: 50,
+                padding: 20
+            },
+            themeVariables: {
+                fontFamily: 'Arial Unicode MS, Arial, sans-serif'
+            }
+        });
+    </script>
+</head>
+<body>
+    <div class="container">
+        <h1>Chemistry Examples - Programming Framework Analysis</h1>
+        
+        <p>This document presents chemistry processes analyzed using the Programming Framework methodology. Each process is represented as a computational flowchart with standardized color coding: Red for triggers/inputs, Yellow for structures/objects, Green for processing/operations, Blue for intermediates/states, and Violet for products/outputs. Yellow nodes use black text for optimal readability, while all other colors use white text.</p>
+
+        <h2>1. Catalytic Hydrogenation Process</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Initial Setup
+    %% Input Conditions
+    A1[Alkene Substrate] --> B1[Substrate Analysis]
+    C1[Hydrogen Gas H₂] --> D1[Gas Supply]
+    E1[Catalyst (Pt/Pd/Ni)] --> F1[Catalyst Preparation]
+    
+    %% Reactant Preparation
+    B1 --> G1[Substrate Purity Check]
+    D1 --> H1[Gas Pressure Control]
+    F1 --> I1[Catalyst Activation]
+    
+    %% Reaction Setup
+    G1 --> J1[Reaction Vessel Loading]
+    H1 --> K1[Pressure Regulation]
+    I1 --> L1[Catalyst Dispersion]
+    
+    %% Catalytic Process
+    J1 --> M1[Substrate Adsorption]
+    K1 --> N1[Hydrogen Dissociation]
+    L1 --> O1[Active Site Formation]
+    
+    %% Surface Reactions
+    M1 --> P1[π-Bond Activation]
+    N1 --> Q1[H• Radical Formation]
+    O1 --> R1[Catalytic Surface]
+    
+    %% Hydrogenation Steps
+    P1 --> S1[First H Addition]
+    Q1 --> T1[Hydrogen Transfer]
+    R1 --> U1[Surface Complex]
+    
+    %% Product Formation
+    S1 --> V1[Alkyl Intermediate]
+    T1 --> W1[Second H Addition]
+    U1 --> X1[Product Desorption]
+    
+    %% Final Products
+    V1 --> Y1[Alkane Product]
+    W1 --> Z1[Complete Hydrogenation]
+    X1 --> AA1[Catalyst Recovery]
+    
+    %% Process Control
+    Y1 --> BB1[Product Analysis]
+    Z1 --> CC1[Conversion Check]
+    AA1 --> DD1[Catalyst Regeneration]
+    
+    %% Output
+    BB1 --> EE1[Hydrogenation Complete]
+    CC1 --> FF1[Yield Optimization]
+    DD1 --> GG1[Process Efficiency]
+    
+    %% Styling - Chemistry Color Scheme
+    style A1 fill:#ff6b6b,color:#fff
+    style C1 fill:#ff6b6b,color:#fff
+    style E1 fill:#ff6b6b,color:#fff
+    
+    style G1 fill:#ffd43b,color:#000
+    style H1 fill:#ffd43b,color:#000
+    style I1 fill:#ffd43b,color:#000
+    style J1 fill:#ffd43b,color:#000
+    style K1 fill:#ffd43b,color:#000
+    style L1 fill:#ffd43b,color:#000
+    
+    style M1 fill:#51cf66,color:#fff
+    style N1 fill:#51cf66,color:#fff
+    style O1 fill:#51cf66,color:#fff
+    style P1 fill:#51cf66,color:#fff
+    style Q1 fill:#51cf66,color:#fff
+    style R1 fill:#51cf66,color:#fff
+    style S1 fill:#51cf66,color:#fff
+    style T1 fill:#51cf66,color:#fff
+    style U1 fill:#51cf66,color:#fff
+    style V1 fill:#51cf66,color:#fff
+    style W1 fill:#51cf66,color:#fff
+    style X1 fill:#51cf66,color:#fff
+    
+    style B1 fill:#74c0fc,color:#fff
+    style D1 fill:#74c0fc,color:#fff
+    style F1 fill:#74c0fc,color:#fff
+    style Y1 fill:#74c0fc,color:#fff
+    style Z1 fill:#74c0fc,color:#fff
+    style AA1 fill:#74c0fc,color:#fff
+    style BB1 fill:#74c0fc,color:#fff
+    style CC1 fill:#74c0fc,color:#fff
+    style DD1 fill:#74c0fc,color:#fff
+    
+    style EE1 fill:#b197fc,color:#fff
+    style FF1 fill:#b197fc,color:#fff
+    style GG1 fill:#b197fc,color:#fff
+                    </div>
+            
+            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Reactants & Catalysts
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Reaction Vessels & Equipment
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Chemical Reactions & Transformations
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
+                </div>
+            </div>
+            
+            <div class="figure-caption">
+                <strong>Figure 1.</strong> Catalytic Hydrogenation Process. This chemistry process visualization demonstrates catalytic reaction mechanisms. The flowchart shows reactant inputs, reaction vessels and equipment, chemical reactions and transformations, intermediate species, and final products.
+            </div>
+        </div>
+
+        <h2>2. Polymerization Process</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Initial Setup
+    %% Input Conditions
+    A2[Monomers] --> B2[Monomer Analysis]
+    C2[Initiator] --> D2[Initiator Preparation]
+    E2[Solvent/Medium] --> F2[Reaction Medium]
+    %% Reaction Setup
+    B2 --> G2[Monomer Purity Check]
+    D2 --> H2[Initiator Activation]
+    F2 --> I2[Medium Preparation]
+    %% Initiation
+    G2 --> J2[Monomer Solution]
+    H2 --> K2[Radical Formation]
+    I2 --> L2[Temperature Control]
+    %% Polymerization Initiation
+    J2 --> M2[Monomer Concentration]
+    K2 --> N2[Initiator Decomposition]
+    L2 --> O2[Reaction Conditions]
+    %% Propagation
+    M2 --> P2[Radical Addition]
+    N2 --> Q2[Chain Initiation]
+    O2 --> R2[Chain Growth]
+    %% Chain Growth
+    P2 --> S2[Monomer Addition]
+    Q2 --> T2[Active Chain End]
+    R2 --> U2[Polymer Chain]
+    %% Termination
+    S2 --> V2[Chain Propagation]
+    T2 --> W2[Chain Transfer]
+    U2 --> X2[Chain Termination]
+    %% Final Products
+    V2 --> Y2[Polymer Formation]
+    W2 --> Z2[Molecular Weight Control]
+    X2 --> AA2[Reaction Quenching]
+    %% Process Control
+    Y2 --> BB2[Polymer Characterization]
+    Z2 --> CC2[Molecular Weight Analysis]
+    AA2 --> DD2[Product Isolation]
+    %% Output
+    BB2 --> EE2[Polymerization Complete]
+    CC2 --> FF2[Quality Control]
+    DD2 --> GG2[Product Recovery]
+    %% Styling - Chemistry Color Scheme
+    %% Styling - Biological Color Scheme
+    style A2 fill:#ff6b6b,color:#fff
+    style C2 fill:#ff6b6b,color:#fff
+    style E2 fill:#ff6b6b,color:#fff
+    style G2 fill:#ffd43b,color:#000
+    style H2 fill:#ffd43b,color:#000
+    style I2 fill:#ffd43b,color:#000
+    style J2 fill:#ffd43b,color:#000
+    style K2 fill:#ffd43b,color:#000
+    style L2 fill:#ffd43b,color:#000
+    style M2 fill:#51cf66,color:#fff
+    style N2 fill:#51cf66,color:#fff
+    style O2 fill:#51cf66,color:#fff
+    style P2 fill:#51cf66,color:#fff
+    style Q2 fill:#51cf66,color:#fff
+    style R2 fill:#51cf66,color:#fff
+    style S2 fill:#51cf66,color:#fff
+    style T2 fill:#51cf66,color:#fff
+    style U2 fill:#51cf66,color:#fff
+    style V2 fill:#51cf66,color:#fff
+    style W2 fill:#51cf66,color:#fff
+    style X2 fill:#51cf66,color:#fff
+    style B2 fill:#74c0fc,color:#fff
+    style D2 fill:#74c0fc,color:#fff
+    style F2 fill:#74c0fc,color:#fff
+    style Y2 fill:#74c0fc,color:#fff
+    style Z2 fill:#74c0fc,color:#fff
+    style AA2 fill:#74c0fc,color:#fff
+    style BB2 fill:#74c0fc,color:#fff
+    style CC2 fill:#74c0fc,color:#fff
+    style DD2 fill:#74c0fc,color:#fff
+    style EE2 fill:#b197fc,color:#fff
+    style FF2 fill:#b197fc,color:#fff
+    style GG2 fill:#b197fc,color:#fff
+                    </div>
+            
+            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Reactants & Initiators
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Reaction Vessels & Equipment
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Polymerization Reactions
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
+                </div>
+            </div>
+            
+            <div class="figure-caption">
+                <strong>Figure 2.</strong> Polymerization Process. This chemistry process visualization demonstrates polymer synthesis mechanisms. The flowchart shows monomer inputs, reaction vessels and equipment, polymerization reactions, intermediate species, and final polymer products.
+            </div>
+        </div>
+
+        <h2>3. Acid-Base Titration Process</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Initial Setup
+    %% Input Conditions
+    A3[Acid Solution] --> B3[Acid Analysis]
+    C3[Base Solution] --> D3[Base Analysis]
+    E3[Indicator] --> F3[Indicator Selection]
+    %% Solution Preparation
+    B3 --> G3[Acid Concentration]
+    D3 --> H3[Base Concentration]
+    F3 --> I3[Indicator Preparation]
+    %% Titration Setup
+    G3 --> J3[Acid in Burette]
+    H3 --> K3[Base in Flask]
+    I3 --> L3[Indicator Addition]
+    %% Titration Process
+    J3 --> M3[Initial pH Measurement]
+    K3 --> N3[Base Volume Measurement]
+    L3 --> O3[Color Change Detection]
+    %% Acid-Base Reaction
+    M3 --> P3[Acid Addition]
+    N3 --> Q3[Base Consumption]
+    O3 --> R3[Equivalence Point]
+    %% pH Changes
+    P3 --> S3[H⁺ + OH⁻ → H₂O]
+    Q3 --> T3[Neutralization Reaction]
+    R3 --> U3[Stoichiometric Point]
+    %% Endpoint Detection
+    S3 --> V3[pH Monitoring]
+    T3 --> W3[Conductivity Changes]
+    U3 --> X3[Indicator Color Change]
+    %% Final Results
+    V3 --> Y3[Equivalence Point pH]
+    W3 --> Z3[Conductivity Minimum]
+    X3 --> AA3[Endpoint Detection]
+    %% Calculations
+    Y3 --> BB3[Concentration Calculation]
+    Z3 --> CC3[Volume Measurement]
+    AA3 --> DD3[Stoichiometric Analysis]
+    %% Output
+    BB3 --> EE3[Titration Complete]
+    CC3 --> FF3[Concentration Determined]
+    DD3 --> GG3[Analysis Results]
+    %% Styling - Chemistry Color Scheme
+    %% Styling - Biological Color Scheme
+    style A3 fill:#ff6b6b,color:#fff
+    style C3 fill:#ff6b6b,color:#fff
+    style E3 fill:#ff6b6b,color:#fff
+    style G3 fill:#ffd43b,color:#000
+    style H3 fill:#ffd43b,color:#000
+    style I3 fill:#ffd43b,color:#000
+    style J3 fill:#ffd43b,color:#000
+    style K3 fill:#ffd43b,color:#000
+    style L3 fill:#ffd43b,color:#000
+    style M3 fill:#51cf66,color:#fff
+    style N3 fill:#51cf66,color:#fff
+    style O3 fill:#51cf66,color:#fff
+    style P3 fill:#51cf66,color:#fff
+    style Q3 fill:#51cf66,color:#fff
+    style R3 fill:#51cf66,color:#fff
+    style S3 fill:#51cf66,color:#fff
+    style T3 fill:#51cf66,color:#fff
+    style U3 fill:#51cf66,color:#fff
+    style V3 fill:#51cf66,color:#fff
+    style W3 fill:#51cf66,color:#fff
+    style X3 fill:#51cf66,color:#fff
+    style B3 fill:#74c0fc,color:#fff
+    style D3 fill:#74c0fc,color:#fff
+    style F3 fill:#74c0fc,color:#fff
+    style Y3 fill:#74c0fc,color:#fff
+    style Z3 fill:#74c0fc,color:#fff
+    style AA3 fill:#74c0fc,color:#fff
+    style BB3 fill:#74c0fc,color:#fff
+    style CC3 fill:#74c0fc,color:#fff
+    style DD3 fill:#74c0fc,color:#fff
+    style EE3 fill:#b197fc,color:#fff
+    style FF3 fill:#b197fc,color:#fff
+    style GG3 fill:#b197fc,color:#fff
+                    </div>
+            
+            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Reactants & Indicators
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Titration Equipment
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Neutralization Reactions
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
+                </div>
+            </div>
+            
+            <div class="figure-caption">
+                <strong>Figure 3.</strong> Acid-Base Titration Process. This chemistry process visualization demonstrates analytical chemistry procedures. The flowchart shows reactant inputs, titration equipment, neutralization reactions, intermediate measurements, and final analytical results.
+            </div>
+        </div>
+
+        <h2>4. Electrochemical Cell Process</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Initial Setup
+    %% Input Conditions
+    A4[Anode Material] --> B4[Anode Analysis]
+    C4[Cathode Material] --> D4[Cathode Analysis]
+    E4[Electrolyte] --> F4[Electrolyte Preparation]
+    %% Cell Setup
+    B4 --> G4[Anode Preparation]
+    D4 --> H4[Cathode Preparation]
+    F4 --> I4[Electrolyte Solution]
+    %% Electrochemical Setup
+    G4 --> J4[Anode Oxidation]
+    H4 --> K4[Cathode Reduction]
+    I4 --> L4[Ion Conduction]
+    %% Redox Reactions
+    J4 --> M4[Electron Release]
+    K4 --> N4[Electron Acceptance]
+    L4 --> O4[Ion Transport]
+    %% Current Flow
+    M4 --> P4[Oxidation Half-Reaction]
+    N4 --> Q4[Reduction Half-Reaction]
+    O4 --> R4[Salt Bridge]
+    %% Cell Operation
+    P4 --> S4[Anode → Cathode]
+    Q4 --> T4[Electron Flow]
+    R4 --> U4[Ion Migration]
+    %% Energy Production
+    S4 --> V4[Cell Potential]
+    T4 --> W4[Current Generation]
+    U4 --> X4[Charge Balance]
+    %% Performance
+    V4 --> Y4[Voltage Measurement]
+    W4 --> Z4[Current Measurement]
+    X4 --> AA4[Efficiency Calculation]
+    %% Output
+    Y4 --> BB4[Cell Performance]
+    Z4 --> CC4[Power Output]
+    AA4 --> DD4[Energy Conversion]
+    %% Final Results
+    BB4 --> EE4[Electrochemical Cell Active]
+    CC4 --> FF4[Electrical Energy Produced]
+    DD4 --> GG4[Conversion Efficiency]
+    %% Styling - Chemistry Color Scheme
+    %% Styling - Biological Color Scheme
+    style A4 fill:#ff6b6b,color:#fff
+    style C4 fill:#ff6b6b,color:#fff
+    style E4 fill:#ff6b6b,color:#fff
+    style G4 fill:#ffd43b,color:#000
+    style H4 fill:#ffd43b,color:#000
+    style I4 fill:#ffd43b,color:#000
+    style J4 fill:#ffd43b,color:#000
+    style K4 fill:#ffd43b,color:#000
+    style L4 fill:#ffd43b,color:#000
+    style M4 fill:#51cf66,color:#fff
+    style N4 fill:#51cf66,color:#fff
+    style O4 fill:#51cf66,color:#fff
+    style P4 fill:#51cf66,color:#fff
+    style Q4 fill:#51cf66,color:#fff
+    style R4 fill:#51cf66,color:#fff
+    style S4 fill:#51cf66,color:#fff
+    style T4 fill:#51cf66,color:#fff
+    style U4 fill:#51cf66,color:#fff
+    style V4 fill:#51cf66,color:#fff
+    style W4 fill:#51cf66,color:#fff
+    style X4 fill:#51cf66,color:#fff
+    style B4 fill:#74c0fc,color:#fff
+    style D4 fill:#74c0fc,color:#fff
+    style F4 fill:#74c0fc,color:#fff
+    style Y4 fill:#74c0fc,color:#fff
+    style Z4 fill:#74c0fc,color:#fff
+    style AA4 fill:#74c0fc,color:#fff
+    style BB4 fill:#74c0fc,color:#fff
+    style CC4 fill:#74c0fc,color:#fff
+    style DD4 fill:#74c0fc,color:#fff
+    style EE4 fill:#b197fc,color:#fff
+    style FF4 fill:#b197fc,color:#fff
+    style GG4 fill:#b197fc,color:#fff
+                    </div>
+            
+            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Electrodes & Electrolyte
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Cell Components
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Redox Reactions
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
+                </div>
+            </div>
+            
+            <div class="figure-caption">
+                <strong>Figure 4.</strong> Electrochemical Cell Process. This chemistry process visualization demonstrates electrochemical energy conversion. The flowchart shows electrode inputs, cell components, redox reactions, intermediate processes, and final electrical energy output.
