Biophysics

1. Molecular Biophysics
   1. Structure of Biomolecules
      1. Proteins
         1. Protein Folding
            1. Folding pathways and intermediate states
            2. Role of chaperones in protein folding
            3. Misfolding and associated diseases
            4. Folding thermodynamics and kinetics
         2. Dynamic Structure-Function Relationships
            1. Allosteric regulation and conformational changes
            2. Protein domains and motifs
            3. Protein flexibility and dynamics
            4. Post-translational modifications
      2. Nucleic Acids
         1. DNA/RNA Structure and Dynamics
            1. Double-helix structure and its stability factors
            2. Supercoiling and topological states
            3. RNA secondary and tertiary structures
            4. DNA/RNA hydration and ion interactions
         2. DNA Replication and Transcription
            1. Molecular mechanisms of replication
            2. Transcription factors and regulatory elements
            3. Epigenetic modifications affecting transcription
            4. DNA repair mechanisms
      3. Lipids
         1. Membranes Structure and Dynamics
            1. Lipid bilayer asymmetry and fluidity
            2. Membrane protein interactions
            3. Lipid rafts and microdomains
            4. Membrane fusion and fission processes
      4. Carbohydrates
         1. Structural variety and complexity
         2. Glycosylation and cell signaling
         3. Interaction with proteins and lipids
         4. Role in cellular recognition and adhesion
   2. Molecular Interactions
      1. Non-Covalent Interactions
         1. Hydrogen bonds and van der Waals forces
         2. Ionic interactions and electrostatics
         3. Hydrophobic effects in biological systems
         4. Role in molecular recognition and specificity
      2. Binding Kinetics and Thermodynamics
         1. Binding equilibrium and affinity
         2. Kinetic models of molecular interactions
         3. Ligand-receptor interactions and cooperativity
         4. Thermodynamics of ligand binding
      3. Enzyme Catalysis
         1. Transition state theory and enzyme kinetics
         2. Mechanisms of enzyme action
         3. Cofactors and catalysis
         4. Allosteric enzymes and regulation
   3. Molecular Dynamics
      1. Conformational space exploration
      2. Energy landscapes and molecular dynamics simulations
      3. Use of Markov models in predicting molecular pathways
      4. Computational methods for studying biomolecular interactions
   4. Techniques and Tools
      1. Imaging techniques and structural determination
      2. Single-molecule techniques and their applications
      3. Use of spectroscopy in molecular studies
      4. Computational modeling and simulations
   5. Applications
      1. Drug design and interaction prediction
      2. Biomaterials and synthetic biomolecules
      3. Understanding disease mechanisms at a molecular level
      4. Role in biotechnology and synthetic biology