1,720,960 research outputs found
Two-state theory of single-molecule stretching experiments
No full textWe present a statistical mechanics analysis of the finite-size elasticity of model polymers, consisting of domains which can exhibit transitions between more than one stable state at large applied force. The constant-force (Gibbs) and constant-displacement (Helmholtz) formulations of single molecule stretching experiments are shown to converge in the thermodynamic limit. Monte Carlo simulations of continuous three dimensional polymers of variable length are carried out, based on this formulation. We demonstrate that the experimental force-extension curves for short and long polymers are described by a unique universal model, despite the differences in chemistry and rate-dependence of transition forces
Theory and Monte Carlo simulations for the stretching of flexible and semiflexible single polymer chains under external fields
No full textStretching 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
Monte Carlo simulations of single polymer force-extension relations
Full text linkWe 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
Elastic behavior of inhomogeneities with size and shape different from their hosting cavities
No full textIn this paper we consider an application of the Eshelby theory concerning the elastic behavior of prestrained or prestressed inhomogeneities. The theory, in its original version, deals with a configuration where both the ellipsoidal particle and the surrounding matrix are in elastostatic equilibrium if no external loads are applied to the system. Here, we consider slightly different shapes and sizes for the particle and the hosting cavity (whose surfaces are firmly bonded together) and, therefore, we observe a given state of strain (or stress) even without externally applied loads. We develop a complete procedure able to determine the uniform elastic field induced in an arbitrarily prestrained particle subjected to arbitrary remote loadings
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)]
Full text linkNo abstract: this is a "response" to a Comment
Elastic properties of hydrogenated graphene
No full textThere exist three conformers of hydrogenated graphene, referred to as chair-, boat-, or washboard-graphane. These systems have a perfect two-dimensional periodicity mapped onto the graphene scaffold but they are characterized by a sp3 orbital hybridization, have different crystal symmetry, and otherwise behave upon loading. By first-principles calculations we determine their structural and phonon properties, as well as we establish their relative stability. Through continuum elasticity we define a simulation protocol addressed to measure by a computer experiment their linear and nonlinear elastic moduli and we actually compute them by first principles. We argue that all graphane conformers respond to any arbitrarily oriented extension with a much smaller lateral contraction than the one calculated for graphene. Furthermore, we provide evidence that boat-graphane has a small and negative Poisson ratio along the armchair and zigzag principal directions of the carbon honeycomb lattice (axially auxetic elastic behavior). Moreover, we show that chair-graphane admits both softening and hardening hyperelasticity, depending on the direction of applied load
Molecular dynamics of ionic self-diffusion at an MgO grain boundary
No full textThe characterization of self-diffusion in MgO grain boundaries is a materials science problem of general interest, being relevant to the stability and reactivity of MgO layers in artificial nanostructures as well as to the understanding of mass transport and morphological evolution in polycrystalline metal oxides which are employed in many technological applications. In addition, atomic transport in MgO is a key factor to describe the rheology of the Earth’s lower mantle. In this work, we tackle the problem using a classical molecular dynamics model and finite-temperature simulations. To this purpose, we first design a stable grain boundary structure, which is meant to be representative of general internal interfaces in nanocrystalline MgO. The Mg and O self-diffusion coefficients along this grain boundary are then determined as a function of temperature by calculating the mean-square ionic displacement in the boundary region. Two different diffusion regimes at low and high temperature are identified, allowing to obtain the relevant activation enthalpies for migration from the temperature dependance of the diffusion coefficients. Our results prove that Mg diffusion along MgO grain boundaries is sufficiently fast to explain the recently reported development of MgO hollow structures during repeated hydrogen sorption cycles in Mg/MgO nanoparticles
Elasticity of flexible and semiflexible polymers with extensible bonds in the Gibbs and Helmholtz ensembles
No full textStretching 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
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
- …