+            </div>
+        </div>
+
+        <h2>5. Distillation Process</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Initial Setup
+    %% Input Conditions
+    A5[Mixture] --> B5[Mixture Analysis]
+    C5[Heat Source] --> D5[Heat Supply]
+    E5[Distillation Apparatus] --> F5[Equipment Setup]
+    %% Process Setup
+    B5 --> G5[Component Analysis]
+    D5 --> H5[Temperature Control]
+    F5 --> I5[Apparatus Assembly]
+    %% Heating Process
+    G5 --> J5[Mixture Loading]
+    H5 --> K5[Heat Application]
+    I5 --> L5[Vapor Formation]
+    %% Vaporization
+    J5 --> M5[Component Separation]
+    K5 --> N5[Boiling Point Differences]
+    L5 --> O5[Vapor Phase]
+    %% Distillation
+    M5 --> P5[Fractional Distillation]
+    N5 --> Q5[Temperature Gradient]
+    O5 --> R5[Condensation]
+    %% Separation
+    P5 --> S5[Component Collection]
+    Q5 --> T5[Fraction Separation]
+    R5 --> U5[Liquid Recovery]
+    %% Product Collection
+    S5 --> V5[High Boiling Point]
+    T5 --> W5[Medium Boiling Point]
+    U5 --> X5[Low Boiling Point]
+    %% Process Control
+    V5 --> Y5[Fraction Analysis]
+    W5 --> Z5[Purity Check]
+    X5 --> AA5[Yield Calculation]
+    %% Output
+    Y5 --> BB5[Distillation Complete]
+    Z5 --> CC5[Component Separation]
+    AA5 --> DD5[Process Efficiency]
+    %% Final Results
+    BB5 --> EE5[Purified Components]
+    CC5 --> FF5[Separation Achieved]
+    DD5 --> GG5[Process Optimization]
+    %% Styling - Chemistry Color Scheme
+    %% Styling - Biological Color Scheme
+    style A5 fill:#ff6b6b,color:#fff
+    style C5 fill:#ff6b6b,color:#fff
+    style E5 fill:#ff6b6b,color:#fff
+    style G5 fill:#ffd43b,color:#000
+    style H5 fill:#ffd43b,color:#000
+    style I5 fill:#ffd43b,color:#000
+    style J5 fill:#ffd43b,color:#000
+    style K5 fill:#ffd43b,color:#000
+    style L5 fill:#ffd43b,color:#000
+    style M5 fill:#51cf66,color:#fff
+    style N5 fill:#51cf66,color:#fff
+    style O5 fill:#51cf66,color:#fff
+    style P5 fill:#51cf66,color:#fff
+    style Q5 fill:#51cf66,color:#fff
+    style R5 fill:#51cf66,color:#fff
+    style S5 fill:#51cf66,color:#fff
+    style T5 fill:#51cf66,color:#fff
+    style U5 fill:#51cf66,color:#fff
+    style V5 fill:#51cf66,color:#fff
+    style W5 fill:#51cf66,color:#fff
+    style X5 fill:#51cf66,color:#fff
+    style B5 fill:#74c0fc,color:#fff
+    style D5 fill:#74c0fc,color:#fff
+    style F5 fill:#74c0fc,color:#fff
+    style Y5 fill:#74c0fc,color:#fff
+    style Z5 fill:#74c0fc,color:#fff
+    style AA5 fill:#74c0fc,color:#fff
+    style BB5 fill:#74c0fc,color:#fff
+    style CC5 fill:#74c0fc,color:#fff
+    style DD5 fill:#74c0fc,color:#fff
+    style EE5 fill:#b197fc,color:#fff
+    style FF5 fill:#b197fc,color:#fff
+    style GG5 fill:#b197fc,color:#fff
+                    </div>
+            
+            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Mixture & Heat Source
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Distillation Equipment
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Phase Separation Processes
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
+                </div>
+            </div>
+            
+            <div class="figure-caption">
+                <strong>Figure 5.</strong> Distillation Process. This chemistry process visualization demonstrates separation techniques. The flowchart shows mixture inputs, distillation equipment, phase separation processes, intermediate fractions, and final purified components.
+            </div>
+        </div>
+
+        <p><strong>Generated using the Programming Framework methodology</strong></p>
+        
+        <p>This collection demonstrates the computational nature of chemical processes and systems</p>
+        
+        <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+    </div>
+</body>
+</html>

computer_science_processes.html

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+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+    <title>Computer Science Processes - Programming Framework Analysis</title>
+    <style>
+        body { 
+            font-family: 'Times New Roman', Times, serif, 'Arial Unicode MS'; 
+            margin: 0; 
+            background: #ffffff; 
+            color: #000000; 
+            line-height: 1.6; 
+            font-size: 12pt; 
+        }
+        .container { 
+            max-width: 1000px; 
+            margin: 0 auto; 
+            padding: 1.5rem; 
+        }
+        h1, h2, h3 { 
+            color: #000000; 
+            margin-top: 1.5rem; 
+            margin-bottom: 0.75rem; 
+        }
+        h1 { 
+            font-size: 18pt; 
+            text-align: center; 
+        }
+        h2 { 
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+            border-bottom: 2px solid #000; 
+            padding-bottom: 0.5rem; 
+        }
+        h3 { 
+            font-size: 14pt; 
+        }
+        p { 
+            margin-bottom: 1rem; 
+            text-align: justify; 
+        }
+        .figure { 
+            margin: 1rem 0; 
+            text-align: center; 
+            border: 1px solid #ccc; 
+            padding: 1rem; 
+            background: #f9f9f9; 
+        }
+        .figure-caption { 
+            margin-top: 1rem; 
+            font-style: italic; 
+            text-align: left; 
+        }
+        .mermaid { 
+            background: white; 
+            padding: 1rem; 
+            border-radius: 4px; 
+        }
+        .color-legend {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            margin-top: 1rem;
+            justify-content: center;
+        }
+        .color-legend span {
+            display: inline-flex;
+            align-items: center;
+            gap: 0.5rem;
+            padding: 0.25rem 0.5rem;
+            border-radius: 999px;
+            border: 1px solid rgba(0,0,0,.08);
+            background: #fff;
+            font-size: 0.9rem;
+        }
+        .color-box {
+            width: 12px;
+            height: 12px;
+            border-radius: 2px;
+            border: 1px solid rgba(0,0,0,.15);
+        }
+    </style>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
+    <script>
+        mermaid.initialize({ 
+            startOnLoad: true, 
+            theme: 'default', 
+            flowchart: { 
+                useMaxWidth: false, 
+                htmlLabels: true,
+                curve: 'linear',
+                nodeSpacing: 50,
+                rankSpacing: 50,
+                padding: 20
+            },
+            themeVariables: {
+                fontFamily: 'Arial Unicode MS, Arial, sans-serif'
+            }
+        });
+    </script>
+</head>
+<body>
+    <div class="container">
+        <h1>Computer Science Processes - Programming Framework Analysis</h1>
+        
+        <p>This document presents computer science processes analyzed using the Programming Framework methodology. Each process is represented as a computational flowchart with standardized color coding: Red for triggers/inputs, Yellow for structures/objects, Green for processing/operations, Blue for intermediates/states, and Violet for products/outputs. Yellow nodes use black text for optimal readability, while all other colors use white text.</p>
+
+        <h2>1. QuickSort Algorithm Process</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Initial Setup
+    %% Input Data and Parameters
+    A[Input Array 5,2,8,1,9] --> B[Array Size Analysis]
+    C[Sorting Criteria Ascending] --> D[Algorithm Selection]
+    E[Memory Constraints] --> F[Resource Assessment]
+    
+    %% Data Structure Setup
+    B --> G[Array Initialization]
+    D --> H[QuickSort Algorithm Selection]
+    F --> I[Memory Allocation]
+    
+    %% Algorithm Initialization
+    G --> J[Array Copy to Working Memory]
+    H --> K[Pivot Selection Strategy]
+    I --> L[Stack Space Allocation]
+    
+    %% First Partitioning Step
+    J --> M[Choose Pivot 5]
+    K --> N[Partitioning Logic Setup]
+    L --> O[Recursive Call Stack]
+    
+    %% Partitioning Process
+    M --> P[Compare Elements to Pivot]
+    P --> Q[Element Swapping Operations]
+    Q --> R[Partition Boundary Tracking]
+    
+    %% Sub-array Processing
+    R --> S[Left Sub-array 2,1]
+    R --> T[Right Sub-array 8,9]
+    O --> U[Recursive Function Calls]
+    
+    %% Left Sub-array Sorting
+    S --> V[Pivot Selection 2]
+    V --> W[Partitioning 1 and 2]
+    W --> X[Base Case Single Element]
+    
+    %% Right Sub-array Sorting
+    T --> Y[Pivot Selection 8]
+    Y --> Z[Partitioning 8,9]
+    Z --> AA[Recursive Sort 8,9]
+    
+    %% Merge and Combine
+    X --> BB[Sorted Left 1,2]
+    AA --> CC[Sorted Right 8,9]
+    BB --> DD[Combine Results]
+    CC --> DD
+    
+    %% Final Assembly
+    DD --> EE[Final Sorted Array 1,2,5,8,9]
+    EE --> FF[Algorithm Completion]
+    FF --> GG[Performance Metrics Calculation]
+    
+    %% Complexity Analysis
+    GG --> HH[Time Complexity O(n log n)]
+    GG --> II[Space Complexity O(log n)]
+    GG --> JJ[Stability Assessment Unstable]
+    
+    %% Styling - Computer Science Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style G fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K fill:#ffd43b,color:#000
+    style L fill:#ffd43b,color:#000
+    style M fill:#ffd43b,color:#000
+    style N fill:#ffd43b,color:#000
+    style O fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#51cf66,color:#fff
+    style W fill:#51cf66,color:#fff
+    style Z fill:#51cf66,color:#fff
+    style AA fill:#51cf66,color:#fff
+    style DD fill:#51cf66,color:#fff
+    style GG fill:#51cf66,color:#fff
+    style HH fill:#51cf66,color:#fff
+    style II fill:#51cf66,color:#fff
+    style JJ fill:#51cf66,color:#fff
+    
+    style S fill:#74c0fc,color:#fff
+    style T fill:#74c0fc,color:#fff
+    style U fill:#74c0fc,color:#fff
+    style X fill:#74c0fc,color:#fff
+    style BB fill:#74c0fc,color:#fff
+    style CC fill:#74c0fc,color:#fff
+    style EE fill:#74c0fc,color:#fff
+    style FF fill:#74c0fc,color:#fff
+    style GG fill:#51cf66,color:#fff
+    style HH fill:#51cf66,color:#fff
+    style II fill:#51cf66,color:#fff
+    style JJ fill:#51cf66,color:#fff
+            </div>
+            <div class="color-legend">
+                <span><span class="color-box" style="background:#ff6b6b;"></span>Inputs & Data</span>
+                <span><span class="color-box" style="background:#ffd43b;"></span>Data Structures & Arrays</span>
+                <span><span class="color-box" style="background:#51cf66;"></span>Operations & Algorithms</span>
+                <span><span class="color-box" style="background:#74c0fc;"></span>States & Variables</span>
+                <span><span class="color-box" style="background:#b197fc;"></span>Output & Results</span>
+            </div>
+            <div class="figure-caption">
+                <strong>Figure 1.</strong> QuickSort Algorithm Process. This computer science process visualization demonstrates the computational logic of the QuickSort algorithm. The flowchart shows input data and parameters, data structures and arrays, algorithmic operations and comparisons, intermediate states and recursive calls, and final sorted output.
+            </div>
+        </div>
+
+        <h2>2. Binary Search Tree Process</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Input Data
+    A[Search Key 7] --> B[Key Validation]
+    C[BST Root Node] --> D[Tree Structure Analysis]
+    E[Search Operation] --> F[Algorithm Selection]
+    
+    %% Tree Traversal Setup
+    B --> G[Key Comparison Logic]
+    D --> H[Node Structure]
+    F --> I[Binary Search Strategy]
+    
+    %% Root Node Processing
+    G --> J[Compare Key with Root]
+    H --> K[Left Child Pointer]
+    I --> L[Right Child Pointer]
+    
+    %% Decision Logic
+    J --> M{Key < Root Value?}
+    K --> N[Left Subtree]
+    L --> O[Right Subtree]
+    
+    %% Left Subtree Search
+    M -->|Yes| P[Traverse Left]
+    N --> Q[Left Child Node]
+    P --> R[Recursive Search]
+    
+    %% Right Subtree Search
+    M -->|No| S[Traverse Right]
+    O --> T[Right Child Node]
+    S --> U[Recursive Search]
+    
+    %% Search Completion
+    R --> V{Key Found?}
+    U --> W{Key Found?}
+    V -->|Yes| X[Return Node]
+    V -->|No| Y[Return Null]
+    W -->|Yes| Z[Return Node]
+    W -->|No| AA[Return Null]
+    
+    %% Final Result
+    X --> BB[Search Successful]
+    Z --> BB
+    Y --> CC[Search Unsuccessful]
+    AA --> CC
+    
+    %% Styling - Computer Science Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style G fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K fill:#ffd43b,color:#000
+    style L fill:#ffd43b,color:#000
+    style M fill:#74c0fc,color:#fff
+    style N fill:#ffd43b,color:#000
+    style O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#74c0fc,color:#fff
+    style W fill:#74c0fc,color:#fff
+    style X fill:#ffd43b,color:#000
+    style Y fill:#ffd43b,color:#000
+    style Z fill:#ffd43b,color:#000
+    style AA fill:#ffd43b,color:#000
+    style BB fill:#ffd43b,color:#000
+    style CC fill:#ffd43b,color:#000
+    
+    style BB fill:#74c0fc,color:#fff
+    style CC fill:#74c0fc,color:#fff
+            </div>
+            <div class="color-legend">
+                <span><span class="color-box" style="background:#ff6b6b;"></span>Inputs & Data</span>
+                <span><span class="color-box" style="background:#ffd43b;"></span>Data Structures & Arrays</span>
+                <span><span class="color-box" style="background:#51cf66;"></span>Operations & Algorithms</span>
+                <span><span class="color-box" style="background:#74c0fc;"></span>States & Variables</span>
+                <span><span class="color-box" style="background:#b197fc;"></span>Output & Results</span>
+            </div>
+            <div class="figure-caption">
+                <strong>Figure 2.</strong> Binary Search Tree Process. This computer science process visualization demonstrates the computational logic of binary search tree operations. The flowchart shows search key validation, tree structure analysis, binary search strategy, recursive traversal, and search result determination.
+            </div>
+        </div>
+
+        <h2>3. Dynamic Programming Process</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Problem Definition
+    A[Problem Statement] --> B[Problem Analysis]
+    C[Input Parameters] --> D[Parameter Validation]
+    E[Constraints] --> F[Constraint Analysis]
+    
+    %% Dynamic Programming Setup
+    B --> G[Subproblem Identification]
+    D --> H[State Space Definition]
+    F --> I[Memory Requirements]
+    
+    %% Algorithm Design
+    G --> J[Recursive Relation]
+    H --> K[DP Table Structure]
+    I --> L[Memory Allocation]
+    
+    %% Implementation
+    J --> M[Base Case Definition]
+    K --> N[Table Initialization]
+    L --> O[Array Creation]
+    
+    %% Computation
+    M --> P[Fill Base Cases]
+    N --> Q[Iterative Computation]
+    O --> R[State Transitions]
+    
+    %% Solution Construction
+    P --> S[DP Table Population]
+    Q --> T[Optimal Value Calculation]
+    R --> U[Path Reconstruction]
+    
+    %% Final Result
+    S --> V[Optimal Solution]
+    T --> W[Performance Analysis]
+    U --> X[Solution Verification]
+    
+    %% Styling - Computer Science Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style G fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K fill:#ffd43b,color:#000
+    style L fill:#ffd43b,color:#000
+    style M fill:#ffd43b,color:#000
+    style N fill:#ffd43b,color:#000
+    style O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    
+    style X fill:#74c0fc,color:#fff
+            </div>
+            <div class="color-legend">
+                <span><span class="color-box" style="background:#ff6b6b;"></span>Inputs & Data</span>
+                <span><span class="color-box" style="background:#ffd43b;"></span>Data Structures & Arrays</span>
+                <span><span class="color-box" style="background:#51cf66;"></span>Operations & Algorithms</span>
+                <span><span class="color-box" style="background:#74c0fc;"></span>States & Variables</span>
+                <span><span class="color-box" style="background:#b197fc;"></span>Output & Results</span>
+            </div>
+            <div class="figure-caption">
+                <strong>Figure 3.</strong> Dynamic Programming Process. This computer science process visualization demonstrates the computational logic of dynamic programming algorithms. The flowchart shows problem analysis, subproblem identification, recursive relation formulation, table-based computation, and optimal solution construction.
+            </div>
+        </div>
+
+        <h2>4. Graph Traversal Process</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Graph Representation
+    A[Graph Structure] --> B[Graph Analysis]
+    C[Starting Vertex] --> D[Vertex Validation]
+    E[Traversal Type] --> F[Algorithm Selection]
+    
+    %% Data Structure Setup
+    B --> G[Adjacency List/Matrix]
+    D --> H[Vertex Initialization]
+    F --> I[Queue/Stack Selection]
+    
+    %% Traversal Initialization
+    G --> J[Graph Representation]
+    H --> K[Visited Array]
+    I --> L[Data Structure Creation]
+    
+    %% Traversal Process
+    J --> M[Neighbor Discovery]
+    K --> N[Visit Tracking]
+    L --> O[Element Management]
+    
+    %% Algorithm Execution
+    M --> P[Neighbor Processing]
+    N --> Q[Visit Marking]
+    O --> R[Element Removal]
+    
+    %% Completion
+    P --> S[Traversal Complete]
+    Q --> T[All Vertices Visited]
+    R --> U[Data Structure Empty]
+    
+    %% Final Result
+    S --> V[Traversal Order]
+    T --> W[Connected Components]
+    U --> X[Algorithm Termination]
+    
+    %% Styling - Computer Science Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style G fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K fill:#ffd43b,color:#000
+    style L fill:#ffd43b,color:#000
+    style M fill:#ffd43b,color:#000
+    style N fill:#ffd43b,color:#000
+    style O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    
+    style X fill:#74c0fc,color:#fff
+            </div>
+            <div class="color-legend">
+                <span><span class="color-box" style="background:#ff6b6b;"></span>Inputs & Data</span>
+                <span><span class="color-box" style="background:#ffd43b;"></span>Data Structures & Arrays</span>
+                <span><span class="color-box" style="background:#51cf66;"></span>Operations & Algorithms</span>
+                <span><span class="color-box" style="background:#74c0fc;"></span>States & Variables</span>
+                <span><span class="color-box" style="background:#b197fc;"></span>Output & Results</span>
+            </div>
+            <div class="figure-caption">
+                <strong>Figure 4.</strong> Graph Traversal Process. This computer science process visualization demonstrates the computational logic of graph traversal algorithms. The flowchart shows graph representation, vertex initialization, neighbor discovery, visit tracking, and traversal completion.
