Overcoming timescale and finite-size limitations to compute nucleation rates from small scale Well Tempered Metadynamics simulations

Condensation of a liquid droplet from a supersaturated vapour phase is initiated by a prototypical nucleation event. As such it is challenging to compute its rate from atomistic molecular dynamics simulations. In fact at realistic supersaturation conditions condensation occurs on time scales that far exceed what can be reached with conventional molecular dynamics methods. Another known problem in this context is the distortion of the free energy profile associated to nucleation due to the small, finite size of typical simulation boxes. In this work the problem of time scale is addressed with a recently developed enhanced sampling method while contextually correcting for finite size effects. We demonstrate our approach by studying the condensation of argon, and showing that characteristic nucleation times of the order of magnitude of hours can be reliably calculated, approaching realistic supersaturation conditions, thus bridging the gap between what standard molecular dynamics simulations can do and real physical systems.Comment: 9 pages, 7 figures, additional figures and data provided as supplementary information. Submitted to the Journal of Chemical Physisc

Langevin equation with colored noise for constant-temperature molecular dynamics simulations

We discuss the use of a Langevin equation with a colored (correlated) noise to perform constant-temperature molecular dynamics simulations. Since the equations of motion are linear in nature, it is easy to predict the response of a Hamiltonian system to such a thermostat and to tune at will the relaxation time of modes of different frequency. This allows one to optimize the time needed to thermalize the system and generate independent configurations. We show how this frequency-dependent response can be exploited to control the temperature of Car-Parrinello-like dynamics, keeping at low temperature the electronic degrees of freedom, without affecting the adiabatic separation from the vibrations of the ions

Metadynamics with adaptive Gaussians

Metadynamics is an established sampling method aimed at reconstructing the free-energy surface relative to a set of appropriately chosen collective variables. In standard metadynamics the free-energy surface is filled by the addition of Gaussian potentials of pre-assigned and typically diagonal covariance. Asymptotically the free-energy surface is proportional to the bias deposited. Here we consider the possibility of using Gaussians whose variance is adjusted on the fly to the local properties of the free-energy surface. We suggest two different prescriptions: one is based on the local diffusivity and the other on the local geometrical properties. We further examine the problem of extracting the free-energy surface when using adaptive Gaussians. We show that the standard relation between the bias and the free energy does not hold. In the limit of narrow Gaussians an explicit correction can be evaluated. In the general case we propose to use instead a relation between bias and free energy borrowed from umbrella sampling. This relation holds for all kinds of incrementally deposited bias. We illustrate on the case of alanine dipeptide the advantage of using adaptive Gaussians in conjunction with the new free-energy estimator both in terms of accuracy and speed of convergence.Comment: Reprinted (adapted) with permission from J. Chem. Theory Comput., DOI: 10.1021/ct3002464. Copyright (2012) American Chemical Societ

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

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

We present a method for determining the free energy dependence on a selected number of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting cases. Convergence and errors can be rigorously and easily controlled. The parameters of the simulation can be tuned so as to focus the computational effort only on the physically relevant regions of the order parameter space. The algorithm is tested on the reconstruction of alanine dipeptide free energy landscape

Nuclear quantum effects in solids using a colored-noise thermostat

We present a method, based on a non-Markovian Langevin equation, to include quantum corrections to the classical dynamics of ions in a quasi-harmonic system. By properly fitting the correlation function of the noise, one can vary the fluctuations in positions and momenta as a function of the vibrational frequency, and fit them so as to reproduce the quantum-mechanical behavior, with minimal a priori knowledge of the details of the system. We discuss the application of the thermostat to diamond and to ice Ih. We find that results in agreement with path-integral molecular dynamics can be obtained using only a fraction of the computational effort.Comment: submitted for publicatio

AN INTEGRATED MODEL FOR THE ASSESSMENT OF STRESS-RELATED RISK FACTORS IN HEALTH CARE PROFESSIONALS

5Abstract To assess the risk from exposure to occupational stress and burnout in health care workers (HCW), a cross-sectional study was planned to compare objective data that can represent potential job stressors in hospital wards and subjective symptoms reported by the workers. Medical doctors, nurses and ancillary workers of the Internal Medicine Wards of a large public hospital in Northern Italy participated in the study. Three subjective questionnaires were administered: the Job Content Questionnaire (JCQ), the State-Trait Anxiety Inventory (STAI), the Maslach Burnout Inventory (MBI). In addition, seven objective parameters were collected as average during the 3 months period prior to the study: a) working understaffed; b) ratio number of patients/HCW on service; c) ratio number of HCW on sick leave/ HCW on service; d) number of skipped days off after night shifts; e) days of sick leave; f) number of deceased patients; g) number of accidents at work. A total group of 230 HCW were examined, employed in six different sub-units of the Medical wards. The female workers were 67.8% and the male workers 32.2%, the mean age was 37.4 years (SD 9.3) in the total group of HCW, 35.1 years (SD 7.9) in females and 42.3 years (SD 10.3) in males. The average scores of subjective and objective parameters resulted significantly higher in the same sub-units. The correlation analysis showed that the subjective questionnaires were highly inter-related. The multivariate analysis showed that the days of sick leave were significantly related to the subjective questionnaires, and the subjective subscales of emotional exhaustion (from MBI), job demand and decision latitude (from JCQ) and STAIt were significantly related to some of the objective parameters. These results support the integrated use of multiple subjective and objective assessment as the most appropriate approach for the evaluation of occupational stress.openopenAlbini, Elisa; Zoni, Silvia; Parrinello, Giovanni; Benedetti, Laura; Lucchini, RobertoAlbini, Elisa; Zoni, Silvia; Parrinello, Giovanni; Benedetti, Laura; Lucchini, Robert

Preliminary observations on haemodynamics during physiological stress conditions following 'double-orifice' mitral valve repair

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The double-orifice technique for mitral valve reconstruction: predictors of postoperative outcome

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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