Daniel M. Zuckerman
NotationBasics: States & KineticsBasics: Mass-Action KineticsEquilibrium means Detailed BalanceCycles and ConstraintsCycle LogicAdvanced Cycle Logic
Non-equilibrium: Steady StatesFree Energy is the Energy Available for WorkThermodynamic Connection Between Free Energy and WorkChemical Potential
Underpinnings of Mass Action: The Ideal Gas The Ideal Gas in a Field: Transmembrane Ionic Gradients Conformational Statistical Mechanics Advanced Diffusion and the Fokker-Planck Picture Discrete-state kinetics and Markov models
Binding: Kinetics & ThermodynamicsBinding: Allostery (in a transport cycle)Chemical Reactions: CatalysisReaction Coupling
Energy Storage in Metastable ConditionsSimple Concentration Gradient Across a BilayerIonic Concentration Gradient Across a BilayerATP and other activated carriers
Diffusion FAQ: The basicsAdvanced diffusion and the Smoluchowski/Fokker-Planck picture
Activated CarriersATP: The Great CarrierATP/Motor Thought ExperimentRecycling of ATP and Coupling to Cellular ProcessesEnergy Storage in GradientsSynthesis of ATP by ATP synthase
ChannelsPumps and TransportersSymporters (Co-transporters)Antiporters (Exchanger or Counter-transporter)ATP-driven TransportersStoichiometric Effects in Transport
Molecular MotorsChaperone-aided Protein FoldingPrinciples of SynthesisPhosphorylation, methylation, etcSynthesis of ATP by ATP SynthaseAdvanced Cycle Logic The Ribosome and Error Correction
Signalling Transport The Membrane, Ions, and "Electrostatic Health" Active ("kinetic") proofreading Diffusion basics: Single-particle tracking etc.