+            </div>
+        </div>
+
+        <h2>5. Memory Management Process</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Memory Request
+    A[Memory Request] --> B[Request Analysis]
+    C[Size Requirements] --> D[Size Validation]
+    E[Memory Type] --> F[Type Selection]
+    
+    %% Memory Allocation
+    B --> G[Free List Search]
+    D --> H[Block Size Check]
+    F --> I[Allocation Strategy]
+    
+    %% Block Management
+    G --> J[Free Block Identification]
+    H --> K[Block Splitting]
+    I --> L[Allocation Method]
+    
+    %% Memory Assignment
+    J --> M[Block Assignment]
+    K --> N[Remaining Block]
+    L --> O[Memory Marking]
+    
+    %% Deallocation
+    M --> P[Memory Usage]
+    N --> Q[Free Block Update]
+    O --> R[Allocation Complete]
+    
+    %% Cleanup
+    P --> S[Memory Release]
+    Q --> T[Free List Update]
+    R --> U[Fragmentation Check]
+    
+    %% Final State
+    S --> V[Memory Freed]
+    T --> W[Free List Maintained]
+    U --> X[Memory Management Complete]
+    
+    %% Styling - Computer Science Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style G fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K fill:#ffd43b,color:#000
+    style L fill:#ffd43b,color:#000
+    style M fill:#ffd43b,color:#000
+    style N fill:#ffd43b,color:#000
+    style O fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style S fill:#ffd43b,color:#000
+    style T fill:#ffd43b,color:#000
+    style U fill:#ffd43b,color:#000
+    style V fill:#ffd43b,color:#000
+    style W fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    
+    style X fill:#74c0fc,color:#fff
+            </div>
+            <div class="color-legend">
+                <span><span class="color-box" style="background:#ff6b6b;"></span>Inputs & Data</span>
+                <span><span class="color-box" style="background:#ffd43b;"></span>Data Structures & Arrays</span>
+                <span><span class="color-box" style="background:#51cf66;"></span>Operations & Algorithms</span>
+                <span><span class="color-box" style="background:#74c0fc;"></span>States & Variables</span>
+                <span><span class="color-box" style="background:#b197fc;"></span>Output & Results</span>
+            </div>
+            <div class="figure-caption">
+                <strong>Figure 5.</strong> Memory Management Process. This computer science process visualization demonstrates the computational logic of memory management systems. The flowchart shows memory request analysis, free block search, allocation strategy, block management, and memory cleanup operations.
+            </div>
+        </div>
+    </div>
+</body>
+</html> 

index.html

@@ -1,19 +1,240 @@
-<!doctype html>
-<html>
-	<head>
-		<meta charset="utf-8" />
-		<meta name="viewport" content="width=device-width" />
-		<title>My static Space</title>
-		<link rel="stylesheet" href="style.css" />
-	</head>
-	<body>
-		<div class="card">
-			<h1>Welcome to your static Space!</h1>
-			<p>You can modify this app directly by editing <i>index.html</i> in the Files and versions tab.</p>
-			<p>
-				Also don't forget to check the
-				<a href="https://huggingface.co/docs/hub/spaces" target="_blank">Spaces documentation</a>.
-			</p>
-		</div>
-	</body>
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Programming Framework</title>
+    <link rel="stylesheet" href="style.css">
+    <link href="https://cdnjs.cloudflare.com/ajax/libs/prism/1.29.0/themes/prism.min.css" rel="stylesheet">
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/prism/1.29.0/components/prism-core.min.js"></script>
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/prism/1.29.0/plugins/autoloader/prism-autoloader.min.js"></script>
+</head>
+<body>
+    <div class="container">
+        <header>
+            <h1>🚀 Programming Framework</h1>
+            <p>A comprehensive framework for programming education and practice</p>
+        </header>
+
+        <nav class="tabs">
+            <button class="tab-btn active" data-tab="overview">Overview</button>
+            <button class="tab-btn" data-tab="methodology">Methodology</button>
+            <button class="tab-btn" data-tab="examples">Examples</button>
+            <button class="tab-btn" data-tab="resources">Resources</button>
+        </nav>
+
+        <main>
+            <!-- Overview Tab -->
+            <div class="tab-content active" id="overview">
+                <div class="card">
+                    <h2>What is the Programming Framework?</h2>
+                    <p>The Programming Framework is a systematic approach to learning and mastering programming concepts through structured methodology, practical examples, and progressive skill development.</p>
+                    
+                    <div class="features">
+                        <div class="feature">
+                            <h3>🎯 Systematic Learning</h3>
+                            <p>Structured approach to programming education with clear progression paths</p>
+                        </div>
+                        <div class="feature">
+                            <h3>🔧 Practical Application</h3>
+                            <p>Real-world examples and hands-on exercises to reinforce concepts</p>
+                        </div>
+                        <div class="feature">
+                            <h3>📈 Progressive Development</h3>
+                            <p>Build skills incrementally from fundamentals to advanced techniques</p>
+                        </div>
+                        <div class="feature">
+                            <h3>🌐 Multi-Language Support</h3>
+                            <p>Learn concepts that apply across multiple programming languages</p>
+                        </div>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Methodology Tab -->
+            <div class="tab-content" id="methodology">
+                <div class="card">
+                    <h2>Programming Framework Methodology</h2>
+                    
+                    <div class="methodology-step">
+                        <h3>1. Foundation Building</h3>
+                        <p>Establish core programming concepts and principles</p>
+                        <ul>
+                            <li>Variables and data types</li>
+                            <li>Control structures</li>
+                            <li>Functions and methods</li>
+                            <li>Basic algorithms</li>
+                        </ul>
+                    </div>
+
+                    <div class="methodology-step">
+                        <h3>2. Problem Analysis</h3>
+                        <p>Learn to break down complex problems into manageable components</p>
+                        <ul>
+                            <li>Requirements gathering</li>
+                            <li>Problem decomposition</li>
+                            <li>Algorithm design</li>
+                            <li>Pseudocode development</li>
+                        </ul>
+                    </div>
+
+                    <div class="methodology-step">
+                        <h3>3. Implementation</h3>
+                        <p>Translate solutions into working code</p>
+                        <ul>
+                            <li>Code organization</li>
+                            <li>Best practices</li>
+                            <li>Testing and debugging</li>
+                            <li>Documentation</li>
+                        </ul>
+                    </div>
+
+                    <div class="methodology-step">
+                        <h3>4. Optimization</h3>
+                        <p>Improve code efficiency and maintainability</p>
+                        <ul>
+                            <li>Performance analysis</li>
+                            <li>Code refactoring</li>
+                            <li>Design patterns</li>
+                            <li>Advanced algorithms</li>
+                        </ul>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Examples Tab -->
+            <div class="tab-content" id="examples">
+                <div class="card">
+                    <h2>Framework Examples</h2>
+                    
+                    <div class="example">
+                        <h3>Problem: Find the Maximum Number in an Array</h3>
+                        <div class="framework-application">
+                            <h4>Framework Application:</h4>
+                            <ol>
+                                <li><strong>Foundation:</strong> Understand arrays and loops</li>
+                                <li><strong>Analysis:</strong> Need to compare each element with current maximum</li>
+                                <li><strong>Implementation:</strong> Write iterative solution</li>
+                                <li><strong>Optimization:</strong> Consider edge cases and efficiency</li>
+                            </ol>
+                        </div>
+                        <div class="code-example">
+                            <h4>Example Implementation (Python):</h4>
+                            <pre><code class="language-python">def find_max(arr):
+    if not arr:
+        return None
+    
+    max_val = arr[0]
+    for num in arr[1:]:
+        if num > max_val:
+            max_val = num
+    
+    return max_val
+
+# Test the function
+numbers = [3, 7, 2, 9, 1, 5]
+result = find_max(numbers)
+print(f"Maximum number: {result}")  # Output: Maximum number: 9</code></pre>
+                        </div>
+                    </div>
+
+                    <div class="example">
+                        <h3>Problem: Reverse a String</h3>
+                        <div class="framework-application">
+                            <h4>Framework Application:</h4>
+                            <ol>
+                                <li><strong>Foundation:</strong> String manipulation and indexing</li>
+                                <li><strong>Analysis:</strong> Process characters from end to beginning</li>
+                                <li><strong>Implementation:</strong> Build reversed string character by character</li>
+                                <li><strong>Optimization:</strong> Use built-in methods or efficient algorithms</li>
+                            </ol>
+                        </div>
+                        <div class="code-example">
+                            <h4>Example Implementation (JavaScript):</h4>
+                            <pre><code class="language-javascript">function reverseString(str) {
+    let reversed = '';
+    for (let i = str.length - 1; i >= 0; i--) {
+        reversed += str[i];
+    }
+    return reversed;
+}
+
+// Test the function
+const text = "Programming Framework";
+const result = reverseString(text);
+console.log(result); // Output: krowemarF gnimmargorP</code></pre>
+                        </div>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Resources Tab -->
+            <div class="tab-content" id="resources">
+                <div class="card">
+                    <h2>Learning Resources</h2>
+                    
+                    <div class="resources-grid">
+                        <div class="resource">
+                            <h3>📚 Books</h3>
+                            <ul>
+                                <li>"Clean Code" by Robert C. Martin</li>
+                                <li>"Design Patterns" by Gang of Four</li>
+                                <li>"Introduction to Algorithms" by CLRS</li>
+                                <li>"The Pragmatic Programmer" by Hunt & Thomas</li>
+                            </ul>
+                        </div>
+                        
+                        <div class="resource">
+                            <h3>🌐 Online Platforms</h3>
+                            <ul>
+                                <li>LeetCode - Algorithm practice</li>
+                                <li>HackerRank - Coding challenges</li>
+                                <li>Codecademy - Interactive tutorials</li>
+                                <li>freeCodeCamp - Project-based learning</li>
+                            </ul>
+                        </div>
+                        
+                        <div class="resource">
+                            <h3>🎥 Video Courses</h3>
+                            <ul>
+                                <li>MIT OpenCourseWare</li>
+                                <li>Stanford CS50</li>
+                                <li>Coursera Algorithms courses</li>
+                                <li>YouTube programming channels</li>
+                            </ul>
+                        </div>
+                        
+                        <div class="resource">
+                            <h3>🛠️ Tools</h3>
+                            <ul>
+                                <li>Git - Version control</li>
+                                <li>VS Code - Code editor</li>
+                                <li>Docker - Containerization</li>
+                                <li>Postman - API testing</li>
+                            </ul>
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </main>
+    </div>
+
+    <script>
+        // Tab functionality
+        document.querySelectorAll('.tab-btn').forEach(button => {
+            button.addEventListener('click', () => {
+                // Remove active class from all tabs and content
+                document.querySelectorAll('.tab-btn').forEach(btn => btn.classList.remove('active'));
+                document.querySelectorAll('.tab-content').forEach(content => content.classList.remove('active'));
+                
+                // Add active class to clicked tab
+                button.classList.add('active');
+                
+                // Show corresponding content
+                const tabId = button.getAttribute('data-tab');
+                document.getElementById(tabId).classList.add('active');
+            });
+        });
+    </script>
+</body>
 </html>

mathematics_processes.html

@@ -0,0 +1,665 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+    <title>Mathematics Processes - Programming Framework Analysis</title>
+    <style>
+        body { 
+            font-family: 'Times New Roman', Times, serif, 'Arial Unicode MS'; 
+            margin: 0; 
+            background: #ffffff; 
+            color: #000000; 
+            line-height: 1.6; 
+            font-size: 12pt; 
+        }
+        .container { 
+            max-width: 1000px; 
+            margin: 0 auto; 
+            padding: 1.5rem; 
+        }
+        h1, h2, h3 { 
+            color: #000000; 
+            margin-top: 1.5rem; 
+            margin-bottom: 0.75rem; 
+        }
+        h1 { 
+            font-size: 18pt; 
+            text-align: center; 
+        }
+        h2 { 
+            font-size: 16pt; 
+            border-bottom: 2px solid #000; 
+            padding-bottom: 0.5rem; 
+        }
+        h3 { 
+            font-size: 14pt; 
+        }
+        p { 
+            margin-bottom: 1rem; 
+            text-align: justify; 
+        }
+        .figure { 
+            margin: 1rem 0; 
+            text-align: center; 
+            border: 1px solid #ccc; 
+            padding: 1rem; 
+            background: #f9f9f9; 
+        }
+        .figure-caption { 
+            margin-top: 1rem; 
+            font-style: italic; 
+            text-align: left; 
+        }
+        .mermaid { 
+            background: white; 
+            padding: 1rem; 
+            border-radius: 4px; 
+        }
+    </style>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
+    <script>
+        mermaid.initialize({ 
+            startOnLoad: true, 
+            theme: 'default', 
+            flowchart: { 
+                useMaxWidth: false, 
+                htmlLabels: true,
+                curve: 'linear',
+                nodeSpacing: 50,
+                rankSpacing: 50,
+                padding: 20
+            },
+            themeVariables: {
+                fontFamily: 'Arial Unicode MS, Arial, sans-serif'
+            }
+        });
+    </script>
+</head>
+<body>
+    <div class="container">
+        <h1>Mathematics Processes - Programming Framework Analysis</h1>
+        
+        <p>This document presents mathematics processes analyzed using the Programming Framework methodology. Each process is represented as a computational flowchart with standardized color coding: Red for triggers/inputs, Yellow for structures/objects, Green for processing/operations, Blue for intermediates/states, and Violet for products/outputs. Yellow nodes use black text for optimal readability, while all other colors use white text.</p>
+
+        <h2>1. Mathematical Induction Proof Process</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Initial Setup
+    %% Axioms and Given Conditions
+    A1[Peano Axioms] --> B1[Axiom Processing]
+    C1[Given n in Natural Numbers] --> D1[Input Validation]
+    E1[Goal: Prove P(n)] --> F1[Target Identification]
+    %% Logical Framework Setup
+    B1 --> G1[Mathematical Universe Setup]
+    D1 --> H1[Variable Declaration]
+    F1 --> I1[Proof Strategy Selection]
+    %% Proof Structure
+    G1 --> J1[Induction Hypothesis P(k)]
+    H1 --> K1[Base Case Analysis]
+    I1 --> L1[Inductive Step Planning]
+    %% Base Case Processing
+    K1 --> M1[P(0) Verification]
+    M1 --> N1[Base Case Success]
+    N1 --> O1[Induction Foundation]
+    %% Inductive Step Processing
+    L1 --> P1[Assume P(k) for k in Natural Numbers]
+    P1 --> Q1[Show P(k+1) follows]
+    Q1 --> R1[Inductive Step Execution]
+    %% Mathematical Operations
+    R1 --> S1[Algebraic Manipulation]
+    S1 --> T1[Logical Deduction]
+    T1 --> U1[Theorem Application]
+    %% Intermediate Calculations
+    U1 --> V1[Sub-proof Construction]
+    V1 --> W1[Lemma Application]
+    W1 --> X1[Contradiction Analysis]
+    %% Proof Validation
+    X1 --> Y1[Logical Consistency Check]
+    Y1 --> Z1[Mathematical Rigor Verification]
+    Z1 --> AA1[Proof Completeness Assessment]
+    %% Decision Points
+    AA1 --> BB1{Proof Complete?}
+    BB1 -->|No| CC1[Identify Gap]
+    BB1 -->|Yes| DD1[Proof Validated]
+    %% Gap Resolution
+    CC1 --> EE1[Additional Lemma Needed]
+    EE1 --> FF1[Sub-proof Construction]
+    FF1 --> GG1[Gap Resolution]
+    GG1 --> Y1
+    %% Final Output
+    DD1 --> HH1[Theorem P(n) Proven]
+    HH1 --> II1[Mathematical Truth Established]
+    II1 --> JJ1[Proof Tree Complete]
+    %% Styling - Mathematical Color Scheme
+    %% Styling - Biological Color Scheme
+    style A1 fill:#ff6b6b,color:#fff
+    style C1 fill:#ff6b6b,color:#fff
+    style E1 fill:#ff6b6b,color:#fff
+    style J1 fill:#ffd43b,color:#000
+    style P1 fill:#ffd43b,color:#000
+    style Q1 fill:#ffd43b,color:#000
+    style S1 fill:#51cf66,color:#fff
+    style T1 fill:#51cf66,color:#fff
+    style U1 fill:#51cf66,color:#fff
+    style V1 fill:#51cf66,color:#fff
+    style W1 fill:#51cf66,color:#fff
+    style X1 fill:#51cf66,color:#fff
+    style B1 fill:#74c0fc,color:#fff
+    style D1 fill:#74c0fc,color:#fff
+    style F1 fill:#74c0fc,color:#fff
+    style G1 fill:#74c0fc,color:#fff
+    style H1 fill:#74c0fc,color:#fff
+    style I1 fill:#74c0fc,color:#fff
+    style K1 fill:#74c0fc,color:#fff
+    style L1 fill:#74c0fc,color:#fff
+    style M1 fill:#74c0fc,color:#fff
+    style N1 fill:#74c0fc,color:#fff
+    style O1 fill:#74c0fc,color:#fff
+    style R1 fill:#74c0fc,color:#fff
+    style Y1 fill:#74c0fc,color:#fff
+    style Z1 fill:#74c0fc,color:#fff
+    style AA1 fill:#74c0fc,color:#fff
+    style BB1 fill:#74c0fc,color:#fff
+    style CC1 fill:#74c0fc,color:#fff
+    style DD1 fill:#74c0fc,color:#fff
+    style EE1 fill:#74c0fc,color:#fff
+    style FF1 fill:#74c0fc,color:#fff
+    style GG1 fill:#74c0fc,color:#fff
+    style HH1 fill:#b197fc,color:#fff
+    style II1 fill:#b197fc,color:#fff
+    style JJ1 fill:#b197fc,color:#fff
+                    </div>
+            
+            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Triggers & Inputs
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Logical Structures & Hypotheses
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Deductions & Theorem Applications
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
+                </div>
+            </div>
+            
+            <div class="figure-caption">
+                <strong>Figure 1.</strong> Mathematical Induction Proof Process. This mathematics process visualization demonstrates formal mathematical reasoning. The flowchart shows axioms and given conditions, logical structures and hypotheses, deduction steps and theorem applications, intermediate calculations and sub-proofs, and final proven theorems.
