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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 such that the total Hamiltonian is the sum of V(t) and the Hamiltonian in the absence of external perturbation. Nonequilibrium work theorems such as Jarzynski equality and(More)
An important limitation of nonequilibrium pulling experiments/simulations in recovering free energy differences is the poor convergence of path-ensemble averages. Therefore, a large number of fast-switching trajectories needs to achieve free energy estimates with acceptable accuracy. We propose a method to improve free energy estimates by drastically(More)
Understanding binding mechanisms between enzymes and potential inhibitors and quantifying protein-ligand affinities in terms of binding free energy is of primary importance in drug design studies. In this respect, several approaches based on molecular dynamics simulations, often combined with docking techniques, have been exploited to investigate the(More)
In the preceding paper of this series (Part I [P. Nicolini and D. Frezzato, J. Chem. Phys. 138, 234101 (2013)]) we have unveiled some ubiquitous features encoded in the systems of polynomial differential equations normally applied in the description of homogeneous and isothermal chemical kinetics (mass-action law). Here we proceed by investigating a deeply(More)
Simplification of chemical kinetics description through dimensional reduction is particularly important to achieve an accurate numerical treatment of complex reacting systems, especially when stiff kinetics are considered and a comprehensive picture of the evolving system is required. To this aim several tools have been proposed in the past decades, such as(More)
In this work, ab initio parametrization of water force field is used to get insights into the functional form of empirical potentials to properly model the physics underlying dispersion interactions. We exploited the force matching algorithm to fit the interaction forces obtained with dispersion corrected density functional theory based molecular dynamics(More)
In this work, we deal with general reactive systems involving N species and M elementary reactions under applicability of the mass-action law. Starting from the dynamic variables introduced in two previous works [P. Nicolini and D. Frezzato, J. Chem. Phys. 138(23), 234101 (2013); 138(23), 234102 (2013)], we turn to a new representation in which the system(More)
Owing to specific characteristics engendered by their lamellar structures, transition metal dichalcogenides are posited as being some of the best dry lubricants available. Herein, we report a density functional investigation into the sliding properties and associated phenomena of these materials. Calculated potential energy and charge transfer profiles are(More)
To achieve acceptable accuracy in fast-switching free energy estimates by Jarzynski equality [ Phys. Rev. Lett. 1997 , 78 , 2690 ] or Crooks fluctuation theorem [ J. Stat. Phys. 1998 , 90 , 1481 ], it is often necessary to realize a large number of externally driven trajectories. This is basically due to inefficient calculation of path-ensemble averages(More)
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