Biophysics

  1. Physical Principles in Biology
    1. Thermodynamics and Bioenergetics
      1. The Laws of Thermodynamics in Living Systems
        1. First Law: Conservation of Energy
          1. Second Law: Entropy and Disorder
            1. Third Law: Absolute Zero and Biological Relevance
            2. Gibbs Free Energy and Spontaneity
              1. Definition and Calculation
                1. Coupled Reactions
                  1. Standard vs. Physiological Conditions
                  2. Enthalpy and Entropy in Biological Processes
                    1. Heat Exchange in Biochemical Reactions
                      1. Entropic Contributions to Folding and Binding
                        1. Temperature Dependence of Biological Processes
                        2. Chemical Potential and Equilibria
                          1. Chemical Potential in Solutions
                            1. Equilibrium Constants
                              1. Le Chatelier's Principle in Biology
                              2. ATP and Energy Currency
                                1. Structure and Hydrolysis of ATP
                                  1. ATP Coupling to Cellular Work
                                    1. Energy Charge and Cellular Regulation
                                  2. Statistical Mechanics in Biology
                                    1. Probability and Distributions
                                      1. Microstates and Macrostates
                                        1. Binomial and Poisson Distributions
                                          1. Normal Distribution in Biological Systems
                                          2. The Boltzmann Distribution
                                            1. Energy States and Populations
                                              1. Temperature Dependence
                                                1. Applications to Molecular Systems
                                                2. Partition Functions
                                                  1. Definition and Calculation
                                                    1. Applications to Biological Systems
                                                      1. Relationship to Thermodynamic Properties
                                                      2. Entropy as Statistical Disorder
                                                        1. Relationship to Information Theory
                                                          1. Entropy in Macromolecular Folding
                                                            1. Configurational Entropy
                                                            2. Modeling Molecular Assemblies
                                                              1. Cooperative Binding
                                                                1. Allosteric Transitions
                                                                  1. Hill Coefficients
                                                                2. Quantum Mechanics in Biology
                                                                  1. Quantum Tunneling in Enzymes
                                                                    1. Mechanisms of Tunneling
                                                                      1. Examples in Enzyme Catalysis
                                                                        1. Temperature Independence
                                                                        2. Photosynthesis and Light Harvesting
                                                                          1. Quantum Coherence in Energy Transfer
                                                                            1. Role of Pigments
                                                                              1. Excitonic Coupling
                                                                              2. Electron Transfer Processes
                                                                                1. Marcus Theory
                                                                                  1. Biological Electron Transport Chains
                                                                                    1. Distance Dependence
                                                                                    2. Vision and Photoreception
                                                                                      1. Photon Absorption by Rhodopsin
                                                                                        1. Quantum Yield in Photoreceptors
                                                                                          1. Isomerization Mechanisms
                                                                                        2. Electromagnetism and Bioelectricity
                                                                                          1. Electrostatics in Molecular Interactions
                                                                                            1. Coulomb's Law in Biomolecules
                                                                                              1. Screening and Debye Length
                                                                                                1. Salt Effects on Interactions
                                                                                                2. Dielectric Properties of Biological Matter
                                                                                                  1. Polarizability of Biomolecules
                                                                                                    1. Membrane Capacitance
                                                                                                      1. Frequency-Dependent Dielectric Response
                                                                                                      2. Electric Fields and Potentials in Cells
                                                                                                        1. Membrane Potential
                                                                                                          1. Electrophysiology Basics
                                                                                                            1. Field Effects on Protein Function
                                                                                                          2. Fluid Dynamics and Transport Phenomena
                                                                                                            1. Diffusion and Fick's Laws
                                                                                                              1. Molecular Diffusion
                                                                                                                1. Diffusion Coefficients
                                                                                                                  1. Random Walk Models
                                                                                                                  2. Osmosis and Osmotic Pressure
                                                                                                                    1. Semipermeable Membranes
                                                                                                                      1. Water Potential in Cells
                                                                                                                        1. Osmotic Regulation
                                                                                                                        2. Viscosity and Biological Fluids
                                                                                                                          1. Blood and Cytoplasmic Viscosity
                                                                                                                            1. Non-Newtonian Fluids in Biology
                                                                                                                              1. Shear Rate Effects
                                                                                                                              2. Laminar vs. Turbulent Flow
                                                                                                                                1. Flow Regimes in Blood Vessels
                                                                                                                                  1. Implications for Transport
                                                                                                                                    1. Mixing and Mass Transfer
                                                                                                                                    2. The Reynolds Number in Biological Contexts
                                                                                                                                      1. Calculation and Interpretation
                                                                                                                                        1. Relevance to Organism Size and Flow
                                                                                                                                          1. Scaling Laws

                                                                                                                                      Previous

                                                                                                                                      1. Introduction to Biophysics

                                                                                                                                      Go to top

                                                                                                                                      Next

                                                                                                                                      3. Molecular Biophysics