Biophysics

1. Biophysical Techniques
   1. Spectroscopy
      1. NMR (Nuclear Magnetic Resonance)
         1. Principles of NMR
            1. Magnetic properties of nuclei
            2. Chemical shift and spin-spin coupling
         2. Instrumentation and methods
            1. NMR spectrometers
            2. Pulse sequences
         3. NMR applications
            1. Protein structure determination
            2. Metabolomics
            3. Dynamic studies of biomolecules
      2. X-ray Crystallography
         1. Basics of X-ray diffraction
            1. Bragg's Law
            2. Diffraction patterns
         2. Crystallization of biomolecules
            1. Techniques for crystal growth
            2. Challenges in crystallization
         3. Structural determination
            1. Phase problem and solutions
            2. Model building and refinement
      3. Infrared Spectroscopy
         1. Vibrational modes of molecules
            1. Fundamental vibrational transitions
            2. IR active modes in biological molecules
         2. Infrared spectrometric methods
            1. FTIR (Fourier-transform infrared spectroscopy)
            2. ATR (Attenuated Total Reflectance)
         3. Applications in biophysics
            1. Secondary structure analysis of proteins
            2. Ligand binding studies
      4. UV-Vis Spectroscopy
         1. Electronic transitions in molecules
            1. Absorbance and Beer-Lambert Law
            2. Chromophores in biomolecules
         2. Instruments and techniques
            1. Spectrophotometers
            2. Diode-array spectrometers
         3. Biological applications
            1. Enzyme kinetics
            2. Quantification of nucleic acids and proteins
      5. Circular Dichroism (CD)
         1. Theory of optical activity
            1. Chiral molecules and circularly polarized light
            2. Ellipticity and molar ellipticity
         2. CD instrumentation
            1. Polarimeters
            2. Detectors and data analysis
         3. CD applications in biology
            1. Protein folding and stability
            2. Ligand binding studies
   2. Microscopy
      1. Electron Microscopy
         1. Transmission Electron Microscopy (TEM)
            1. Electron beam interactions
            2. Sample preparation methods
            3. Imaging biological specimens
         2. Scanning Electron Microscopy (SEM)
            1. Surface topography analysis
            2. Sample coatings and conductive surfaces
            3. 3D reconstructions
      2. Optical Microscopy
         1. Fluorescence Microscopy
            1. Fluorophores and fluorescence
            2. Techniques like wide-field and total internal reflection (TIRF)
         2. Confocal Microscopy
            1. Optical sectioning and 3D reconstructions
            2. Pinhole and detector technology
         3. Super-resolution Microscopy
            1. Techniques: STED, PALM, STORM
            2. Applications in studying nanoscale structures
            3. Resolution limits and improvements
   3. Computational Methods
      1. Molecular Dynamics Simulations
         1. Force fields and algorithms
         2. Simulation protocols
            1. Equilibration and production runs
         3. Analysis of simulation data
      2. Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations
         1. Hybrid quantum/classical mechanics
         2. Applications in enzyme catalysis
         3. Methodological challenges and developments
      3. Bioinformatics and Structural Modeling
         1. Sequence alignment and prediction tools
         2. Homology modeling
         3. Protein-protein interaction predictions
   4. Other Techniques
      1. Atomic Force Microscopy (AFM)
         1. Operational principles and capabilities
         2. Imaging and force measurements
         3. Biological applications: single-molecule force spectroscopy
      2. Surface Plasmon Resonance (SPR)
         1. Fundamentals of plasmonics
         2. Real-time interaction analysis
         3. Applications in studying binding kinetics
      3. Single-Molecule Techniques
         1. Optical and magnetic tweezers
            1. Principles of manipulation
            2. Force measurements at the molecular level
         2. Single-molecule fluorescence
            1. Techniques like FRET and smFISH
            2. Applications in tracking molecular interactions