Biophysics

  1. Biophysical Techniques and Methods
    1. Structural Biology Methods
      1. X-ray Crystallography
        1. Principles and Instrumentation
          1. Data Collection and Analysis
            1. Structure Determination
              1. Phase Problem Solutions
              2. Nuclear Magnetic Resonance Spectroscopy
                1. Basic Principles
                  1. Solution vs. Solid-State NMR
                    1. Structure Elucidation
                      1. Dynamics Studies
                      2. Cryo-Electron Microscopy
                        1. Sample Preparation
                          1. Imaging and Data Processing
                            1. Single-Particle Analysis
                              1. Resolution Revolution
                              2. Small-Angle X-ray Scattering
                                1. Principles and Applications
                                  1. Data Interpretation
                                    1. Shape Reconstruction
                                  2. Spectroscopy
                                    1. UV-Visible Spectroscopy
                                      1. Absorption Spectra
                                        1. Applications in Biochemistry
                                          1. Chromophores in Biology
                                          2. Fluorescence Spectroscopy
                                            1. Fluorophores and Labeling
                                              1. Fluorescence Lifetime and Quenching
                                                1. FRET Applications
                                                2. Circular Dichroism
                                                  1. Principles of Optical Activity
                                                    1. Secondary Structure Analysis
                                                      1. Protein Folding Studies
                                                      2. Infrared and Raman Spectroscopy
                                                        1. Vibrational Modes
                                                          1. Structural Information from Spectra
                                                            1. Time-Resolved Studies
                                                          2. Microscopy
                                                            1. Light Microscopy
                                                              1. Brightfield and Phase Contrast
                                                                1. Resolution Limits
                                                                  1. Numerical Aperture
                                                                  2. Fluorescence Microscopy
                                                                    1. Fluorescent Probes
                                                                      1. Imaging Techniques
                                                                        1. Photobleaching and Phototoxicity
                                                                        2. Confocal Microscopy
                                                                          1. Optical Sectioning
                                                                            1. 3D Imaging
                                                                              1. Laser Scanning Systems
                                                                              2. Super-Resolution Microscopy
                                                                                1. STED Microscopy
                                                                                  1. PALM and STORM
                                                                                    1. Applications in Cell Biology
                                                                                    2. Atomic Force Microscopy
                                                                                      1. Surface Topography
                                                                                        1. Force Measurements
                                                                                          1. Single-Molecule Studies
                                                                                          2. Scanning Tunneling Microscopy
                                                                                            1. Principles and Applications
                                                                                              1. Atomic Resolution Imaging
                                                                                            2. Single-Molecule Techniques
                                                                                              1. Optical Tweezers
                                                                                                1. Force Measurement and Manipulation
                                                                                                  1. Calibration Methods
                                                                                                    1. Applications to Biomolecules
                                                                                                    2. Magnetic Tweezers
                                                                                                      1. Torque and Stretching Experiments
                                                                                                        1. DNA Supercoiling Studies
                                                                                                        2. Single-Molecule Fluorescence
                                                                                                          1. Distance Measurements
                                                                                                            1. Conformational Dynamics
                                                                                                              1. Photobleaching Analysis
                                                                                                              2. Patch Clamp Electrophysiology
                                                                                                                1. Ion Channel Recording
                                                                                                                  1. Single-Channel vs. Whole-Cell Techniques
                                                                                                                    1. Voltage and Current Clamp
                                                                                                                  2. Hydrodynamic Methods
                                                                                                                    1. Sedimentation and Centrifugation
                                                                                                                      1. Analytical Ultracentrifugation
                                                                                                                        1. Density Gradient Centrifugation
                                                                                                                          1. Molecular Weight Determination
                                                                                                                          2. Electrophoresis
                                                                                                                            1. Gel Electrophoresis
                                                                                                                              1. Capillary Electrophoresis
                                                                                                                                1. Native vs. Denaturing Conditions
                                                                                                                              2. Computational Biophysics and Modeling
                                                                                                                                1. Molecular Dynamics Simulations
                                                                                                                                  1. Force Fields
                                                                                                                                    1. Simulation Protocols
                                                                                                                                      1. Analysis of Trajectories
                                                                                                                                        1. Enhanced Sampling Methods
                                                                                                                                        2. Monte Carlo Methods
                                                                                                                                          1. Random Sampling Techniques
                                                                                                                                            1. Applications in Protein Folding
                                                                                                                                              1. Metropolis Algorithm
                                                                                                                                              2. Coarse-Grained Modeling
                                                                                                                                                1. Simplified Representations
                                                                                                                                                  1. Applications to Large Systems
                                                                                                                                                    1. Multiscale Modeling
                                                                                                                                                    2. Bioinformatics and Sequence Analysis
                                                                                                                                                      1. Sequence Alignment
                                                                                                                                                        1. Structure Prediction
                                                                                                                                                          1. Homology Modeling
                                                                                                                                                          2. Systems Biology Modeling
                                                                                                                                                            1. Mathematical Modeling of Networks
                                                                                                                                                              1. Parameter Estimation and Validation
                                                                                                                                                                1. Sensitivity Analysis

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                                                                                                                                                            5. Systems and Organismal Biophysics

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                                                                                                                                                            1. Introduction to Biophysics