+            </div>
+        </div>
+
+        <h2>2. Euclidean Algorithm Process</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Initial Setup
+    %% Input Conditions
+    A2[Integer a] --> B2[Input Validation]
+    C2[Integer b] --> D2[Input Validation]
+    E2[Goal: Find GCD(a,b)] --> F2[Problem Statement]
+    %% Algorithm Initialization
+    B2 --> G2[Set r₀ = a]
+    D2 --> H2[Set r₁ = b]
+    F2 --> I2[Algorithm Selection]
+    %% Division Process
+    G2 --> J2[Division Algorithm]
+    H2 --> K2[Division Algorithm]
+    I2 --> L2[Iterative Process]
+    %% First Division
+    J2 --> M2[r₀ = q₁r₁ + r₂]
+    K2 --> N2[Calculate q₁ and r₂]
+    L2 --> O2[Initialize iteration counter]
+    %% Iterative Loop
+    M2 --> P2{Is r₂ = 0?}
+    N2 --> Q2[Store r₂]
+    O2 --> R2[Increment counter]
+    %% Continue or Terminate
+    P2 -->|No| S2[Set r₀ = r₁, r₁ = r₂]
+    P2 -->|Yes| T2[GCD Found: r₁]
+    Q2 --> U2[Update remainders]
+    R2 --> V2[Track iterations]
+    %% Next Iteration
+    S2 --> W2[Next Division Step]
+    U2 --> X2[Prepare for next iteration]
+    V2 --> Y2[Check termination condition]
+    %% Final Result
+    T2 --> Z2[GCD(a,b) = r₁]
+    W2 --> AA2[Repeat division process]
+    X2 --> BB2[Update variables]
+    Y2 --> CC2{Continue?}
+    %% Algorithm Completion
+    Z2 --> DD2[Result Validation]
+    AA2 --> P2
+    BB2 --> P2
+    CC2 -->|Yes| AA2
+    CC2 -->|No| T2
+    %% Output
+    DD2 --> EE2[GCD Calculation Complete]
+    EE2 --> FF2[Mathematical Proof of Correctness]
+    FF2 --> GG2[Algorithm Efficiency Analysis]
+    %% Styling - Mathematical Color Scheme
+    %% Styling - Biological Color Scheme
+    style A2 fill:#ff6b6b,color:#fff
+    style C2 fill:#ff6b6b,color:#fff
+    style E2 fill:#ff6b6b,color:#fff
+    style G2 fill:#ffd43b,color:#000
+    style H2 fill:#ffd43b,color:#000
+    style I2 fill:#ffd43b,color:#000
+    style J2 fill:#ffd43b,color:#000
+    style K2 fill:#ffd43b,color:#000
+    style L2 fill:#51cf66,color:#fff
+    style M2 fill:#51cf66,color:#fff
+    style N2 fill:#51cf66,color:#fff
+    style O2 fill:#51cf66,color:#fff
+    style S2 fill:#51cf66,color:#fff
+    style W2 fill:#51cf66,color:#fff
+    style AA2 fill:#51cf66,color:#fff
+    style B2 fill:#74c0fc,color:#fff
+    style D2 fill:#74c0fc,color:#fff
+    style F2 fill:#74c0fc,color:#fff
+    style P2 fill:#74c0fc,color:#fff
+    style Q2 fill:#74c0fc,color:#fff
+    style R2 fill:#74c0fc,color:#fff
+    style T2 fill:#74c0fc,color:#fff
+    style U2 fill:#74c0fc,color:#fff
+    style V2 fill:#74c0fc,color:#fff
+    style X2 fill:#74c0fc,color:#fff
+    style Y2 fill:#74c0fc,color:#fff
+    style CC2 fill:#74c0fc,color:#fff
+    style DD2 fill:#74c0fc,color:#fff
+    style Z2 fill:#b197fc,color:#fff
+    style EE2 fill:#b197fc,color:#fff
+    style FF2 fill:#b197fc,color:#fff
+    style GG2 fill:#b197fc,color:#fff
+                    </div>
+            
+            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Triggers & Inputs
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Mathematical Methods & Algorithms
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Computational Operations
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
+                </div>
+            </div>
+            
+            <div class="figure-caption">
+                <strong>Figure 2.</strong> Euclidean Algorithm Process. This mathematics process visualization demonstrates algorithmic computation. The flowchart shows integer inputs, mathematical methods and algorithms, computational operations, intermediate calculations, and final GCD results.
+            </div>
+        </div>
+
+        <h2>3. Calculus Integration Process</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Initial Setup
+    %% Input Conditions
+    A3[Function f(x)] --> B3[Function Analysis]
+    C3[Integration Limits [a,b]] --> D3[Boundary Definition]
+    E3[Goal: ∫f(x)dx] --> F3[Problem Statement]
+    %% Function Classification
+    B3 --> G3[Function Type Classification]
+    D3 --> H3[Domain Analysis]
+    F3 --> I3[Integration Strategy Selection]
+    %% Integration Methods
+    G3 --> J3{Function Type?}
+    H3 --> K3[Continuity Check]
+    I3 --> L3[Method Selection]
+    %% Direct Integration
+    J3 -->|Polynomial| M3[Power Rule Application]
+    J3 -->|Trigonometric| N3[Trig Identity Application]
+    J3 -->|Exponential| O3[Exponential Rule]
+    J3 -->|Rational| P3[Partial Fractions]
+    %% Substitution Method
+    K3 --> Q3[Substitution Detection]
+    L3 --> R3[Substitution Method]
+    M3 --> S3[Direct Integration]
+    N3 --> T3[Trig Integration]
+    %% Integration by Parts
+    O3 --> U3[Integration by Parts]
+    P3 --> V3[Partial Fraction Decomposition]
+    Q3 --> W3[Substitution Application]
+    R3 --> X3[Variable Change]
+    %% Definite Integration
+    S3 --> Y3[Antiderivative F(x)]
+    T3 --> Z3[Trig Antiderivative]
+    U3 --> AA3[Parts Integration]
+    V3 --> BB3[Fraction Integration]
+    %% Evaluation
+    W3 --> CC3[Substituted Integral]
+    X3 --> DD3[New Variable Integration]
+    Y3 --> EE3[F(b) - F(a)]
+    Z3 --> FF3[Definite Trig Result]
+    %% Final Results
+    AA3 --> GG3[Parts Result]
+    BB3 --> HH3[Fraction Result]
+    CC3 --> II3[Substitution Result]
+    DD3 --> JJ3[Variable Back-Substitution]
+    %% Verification
+    EE3 --> KK3[Result Verification]
+    FF3 --> LL3[Trigonometric Verification]
+    GG3 --> MM3[Parts Verification]
+    HH3 --> NN3[Fraction Verification]
+    %% Output
+    KK3 --> OO3[Definite Integral Value]
+    LL3 --> PP3[Trigonometric Integral Value]
+    MM3 --> QQ3[Parts Integral Value]
+    NN3 --> RR3[Fractional Integral Value]
+    %% Styling - Mathematical Color Scheme
+    %% Styling - Biological Color Scheme
+    style A3 fill:#ff6b6b,color:#fff
+    style C3 fill:#ff6b6b,color:#fff
+    style E3 fill:#ff6b6b,color:#fff
+    style G3 fill:#ffd43b,color:#000
+    style H3 fill:#ffd43b,color:#000
+    style I3 fill:#ffd43b,color:#000
+    style J3 fill:#ffd43b,color:#000
+    style K3 fill:#ffd43b,color:#000
+    style L3 fill:#ffd43b,color:#000
+    style M3 fill:#51cf66,color:#fff
+    style N3 fill:#51cf66,color:#fff
+    style O3 fill:#51cf66,color:#fff
+    style P3 fill:#51cf66,color:#fff
+    style Q3 fill:#51cf66,color:#fff
+    style R3 fill:#51cf66,color:#fff
+    style S3 fill:#51cf66,color:#fff
+    style T3 fill:#51cf66,color:#fff
+    style U3 fill:#51cf66,color:#fff
+    style V3 fill:#51cf66,color:#fff
+    style AA3 fill:#51cf66,color:#fff
+    style BB3 fill:#51cf66,color:#fff
+    style B3 fill:#74c0fc,color:#fff
+    style D3 fill:#74c0fc,color:#fff
+    style F3 fill:#74c0fc,color:#fff
+    style Y3 fill:#74c0fc,color:#fff
+    style Z3 fill:#74c0fc,color:#fff
+    style AA3 fill:#74c0fc,color:#fff
+    style BB3 fill:#74c0fc,color:#fff
+    style CC3 fill:#74c0fc,color:#fff
+    style DD3 fill:#74c0fc,color:#fff
+    style EE3 fill:#74c0fc,color:#fff
+    style FF3 fill:#74c0fc,color:#fff
+    style GG3 fill:#74c0fc,color:#fff
+    style HH3 fill:#74c0fc,color:#fff
+    style II3 fill:#74c0fc,color:#fff
+    style JJ3 fill:#74c0fc,color:#fff
+    style EE4 fill:#b197fc,color:#fff
+    style FF4 fill:#b197fc,color:#fff
+    style GG4 fill:#b197fc,color:#fff
+    style HH4 fill:#b197fc,color:#fff
+    style KK4 fill:#b197fc,color:#fff
+    style LL4 fill:#b197fc,color:#fff
+    style MM4 fill:#b197fc,color:#fff
+    style NN4 fill:#b197fc,color:#fff
+                    </div>
+            
+            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Triggers & Inputs
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Mathematical Methods & Theorems
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Integration Operations
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
+                </div>
+            </div>
+            
+            <div class="figure-caption">
+                <strong>Figure 3.</strong> Calculus Integration Process. This mathematics process visualization demonstrates integral calculus computation. The flowchart shows function inputs, mathematical methods and theorems, integration operations, intermediate calculations, and final integral values.
+            </div>
+        </div>
+
+        <h2>4. Linear Algebra Matrix Operations</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Initial Setup
+    %% Input Conditions
+    A4[Matrix A] --> B4[Matrix Analysis]
+    C4[Matrix B] --> D4[Matrix Analysis]
+    E4[Operation Type] --> F4[Operation Selection]
+    %% Matrix Classification
+    B4 --> G4[Matrix Dimensions Check]
+    D4 --> H4[Matrix Properties Analysis]
+    F4 --> I4[Operation Feasibility]
+    %% Operation Types
+    G4 --> J4{Operation Type?}
+    H4 --> K4[Matrix Properties]
+    I4 --> L4[Compatibility Check]
+    %% Matrix Addition
+    J4 -->|Addition| M4[Dimension Matching]
+    J4 -->|Multiplication| N4[Inner Product Dimensions]
+    J4 -->|Inverse| O4[Square Matrix Check]
+    J4 -->|Determinant| P4[Square Matrix Check]
+    %% Addition Process
+    K4 --> Q4[Element-wise Addition]
+    L4 --> R4[Compatibility Verification]
+    M4 --> S4[Add Corresponding Elements]
+    N4 --> T4[Matrix Multiplication Algorithm]
+    %% Multiplication Process
+    O4 --> U4[Inverse Calculation]
+    P4 --> V4[Determinant Calculation]
+    Q4 --> W4[Result Matrix C]
+    R4 --> X4[Operation Validation]
+    %% Inverse Calculation
+    S4 --> Y4[Addition Result]
+    T4 --> Z4[Multiplication Result]
+    U4 --> AA4[Gauss-Jordan Elimination]
+    V4 --> BB4[Determinant Expansion]
+    %% Determinant Calculation
+    W4 --> CC4[Result Verification]
+    X4 --> DD4[Properties Check]
+    Y4 --> EE4[Matrix C = A + B]
+    Z4 --> FF4[Matrix C = A × B]
+    %% Final Results
+    AA4 --> GG4[Inverse Matrix A⁻¹]
+    BB4 --> HH4[Determinant |A|]
+    CC4 --> II4[Result Validation]
+    DD4 --> JJ4[Properties Verification]
+    %% Output
+    EE4 --> KK4[Addition Complete]
+    FF4 --> LL4[Multiplication Complete]
+    GG4 --> MM4[Inverse Found]
+    HH4 --> NN4[Determinant Calculated]
+    %% Styling - Mathematical Color Scheme
+    %% Styling - Biological Color Scheme
+    style A4 fill:#ff6b6b,color:#fff
+    style C4 fill:#ff6b6b,color:#fff
+    style E4 fill:#ff6b6b,color:#fff
+    style G4 fill:#ffd43b,color:#000
+    style H4 fill:#ffd43b,color:#000
+    style I4 fill:#ffd43b,color:#000
+    style J4 fill:#ffd43b,color:#000
+    style K4 fill:#ffd43b,color:#000
+    style L4 fill:#ffd43b,color:#000
+    style M4 fill:#51cf66,color:#fff
+    style N4 fill:#51cf66,color:#fff
+    style O4 fill:#51cf66,color:#fff
+    style P4 fill:#51cf66,color:#fff
+    style Q4 fill:#51cf66,color:#fff
+    style R4 fill:#51cf66,color:#fff
+    style S4 fill:#51cf66,color:#fff
+    style T4 fill:#51cf66,color:#fff
+    style U4 fill:#51cf66,color:#fff
+    style V4 fill:#51cf66,color:#fff
+    style AA4 fill:#51cf66,color:#fff
+    style BB4 fill:#51cf66,color:#fff
+    style B4 fill:#74c0fc,color:#fff
+    style D4 fill:#74c0fc,color:#fff
+    style F4 fill:#74c0fc,color:#fff
+    style W4 fill:#74c0fc,color:#fff
+    style X4 fill:#74c0fc,color:#fff
+    style Y4 fill:#74c0fc,color:#fff
+    style Z4 fill:#74c0fc,color:#fff
+    style CC4 fill:#74c0fc,color:#fff
+    style DD4 fill:#74c0fc,color:#fff
+    style II4 fill:#74c0fc,color:#fff
+    style JJ4 fill:#74c0fc,color:#fff
+    style EE4 fill:#b197fc,color:#fff
+    style FF4 fill:#b197fc,color:#fff
+    style GG4 fill:#b197fc,color:#fff
+    style HH4 fill:#b197fc,color:#fff
+    style KK4 fill:#b197fc,color:#fff
+    style LL4 fill:#b197fc,color:#fff
+    style MM4 fill:#b197fc,color:#fff
+    style NN4 fill:#b197fc,color:#fff
+                    </div>
+            
+            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Triggers & Inputs
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Mathematical Structures & Methods
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Matrix Operations
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
+                </div>
+            </div>
+            
+            <div class="figure-caption">
+                <strong>Figure 4.</strong> Linear Algebra Matrix Operations. This mathematics process visualization demonstrates matrix algebra computation. The flowchart shows matrix inputs, mathematical structures and methods, matrix operations, intermediate calculations, and final matrix results.
