Canonical sampling through velocity-rescaling

We present a new molecular dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains constant during the evolution. In numerical applications this quantity can be used to measure the accuracy of the sampling. We illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liquid phases. Its performance is excellent and largely independent on the thermostat parameter also with regard to the dynamic properties

Tautomeric equilibrium in condensed phases

We present an ab initio molecular dynamics (MD) investigation of the tautomeric equilibrium for aqueous solutions of glycine and acetone at realistic experimental conditions. Metadynamics is used to accelerate proton migration among tautomeric centers. Due to the formation of complex water-ion structures involved the proton dynamics in the aqueous environment, standard enhanced sampling approaches may face severe limitations in providing a general description of the phenomenon. Recently, we developed a set of Collective Variables (CVs) designed to study protons transfer reactions in complex condensed systems [Grifoni et al. PNAS, 2019, 116(10), 4054-4057]. In this work we applied this approach to study proton dissociation dynamics leading to tautomeric interconversion of biologically and chemically relevant prototypical systems, namely glycine and acetone in water. Although relatively simple from a chemical point of view, the results show that even for these small systems complex reaction pathways and non-trivial conversion dynamics are observed. The generality of our method allows obtaining these results without providing any prior information on the dissociation dynamics but only the atomic species that can exchange protons in the process. Our results agree with literature estimates and demonstrate the general applicability of this method in the study of tautomeric reactions

Reconstructing the Density of States by History-Dependent Metadynamics

We present a novel method for the calculation of the energy density of states D(E) for systems described by classical statistical mechanics. The method builds on an extension of a recently proposed strategy that allows the free energy profile of a canonical system to be recovered within a pre-assigned accuracy,[A. Laio and M. Parrinello, PNAS 2002]. The method allows a good control over the error on the recovered system entropy. This fact is exploited to obtain D(E) more efficiently by combining measurements at different temperatures. The accuracy and efficiency of the method are tested for the two-dimensional Ising model (up to size 50x50) by comparison with both exact results and previous studies. This method is a general one and should be applicable to more realistic model systems

Fish Welfare in Aquaculture: Physiological and Immunological Activities for Diets, Social and Spatial Stress on Mediterranean Aqua Cultured Species

Welfare assessment currently is less well-characterized for aquatic animals and the clas- sical methodologies used for terrestrial animals are not adequate to improve our knowledge about fish well-being. Among different approaches, the status of organism responses can be carried out using different physiological and biochemical tools. Here, we present the state of the art regarding fish welfare, methodologies, and experimental results with a particular focus on two important Mediterranean aquaculture species, Sparus aurata and Dicentrarchus labrax. We introduce an approach using physiological stress-indicators, growth performance and swimming activity to investigate the effects of the implantation of electronic tags to facilitate the application of telemetry for aquaculture purposes. The application of telemetry to research on aquatic organisms has expanded recently, and its utilization needs to be better understood. The mentioned approaches have been discussed for application in different aquaculture methodologies. Moreover, social stress and territoriality are relevant factors in the evaluation of gregarious species that may have consequences on the conditions of animals farmed in captivity. These aspects, that may impair the ability of fish to respond to various stimuli or negatively influence the flesh quality, here are analysed through behavioural observation, flanked by the physiological and immunological approach

Accurate sampling using Langevin dynamics

We show how to derive a simple integrator for the Langevin equation and illustrate how it is possible to check the accuracy of the obtained distribution on the fly, using the concept of effective energy introduced in a recent paper [J. Chem. Phys. 126, 014101 (2007)]. Our integrator leads to correct sampling also in the difficult high-friction limit. We also show how these ideas can be applied in practical simulations, using a Lennard-Jones crystal as a paradigmatic case

Metric tensor as the dynamical variable for variable cell-shape molecular dynamics

We propose a new variable cell-shape molecular dynamics algorithm where the dynamical variables associated with the cell are the six independent dot products between the vectors defining the cell instead of the nine cartesian components of those vectors. Our choice of the metric tensor as the dynamical variable automatically eliminates the cell orientation from the dynamics. Furthermore, choosing for the cell kinetic energy a simple scalar that is quadratic in the time derivatives of the metric tensor, makes the dynamics invariant with respect to the choice of the simulation cell edges. Choosing the densitary character of that scalar allows us to have a dynamics that obeys the virial theorem. We derive the equations of motion for the two conditions of constant external pressure and constant thermodynamic tension. We also show that using the metric as variable is convenient for structural optimization under those two conditions. We use simulations for Ar with Lennard-Jones parameters and for Si with forces and stresses calculated from first-principles of density functional theory to illustrate the applications of the method.Comment: 10 pages + 6 figures, Latex, to be published in Physical Review

Elastic Constants of Quantum Solids by Path Integral Simulations

Two methods are proposed to evaluate the second-order elastic constants of quantum mechanically treated solids. One method is based on path-integral simulations in the (NVT) ensemble using an estimator for elastic constants. The other method is based on simulations in the (NpT) ensemble exploiting the relationship between strain fluctuations and elastic constants. The strengths and weaknesses of the methods are discussed thoroughly. We show how one can reduce statistical and systematic errors associated with so-called primitive estimators. The methods are then applied to solid argon at atmospheric pressures and solid helium 3 (hcp, fcc, and bcc) under varying pressures. Good agreement with available experimental data on elastic constants is found for helium 3. Predictions are made for the thermal expectation value of the kinetic energy of solid helium 3.Comment: 9 pages doublecolumn, 6 figures, submitted to PR

Stacking-fault energies for Ag, Cu, and Ni from empirical tight-binding potentials

The intrinsic stacking-fault energies and free energies for Ag, Cu, and Ni are derived from molecular-dynamics simulations using the empirical tight-binding potentials of Cleri and Rosato [Phys. Rev. B 48, 22 (1993)]. While the results show significant deviations from experimental data, the general trend between the elements remains correct. This allows to use the potentials for qualitative comparisons between metals with high and low stacking-fault energies. Moreover, the effect of stacking faults on the local vibrational properties near the fault is examined. It turns out that the stacking fault has the strongest effect on modes in the center of the transverse peak and its effect is localized in a region of approximately eight monolayers around the defect.Comment: 5 pages, 2 figures, accepted for publication in Phys. Rev.

Nonperturbative Gauge Fixing and Perturbation Theory

We compare the gauge-fixing approach proposed by Jona-Lasinio and Parrinello, and by Zwanziger (JPLZ) with the standard Fadeev-Popov procedure, and demonstrate perturbative equality of gauge-invariant quantities, up to irrelevant terms induced by the cutoff. We also show how a set of local, renormalizable Feynman rules can be constructed for the JPLZ procedure.Comment: 9 pages, latex, version to appear in Phys. Rev.