Response to “Comment on ‘Elasticity of flexible and semiflexible polymers with extensible bonds in the Gibbs and Helmholtz ensembles”’ [J. Chem. Phys. 138, 157101 (2013)]

No abstract: this is a "response" to a Comment

Monte Carlo simulations of single polymer force-extension relations

We present Monte Carlo simulations for studying the statistical mechanics of arbitrarily long single molecules under stretching. In many cases in which the thermodynamic limit is not satisfied, different statistical ensembles yield different macroscopic force-displacement curves. In this work we provide a description of the Monte Carlo simulations and discuss in details the assumptions adopted

Theory and Monte Carlo simulations for the stretching of flexible and semiflexible single polymer chains under external fields

Stretching experiments on single molecules of arbitrary length opened the way for studying the statistical mechanics of small systems. In many cases in which the thermodynamic limit is not satisfied, different macroscopic boundary conditions, corresponding to different statistical mechanics ensembles, yield different force-displacement curves. We formulate analytical expressions and develop Monte Carlo simulations to quantitatively evaluate the difference between the Helmholtz and the Gibbs ensembles for a wide range of polymer models of biological relevance. We consider generalizations of the freely jointed chain and of the worm-like chain models with extensible bonds. In all cases we show that the convergence to the thermodynamic limit upon increasing contour length is described by a suitable power law and a specific scaling exponent, characteristic of each model. (C) 2012 American Institute of Physics

Hydrogen storage in MgH2 matrices: A study of Mg-MgH2 interface using CPMD code on ENEA-GRID

The remarkable ability of magnesium to store significant quantities of hydrogen, in the form (MgH2), has fostered intense research efforts in the last years in view of its future applications where light and safe hydrogen-storage media are needed. However, further research is needed since Mg has a high operation temperature and slow absorption kinetics that prevent for the moment the use in practical applications. To improve and optimize the performances of this material a detailed knowledge of the hydrogen diffusion mechanism at the atomic level is needed. Experiments can only provide indirect evidences of the atomic rearrangement during the desorption process. For these reasons a detailed computational study of MgH2 is invoked to characterize the dynamics of hydrogen during desorption. Further insights are gained by characterizing the Mg-MgH2 interface which is supposed to play a major role in the hydrogen diffusion during absorption and desorption cycles. By means of accurate ab initio molecular dynamics simulations based on the density-functional theory with norm-conserving pseudopotentials and plane-wave expansion (CPMD code) an interface is designed and studied. Extensive electronic structure calculations are used to characterize the equilibrium properties and the behavior of the surfaces in terms of total energy considerations and atomic diffusion

Elasticity of flexible and semiflexible polymers with extensible bonds in the Gibbs and Helmholtz ensembles

Stretching experiments on single molecules of arbitrary length opened the way for studying the statistical mechanics of small systems. In many cases in which the thermodynamic limit is not satisfied, different macroscopic boundary conditions, corresponding to different statistical mechanics ensembles, yield different force-displacement curves. We formulate analytical expressions and develop Monte Carlo simulations to quantitatively evaluate the difference between the Helmholtz and the Gibbs ensembles for a wide range of polymer models of biological relevance. We consider generalizations of the freely jointed chain and of the worm-like chain models with extensible bonds. In all cases we show that the convergence to the thermodynamic limit upon increasing contour length is described by a suitable power law and a specific scaling exponent, characteristic of each model

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.

Interplay of Strain Relaxation and Chemically Induced Diffusion Barriers: Nanostructure Formation in 2D Alloys

We study the formation of nanostructures with alternating stripes composed of bulk-immiscible adsorbates during submonolayer heteroepitaxy. We evaluate the influence of two mechanisms considered in the literature: (i) strain relaxation by alternating arrangement of the adsorbate species, and (ii) kinetic segregation due to chemically induced diffusion barriers. A model ternary system of two adsorbates with opposite misfit relative to the substrate, and symmetric binding is investigated by off-lattice as well as lattice kinetic Monte Carlo simulations. We find that neither of the mechanisms (i) or (ii) alone can account for known experimental observations. Rather, a combination of both is needed. We present an off-lattice model which allows for a qualitative reproduction of stripe patterns as well as island ramification in agreement with recent experimental observations for CoAg/Ru(0001) [R. Q. Hwang, Phys. Rev. Lett. 76, 4757 (1996)]. The quantitative dependencies of stripe width and degree of island ramification on the misfit and interaction strength between the two adsorbate types are presented. Attempts to capture essential features in a simplified lattice gas model show that a detailed incorporation of non-local effects is required.Comment: 24 pages, 12 figure

Magic structures of helical multi-shell zirconium nanowires

The structures of free-standing zirconium nanowires with 0.6$-$2.8 nm in diameter are systematically studied by using genetic algorithm simulations with a tight-binding many body potential. Several multi-shell growth sequences with cylindrical structures are obtained. These multi-shell structures are composed of coaxial atomic shells with the three- and four-strands helical, centered pentagonal and hexagonal, and parallel double-chain-core curved surface epitaxy. Under the same growth sequence, the numbers of atomic strands in inner- and outer-shell show even-odd coupling and usually differ by five. The size and structure dependence of angular correlation functions and vibrational properties of zirconium nanowire are also discussed.Comment: 14 pages, 4 figure

Surfactant effect in heteroepitaxial growth. The Pb - Co/Cu(111) case

A MonteCarlo simulations study has been performed in order to study the effect of Pb as surfactant on the initial growth stage of Co/Cu(111). The main characteristics of Co growing over Cu(111) face, i.e. the decorated double layer steps, the multiple layer islands and the pools of vacancies, disappear with the pre-evaporation of a Pb monolayer. Through MC simulations, a full picture of these complex processes is obtained. Co quickly diffuses through the Pb monolayer exchanging place with Cu atoms at the substrate. The exchange process diffusion inhibits the formation of pure Co islands, reducing the surface stress and then the formation of multilayer islands and the pools of vacancies. On the other hand, the random exchange also suppress the nucleation preferential sites generated by Co atoms at Cu steps, responsible of the step decoration.Comment: 4 pages, latex, 2 figures embedded in the tex

Continuum field description of crack propagation

We develop continuum field model for crack propagation in brittle amorphous solids. The model is represented by equations for elastic displacements combined with the order parameter equation which accounts for the dynamics of defects. This model captures all important phenomenology of crack propagation: crack initiation, propagation, dynamic fracture instability, sound emission, crack branching and fragmentation.Comment: 4 pages, 5 figures, submitted to Phys. Rev. Lett. Additional information can be obtained from http://gershwin.msd.anl.gov/theor