Description |
1 online resource (xxi, 324 pages) : illustrations |
Contents |
Chapter 1. Proteins Don't Know Biology -- Prologue: Statistical Physics of Candy, Dirt, and Biology -- Guiding Principles -- About This Book -- Molecular Prologue: A Day in the Life of Butane -- What Does Equilibrium Mean to a Protein? -- A Word on Experiments -- Making Movies: Basic Molecular Dynamics Simulation -- Basic Protein Geometry -- A Note on the Chapters -- Chapter 2. The Heart of It All: Probability Theory -- Introduction -- Basics of One-Dimensional Distributions -- Fluctuations and Error -- Two+ Dimensions: Projection and Correlation -- Simple Statistics Help Reveal a Motor Protein's Mechanism -- Additional Problems: Trajectory Analysis -- Chapter 3. Big Lessons from Simple Systems: Equilibrium Statistical Mechanics in One Dimension -- Introduction -- Energy Landscapes Are Probability Distributions -- States, Not Configurations -- Free Energy: It's Just Common Sense If You Believe in Probability -- Entropy: It's Just a Name -- Summing Up -- Molecular Intuition from Simple Systems -- Loose Ends: Proper Dimensions, Kinetic Energy -- Chapter 4. Nature Doesn't Calculate Partition Functions: Elementary Dynamics and Equilibrium -- Introduction -- Newtonian Dynamics: Deterministic but Not Predictable -- Barrier Crossing--Activated Processes -- Flux Balance: The Definition of Equilibrium -- Simple Diffusion, Again -- More on Stochastic Dynamics: The Langevin Equation -- Key Tools: The Correlation Time and Function -- Tying It All Together -- So Many Ways to ERR: Dynamics in Molecular Simulation -- Mini-Project: Double-Well Dynamics -- Chapter 5. Molecules Are Correlated! Multidimensional Statistical Mechanics -- Introduction -- A More-Than-Two-Dimensional Prelude -- Coordinates and Force Fields -- The Single-Molecule Partition Function -- Multimolecular Systems -- The Free Energy Still Gives the Probability -- Summary -- Chapter 6. From Complexity to Simplicity: The Potential of Mean Force -- Introduction: PMFs Are Everywhere -- The Potential of Mean Force Is Like a Free Energy -- The PMF May Not Yield the Reaction Rate or Transition State -- The Radial Distribution Function -- PMFs Are the Typical Basis for "Knowledge-Based" ("Statistical") Potentials -- Summary: The Meaning, Uses, and Limitations of the PMF -- Chapter 7. What's Free about "Free" Energy? Essential Thermodynamics -- Introduction -- Statistical Thermodynamics: Can You Take a Derivative? -- You Love the Ideal Gas -- Boring but True: The First Law Describes Energy Conservation -- G vs. F: Other Free Energies and Why They (Sort of ) Matter -- Overview of Free Energies and Derivatives -- The Second Law and (Sometimes) Free Energy Minimization -- Calorimetry: A Key Thermodynamic Technique -- The Bare-Bones Essentials of Thermodynamics -- Key Topics Omitted from This Chapter -- Chapter 8. The Most Important Molecule: Electro-Statistics of Water -- Basics of Water Structure -- Water Molecules Are Structural Elements in Many Crystal Structures -- The pH of Water and Acid-Base Ideas -- Hydrophobic Effect -- Water Is a Strong Dielectric -- Charges in Water + Salt = Screening -- A Brief Word on Solubility -- Summary -- Additional Problem: Understanding Differential Electrostatics -- Chapter 9. Basics of Binding and Allostery -- A Dynamical View of Binding: On- and Off-Rates -- Macroscopic Equilibrium and the Binding Constant -- A Structural-Thermodynamic View of Binding -- Understanding Relative Affinities: ∆∆G and Thermodynamic Cycles -- Energy Storage in "Fuels" Like ATP -- Direct Statistical Mechanics Description of Binding -- Allostery and Cooperativity -- Elementary Enzymatic Catalysis -- pH AND pKa -- Summary -- Chapter 10. Kinetics of Conformational Change and Protein Folding -- Introduction: Basins, Substates, and States -- Kinetic Analysis of Multistate Systems -- Conformational and Allosteric Changes in Proteins -- Protein Folding -- Summary -- Chapter 11. Ensemble Dynamics: From Trajectories to Diffusion and Kinetics -- Introduction: Back to Trajectories and Ensembles -- One-Dimensional Ensemble Dynamics -- Four Key Trajectory Ensembles -- From Trajectory Ensembles to Observables -- Diffusion and Beyond: Evolving Probability Distributions -- The Jarzynski Relation and Single-Molecule Phenomena -- Summary -- Chapter 12. A Statistical Perspective on Biomolecular Simulation -- Introduction: Ideas, Not Recipes -- First, Choose Your Model: Detailed or Simplified -- "Basic" Simulations Emulate Dynamics -- Metropolis Monte Carlo: A Basic Method and Variations -- Another Basic Method: Reweighting and Its Variations -- Discrete-State Simulations -- How to Judge Equilibrium Simulation Quality -- Free Energy and PMF Calculations -- Path Ensembles: Sampling Trajectories -- Protein Folding: Dynamics and Structure Prediction -- Summary -- Index |