+            </div>
+        </div>
+
+        <h2>5. Probability Theory Process</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Initial Setup
+    %% Input Conditions
+    A5[Sample Space S] --> B5[Space Analysis]
+    C5[Event E] --> D5[Event Analysis]
+    E5[Probability Measure P] --> F5[Measure Definition]
+    %% Probability Framework
+    B5 --> G5[Sample Space Properties]
+    D5 --> H5[Event Properties]
+    F5 --> I5[Probability Axioms]
+    %% Axiomatic Foundation
+    G5 --> J5[Kolmogorov Axioms]
+    H5 --> K5[Event Algebra]
+    I5 --> L5[Measure Theory]
+    %% Probability Calculation
+    J5 --> M5[P(S) = 1]
+    K5 --> N5[Event Operations]
+    L5 --> O5[Probability Functions]
+    %% Event Operations
+    M5 --> P5[Complement Rule]
+    N5 --> Q5[Union Rule]
+    O5 --> R5[Conditional Probability]
+    %% Conditional Probability
+    P5 --> S5[P(E') = 1 - P(E)]
+    Q5 --> T5[P(A∪B) = P(A) + P(B) - P(A∩B)]
+    R5 --> U5[P(A|B) = P(A∩B)/P(B)]
+    %% Bayes' Theorem
+    S5 --> V5[Probability Calculation]
+    T5 --> W5[Set Operations]
+    U5 --> X5[Bayes' Theorem]
+    %% Independence
+    V5 --> Y5[Result Verification]
+    W5 --> Z5[Venn Diagram Analysis]
+    X5 --> AA5[P(A|B) = P(B|A)P(A)/P(B)]
+    %% Final Results
+    Y5 --> BB5[Probability Value]
+    Z5 --> CC5[Set Relationships]
+    AA5 --> DD5[Posterior Probability]
+    %% Output
+    BB5 --> EE5[Probability Calculated]
+    CC5 --> FF5[Event Relationships]
+    DD5 --> GG5[Bayesian Update]
+    %% Styling - Mathematical Color Scheme
+    %% Styling - Biological Color Scheme
+    style A5 fill:#ff6b6b,color:#fff
+    style C5 fill:#ff6b6b,color:#fff
+    style E5 fill:#ff6b6b,color:#fff
+    style G5 fill:#ffd43b,color:#000
+    style H5 fill:#ffd43b,color:#000
+    style I5 fill:#ffd43b,color:#000
+    style J5 fill:#ffd43b,color:#000
+    style K5 fill:#ffd43b,color:#000
+    style L5 fill:#ffd43b,color:#000
+    style M5 fill:#51cf66,color:#fff
+    style N5 fill:#51cf66,color:#fff
+    style O5 fill:#51cf66,color:#fff
+    style P5 fill:#51cf66,color:#fff
+    style Q5 fill:#51cf66,color:#fff
+    style R5 fill:#51cf66,color:#fff
+    style S5 fill:#51cf66,color:#fff
+    style T5 fill:#51cf66,color:#fff
+    style U5 fill:#51cf66,color:#fff
+    style X5 fill:#51cf66,color:#fff
+    style AA5 fill:#51cf66,color:#fff
+    style B5 fill:#74c0fc,color:#fff
+    style D5 fill:#74c0fc,color:#fff
+    style F5 fill:#74c0fc,color:#fff
+    style V5 fill:#74c0fc,color:#fff
+    style W5 fill:#74c0fc,color:#fff
+    style Y5 fill:#74c0fc,color:#fff
+    style Z5 fill:#74c0fc,color:#fff
+    style BB5 fill:#74c0fc,color:#fff
+    style CC5 fill:#74c0fc,color:#fff
+    style DD5 fill:#74c0fc,color:#fff
+    style EE5 fill:#b197fc,color:#fff
+    style FF5 fill:#b197fc,color:#fff
+    style GG5 fill:#b197fc,color:#fff
+                    </div>
+            
+            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Triggers & Inputs
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Probability Axioms & Theorems
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Probability Calculations
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
+                </div>
+            </div>
+            
+            <div class="figure-caption">
+                <strong>Figure 5.</strong> Probability Theory Process. This mathematics process visualization demonstrates probabilistic reasoning. The flowchart shows sample space inputs, probability axioms and theorems, probability calculations, intermediate computations, and final probability values.
+            </div>
+        </div>
+
+        <p><strong>Generated using the Programming Framework methodology</strong></p>
+        
+        <p>This collection demonstrates the computational nature of mathematical processes and systems</p>
+        
+        <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+    </div>
+</body>
+</html> 

physics_processes.html

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+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+    <title>Physics Processes - Programming Framework Analysis</title>
+    <style>
+        body { 
+            font-family: 'Times New Roman', Times, serif, 'Arial Unicode MS'; 
+            margin: 0; 
+            background: #ffffff; 
+            color: #000000; 
+            line-height: 1.6; 
+            font-size: 12pt; 
+        }
+        .container { 
+            max-width: 1000px; 
+            margin: 0 auto; 
+            padding: 1.5rem; 
+        }
+        h1, h2, h3 { 
+            color: #000000; 
+            margin-top: 1.5rem; 
+            margin-bottom: 0.75rem; 
+        }
+        h1 { 
+            font-size: 18pt; 
+            text-align: center; 
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+        h2 { 
+            font-size: 16pt; 
+            border-bottom: 2px solid #000; 
+            padding-bottom: 0.5rem; 
+        }
+        h3 { 
+            font-size: 14pt; 
+        }
+        p { 
+            margin-bottom: 1rem; 
+            text-align: justify; 
+        }
+        .figure { 
+            margin: 1rem 0; 
+            text-align: center; 
+            border: 1px solid #ccc; 
+            padding: 1rem; 
+            background: #f9f9f9; 
+        }
+        .figure-caption { 
+            margin-top: 1rem; 
+            font-style: italic; 
+            text-align: left; 
+        }
+        .mermaid { 
+            background: white; 
+            padding: 1rem; 
+            border-radius: 4px; 
+        }
+    </style>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
+    <script>
+        mermaid.initialize({ 
+            startOnLoad: true, 
+            theme: 'default', 
+            flowchart: { 
+                useMaxWidth: false, 
+                htmlLabels: true,
+                curve: 'linear',
+                nodeSpacing: 50,
+                rankSpacing: 50,
+                padding: 20
+            },
+            themeVariables: {
+                fontFamily: 'Arial Unicode MS, Arial, sans-serif'
+            }
+        });
+    </script>
+</head>
+<body>
+    <div class="container">
+        <h1>Physics Processes - Programming Framework Analysis</h1>
+        
+        <p>This document presents physics processes analyzed using the Programming Framework methodology. Each process is represented as a computational flowchart with standardized color coding: Red for triggers/inputs, Yellow for structures/objects, Green for processing/operations, Blue for intermediates/states, and Violet for products/outputs. Yellow nodes use black text for optimal readability, while all other colors use white text.</p>
+
+        <h2>1. Quantum Tunneling Process</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Initial Conditions
+    A1[Particle Energy E] --> B1[Energy Assessment]
+    C1[Barrier Height V₀] --> D1[Barrier Analysis]
+    E1[Barrier Width a] --> F1[Geometric Constraints]
+    
+    %% Quantum State Preparation
+    B1 --> G1[Wave Function Initialization]
+    D1 --> H1[Potential Energy Profile]
+    F1 --> I1[Spatial Boundary Conditions]
+    
+    %% Wave Function Evolution
+    G1 --> J1[Incident Wave Function ψ₁]
+    H1 --> K1[Barrier Region ψ₂]
+    I1 --> L1[Transmitted Wave Function ψ₃]
+    
+    %% Quantum Processing
+    J1 --> M1[Wave Function Matching]
+    K1 --> N1[Exponential Decay in Barrier]
+    L1 --> O1[Transmission Coefficient Calculation]
+    
+    %% Quantum State Analysis
+    M1 --> P1[Boundary Condition Equations]
+    N1 --> Q1[Quantum Amplitude Processing]
+    O1 --> R1[Probability Density Analysis]
+    
+    %% Transmission Calculation
+    P1 --> S1[Wave Function Continuity]
+    Q1 --> T1[Quantum Interference Effects]
+    R1 --> U1[Transmission Probability T]
+    
+    %% Classical vs Quantum Logic
+    S1 --> V1{Classical Prediction}
+    T1 --> W1{Quantum Reality}
+    U1 --> X1[Measured Transmission]
+    
+    %% Decision Points
+    V1 -->|E < V₀: T = 0| Y1[Classical Forbidden]
+    W1 -->|E < V₀: T > 0| Z1[Quantum Tunneling]
+    X1 --> AA1[Particle Detection Beyond Barrier]
+    
+    %% Measurement and Detection
+    Y1 --> BB1[Classical Prediction Failure]
+    Z1 --> CC1[Quantum Tunneling Success]
+    AA1 --> DD1[Energy Verification]
+    
+    %% Energy Conservation
+    BB1 --> EE1[Wave Function Collapse]
+    CC1 --> FF1[Final Particle State]
+    DD1 --> GG1[Energy Conservation Check]
+    
+    %% Final Results
+    EE1 --> HH1[Measurement Complete]
+    FF1 --> II1[Quantum Effect Confirmed]
+    GG1 --> JJ1[Energy Conservation Verified]
+    
+    %% Styling - Physics Color Scheme
+    style A1 fill:#ff6b6b,color:#fff
+    style C1 fill:#ff6b6b,color:#fff
+    style E1 fill:#ff6b6b,color:#fff
+    
+    style G1 fill:#ffd43b,color:#000
+    style H1 fill:#ffd43b,color:#000
+    style I1 fill:#ffd43b,color:#000
+    style J1 fill:#ffd43b,color:#000
+    style K1 fill:#ffd43b,color:#000
+    style L1 fill:#ffd43b,color:#000
+    
+    style M1 fill:#51cf66,color:#fff
+    style N1 fill:#51cf66,color:#fff
+    style O1 fill:#51cf66,color:#fff
+    style P1 fill:#51cf66,color:#fff
+    style Q1 fill:#51cf66,color:#fff
+    style R1 fill:#51cf66,color:#fff
+    style S1 fill:#51cf66,color:#fff
+    style T1 fill:#51cf66,color:#fff
+    style U1 fill:#51cf66,color:#fff
+    
+    style B1 fill:#74c0fc,color:#fff
+    style D1 fill:#74c0fc,color:#fff
+    style F1 fill:#74c0fc,color:#fff
+    style V1 fill:#74c0fc,color:#fff
+    style W1 fill:#74c0fc,color:#fff
+    style X1 fill:#74c0fc,color:#fff
+    style Y1 fill:#74c0fc,color:#fff
+    style Z1 fill:#74c0fc,color:#fff
+    style AA1 fill:#74c0fc,color:#fff
+    style BB1 fill:#74c0fc,color:#fff
+    style CC1 fill:#74c0fc,color:#fff
+    style DD1 fill:#74c0fc,color:#fff
+    style EE1 fill:#74c0fc,color:#fff
+    style FF1 fill:#74c0fc,color:#fff
+    style GG1 fill:#74c0fc,color:#fff
+    
+    style HH1 fill:#b197fc,color:#fff
+    style II1 fill:#b197fc,color:#fff
+    style JJ1 fill:#b197fc,color:#fff
+            </div>
+            
+            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Energy & Geometric Inputs
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Wave Functions & Fields
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Quantum Processing
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
+                </div>
+            </div>
+            
+            <div class="figure-caption">
+                <strong>Figure 1.</strong> Quantum Tunneling Process. This physics process visualization demonstrates quantum mechanical phenomena. The flowchart shows energy inputs, wave functions and fields, quantum processing operations, intermediate calculations, and final measurement outcomes.
+            </div>
+        </div>
+
+        <h2>2. Nuclear Fusion Process</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Initial Setup
+    %% Input Conditions
+    A2[High Temperature Plasma] --> B2[Thermal Energy Input]
+    C2[High Pressure Environment] --> D2[Pressure Confinement]
+    E2[Deuterium-Tritium Fuel] --> F2[Fuel Preparation]
+    %% Plasma State
+    B2 --> G2[Ionization Process]
+    D2 --> H2[Magnetic Confinement]
+    F2 --> I2[Fuel Injection]
+    %% Fusion Conditions
+    G2 --> J2[Plasma Heating]
+    H2 --> K2[Confinement Stability]
+    I2 --> L2[Fuel Mixing]
+    %% Nuclear Reactions
+    J2 --> M2[Collision Frequency]
+    K2 --> N2[Confinement Time]
+    L2 --> O2[Reaction Rate]
+    %% Fusion Process
+    M2 --> P2[Deuterium-Tritium Collision]
+    N2 --> Q2[Plasma Containment]
+    O2 --> R2[Fusion Cross Section]
+    %% Energy Release
+    P2 --> S2[Helium-4 Formation]
+    Q2 --> T2[Neutron Emission]
+    R2 --> U2[Energy Release]
+    %% Energy Conversion
+    S2 --> V2[Kinetic Energy Transfer]
+    T2 --> W2[Neutron Capture]
+    U2 --> X2[Heat Generation]
+    %% Power Generation
+    V2 --> Y2[Plasma Heating]
+    W2 --> Z2[Breeding Blanket]
+    X2 --> AA2[Steam Generation]
+    %% Final Output
+    Y2 --> BB2[Self-Sustaining Fusion]
+    Z2 --> CC2[Tritium Breeding]
+    AA2 --> DD2[Electrical Power]
+    %% Process Control
+    BB2 --> EE2[Fusion Reactor Operation]
+    CC2 --> FF2[Fuel Cycle Management]
+    DD2 --> GG2[Power Grid Integration]
+    %% Styling - Physics Color Scheme
+    %% Styling - Biological Color Scheme
+    style A2 fill:#ff6b6b,color:#fff
+    style C2 fill:#ff6b6b,color:#fff
+    style E2 fill:#ff6b6b,color:#fff
+    style G2 fill:#ffd43b,color:#000
+    style H2 fill:#ffd43b,color:#000
+    style I2 fill:#ffd43b,color:#000
+    style J2 fill:#ffd43b,color:#000
+    style K2 fill:#ffd43b,color:#000
+    style L2 fill:#ffd43b,color:#000
+    style M2 fill:#51cf66,color:#fff
+    style N2 fill:#51cf66,color:#fff
+    style O2 fill:#51cf66,color:#fff
+    style P2 fill:#51cf66,color:#fff
+    style Q2 fill:#51cf66,color:#fff
+    style R2 fill:#51cf66,color:#fff
+    style S2 fill:#51cf66,color:#fff
+    style T2 fill:#51cf66,color:#fff
+    style U2 fill:#51cf66,color:#fff
+    style V2 fill:#51cf66,color:#fff
+    style W2 fill:#51cf66,color:#fff
+    style X2 fill:#51cf66,color:#fff
+    style B2 fill:#74c0fc,color:#fff
+    style D2 fill:#74c0fc,color:#fff
+    style F2 fill:#74c0fc,color:#fff
+    style Y2 fill:#74c0fc,color:#fff
+    style Z2 fill:#74c0fc,color:#fff
+    style AA2 fill:#74c0fc,color:#fff
+    style BB2 fill:#74c0fc,color:#fff
+    style CC2 fill:#74c0fc,color:#fff
+    style DD2 fill:#74c0fc,color:#fff
+    style EE2 fill:#74c0fc,color:#fff
+    style FF2 fill:#74c0fc,color:#fff
+    style GG2 fill:#74c0fc,color:#fff
+    style HH2 fill:#b197fc,color:#fff
+    style II2 fill:#b197fc,color:#fff
+    style JJ2 fill:#b197fc,color:#fff
+                    </div>
+            
+            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Plasma & Fuel Inputs
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Confinement Systems
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Nuclear Fusion Reactions
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
+                </div>
+            </div>
+            
+            <div class="figure-caption">
+                <strong>Figure 2.</strong> Nuclear Fusion Process. This physics process visualization demonstrates nuclear energy production. The flowchart shows plasma inputs, confinement systems, nuclear fusion reactions, intermediate processes, and final energy output.
+            </div>
+        </div>
+
+        <h2>3. Electromagnetic Wave Propagation</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Initial Setup
+    %% Input Conditions
+    A3[Electromagnetic Source] --> B3[Source Analysis]
+    C3[Medium Properties] --> D3[Medium Analysis]
+    E3[Boundary Conditions] --> F3[Boundary Definition]
+    %% Wave Generation
+    B3 --> G3[Electric Field Generation]
+    D3 --> H3[Dielectric Properties]
+    F3 --> I3[Interface Conditions]
+    %% Wave Propagation
+    G3 --> J3[Maxwell's Equations]
+    H3 --> K3[Wave Speed Calculation]
+    I3 --> L3[Reflection/Refraction]
+    %% Field Evolution
+    J3 --> M3[Electric Field E]
+    K3 --> N3[Magnetic Field B]
+    L3 --> O3[Wave Vector k]
+    %% Wave Dynamics
+    M3 --> P3[Field Oscillation]
+    N3 --> Q3[Energy Density]
+    O3 --> R3[Phase Velocity]
+    %% Energy Transport
+    P3 --> S3[Poynting Vector]
+    Q3 --> T3[Energy Conservation]
+    R3 --> U3[Group Velocity]
+    %% Wave Interaction
+    S3 --> V3[Energy Flux]
+    T3 --> W3[Power Transmission]
+    U3 --> X3[Dispersion Effects]
+    %% Detection
+    V3 --> Y3[Wave Detection]
+    W3 --> Z3[Signal Processing]
+    X3 --> AA3[Interference Patterns]
+    %% Final Results
+    Y3 --> BB3[Wave Amplitude]
+    Z3 --> CC3[Phase Information]
+    AA3 --> DD3[Interference Fringes]
+    %% Output
+    BB3 --> EE3[Electromagnetic Wave Detected]
+    CC3 --> FF3[Phase Information Extracted]
+    DD3 --> GG3[Interference Pattern Analyzed]
+    %% Styling - Physics Color Scheme
+    %% Styling - Biological Color Scheme
+    style A3 fill:#ff6b6b,color:#fff
+    style C3 fill:#ff6b6b,color:#fff
+    style E3 fill:#ff6b6b,color:#fff
+    style G3 fill:#ffd43b,color:#000
+    style H3 fill:#ffd43b,color:#000
+    style I3 fill:#ffd43b,color:#000
+    style J3 fill:#ffd43b,color:#000
+    style K3 fill:#ffd43b,color:#000
+    style L3 fill:#ffd43b,color:#000
+    style M3 fill:#51cf66,color:#fff
+    style N3 fill:#51cf66,color:#fff
+    style O3 fill:#51cf66,color:#fff
+    style P3 fill:#51cf66,color:#fff
+    style Q3 fill:#51cf66,color:#fff
+    style R3 fill:#51cf66,color:#fff
+    style S3 fill:#51cf66,color:#fff
+    style T3 fill:#51cf66,color:#fff
+    style U3 fill:#51cf66,color:#fff
+    style V3 fill:#51cf66,color:#fff
+    style W3 fill:#51cf66,color:#fff
+    style X3 fill:#51cf66,color:#fff
+    style B3 fill:#74c0fc,color:#fff
+    style D3 fill:#74c0fc,color:#fff
+    style F3 fill:#74c0fc,color:#fff
+    style Y3 fill:#74c0fc,color:#fff
+    style Z3 fill:#74c0fc,color:#fff
+    style AA3 fill:#74c0fc,color:#fff
+    style BB3 fill:#74c0fc,color:#fff
+    style CC3 fill:#74c0fc,color:#fff
+    style DD3 fill:#74c0fc,color:#fff
+    style EE3 fill:#74c0fc,color:#fff
+    style FF3 fill:#74c0fc,color:#fff
+    style GG3 fill:#74c0fc,color:#fff
+    style HH3 fill:#b197fc,color:#fff
+    style II3 fill:#b197fc,color:#fff
+    style JJ3 fill:#b197fc,color:#fff
+                    </div>
+            
+            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Source & Medium Inputs
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Electromagnetic Fields
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Wave Propagation
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
+                </div>
+            </div>
+            
+            <div class="figure-caption">
+                <strong>Figure 3.</strong> Electromagnetic Wave Propagation. This physics process visualization demonstrates electromagnetic wave dynamics. The flowchart shows source inputs, electromagnetic fields, wave propagation processes, intermediate calculations, and final detection results.
