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| Preface | |
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| Basic thermodynamic and biochemical concepts | |
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| Fundamental thermodynamic concepts | |
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| States of matter | |
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| Pressure | |
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| Temperature | |
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| Volume, mass, and number | |
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| Properties of gasesThe ideal gas lawsGas Mixtures | |
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| Kinetic energy of gases | |
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| Real GasesLiquifying gases for low temperature spectroscopy | |
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| Molecular Basis for Life | |
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| Cell Membranes | |
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| Amino acids | |
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| Classification of amino acids by their side chains | |
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| DNA and RNA | |
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| First law of thermodynamics | |
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| Systems | |
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| State Functions | |
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| First law of thermodynamics | |
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| Research Direction: Drug design IWork | |
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| Specific heat | |
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| Internal energy for an ideal gas | |
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| Enthalpy | |
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| Dependence of specific heat on enthalpy | |
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| Derivative box: State Functions described using partial derivatives | |
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| Enthalpy changes of biochemical reactions | |
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| Research Direction: Global climate change | |
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| Second law of thermodynamicsEntropy | |
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| Entropy changes for reversible and irreversible processes | |
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| The second law of thermodynamics | |
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| Interpretation of entropy | |
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| Third law of thermodynamics | |
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| Gibbs energy | |
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| Relationship between the Gibbs free energy and the equilibrium constant | |
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| Research Direction: Drug design IIGibbs free energy for an ideal gas | |
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| Using the Gibbs free energy | |
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| Carnot cycle and hybrid cars | |
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| Derivative box: Entropy as a state function | |
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| Research Direction: Nitrogen fixation | |
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| Phase diagrams, mixtures and chemical potential | |
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| Substances may exist in different phases | |
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| Phase diagrams and transitions | |
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| Chemical potential | |
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| Properties of lipids described using the chemical potential | |
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| Research Direction: lipid rafts | |
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| Determination of micelle formation using surface tension | |
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| Mixtures Raoult's law Osmosis | |
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| Research Direction: Protein crystallization | |
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| Equilibria and reactions involving protons | |
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| Gibbs free energy minimum | |
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| Derivative box: Relationship between the Gibbs energy and equilibrium constant | |
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| Response of the equilibrium constant to condition changes | |
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| Acid-base equilibria | |
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| Protonation states of amino acid residues | |
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| BuffersBuffering in the cardiovascular system | |
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| Research Direction: Proton coupled electron transfer and pathways | |
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| Oxidation/reduction reactions and bioenergetics | |
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| Oxidation/reduction reactionsElectrochemical cells | |
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| The Nernst Equation: Midpoint potentials | |
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| Gibbs energy of formation and activity | |
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| Ionic strength | |
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| Adenosine triphosphate, ATP Chemiosmotic hypothesis | |
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| Research Direction: Respiratory chain | |
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| Research Direction: ATP synthase | |
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| Kinetics and enzymesThe rate of a chemical reaction | |
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| Parallel first-order reactions | |
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| Sequential first order reactions | |
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| Second-order reactions | |
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| The order of a reaction | |
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| Reactions that approach equilibrium | |
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| Activation energy | |
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| Research Direction: Electron transfer I: Energetics | |
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| Derivative box Derivation of Marcus relationship | |
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| Enzymes | |
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| Enzymes lower the activation energy | |
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| Enzyme mechanisms | |
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| Research Directions: Dynamics in enzyme mechanism | |
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| Michaelis-Menten mechanism | |
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| Lineweaver-Burk equation | |
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| Enzyme activity | |
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| Research direction: The RNA world | |
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| The Boltzmann distribution and statistical thermodynamics | |
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| ProbabilityBoltzmann distribution | |
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| Partition function | |
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| Statistical thermodynamics | |
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| Research Direction: Protein folding and prionsPrions | |
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| Quantum theory: Introduction and principles | |
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| Classical concepts | |
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| Experimental failures of classical physics | |
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| Blackbody radiationPhotoelectric effectAtomic spectra | |
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| Principles of quantum theory | |
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| Wave Particle Duality Schrodinger's Equation | |
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| Born Interpretation | |
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| General approach for solving Schrodinger's equation | |
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| Interpretation of quantum mechanics | |
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| Heisenberg Uncertainty Principle | |
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| A quantum mechanical world | |
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| Research Direction: Schrodinger's cat | |
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| Particle in box and tunneling | |
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| One-dimensional particle in the box | |
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| Properties of the solutions | |
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| Energy and wave function Symmetry | |
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| Wavelength | |
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| Probability | |
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| Average or expectation value | |
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| Transitions | |
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| Research Direction: Carotenoids Two-dimensional particle in a box Tunneling | |
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| Research Direction: Probing biological membranes | |
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| Research Direction: Electron transfer II: Distance dependence | |
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| Vibrational motion and infrared spectroscopy | |
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| Simple Harmonic Oscillator: Classical theory | |
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| Potential energy for the simple harmonic oscillator | |
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| Simple Ha | |