by Tony Lelièvre (CERMICS & INRIA Rocquencourt, France) , Gabriel Stoltz (CERMICS & INRIA Rocquencourt, France) , & Mathias Rousset (INRIA Lille, France)

This monograph provides a general introduction to advanced computational methods for free energy calculations, from the systematic and rigorous point of view of applied mathematics. Free energy calculations in molecular dynamics have become an outstanding and increasingly broad computational field in physics, chemistry and molecular biology within the past few years, by making possible the analysis of complex molecular systems. This work proposes a new, general and rigorous presentation, intended both for practitioners interested in a mathematical treatment, and for applied mathematicians interested in molecular dynamics.

• Sampling Methods
• Stochastic Differential Equations
• Meta-Stability
• Free Energy Perturbation
• Thermodynamic Integration
• Constrained Dynamics
• Non-Equilibrium Methods
• Fluctuation Identities
• Jarzynski Identity
• Adaptive Techniques
• Long Time Convergence
• Replica Selection Methods
• Selection Mechanisms
• Parallel Computation