+            </div>
+        </div>
+
+        <h2>4. Thermodynamic Cycle Process</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Initial Setup
+    %% Input Conditions
+    A4[Heat Source] --> B4[Heat Supply]
+    C4[Working Fluid] --> D4[Fluid Properties]
+    E4[System Boundaries] --> F4[Boundary Definition]
+    %% Initial State
+    B4 --> G4[High Temperature Reservoir]
+    D4 --> H4[Fluid State Analysis]
+    F4 --> I4[System Isolation]
+    %% Isothermal Expansion
+    G4 --> J4[Heat Addition Q₁]
+    H4 --> K4[Volume Expansion]
+    I4 --> L4[Work Output W₁]
+    %% Adiabatic Expansion
+    J4 --> M4[Temperature Decrease]
+    K4 --> N4[Pressure Reduction]
+    L4 --> O4[Work Output W₂]
+    %% Isothermal Compression
+    M4 --> P4[Heat Rejection Q₂]
+    N4 --> Q4[Volume Compression]
+    O4 --> R4[Work Input W₃]
+    %% Adiabatic Compression
+    P4 --> S4[Temperature Increase]
+    Q4 --> T4[Pressure Increase]
+    R4 --> U4[Work Input W₄]
+    %% Cycle Completion
+    S4 --> V4[Return to Initial State]
+    T4 --> W4[System Reset]
+    U4 --> X4[Net Work Output]
+    %% Efficiency Calculation
+    V4 --> Y4[Cycle Efficiency η]
+    W4 --> Z4[Energy Conservation]
+    X4 --> AA4[Power Generation]
+    %% Final Results
+    Y4 --> BB4[Thermal Efficiency]
+    Z4 --> CC4[Energy Balance]
+    AA4 --> DD4[Mechanical Power]
+    %% Output
+    BB4 --> EE4[Thermodynamic Cycle Complete]
+    CC4 --> FF4[Energy Conversion Efficient]
+    DD4 --> GG4[Power Output Maximized]
+    %% Styling - Physics Color Scheme
+    %% Styling - Biological Color Scheme
+    style A4 fill:#ff6b6b,color:#fff
+    style C4 fill:#ff6b6b,color:#fff
+    style E4 fill:#ff6b6b,color:#fff
+    style G4 fill:#ffd43b,color:#000
+    style H4 fill:#ffd43b,color:#000
+    style I4 fill:#ffd43b,color:#000
+    style J4 fill:#ffd43b,color:#000
+    style K4 fill:#ffd43b,color:#000
+    style L4 fill:#ffd43b,color:#000
+    style M4 fill:#51cf66,color:#fff
+    style N4 fill:#51cf66,color:#fff
+    style O4 fill:#51cf66,color:#fff
+    style P4 fill:#51cf66,color:#fff
+    style Q4 fill:#51cf66,color:#fff
+    style R4 fill:#51cf66,color:#fff
+    style S4 fill:#51cf66,color:#fff
+    style T4 fill:#51cf66,color:#fff
+    style U4 fill:#51cf66,color:#fff
+    style V4 fill:#51cf66,color:#fff
+    style W4 fill:#51cf66,color:#fff
+    style X4 fill:#51cf66,color:#fff
+    style B4 fill:#74c0fc,color:#fff
+    style D4 fill:#74c0fc,color:#fff
+    style F4 fill:#74c0fc,color:#fff
+    style Y4 fill:#74c0fc,color:#fff
+    style Z4 fill:#74c0fc,color:#fff
+    style AA4 fill:#74c0fc,color:#fff
+    style BB4 fill:#74c0fc,color:#fff
+    style CC4 fill:#74c0fc,color:#fff
+    style DD4 fill:#74c0fc,color:#fff
+    style EE4 fill:#74c0fc,color:#fff
+    style FF4 fill:#74c0fc,color:#fff
+    style GG4 fill:#74c0fc,color:#fff
+    style HH4 fill:#b197fc,color:#fff
+    style II4 fill:#b197fc,color:#fff
+    style JJ4 fill:#b197fc,color:#fff
+                    </div>
+            
+            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Heat & Fluid Inputs
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Thermodynamic Systems
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Thermodynamic Processes
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
+                </div>
+            </div>
+            
+            <div class="figure-caption">
+                <strong>Figure 4.</strong> Thermodynamic Cycle Process. This physics process visualization demonstrates energy conversion cycles. The flowchart shows heat inputs, thermodynamic systems, thermodynamic processes, intermediate states, and final power output.
+            </div>
+        </div>
+
+        <h2>5. Particle Accelerator Process</h2>
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Initial Setup
+    %% Input Conditions
+    A5[Particle Source] --> B5[Source Analysis]
+    C5[Accelerating Fields] --> D5[Field Generation]
+    E5[Beam Optics] --> F5[Optics Setup]
+    %% Particle Preparation
+    B5 --> G5[Particle Generation]
+    D5 --> H5[Electric Field E]
+    F5 --> I5[Magnetic Field B]
+    %% Initial Acceleration
+    G5 --> J5[Particle Injection]
+    H5 --> K5[Linear Acceleration]
+    I5 --> L5[Beam Focusing]
+    %% Acceleration Process
+    J5 --> M5[Velocity Increase]
+    K5 --> N5[Energy Gain]
+    L5 --> O5[Beam Confinement]
+    %% Circular Motion
+    M5 --> P5[Centripetal Force]
+    N5 --> Q5[Relativistic Effects]
+    O5 --> R5[Orbital Motion]
+    %% Energy Build-up
+    P5 --> S5[Radius of Curvature]
+    Q5 --> T5[Mass Increase]
+    R5 --> U5[Angular Velocity]
+    %% Beam Dynamics
+    S5 --> V5[Beam Stability]
+    T5 --> W5[Energy Synchronization]
+    U5 --> X5[Revolution Frequency]
+    %% Collision Process
+    V5 --> Y5[Beam Crossing]
+    W5 --> Z5[Particle Collisions]
+    X5 --> AA5[Reaction Products]
+    %% Detection
+    Y5 --> BB5[Collision Detection]
+    Z5 --> CC5[Particle Tracking]
+    AA5 --> DD5[Energy Measurement]
+    %% Final Results
+    BB5 --> EE5[Collision Events]
+    CC5 --> FF5[Particle Trajectories]
+    DD5 --> GG5[Energy Distribution]
+    %% Output
+    EE5 --> HH5[Particle Accelerator Active]
+    FF5 --> II5[Beam Dynamics Analyzed]
+    GG5 --> JJ5[Physics Data Collected]
+    %% Styling - Physics Color Scheme
+    %% Styling - Biological Color Scheme
+    style A5 fill:#ff6b6b,color:#fff
+    style C5 fill:#ff6b6b,color:#fff
+    style E5 fill:#ff6b6b,color:#fff
+    style G5 fill:#ffd43b,color:#000
+    style H5 fill:#ffd43b,color:#000
+    style I5 fill:#ffd43b,color:#000
+    style J5 fill:#ffd43b,color:#000
+    style K5 fill:#ffd43b,color:#000
+    style L5 fill:#ffd43b,color:#000
+    style M5 fill:#51cf66,color:#fff
+    style N5 fill:#51cf66,color:#fff
+    style O5 fill:#51cf66,color:#fff
+    style P5 fill:#51cf66,color:#fff
+    style Q5 fill:#51cf66,color:#fff
+    style R5 fill:#51cf66,color:#fff
+    style S5 fill:#51cf66,color:#fff
+    style T5 fill:#51cf66,color:#fff
+    style U5 fill:#51cf66,color:#fff
+    style V5 fill:#51cf66,color:#fff
+    style W5 fill:#51cf66,color:#fff
+    style X5 fill:#51cf66,color:#fff
+    style B5 fill:#74c0fc,color:#fff
+    style D5 fill:#74c0fc,color:#fff
+    style F5 fill:#74c0fc,color:#fff
+    style Y5 fill:#74c0fc,color:#fff
+    style Z5 fill:#74c0fc,color:#fff
+    style AA5 fill:#74c0fc,color:#fff
+    style BB5 fill:#74c0fc,color:#fff
+    style CC5 fill:#74c0fc,color:#fff
+    style DD5 fill:#74c0fc,color:#fff
+    style EE5 fill:#74c0fc,color:#fff
+    style FF5 fill:#74c0fc,color:#fff
+    style GG5 fill:#74c0fc,color:#fff
+    style HH5 fill:#b197fc,color:#fff
+    style II5 fill:#b197fc,color:#fff
+    style JJ5 fill:#b197fc,color:#fff
+                    </div>
+            
+            <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Particle & Field Inputs
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Accelerating Fields
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Acceleration Processes
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
+                </div>
+            </div>
+            
+            <div class="figure-caption">
+                <strong>Figure 5.</strong> Particle Accelerator Process. This physics process visualization demonstrates particle acceleration mechanisms. The flowchart shows particle inputs, accelerating fields, acceleration processes, intermediate states, and final collision data.
+            </div>
+        </div>
+
+        <p><strong>Generated using the Programming Framework methodology</strong></p>
+        
+        <p>This collection demonstrates the computational nature of physical processes and systems</p>
+        
+        <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
+    </div>
+</body>
+</html> 

programming_framework_article.html

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+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+    <title>A Programming Framework for Complex Systems: From Biology to Mathematics</title>
+    <style>
+        body { font-family: 'Times New Roman', Times, serif; margin: 0; background: #ffffff; color: #000000; line-height: 1.6; font-size: 12pt; }
+        .container { max-width: 800px; margin: 0 auto; padding: 1.5rem; }
+        h1, h2, h3 { color: #000000; margin-top: 1.5rem; margin-bottom: 0.75rem; }
+        h1 { font-size: 18pt; text-align: center; }
+        h2 { font-size: 16pt; border-bottom: 2px solid #000; padding-bottom: 0.5rem; }
+        h3 { font-size: 14pt; }
+        p { margin-bottom: 1rem; text-align: justify; }
+        .figure { margin: 1rem 0; text-align: center; border: 1px solid #ccc; padding: 1rem; background: #f9f9f9; }
+        .figure-caption { margin-top: 1rem; font-style: italic; text-align: left; }
+        .mermaid { background: white; padding: 1rem; border-radius: 4px; }
+    </style>
+    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
+    <script>
+        mermaid.initialize({ startOnLoad: true, theme: 'default', flowchart: { useMaxWidth: true, htmlLabels: true } });
+    </script>
+</head>
+<body>
+    <div class="container">
+        <h1>A Programming Framework for Complex Systems: From Biology to Mathematics</h1>
+        
+        <div style="text-align: center; margin: 2rem 0; font-size: 14pt;">
+            <p><strong>Gary Welz</strong></p>
+            <p style="font-size: 12pt; color: #666; margin-top: 0.5rem;">
+                Retired Faculty Member<br>
+                John Jay College, CUNY (Department of Mathematics and Computer Science)<br>
+                Borough of Manhattan Community College, CUNY<br>
+                CUNY Graduate Center (New Media Lab)<br>
+                Email: gwelz@jjay.cuny.edu
+            </p>
+        </div>
+
+        <p><strong>Abstract.</strong> We present a systematic visualization methodology—the Programming Framework—for analyzing complex systems across multiple domains. Using Mermaid Markdown syntax and large language model (LLM) processing, we demonstrate the framework's application to representative biological and chemical systems. The methodology leverages text-based process descriptions to generate standardized flowchart representations, enabling systematic comparison and pattern recognition across traditionally separate disciplines. Analysis of 297 representative processes reveals common computational patterns that may transcend domain boundaries. The complete dataset and methodology are publicly available through the Genome Logic Modeling Project (GLMP) Hugging Face Space, serving as the primary evidence base for this methodology.</p>
+
+        <h2>Introduction</h2>
+        <p>Complex systems across biology, chemistry, and physics exhibit remarkable similarities in their organizational principles despite operating at vastly different scales and domains. Traditional analysis methods often remain siloed within specific disciplines, limiting our ability to identify common patterns and computational logic that govern system behavior. Here, we present the Programming Framework, a systematic methodology that translates complex system dynamics into standardized computational representations using Mermaid Markdown syntax and LLM processing.</p>
+
+        <p>The framework builds upon three decades of computational biology research, beginning with early explorations of the genome-as-program metaphor in the 1990s. The author's 1995 work on the β-galactosidase regulation system represented one of the first attempts to model genetic regulation using computational logic constructs, creating flowcharts that depicted biological processes as decision trees with conditional branches, feedback loops, and termination conditions. This early work, discussed on the bionet.genome.chromosome newsgroup with computational biologists including Robert Robbins of Johns Hopkins University, established foundational concepts that continue to influence modern computational biology.</p>
+
+        <p>The framework employs a visual programming language based on flowchart logic, where system components are categorized into five functional classes with domain-specific color coding. This color-coded system enables rapid identification of system architecture and computational logic patterns. The classification system bridges biological and chemical domains: biological catalysts include enzymes and regulatory proteins, while chemical catalysts include industrial catalysts and recovery systems; biological intermediates include metabolites and signaling molecules, while chemical intermediates include reaction species and process streams.</p>
+
+        <h2>Universal Color Scheme</h2>
+        <p>This document presents complex systems analyzed using the Programming Framework methodology. Each process is represented as a computational flowchart with standardized color coding: Red for triggers/inputs, Yellow for structures/objects, Green for processing/operations, Blue for intermediates/states, and Violet for products/outputs. Yellow nodes use black text for optimal readability, while all other colors use white text.</p>
+
+        <div style="background: #f8f9fa; padding: 1.5rem; border-radius: 8px; margin: 1.5rem 0; border-left: 4px solid #007bff;">
+            <h3 style="margin-top: 0; color: #007bff;">Universal Color Coding System</h3>
+            <div style="overflow-x: auto;">
+                <table style="width: 100%; border-collapse: collapse; margin: 1rem 0; background: white; border-radius: 8px; overflow: hidden; box-shadow: 0 2px 8px rgba(0,0,0,0.1);">
+                    <thead>
+                        <tr style="background: #007bff; color: white;">
+                            <th style="padding: 1rem; text-align: left; border: 1px solid #dee2e6; font-weight: 600;">Color Category</th>
+                            <th style="padding: 1rem; text-align: center; border: 1px solid #dee2e6; font-weight: 600;">Biology</th>
+                            <th style="padding: 1rem; text-align: center; border: 1px solid #dee2e6; font-weight: 600;">Chemistry</th>
+                            <th style="padding: 1rem; text-align: center; border: 1px solid #dee2e6; font-weight: 600;">Computer Science</th>
+                            <th style="padding: 1rem; text-align: center; border: 1px solid #dee2e6; font-weight: 600;">Physics</th>
+                            <th style="padding: 1rem; text-align: center; border: 1px solid #dee2e6; font-weight: 600;">Mathematics</th>
+                        </tr>
+                    </thead>
+                    <tbody>
+                        <tr style="background: rgba(255, 107, 107, 0.1);">
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; font-weight: 600; text-align: center;">
+                                <span style="width: 20px; height: 20px; border-radius: 4px; background: #ff6b6b; border: 1px solid #333; display: inline-block; margin-bottom: 0.5rem;"></span><br>
+                                Red<br><span style="font-size: 0.8em; font-weight: normal; color: #666;">(#ff6b6b)</span><br><span style="font-size: 0.8em; font-weight: normal; color: #666;">Triggers & Inputs</span>
+                            </td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Environmental signals<br>Nutrient availability<br>Stress conditions<br>Hormonal cues</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Reactant supply<br>Temperature<br>Pressure<br>Catalyst addition</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Input data<br>User commands<br>System parameters<br>External APIs</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Energy input<br>Force application<br>Field strength<br>Initial conditions</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Axioms<br>Given conditions<br>Initial values<br>Boundary conditions</td>
+                        </tr>
+                        <tr style="background: rgba(255, 212, 59, 0.1);">
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; font-weight: 600; text-align: center;">
+                                <span style="width: 20px; height: 20px; border-radius: 4px; background: #ffd43b; border: 1px solid #333; display: inline-block; margin-bottom: 0.5rem;"></span><br>
+                                Yellow<br><span style="font-size: 0.8em; font-weight: normal; color: #666;">(#ffd43b)</span><br><span style="font-size: 0.8em; font-weight: normal; color: #666;">Structures & Objects</span>
+                            </td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Enzymes<br>Receptor proteins<br>Regulatory complexes<br>Structural proteins</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Catalysts<br>Reaction vessels<br>Separation media<br>Analytical instruments</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Data structures<br>Algorithms<br>Functions<br>Classes</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Fields<br>Particles<br>Waves<br>Measurement devices</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Theorems<br>Methods<br>Formulas<br>Logical frameworks</td>
+                        </tr>
+                        <tr style="background: rgba(81, 207, 102, 0.1);">
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; font-weight: 600; text-align: center;">
+                                <span style="width: 20px; height: 20px; border-radius: 4px; background: #51cf66; border: 1px solid #333; display: inline-block; margin-bottom: 0.5rem;"></span><br>
+                                Green<br><span style="font-size: 0.8em; font-weight: normal; color: #666;">(#51cf66)</span><br><span style="font-size: 0.8em; font-weight: normal; color: #666;">Processing & Operations</span>
+                            </td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Metabolic reactions<br>Signal transduction<br>Gene expression<br>Protein synthesis</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Chemical reactions<br>Equilibrium shifts<br>Phase changes<br>Kinetic processes</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Algorithm execution<br>Data processing<br>Logical operations<br>Control flow</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Wave propagation<br>Quantum operations<br>Energy transfer<br>Force interactions</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Logical steps<br>Calculations<br>Proof construction<br>Deductive reasoning</td>
+                        </tr>
+                        <tr style="background: rgba(116, 192, 252, 0.1);">
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; font-weight: 600; text-align: center;">
+                                <span style="width: 20px; height: 20px; border-radius: 4px; background: #74c0fc; border: 1px solid #333; display: inline-block; margin-bottom: 0.5rem;"></span><br>
+                                Blue<br><span style="font-size: 0.8em; font-weight: normal; color: #666;">(#74c0fc)</span><br><span style="font-size: 0.8em; font-weight: normal; color: #666;">Intermediates & States</span>
+                            </td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Metabolites<br>Signaling molecules<br>Protein complexes<br>Regulatory states</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Reaction intermediates<br>Transition states<br>Product mixtures<br>Process streams</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Variables<br>Memory states<br>Function calls<br>Data transformations</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Quantum states<br>Energy levels<br>Wave functions<br>Measurement results</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Intermediate results<br>Sub-proofs<br>Calculated values<br>Logical states</td>
+                        </tr>
+                        <tr style="background: rgba(177, 151, 252, 0.1);">
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; font-weight: 600; text-align: center;">
+                                <span style="width: 20px; height: 20px; border-radius: 4px; background: #b197fc; border: 1px solid #333; display: inline-block; margin-bottom: 0.5rem;"></span><br>
+                                Violet<br><span style="font-size: 0.8em; font-weight: normal; color: #666;">(#b197fc)</span><br><span style="font-size: 0.8em; font-weight: normal; color: #666;">Products & Outputs</span>
+                            </td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Biomolecules<br>Cellular responses<br>Organismal behaviors<br>Population changes</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Final products<br>Reaction yields<br>Process outputs<br>Analytical results</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Program outputs<br>Computed results<br>System responses<br>User interfaces</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Measured quantities<br>Physical phenomena<br>Energy states<br>System behaviors</td>
+                            <td style="padding: 1rem; border: 1px solid #dee2e6; text-align: center;">Proven theorems<br>Mathematical results<br>Logical conclusions<br>Computed solutions</td>
+                        </tr>
+                    </tbody>
+                </table>
+            </div>
+            <div style="background: #fff3cd; padding: 1rem; border-radius: 6px; margin-top: 1rem; border-left: 4px solid #ffc107;">
+                <p style="margin: 0; font-size: 0.9em;"><strong>Note:</strong> Yellow nodes use black text for optimal readability, while all other colors use white text.</p>
+            </div>
+        </div>
+
+        <h2>Methodology</h2>
+        <p>The Programming Framework methodology involves systematic analysis of complex systems through the following steps:</p>
+
+        <div style="background: #e8f5e8; padding: 1.5rem; border-radius: 8px; margin: 1.5rem 0; border-left: 4px solid #28a745;">
+            <h3 style="margin-top: 0; color: #28a745;">Analysis Process</h3>
+            <ol style="margin: 0; padding-left: 1.5rem;">
+                <li><strong>System Identification:</strong> Identify the biological, chemical, or physical system to be analyzed</li>
+                <li><strong>Component Categorization:</strong> Classify system components into the five functional categories</li>
+                <li><strong>Flowchart Construction:</strong> Create Mermaid flowcharts with appropriate color coding</li>
+                <li><strong>Logic Verification:</strong> Verify computational logic and system dynamics</li>
+                <li><strong>Cross-Disciplinary Comparison:</strong> Identify patterns across different domains</li>
+            </ol>
+        </div>
+
+        <div style="background: #fff3cd; padding: 1.5rem; border-radius: 8px; margin: 1.5rem 0; border-left: 4px solid #ffc107;">
+            <h3 style="margin-top: 0; color: #856404;">Sample Analysis Prompt</h3>
+            <p style="margin: 0; font-family: monospace; background: #f8f9fa; padding: 1rem; border-radius: 4px; border: 1px solid #dee2e6;">
+                "Analyze the [system name] using the Programming Framework methodology. Create a Mermaid Markdown or mmd file that will enable the creation in html of a computational flowchart showing how environmental inputs are processed through regulatory mechanisms to produce specific outputs. Use the universal color scheme: Red for triggers/inputs, Yellow for structures/catalysts, Green for processing operations, Blue for intermediates, and Violet for products. Include a discipline-specific color key beneath the flowchart."
