Cargando…
Statistical physics of biomolecules : an introduction /
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...
| Clasificación: | Libro Electrónico |
|---|---|
| Autor principal: | |
| Formato: | Electrónico eBook |
| Idioma: | Inglés |
| Publicado: |
Boca Raton, FL :
CRC Press/Taylor & Francis,
©2010.
|
| Temas: | |
| Acceso en línea: | Texto completo |
Tabla de Contenidos:
- 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.