Towards bulk thermodynamics via non-equilibrium methods: gaseous methane as a case study

Zerbetto, Mirco; Frezzato, Diego

doi:10.1039/c4cp03815k

Cited by 7 publications

(4 citation statements)

References 47 publications

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“…Furthermore, we outline the almost full compatibility of EBDF with early path-sampling techniques developed in the framework of nonequilibrium simulation schemes. [27][28][29]58 In this respect, the relative simplicity of the method may easily allow implementation into modern simulation programs devised for performing steered molecular dynamics simulations. 59 The method here presented can be extended to molecular systems straightforwardly.…”

Section: Discussionmentioning

confidence: 99%

Elastic Barrier Dynamical Freezing in Free Energy Calculations: A Way To Speed Up Nonequilibrium Molecular Dynamics Simulations by Orders of Magnitude

Giovannelli

Cardini

Chelli

2016

J. Chem. Theory Comput.

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An important issue concerning computer simulations addressed to free energy estimates via nonequilibrium work theorems, such as the Jarzynski equality [Phys. Rev. Lett. 1997, 78, 2690], is the computational effort required to achieve results with acceptable accuracy. In this respect, the dynamical freezing approach [Phys. Rev. E 2009, 80, 041124] has been shown to improve the efficiency of this kind of simulations, by blocking the dynamics of particles located outside an established mobility region. In this report, we show that dynamical freezing produces a systematic spurious decrease of the particle density inside the mobility region. As a consequence, the requirements to apply nonequilibrium work theorems are only approximately met. Starting from these considerations, we have developed a simulation scheme, called "elastic barrier dynamical freezing", according to which a stiff potential-energy barrier is enforced at the boundaries of the mobility region, preventing the particles from leaving this region of space during the nonequilibrium trajectories. The method, tested on the calculation of the distance-dependent free energy of a dimer immersed into a Lennard-Jones fluid, provides an accuracy comparable to the conventional steered molecular dynamics, with a computational speedup exceeding a few orders of magnitude.

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Section: Discussionmentioning

confidence: 99%

Elastic Barrier Dynamical Freezing in Free Energy Calculations: A Way To Speed Up Nonequilibrium Molecular Dynamics Simulations by Orders of Magnitude

Giovannelli

Cardini

Chelli

2016

J. Chem. Theory Comput.

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“…The torsion free energy profile about each bond of the probe chain has been constructed by employing the nonequilibrium statistical tool described in refs and and implemented in the C++ library JEFREE, recently developed by some of us and used to perform the calculations. Details about this specific implementation are given in the SI-Sec9.…”

Section: Experimental Details and Discussionmentioning

confidence: 99%

Conformational Mobility in Monolayer-Protected Nanoparticles: From Torsional Free Energy Profiles to NMR Relaxation

et al. 2015

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In this work, we develop a self-consistent route to inspect the conformational mobility of single chains in gold nanoparticles passivated with a monolayer of decanethiols. The approach is based on the match between a theoretical modeling under a coarse-grained level (i.e., system definition, buildup of the free energy profiles along relevant coordinates, modeling/parametrization of the friction, production of stochastic trajectories) and experimental spectroscopic investigations. The agreement between calculated and experimental values of 13 C NMR longitudinal relaxation times supports the theoretical assumptions and the model parametrization. On physical grounds, it emerges that the mobility of the single chains resembles that of an ideal chain made of connected n-butane-like bonds.

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“…10 and to the documentary file 11 (for a recent application of the method see also ref. 28), while here we only give a basic overview.…”

Section: The Jefree Softwarementioning

confidence: 99%

Probing the conformational energetics of alkyl thiols on gold surfaces by means of a morphing/steering non-equilibrium tool

Piserchia

Zerbetto

Frezzato

2015

Phys. Chem. Chem. Phys.

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In this work we show that a non-equilibrium statistical tool based on Jarzynski's equality (JE) can be applied to achieve a sufficiently accurate mapping of the torsion free energy, bond-by-bond, for an alkyl thiol ligand tethered to a gold surface and sensing the presence of the surrounding cluster of similar chains. The strength of our approach is the employment of a strategy to let grow the internal energetics of the whole system (namely, the "energy morphing" stage recently presented by us in J. Comput. Chem., 2014, 35, 1865-1881) before initiating the rotational steering, which yields accurate results in terms of statistical uncertainties and bias on the free energy profiles. The work is mainly methodological and illustrates the feasibility of this kind of inspection on nanoscale molecular clusters with conformational flexibility. The outcomes for the archetype of self-assembled-monolayers considered here, a regular pattern of 10-carbon alkyl thiols on an ideal gold surface, give information on the conformational mobility of the ligands. Notably, such information is unlikely to be obtained by means of standard equilibrium techniques or by conventional molecular dynamics simulations.

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Towards bulk thermodynamics via non-equilibrium methods: gaseous methane as a case study

Cited by 7 publications

References 47 publications

Elastic Barrier Dynamical Freezing in Free Energy Calculations: A Way To Speed Up Nonequilibrium Molecular Dynamics Simulations by Orders of Magnitude

Elastic Barrier Dynamical Freezing in Free Energy Calculations: A Way To Speed Up Nonequilibrium Molecular Dynamics Simulations by Orders of Magnitude

Conformational Mobility in Monolayer-Protected Nanoparticles: From Torsional Free Energy Profiles to NMR Relaxation

Probing the conformational energetics of alkyl thiols on gold surfaces by means of a morphing/steering non-equilibrium tool

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