| 12.1 |
Molecular Motors: Theory |
| 12.1.1 |
Protein Motion as a Simple Random Walk |
| 12.1.2 |
Polymer Growth |
| 12.1.3 |
Sample Paths of Polymer Growth |
| 12.1.4 |
The Statistical Behavior of Polymer Growth |
| 12.2 |
Modeling Molecular Motions |
| 12.2.1 |
The Langevin Equation |
| 12.2.2 |
Numerical Simulation of the Langevin Equation |
| 12.2.3 |
The Smoluchowski Model |
| 12.2.4 |
First Passage Time |
| 12.3 |
Modeling Chemical Reactions |
| 12.4 |
A Mecanochemical Model |
| 12.5 |
Numerical Simulation of Protein Motion |
| 12.5.1 |
Numerical Algorithm that Preserves Detailed Balance |
| 12.5.2 |
Boundary Conditions |
| 12.5.3 |
Numerical Stability |
| 12.5.4 |
Implicit Discretization |
| 12.6 |
Derivations and Comments |
| 12.6.1 |
The Drag Coefficient |
| 12.6.2 |
The Equipartition Theorem |
| 12.6.3 |
A Numerical Method for the Lengevin Equation |
| 12.6.4 |
Some Connections with Thermodynamics |
| 12.6.5 |
Jumping Beans and Entropy |
| 12.6.6 |
Jump Rates |
| 12.6.7 |
Jump Rates at an Absorbing Boundary |
| 12.7 |
Exercises |