+            </p>
+        </div>
+
+        <div style="background: #d1ecf1; padding: 1.5rem; border-radius: 8px; margin: 1.5rem 0; border-left: 4px solid #17a2b8;">
+            <h3 style="margin-top: 0; color: #0c5460;">Key Applications</h3>
+            <ul style="margin: 0; padding-left: 1.5rem;">
+                <li><strong>Biological Systems:</strong> Gene regulation, metabolic pathways, signal transduction</li>
+                <li><strong>Chemical Processes:</strong> Catalytic reactions, equilibrium systems, kinetic analysis</li>
+                <li><strong>Physical Systems:</strong> Quantum processes, thermodynamic cycles, wave phenomena</li>
+                <li><strong>Computer Science:</strong> Algorithm analysis, data structures, computational complexity</li>
+                <li><strong>Mathematical Systems:</strong> Proof construction, logical frameworks, theorem development</li>
+            </ul>
+        </div>
+
+        <h2>Technical Foundation</h2>
+        <p>The Programming Framework builds upon Mermaid Markdown (MMD), a text-based diagram generation syntax developed by Knut Sveidqvist in 2014. MMD enables the creation of complex flowcharts and diagrams from simple text descriptions, similar to how Markdown simplifies text formatting. This technical innovation was critical for our methodology, as it allows for:</p>
+
+        <div style="background: #f8f9fa; padding: 1.5rem; border-radius: 8px; margin: 1.5rem 0; border-left: 4px solid #6c757d;">
+            <h3 style="margin-top: 0; color: #495057;">Mermaid Markdown Capabilities</h3>
+            <ol style="margin: 0; padding-left: 1.5rem;">
+                <li><strong>Text-to-Diagram Conversion:</strong> Process descriptions from scientific literature can be directly converted into visual representations</li>
+                <li><strong>Standardized Syntax:</strong> Consistent formatting across different systems and domains</li>
+                <li><strong>Automated Generation:</strong> LLMs can rapidly process text descriptions and generate MMD code</li>
+                <li><strong>Cross-Platform Compatibility:</strong> MMD integrates with documentation platforms and can be rendered in multiple formats</li>
+                <li><strong>Automatic Color Coding:</strong> Canvas automatically derives color categories from MMD syntax, ensuring consistent visual representation</li>
+            </ol>
+        </div>
+
+        <h2>Historical Evolution: From 1995 to 2025</h2>
+        <p>The Programming Framework represents the culmination of a 30-year evolution in computational biology visualization. The author's 1995 β-galactosidase flowchart, created using manual tools and requiring months of research, represented one of the first attempts to model genetic regulation using computational logic constructs. This early work established the conceptual foundation for treating biological processes as executable programs with conditional logic, feedback loops, and decision points.</p>
+
+        <p>The transformation from 1995 to 2025 demonstrates the democratization of computational biology through technological convergence. What once required months of manual research and specialized tools can now be accomplished in hours through the combination of Mermaid Markdown syntax, LLM processing, and human biological insight. This evolution enables systematic analysis of hundreds of biological processes rather than individual case studies, representing a fundamental shift in the scale and scope of computational biology research.</p>
+
+        <div style="background: #fff3cd; padding: 1.5rem; border-radius: 8px; margin: 1.5rem 0; border-left: 4px solid #ffc107;">
+            <h3 style="margin-top: 0; color: #856404;">Evolution Timeline</h3>
+            <div style="display: grid; grid-template-columns: 1fr 1fr; gap: 1rem; margin: 1rem 0;">
+                <div style="background: #fff; padding: 1rem; border-radius: 6px; border: 1px solid #dee2e6;">
+                    <h4 style="margin-top: 0; color: #856404;">1995: Manual Creation</h4>
+                    <ul style="margin: 0; padding-left: 1rem; font-size: 0.9em;">
+                        <li>Months of research and reading</li>
+                        <li>Manual flowchart creation with Inspiration</li>
+                        <li>Single process analysis</li>
+                        <li>Community discussion on bionet.genome.chromosome</li>
+                        <li>Foundation for computational biology</li>
+                    </ul>
+                </div>
+                <div style="background: #fff; padding: 1rem; border-radius: 6px; border: 1px solid #dee2e6;">
+                    <h4 style="margin-top: 0; color: #856404;">2025: AI-Assisted Analysis</h4>
+                    <ul style="margin: 0; padding-left: 1rem; font-size: 0.9em;">
+                        <li>Hours of AI-assisted processing</li>
+                        <li>Automated Mermaid Markdown generation</li>
+                        <li>Systematic analysis of 297+ processes</li>
+                        <li>Cross-disciplinary pattern recognition</li>
+                        <li>Universal computational framework</li>
+                    </ul>
+                </div>
+            </div>
+        </div>
+
+        <h2>Dataset and Evidence Base</h2>
+        <p>We analyzed a comprehensive dataset of biological processes spanning multiple organisms and systems: 110 processes from <em>Saccharomyces cerevisiae</em> (yeast) covering DNA replication, cell cycle control, signal transduction, energy metabolism, and stress responses; multiple processes from <em>Escherichia coli</em> including DNA replication, gene regulation, central metabolism, motility, and specialized systems like the lac operon; and advanced systems including photosynthesis, bacterial sporulation, circadian clocks, and viral decision switches.</p>
+
+        <p>Each process was translated into the Programming Framework format using LLM processing of published scientific descriptions, enabling systematic pattern identification and computational logic analysis across diverse biological systems. The complete dataset comprising 297 total processes across 36 individual collections is publicly available through the Genome Logic Modeling Project (GLMP) Hugging Face Space, serving as the primary evidence base for this methodology.</p>
+
+        <h2>Representative Applications</h2>
+
+        <h3>Case Study: β-Galactosidase Analysis (2025)</h3>
+        <p>The β-galactosidase system represents one of the most well-characterized examples of genetic regulation in molecular biology. Using modern tools and AI assistance, we can now create sophisticated and detailed visualizations that demonstrate the full computational complexity of the lac operon system. This represents the current state of the Programming Framework methodology, showing how environmental inputs (lactose, glucose, energy status) are processed through regulatory logic gates to control gene expression and metabolic pathways:</p>
+
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Initial Setup
+    %% Environmental Inputs
+    A[Lactose in Environment] --> B[Lactose Transport]
+    C[Glucose in Environment] --> D[Glucose Transport]
+    E[Low Energy Status] --> F[Energy Stress Signal]
+    %% Transport Processes
+    B --> G[Lactose Permease LacY]
+    G --> H[Lactose Inside Cell]
+    H --> I[Lactose Availability]
+    D --> J[Glucose Transporters]
+    J --> K[Glucose Inside Cell]
+    K --> L[High Glucose Status]
+    %% Regulatory Logic Gates
+    I --> M{Is Lactose Present?}
+    L --> N{Is Glucose Present?}
+    F --> O{Is Energy Low?}
+    %% Repressor Logic
+    M -->|No| P[Lac Repressor Active]
+    M -->|Yes| Q[Lac Repressor Inactive]
+    P --> R[Repressor Binds Operator]
+    R --> S[Transcription Blocked]
+    Q --> T[Repressor Released]
+    T --> U[Operator Free]
+    %% CAP-cAMP Logic
+    N -->|Yes| V[Low cAMP Levels]
+    N -->|No| W[High cAMP Levels]
+    O --> W
+    W --> X[cAMP-CAP Complex]
+    V --> Y[No CAP Binding]
+    X --> Z[CAP Binds Promoter]
+    Y --> AA[No CAP Binding]
+    %% Transcription Control
+    U --> BB{Operator Free?}
+    Z --> CC{CAP Bound?}
+    BB -->|Yes| DD[RNA Polymerase Binding]
+    BB -->|No| EE[Transcription Blocked]
+    CC -->|Yes| FF[Strong Transcription]
+    CC -->|No| GG[Weak Transcription]
+    %% Gene Expression
+    DD --> HH[Transcription Initiation]
+    FF --> II[lacZ mRNA Synthesis]
+    FF --> JJ[lacY mRNA Synthesis]
+    FF --> KK[lacA mRNA Synthesis]
+    %% Protein Synthesis
+    II --> LL[LacZ Translation]
+    JJ --> MM[LacY Translation]
+    KK --> NN[LacA Translation]
+    %% Functional Proteins
+    LL --> OO[Beta-Galactosidase Enzyme]
+    MM --> PP[Lactose Permease]
+    NN --> QQ[Galactoside Acetyltransferase]
+    %% Metabolic Functions
+    OO --> RR[Lactose Hydrolysis]
+    PP --> SS[Lactose Transport]
+    QQ --> TT[Galactoside Modification]
+    %% Final Products
+    RR --> UU[Glucose + Galactose]
+    SS --> VV[Lactose Uptake]
+    TT --> WW[Detoxification]
+    %% Energy Production
+    UU --> XX[Glycolysis]
+    VV --> YY[Lactose Processing]
+    WW --> ZZ[Cell Protection]
+    %% System Equilibrium
+    XX --> AAA[Energy Production]
+    YY --> BBB[Lactose Consumption]
+    ZZ --> CCC[Cell Survival]
+    %% Feedback Control
+    AAA --> DDD[Energy Status Improved]
+    BBB --> EEE[Lactose Depletion]
+    CCC --> FFF[Reduced Energy Stress]
+    %% Dynamic Equilibrium
+    DDD --> GGG[Reduced Lactose Signal]
+    EEE --> HHH[Maintained Homeostasis]
+    FFF --> III[System Equilibrium]
+    %% Styling - Biological Color Scheme
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style G fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#ffd43b,color:#000
+    style X fill:#ffd43b,color:#000
+    style OO fill:#ffd43b,color:#000
+    style PP fill:#ffd43b,color:#000
+    style QQ fill:#ffd43b,color:#000
+    style B fill:#51cf66,color:#fff
+    style D fill:#51cf66,color:#fff
+    style F fill:#51cf66,color:#fff
+    style H fill:#51cf66,color:#fff
+    style K fill:#51cf66,color:#fff
+    style R fill:#51cf66,color:#fff
+    style T fill:#51cf66,color:#fff
+    style W fill:#51cf66,color:#fff
+    style Z fill:#51cf66,color:#fff
+    style DD fill:#51cf66,color:#fff
+    style FF fill:#51cf66,color:#fff
+    style HH fill:#51cf66,color:#fff
+    style II fill:#51cf66,color:#fff
+    style JJ fill:#51cf66,color:#fff
+    style KK fill:#51cf66,color:#fff
+    style LL fill:#51cf66,color:#fff
+    style MM fill:#51cf66,color:#fff
+    style NN fill:#51cf66,color:#fff
+    style RR fill:#51cf66,color:#fff
+    style SS fill:#51cf66,color:#fff
+    style TT fill:#51cf66,color:#fff
+    style XX fill:#51cf66,color:#fff
+    style YY fill:#51cf66,color:#fff
+    style ZZ fill:#51cf66,color:#fff
+    style DDD fill:#51cf66,color:#fff
+    style EEE fill:#51cf66,color:#fff
+    style FFF fill:#51cf66,color:#fff
+    style I fill:#74c0fc,color:#fff
+    style L fill:#74c0fc,color:#fff
+    style U fill:#74c0fc,color:#fff
+    style AA fill:#74c0fc,color:#fff
+    style UU fill:#74c0fc,color:#fff
+    style VV fill:#74c0fc,color:#fff
+    style WW fill:#74c0fc,color:#fff
+    style AAA fill:#74c0fc,color:#fff
+    style BBB fill:#74c0fc,color:#fff
+    style CCC fill:#74c0fc,color:#fff
+    style GGG fill:#74c0fc,color:#fff
+    style HHH fill:#74c0fc,color:#fff
+    style III fill:#74c0fc,color:#fff
+    style M fill:#b197fc,color:#fff
+    style N fill:#b197fc,color:#fff
+    style O fill:#b197fc,color:#fff
+    style BB fill:#b197fc,color:#fff
+    style CC fill:#b197fc,color:#fff
+    style EE fill:#b197fc,color:#fff
+    style GG fill:#b197fc,color:#fff
+                    </div>
+            <div style="display: grid; grid-template-columns: repeat(auto-fit,minmax(140px,1fr)); gap: .5rem 1rem; margin: 1rem 0 0; font-size: 10pt; color: #333;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Triggers & Conditions
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Catalysts & Enzymes
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Chemical Processing
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
+                </div>
+            </div>
+            <div class="figure-caption">
+                <strong>Figure 1.</strong> 2025 β-Galactosidase Regulation Flowchart - Current Framework. This comprehensive computational flowchart demonstrates the Programming Framework's ability to represent complex genetic regulatory networks with complete feedback loops and system equilibrium. The visualization shows environmental inputs, regulatory complexes and enzymes, intermediate states and logic gates, functional outputs, and key regulatory proteins, revealing the sophisticated computational logic underlying lactose metabolism in E. coli including CAP-cAMP regulation, protein synthesis, and dynamic feedback control.
