Fluctuation theorems, developed over the past 15 years, have resulted in fundamental
breakthroughs in our understanding of how irreversibility emerges from reversible dynamics …

When a macroscopic system in contact with a heat reservoir is driven away from equilibrium,
the second law of thermodynamics places a strict bound on the amount of work performed …

Molecular dynamics simulations enable access to free energy differences governing the
driving force underlying all biological processes. In the current chapter we describe …

A series of computational methods for p K a shift prediction are extensively tested on a set of
benchmark protein systems, aiming at identifying pitfalls and evaluating their performance …

The combination of free energy simulations in the alchemical and configurational spaces
provides a feasible route to access the thermodynamic profiles under a computationally …

The indirect free energy simulation at quantum mechanics (QM)/molecular mechanics (MM)
levels provides a feasible alternative to direct QM/MM simulations. The main idea under the …

In contrast to other sirtuins (NAD+-dependent class III lysine deacylases), inhibition of Sirt5
is poorly investigated, yet. Our present work is based on the recently identified Sirt5 inhibitor …

In this article we present a potential of mean force estimator based on measurements of the
work performed on a system during out of equilibrium realizations of a process. More …

The Jarzynski identity [C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)] and the Crooks
equation [GE Crooks, J. Stat. Phys. 90, 1481 (1998)] relate thermodynamic free energy …

The hydration free energy (HFE) is a critical property for predicting and understanding
chemical and biological processes in aqueous solution. There are a number of …