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 …

An azobenzene-capped DNA hairpin coupled to an AFM is presented as an optically
triggered single-molecule motor. The photoinduced trans to cis isomerization of azobenzene …

The present paper is intended to be a comprehensive assessment and rationalization, from
a statistical mechanics perspective, of existing alchemical theories for binding free energy …

The indirect method for the construction of quantum mechanics (QM)/molecular mechanics
(MM) free energy landscapes provides a cheaper alternative for free energy simulations at …

In this paper, we present an improved method for obtaining unbiased estimates of the free
energy difference between two thermodynamic states using the work distribution measured …

We present non equilibrium molecular dynamics experiments of the unfolding and refolding
of a single molecule alanine decapeptide in vacuo subject to a Nosé thermostat. Forward …

In the framework of single-molecule pulling experiments, the system is typically driven out of
equilibrium by a time-dependent external potential V (t) acting on a collective coordinate …

In recent years, a number of techniques have been developed that allow us to access the
properties of single molecules; for example, see Refs [1–8]. These windows into the single …

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