Showing papers by "Fabrizio Cleri published in 2013"

Thermal conductivity from approach-to-equilibrium molecular dynamics

Abstract: We use molecular dynamics simulations to study the thermal transport properties of a range of poor to good thermal conductors by a method in which two portions are delimited and heated at two different temperatures before the approach-to-equilibrium in the whole structure is monitored. The numerical results are compared to the corresponding solution of the heat equation. Based on this comparison, the observed exponential decay of the temperature difference is interpreted and used to extract the thermal conductivity of homogeneous materials. The method is first applied to bulk silicon and an excellent agreement with previous calculations is obtained. Finally, we predict the thermal conductivity of germanium and α-quartz.

Two-state theory of single-molecule stretching experiments

Abstract: We present a statistical mechanics analysis of the finite-size elasticity of model polymers, consisting of domains that 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.

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)]

Abstract: Two different statistical ensembles can be considered for extending a single polymer chain: the Gibbs (or isotensional) ensemble characterized by a deterministic force applied to the free end of the chain (the other being fixed in a given reference frame), and the Helmholtz (or isometric) ensemble obtained with both the ends of the polymers tethered at two different points of the space. When the thermodynamic limit is satisfied (the number of monomers approaches infinity) these ensembles are equivalent from the thermodynamic point of view: it means that the constitutive equations (vector force-extension relations) assume the same mathematical form in both isotensional and isometric conditions. Equivalently, the Helmholtz and Gibbs free energies are linked by a Legendre transform. We explain that this general result is coherent with some “forms of inequivalence” observed by defining different average values of force and position vectors. However, this fact does not indicate thermodynamic inequivalence as largely discussed in the present Response.

Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation

Abstract: We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm long nanowires, based on a repeated TC5 sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual stacked C*C+ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression and bending deformation with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young's and bending moduli of the nanowire, as wel as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to that of a metal. Besides their yet to be clarified biological significance, i-motif nanowires may qualify as interesting candidates for nanotechnology templates, due to such outstanding mechanical properties.

Silicon Nanotweezers with a microfluidic cavity for the real time characterization of DNA damage under therapeutic radiation beams

Abstract: We report the biomechanical characterization of λ-DNA bundle exposed to a therapeutic radiation beam by silicon Nanotweezers. The micromechanical device endures the harsh environment of radiation beams, and still retains molecular-level detection accuracy. The real-time DNA bundle degradation is observed in terms of biomechanical stiffness and viscosity reduction, both in air and in solution. These results pave the way for both fundamental and clinical studies of DNA degradation mechanisms under ionizing radiation for improved tumor treatment.

Real time bio mechanical characterization of DNA damage under therapeutic radiation beams

Abstract: We report the first real-time biomechanical measurement of DNA bundle degradation in solution when exposed to a therapeutic radiation beam. The Silicon Nano Tweezers and their microfluidic endure the harsh environment of radiation beams and still retain molecular-level accuracy. This result paves the way for both fundamental and clinical studies of DNA degradation under radiation for improved tumor treatment.

4422 - STRESS AND STRAIN FIELDS OF A CRACK-INCLUSION PAIR IN β-SiC: AN ATOMISTIC INVESTIGATION OF NONLINEARITY EFFECTS

Abstract: We investigate the interaction of a microcrack and an inclusion in monocrystal β-SiC under plane strain loading condition. By means of molecular dynamics simulations we are able to represent properly the mechanical loads and to calculate the stress and strain fields when the distance of the microcrack and the inclusion is varied. When the crack-inclusion distance is large respect to the dimension of the isolated defects our results are consistent with the basic results of the linear elastic fracture mechanics, and provide a deeper insight at the nanoscale. At small crack-inclusion distances the stress and strain fields are not additive respect to the isolated microcrack and inclusion and we calculate such a defect of linearity. We find power law dependence of the stress and strain defect of linearity on the relative distance of the microcrack and the inclusion.

5048 - atomistic simulations on fracture events in nanostructured silicon carbide

Abstract: We present the conceptual framework of atomistic simulations applied to the investigation of mechanical properties of materials. As a show-case application, we discuss a fracture event in bulk silicon carbide when a hard nanofiber inclusion of diamond is present in the neighborhood of a microcrack. We show that, for suitable distances between the two defects, the nanofiber inhibits the propagation of a fracture event from the microcrack tip. This result is consistent with the suggestion that fiber reinforcement could provide increased fracture thoughness in ceramic materials.