Summary |
Proteins Don't Know BiologyPrologue: Statistical Physics of Candy, Dirt, and Biology Guiding Principles About This Book Molecular Prologue: A Day in the Life of Butane What Does Equilibrium Mean to a Protein? A Word on Experiments Making Movies: Basic Molecular Dynamics Simulation Basic Protein Geometry A Note on the Chapters The Heart of It All: Probability Theory Introduction Basics of One-Dimensional Distributions Fluctuations and Error Two+ Dimensions: Projection and Correlation Simple Statistics Help Reveal a Motor Protein's Mechanism Additional Problems: Trajectory Analysis Big Lessons from Simple Systems: Equilibrium Statistical Mechanics in One DimensionIntroduction Energy Landscapes Are Probability Distributions States, Not Configurations Free Energy: It's Just Common Sense If You Believe in Probability Entropy: It's Just a Name Summing Up Molecular Intuition from Simple Systems Loose Ends: Proper Dimensions, Kinetic Energy Nature Doesn't Calculate Partition Functions: Elementary Dynamics and Equilibrium Introduction Newtonian Dynamics: Deterministic but Not Predictable Barrier Crossing-Activated Processes Flux Balance: The Definition of Equilibrium Simple Diffusion, Again More on Stochastic Dynamics: The Langevin Equation Key Tools: The Correlation Time and Function Tying It All Together So Many Ways to ERR: Dynamics in Molecular Simulation Mini-Project: Double-Well Dynamics Molecules Are Correlated! Multidimensional Statistical Mechanics Introduction A More-Than-Two-Dimensional Prelude Coordinates and Force Fields The Single-Molecule Partition Function Multimolecular Systems The Free Energy Still Gives the Probability Summary From Complexity to Simplicity: The Potential of Mean Force Introduction: PMFs Are Everywhere The Potential of Mean Force Is Like a Free Energy The PMF May Not Yield the Reaction Rate or Transition State The Radial |
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Probability Distributions The Jarzynski Relation and Single-Molecule Phenomena Summary A Statistical Perspective on Biomolecular Simulation Introduction: Ideas, Not Recipes First, Choose Your Model: Detailed or Simplified "Basic" Simulations Emulate Dynamics Metropolis Monte Carlo: A Basic Method and Variations Another Basic Method: Reweighting and Its Variations Discrete-State Simulations How to Judge Equilibrium Simulation Quality Free Energy and PMF Calculations Path Ensembles: Sampling Trajectories Protein Folding: Dynamics and Structure Prediction Summary Index |
Bibliography |
Includes bibliographical references and index |
Notes |
Print version record |
Subject |
Biophysics.
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Statistical physics.
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Biomolecules.
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Bioinformatics.
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Computational biology.
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Statistics.
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Biophysics
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Computational Biology
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Statistics as Topic
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statistics.
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SCIENCE -- Life Sciences -- Biochemistry.
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Statistics
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Computational biology
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Bioinformatics
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Biomolecules
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Biophysics
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Statistical physics
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Form |
Electronic book
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ISBN |
9781420073799 |
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1420073796 |
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