+            </div>
+        </div>
+
+        <h3>Case Study: Algorithm Execution Analysis</h3>
+        <p>To demonstrate the framework's applicability to computer science, we applied the methodology to algorithm execution, specifically a sorting algorithm. This example shows how the same computational logic can be applied to fundamental computer science processes:</p>
+
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    A[Input Array] --> B[Data Validation]
+    B --> C[Algorithm Selection]
+    C --> D[QuickSort Algorithm]
+    D --> E[Pivot Selection]
+    E --> F[Partition Operation]
+    F --> G[Recursive Calls]
+    G --> H[Sub-array Sorting]
+    H --> I[Array Merging]
+    I --> J[Sorted Output]
+    
+    %% Error Handling
+    B --> K[Valid Input Check]
+    K --> L[Error Handling]
+    K --> C
+    
+    %% Performance Analysis
+    J --> M[Performance Analysis]
+    M --> N[Time Complexity Analysis]
+    M --> O[Space Complexity Analysis]
+    
+    %% Styling
+    style A fill:#ff6b6b,color:#fff
+    style J fill:#b197fc,color:#fff
+    style N fill:#b197fc,color:#fff
+    style O fill:#b197fc,color:#fff
+    
+    style B fill:#ffd43b,color:#000
+    style C fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style E fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style G fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style L fill:#ffd43b,color:#000
+    style M fill:#ffd43b,color:#000
+    
+    style K fill:#74c0fc,color:#fff
+            </div>
+            <div style="display: grid; grid-template-columns: repeat(auto-fit,minmax(140px,1fr)); gap: .5rem 1rem; margin: 1rem 0 0; font-size: 10pt; color: #333;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Inputs & Data
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Data Structures & Arrays
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Operations & Algorithms
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>States & Variables
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Output & Results
+                </div>
+            </div>
+            <div class="figure-caption">
+                <strong>Figure 2.</strong> QuickSort Algorithm Process. This computer science process visualization demonstrates the computational logic of the QuickSort algorithm. The flowchart shows input data and parameters, data structures and arrays, algorithmic operations and comparisons, intermediate states and recursive calls, and final sorted output, revealing the computational logic underlying algorithm execution and complexity analysis.
+            </div>
+        </div>
+
+        <h3>Case Study: Water Electrolysis Analysis</h3>
+        <p>To demonstrate the framework's applicability beyond biological systems, we applied the methodology to water electrolysis, a fundamental chemical process. This example shows how the same computational logic can be applied to physical chemistry systems:</p>
+
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Initial Setup
+    %% Input Materials
+    A[Water Supply] --> B[Water Purification]
+    C[Electrical Power] --> D[Power Regulation]
+    E[Electrolyte Supply] --> F[Electrolyte Preparation]
+    %% Material Preparation
+    B --> G[Purified Water]
+    D --> H[Controlled Voltage]
+    F --> I[Electrolyte Solution]
+    %% Electrolysis Setup
+    G --> J[Anode Compartment]
+    G --> K[Cathode Compartment]
+    I --> L[Electrolyte Circulation]
+    H --> M[Electron Flow]
+    %% Anode Reactions
+    J --> N[Water Oxidation at Anode]
+    N --> O[Oxygen Gas Evolution]
+    N --> P[Proton Release]
+    N --> Q[Electron Transfer]
+    %% Cathode Reactions
+    K --> R[Proton Reduction at Cathode]
+    R --> S[Hydrogen Gas Evolution]
+    R --> T[Electron Consumption]
+    %% Gas Collection
+    O --> U[Oxygen Collection]
+    S --> V[Hydrogen Collection]
+    %% Gas Processing
+    U --> W[Oxygen Drying]
+    V --> X[Hydrogen Drying]
+    W --> Y[Oxygen Compression]
+    X --> Z[Hydrogen Compression]
+    %% Final Products
+    Y --> AA[Compressed Oxygen Gas]
+    Z --> BB[Compressed Hydrogen Gas]
+    %% System Monitoring
+    M --> CC[Current Monitoring]
+    L --> DD[Temperature Control]
+    %% Process Control
+    CC --> EE[Voltage Regulation]
+    DD --> FF[Pressure Monitoring]
+    %% Efficiency Analysis
+    EE --> GG[Energy Efficiency]
+    FF --> HH[Process Optimization]
+    %% Final Output
+    GG --> II[Electrolysis Process Complete]
+    HH --> JJ[Hydrogen Production Optimized]
+    %% Styling - Chemistry Color Scheme
+    %% Styling - Biological Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    style B fill:#ffd43b,color:#000
+    style D fill:#ffd43b,color:#000
+    style F fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K fill:#ffd43b,color:#000
+    style N fill:#ffd43b,color:#000
+    style R fill:#ffd43b,color:#000
+    style G fill:#51cf66,color:#fff
+    style H fill:#51cf66,color:#fff
+    style I fill:#51cf66,color:#fff
+    style L fill:#51cf66,color:#fff
+    style M fill:#51cf66,color:#fff
+    style O fill:#51cf66,color:#fff
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style S fill:#51cf66,color:#fff
+    style T fill:#51cf66,color:#fff
+    style U fill:#51cf66,color:#fff
+    style V fill:#51cf66,color:#fff
+    style W fill:#51cf66,color:#fff
+    style X fill:#51cf66,color:#fff
+    style Y fill:#51cf66,color:#fff
+    style Z fill:#51cf66,color:#fff
+    style CC fill:#51cf66,color:#fff
+    style DD fill:#51cf66,color:#fff
+    style EE fill:#51cf66,color:#fff
+    style FF fill:#51cf66,color:#fff
+    style GG fill:#51cf66,color:#fff
+    style HH fill:#51cf66,color:#fff
+    style AA fill:#74c0fc,color:#fff
+    style BB fill:#74c0fc,color:#fff
+    style II fill:#74c0fc,color:#fff
+    style JJ fill:#74c0fc,color:#fff
+    style CC fill:#b197fc,color:#fff
+    style DD fill:#b197fc,color:#fff
+    style EE fill:#b197fc,color:#fff
+    style FF fill:#b197fc,color:#fff
+                    </div>
+            <div style="display: grid; grid-template-columns: repeat(auto-fit,minmax(140px,1fr)); gap: .5rem 1rem; margin: 1rem 0 0; font-size: 10pt; color: #333;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Reactants & Conditions
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Catalysts & Enzymes
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Chemical Reactions
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
+                </div>
+            </div>
+            <div class="figure-caption">
+                <strong>Figure 3.</strong> Water Electrolysis Process Flowchart. This detailed chemical process visualization demonstrates the framework's cross-disciplinary applicability. The flowchart shows electrical inputs, electrode catalysts, intermediate reactions, and gas products, revealing the computational logic of electrochemical water splitting with comprehensive process control and optimization.
+            </div>
+        </div>
+
+        <h3>Case Study: Quantum Tunneling Analysis</h3>
+        <p>To demonstrate the framework's applicability to fundamental physics, we applied the methodology to quantum tunneling, a phenomenon where particles can pass through classically forbidden energy barriers. This example shows how the same computational logic can be applied to quantum mechanical systems:</p>
+
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    %% Initial Conditions
+    A[Particle Energy E] --> B[Energy Assessment]
+    C[Barrier Height V₀] --> D[Barrier Analysis]
+    E[Barrier Width a] --> F[Geometric Constraints]
+    
+    %% Quantum State Preparation
+    B --> G[Wave Function Initialization]
+    D --> H[Potential Energy Profile]
+    F --> I[Spatial Boundary Conditions]
+    
+    %% Wave Function Evolution
+    G --> J[Incident Wave Function ψ₁]
+    H --> K[Barrier Region ψ₂]
+    I --> L[Transmitted Wave Function ψ₃]
+    
+    %% Quantum Processing
+    J --> M[Wave Function Matching]
+    K --> N[Exponential Decay in Barrier]
+    L --> O[Transmission Coefficient Calculation]
+    
+    %% Quantum State Analysis
+    M --> P[Boundary Condition Equations]
+    N --> Q[Quantum Amplitude Processing]
+    O --> R[Probability Density Analysis]
+    
+    %% Transmission Calculation
+    P --> S[Wave Function Continuity]
+    Q --> T[Quantum Interference Effects]
+    R --> U[Transmission Probability T]
+    
+    %% Classical vs Quantum Logic
+    S --> V{Classical Prediction}
+    T --> W{Quantum Reality}
+    U --> X[Measured Transmission]
+    
+    %% Decision Points
+    V -->|E < V₀: T = 0| Y[Classical Forbidden]
+    W -->|E < V₀: T > 0| Z[Quantum Tunneling]
+    X --> AA[Particle Detection Beyond Barrier]
+    
+    %% Measurement and Detection
+    Y --> BB[Classical Prediction Failure]
+    Z --> CC[Quantum Tunneling Success]
+    AA --> DD[Energy Verification]
+    
+    %% Energy Conservation
+    BB --> EE[Wave Function Collapse]
+    CC --> FF[Final Particle State]
+    DD --> GG[Energy Conservation Check]
+    
+    %% Final Results
+    EE --> HH[Measurement Complete]
+    FF --> II[Quantum Effect Confirmed]
+    GG --> JJ[Energy Conservation Verified]
+    
+    %% Styling - Physics Color Scheme
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    
+    style G fill:#ffd43b,color:#000
+    style H fill:#ffd43b,color:#000
+    style I fill:#ffd43b,color:#000
+    style J fill:#ffd43b,color:#000
+    style K fill:#ffd43b,color:#000
+    style L fill:#ffd43b,color:#000
+    
+    style B fill:#51cf66,color:#fff
+    style D fill:#51cf66,color:#fff
+    style F fill:#51cf66,color:#fff
+    style M fill:#51cf66,color:#fff
+    style N fill:#51cf66,color:#fff
+    style O fill:#51cf66,color:#fff
+    style P fill:#51cf66,color:#fff
+    style Q fill:#51cf66,color:#fff
+    style R fill:#51cf66,color:#fff
+    style S fill:#51cf66,color:#fff
+    style T fill:#51cf66,color:#fff
+    style U fill:#51cf66,color:#fff
+    
+    style V fill:#74c0fc,color:#fff
+    style W fill:#74c0fc,color:#fff
+    style X fill:#74c0fc,color:#fff
+    style Y fill:#74c0fc,color:#fff
+    style Z fill:#74c0fc,color:#fff
+    style AA fill:#74c0fc,color:#fff
+    style BB fill:#74c0fc,color:#fff
+    style CC fill:#74c0fc,color:#fff
+    style DD fill:#74c0fc,color:#fff
+    style EE fill:#74c0fc,color:#fff
+    style FF fill:#74c0fc,color:#fff
+    style GG fill:#74c0fc,color:#fff
+    
+    style HH fill:#b197fc,color:#fff
+    style II fill:#b197fc,color:#fff
+    style JJ fill:#b197fc,color:#fff
+            </div>
+            <div style="display: grid; grid-template-columns: repeat(auto-fit,minmax(140px,1fr)); gap: .5rem 1rem; margin: 1rem 0 0; font-size: 10pt; color: #333;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Triggers & Conditions
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Wave Functions & Fields
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Quantum Processing
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Products
+                </div>
+            </div>
+            <div class="figure-caption">
+                <strong>Figure 4.</strong> Quantum Tunneling Process Flowchart. This physics process visualization demonstrates the framework's applicability to quantum mechanical systems. The flowchart shows energy inputs, wave functions and fields, quantum processing operations, intermediate calculations, and final measurement outcomes, revealing the computational logic underlying quantum tunneling phenomena.
+            </div>
+        </div>
+
+        <h3>Case Study: Mathematical Proof Tree Analysis</h3>
+        <p>To demonstrate the framework's applicability to pure mathematics, we applied the methodology to mathematical proof construction, a fundamental process in mathematical logic. This example shows how the same computational logic can be applied to formal mathematical reasoning. The framework could similarly be applied to algorithm analysis, group theory operations, calculus processes, and other mathematical domains:</p>
+
+        <div class="figure">
+            <div class="mermaid">
+graph TD
+    A[Peano Axioms] --> B[Axiom Processing]
+    C[Given n in Natural Numbers] --> D[Input Validation]
+    E[Goal: Prove P of n] --> F[Target Identification]
+    
+    B --> G[Mathematical Universe Setup]
+    D --> H[Variable Declaration]
+    F --> I[Proof Strategy Selection]
+    
+    G --> J[Induction Hypothesis P of k]
+    H --> K[Base Case Analysis]
+    I --> L[Inductive Step Planning]
+    
+    K --> M[P of 0 Verification]
+    M --> N[Base Case Success]
+    N --> O[Induction Foundation]
+    
+    L --> P[Assume P of k for k in Natural Numbers]
+    P --> Q[Show P of k plus 1 follows]
+    Q --> R[Inductive Step Execution]
+    
+    R --> S[Algebraic Manipulation]
+    S --> T[Logical Deduction]
+    T --> U[Theorem Application]
+    
+    U --> V[Sub-proof Construction]
+    V --> W[Lemma Application]
+    W --> X[Contradiction Analysis]
+    
+    X --> Y[Logical Consistency Check]
+    Y --> Z[Mathematical Rigor Verification]
+    Z --> AA[Proof Completeness Assessment]
+    
+    AA --> BB[Proof Complete Check]
+    BB --> CC[Identify Gap]
+    BB --> DD[Proof Validated]
+    
+    CC --> EE[Additional Lemma Needed]
+    EE --> FF[Sub-proof Construction]
+    FF --> GG[Gap Resolution]
+    GG --> Y
+    
+    DD --> HH[Theorem P of n Proven]
+    HH --> II[Mathematical Truth Established]
+    II --> JJ[Proof Tree Complete]
+    
+    %% Styling
+    style A fill:#ff6b6b,color:#fff
+    style C fill:#ff6b6b,color:#fff
+    style E fill:#ff6b6b,color:#fff
+    
+    style J fill:#ffd43b,color:#000
+    style P fill:#ffd43b,color:#000
+    style Q fill:#ffd43b,color:#000
+    style S fill:#51cf66,color:#fff
+    style T fill:#51cf66,color:#fff
+    style U fill:#51cf66,color:#fff
+    style V fill:#51cf66,color:#fff
+    style W fill:#51cf66,color:#fff
+    style X fill:#51cf66,color:#fff
+    
+    style B fill:#74c0fc,color:#fff
+    style D fill:#74c0fc,color:#fff
+    style F fill:#74c0fc,color:#fff
+    style G fill:#74c0fc,color:#fff
+    style H fill:#74c0fc,color:#fff
+    style I fill:#74c0fc,color:#fff
+    style K fill:#74c0fc,color:#fff
+    style L fill:#74c0fc,color:#fff
+    style M fill:#74c0fc,color:#fff
+    style N fill:#74c0fc,color:#fff
+    style O fill:#74c0fc,color:#fff
+    style R fill:#74c0fc,color:#fff
+    style Y fill:#74c0fc,color:#fff
+    style Z fill:#74c0fc,color:#fff
+    style AA fill:#74c0fc,color:#fff
+    style BB fill:#74c0fc,color:#fff
+    style CC fill:#74c0fc,color:#fff
+    style DD fill:#74c0fc,color:#fff
+    style EE fill:#74c0fc,color:#fff
+    style FF fill:#74c0fc,color:#fff
+    style GG fill:#74c0fc,color:#fff
+    
+    style HH fill:#b197fc,color:#fff
+    style II fill:#b197fc,color:#fff
+    style JJ fill:#b197fc,color:#fff
+            </div>
+            <div style="display: grid; grid-template-columns: repeat(auto-fit,minmax(140px,1fr)); gap: .5rem 1rem; margin: 1rem 0 0; font-size: 10pt; color: #333;">
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ff6b6b;"></span>Axioms & Assumptions
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#ffd43b;"></span>Logical Structures & Hypotheses
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#51cf66;"></span>Deductions & Theorem Applications
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#74c0fc;"></span>Intermediates
+                </div>
+                <div style="display:inline-flex; align-items:center; gap:.5rem; padding:.25rem .5rem; border-radius: 999px; border: 1px solid rgba(0,0,0,.08); background:#fff;">
+                    <span style="width: 12px; height: 12px; border-radius: 2px; border:1px solid rgba(0,0,0,.15); background:#b197fc;"></span>Conclusions
+                </div>
+            </div>
+            <div class="figure-caption">
+                <strong>Figure 5.</strong> Mathematical Induction Proof Process. This mathematics process visualization demonstrates formal mathematical reasoning. The flowchart shows axioms and given conditions, logical structures and hypotheses, deduction steps and theorem applications, intermediate calculations and sub-proofs, and final proven theorems, revealing the computational logic underlying mathematical proof construction.
+            </div>
+        </div>
+
+        <h2>Conclusion</h2>
+        <p>The Programming Framework represents a systematic approach to complex system visualization that bridges traditional disciplinary boundaries. By providing a standardized language for describing system dynamics, the framework enables systematic comparison and pattern recognition across diverse domains.</p>
+
+        <p>The successful application to both biological networks and industrial chemical processes demonstrates the framework's potential for cross-disciplinary analysis. Future work will extend the framework to additional domains, develop automated analysis tools, and explore applications in synthetic biology and systems engineering.</p>
+
+        <p>This methodology contributes to the development of unified approaches to complex systems, where common computational principles can be identified and applied across traditionally separate disciplines. The framework's accessibility and standardization make it a valuable tool for researchers, educators, and students working across the boundaries of biology, chemistry, and computational science.</p>
+    </div>
+</body>
+</html>

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