Stochastic thermodynamics as reviewed here systematically provides a framework for
extending the notions of classical thermodynamics such as work, heat and entropy …

The calculation of free‐energy differences is one of the main challenges in computational
biology and biochemistry. Umbrella sampling, biased molecular dynamics (MD), is one of …

In the host of numerical schemes devised to calculate free energy differences by way of
geometric transformations, the adaptive biasing force algorithm has emerged as a promising …

As access to computational resources continues to increase, free-energy calculations have
emerged as a powerful tool that can play a predictive role in a wide range of research areas …

Steered molecular dynamics (SMD) permits efficient investigations of molecular processes
by focusing on selected degrees of freedom. We explain how one can, in the framework of …

Atomic force microscopes and optical tweezers are widely used to probe the mechanical
properties of individual molecules and molecular interactions, by exerting mechanical forces …

Calculation of free energy is of great importance for understanding the kinetics and the
structural determinants of biomolecular processes, such as transition between different …

This monograph provides a general introduction to advanced computational methods for
free energy calculations, from the systematic and rigorous point of view of applied …

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We present a maximum likelihood argument for the Bennett acceptance ratio method, and
derive a simple formula for the variance of free energy estimates generated using this …