Molecular Biophysics Masterclass: The Physics of Life

What makes life work at the molecular level?

This course answers that question by diving deep into the physics that governs biological molecules—from DNA and proteins to membranes and drugs. Unlock the molecular secrets of life with this in-depth course on Biophysics. Spanning over 300+  video concepts, this course offers a comprehensive journey through the physical principles that govern biological molecules, their interactions, and their roles in life processes.

It begins with the foundational principles of molecular biophysics, exploring the unique properties of water, the structure of DNA and RNA, and the central dogma that connects genetic information to cellular function. From there, it delves into the forces that drive molecular interactions—electrostatics, hydrogen bonding, and quantum effects—and how these are modeled computationally to simulate real biological systems.

As the course progresses, learners are introduced to the thermodynamic principles that underpin molecular stability and change. Concepts like entropy, free energy, and energy landscapes are unpacked in the context of protein folding, phase transitions, and molecular flexibility. The course then transitions into the structural world of proteins, examining the roles of amino acids, the formation of helices and sheets, and the challenges of misfolding and prion diseases.

A significant portion of the course is dedicated to molecular dynamics simulations, teaching how biomolecules are modeled over time using algorithms, ensembles, and boundary conditions. Students learn to interpret simulation data and apply it to biological questions, from protein folding pathways to binding free energy calculations.

The course also explores the architectural diversity of proteins—fibrous, globular, and membrane-bound—highlighting structural motifs and folding patterns that define their function. Membrane biology is examined in depth, including lipid bilayer dynamics, membrane protein topology, ion channels, and signal transduction mechanisms.

Evolutionary perspectives are integrated through discussions on protein fold classification, stability principles, and the role of mutations. Bioinformatics tools are introduced to analyze sequences, predict structures, and model evolutionary relationships, culminating in advanced techniques like homology modeling and deep learning with AlphaFold.

In the final chapters, the course shifts toward practical applications in drug discovery. Learners explore the full pipeline from target identification to lead optimization, including experimental and virtual screening, docking, pharmacophore modeling, and fragment-based design. Real-world case studies illustrate how molecular biophysics drives innovation in medicine.

A bonus section on lipid-protein interactions offers a deep dive into membrane biophysics, covering hydrophobic mismatch, cholesterol effects, lipid rafts, and the role of lipid nanoparticles in vaccine delivery. Throughout the course, learners are guided by clear explanations, visual simulations, and study questions that reinforce understanding and encourage exploration.

This course is ideal for students, researchers, and professionals in biology, chemistry, physics, and biomedical sciences who want to understand the physical principles behind life’s molecular processes and apply them to real-world challenges in science and medicine.

Course Breakdown

Section 1: Introduction to Molecular Biophysics

• Water’s unique properties
• DNA components, structure, and Chargaff’s ratio
• RNA types and the central dogma
• Protein basics and structure determination

Section 2: Molecular Interactions and Modeling

• Electron-based interactions and quantum chemistry
• Force fields, torsions, and Ramachandran plots
• Hydrogen bonding and energy landscapes

Section 3: Thermodynamics and Entropy

• Boltzmann distribution and Maxwell-Boltzmann velocities
• Free energy, entropy, and phase transitions
• Thermodynamic definitions and applications in biology

Section 4: Protein Folding and Stability

• Hydrophobic effect and folding collapse
• Energy landscapes and statistical mechanics
• Alpha helix and beta sheet stability
• Electrostatics and phase transitions

Section 5: Amino Acids and Structural Motifs

• Amino acid properties and classifications
• Helices, sheets, and folding kinetics
• Misfolding and prion diseases

Section 6: Molecular Dynamics Simulations

• Simulation principles and algorithms
• Ensembles, solvation, and boundary conditions
• Free energy calculations and Markov models

Section 7: Protein Architecture and Folding Patterns

• Fibrous, globular, and membrane proteins
• Structural motifs: Greek Key, TIM barrel, Rossman fold
• Disordered proteins and folding diversity

Section 8: Membrane Biology and Transport

• Lipid bilayers and membrane protein topology
• Ion channels, pumps, and signaling pathways
• GPCRs, RTKs, and mRNA vaccine delivery

Section 9: Evolution and Protein Fold Classification

• Fold databases (CATH, SCOP)
• Evolutionary pressures and stability principles
• Folding defects and conformational transitions

Section 10: Folding Models and Kinetics

• Molten globules and folding pathways
• Diffusion-collision, hydrophobic collapse, nucleation-condensation
• Chevron plots and phi-value analysis

Section 11: Bioinformatics and Structure Prediction

• DNA sequencing and mutation analysis
• Homology modeling and deep learning (AlphaFold)
• Phylogenetics and scoring matrices

Section 12: Drug Discovery and Molecular Design

• Target identification and binding site analysis
• Screening methods: experimental and virtual
• Docking, pharmacophores, and lead optimization

Section 13: Advanced Topics in Drug Design

• Free energy simulations and peptide drugs
• Ion channel modulation and protein fold design
• Case studies and biological drug development

Bonus Section: Lipid-Protein Interactions

• Hydrophobic mismatch and membrane adaptation
• Snorkeling, anchoring residues, and voltage sensors
• Cholesterol, lipid rafts, and nanodiscs
• Experimental techniques and vaccine delivery systems