Interactive visual explorations of Bioinformatics & Computational Biology concepts.
View Portfolio → bushra-khan49.github.io/Portfolio-Projects
| Topic | Title | Live Link |
|---|---|---|
| Domain 1 · Topic 0 | The DNA | Open → |
| Domain 1 · Topic 1 | Replication | Open → |
| Domain 1 · Topic 2 | Fidelity Safeguards | Open → |
| Domain 1 · Topic 3 | Okazaki Fragments | Open → |
| Domain 1 · Topic 4 | Thermodynamics of Fidelity | Open → |
| Domain 1 · Topic 5 | The Physics of Base Pairing | Open → |
An interactive, scroll-driven 3D visualization covering:
- DNA Primary Structure & Nucleotides
- Purines vs Pyrimidines (with RNA/Uracil comparison)
- Base Pairing & Hydrogen Bonds
- Antiparallel Strands & Directionality
- Chromatin Packaging & Histone H1
- Major & Minor Grooves (labeled)
- Bioinformatics Applications (connected to structural biology)
An interactive visualizer explaining the molecular machinery and mechanics of DNA replication:
- The Replication Machinery: Helicase, Primase, Polymerase, Ligase, Topoisomerase
- Mechanics: Semi-conservative replication & Bidirectional forks
- Directionality: 5' → 3' synthesis and the 3'-OH requirement
- Strand Asymmetry: Leading vs Lagging strand (Okazaki fragments)
- Loop-and-Release: How the replisome copies both strands simultaneously
- Bioinformatics: Connecting replication mechanics to read mapping, variant calling, and mutation models
An interactive visualizer exploring DNA error prevention, proofreading, and mismatch repair:
- Chemistry Limitations: Why hydrogen bonding alone only gives 1 error per 100-1000 bases.
- Layer 1 (Presynthetic): Active-site geometry, induced fit, and preventing incorrect bonding.
- Layer 2 (Proofreading): 3' → 5' exonuclease activity (the molecular backspace).
- Layer 3 (Mismatch Repair): Detecting distortions and identifying the new strand (methylation/nicks).
- Bioinformatics: How fidelity underpins variant calling accuracy, read mapping, and evolutionary models.
An interactive visualizer detailing the mechanics of lagging strand synthesis:
- The Lagging Strand Problem: Why DNA polymerase's 5' → 3' requirement forces discontinuous synthesis.
- RNA Primers: The essential role of Primase in starting each fragment.
- Ligation: How DNA Ligase seals the nicks to create a continuous sugar-phosphate backbone.
- Bioinformatics: The impact of fragmentation on short-read sequencing technologies, genome assembly, and alignment algorithms.
An interactive exploration of the physical chemistry governing replication accuracy:
- Thermodynamic Forces: Entropy, Enthalpy, and the physical driving forces of replication.
- Energy Balance: The energetic cost of correct base pairing versus the penalty of a mispair.
- Bioinformatics: How molecular thermodynamics dictates evolutionary mutation rates, transition/transversion ratios, and substitution matrices (BLOSUM/PAM).
A deep dive into the chemical thermodynamics and energetic landscapes of DNA base calling:
- Hydrogen Bonding Enthalpy: The energy released by canonical G-C and A-T bonds (Coulomb's Law).
- The Hydration Shell: Solvation penalties, stripping water molecules, and the "thermodynamic toll booth".
- Gibbs Free Energy Landscape: 3D topological surfaces and conformational reaction coordinates.
- Boltzmann Distribution: How a tiny (\Delta\Delta G) difference creates a massive exponential difference in binding probability ((P \propto e^{-\Delta G/RT})).
- Drug Discovery: Connections to computational molecular docking (AutoDock Vina) and rational drug design.
- Bioinformatics Failures: Why thermodynamics is the bedrock for variant calling and genome assembly, and what happens if it fails.
More topics coming soon.