Showing papers by "Fabrizio Cleri published in 2017"
TL;DR: In this paper, a transient thermal regime is achieved in glassy GeTe4 by first-principles molecular dynamics following the recently proposed "approach-to-equilibrium" methodology.
Abstract: A transient thermal regime is achieved in glassy GeTe4 by first-principles molecular dynamics following the recently proposed "approach-to-equilibrium" methodology. The temporal and spatial evolution of the temperature do comply with the time-dependent solution of the heat equation. We demonstrate that the time scales required to create the hot and the cold parts of the system and observe the resulting approach to equilibrium are accessible to first-principles molecular dynamics. Such a strategy provides the thermal conductivity from the characteristic decay time. We rationalize in detail the impact on the thermal conductivity of the initial temperature difference, the equilibration duration, and the main simulation features.
28 citations
TL;DR: In this article, the physicochemical properties of the passivated B-Si(111)-(√3x √3) R30° surface have been described, which enable the self-assembly of molecules into a rich variety of extended and regular structures on silicon.
25 citations
TL;DR: This work focuses on the molecular-scale dynamics of the events immediately following the production of single- and double-strand breaks, since this early-stage evolution of the damage is crucial to determine the subsequent fate of the DNA fragment, and establishes the necessary conditions for the events ultimately leading to DNA fragmentation.
Abstract: Damage to the DNA backbone occurs from natural sources, and with exceedingly large density during radiotherapy, as typically used for cancer treatment. Here, we focus on the molecular-scale dynamics of the events immediately following the production of single- and double-strand breaks, since this early-stage evolution of the damage is crucial to determine the subsequent fate of the DNA fragment. While multiple cleavage of phosphodiester bonds is the first step, however the remaining hydrogen-bond and π-stacking interactions maintain a considerable DNA cohesion, and determine further defect evolution. We use all-atom molecular dynamics to simulate the force spectra and thermal stability of different single- and multiple-defect configurations, in a random 31 bp DNA sequence. Simulations reveal a complex dynamical behaviour of the defects, where collective bond-rearrangement phenomena dominate with respect to simple bond cleavage. Defects are stable against thermal disruption, unless very closely spaced. We establish the necessary conditions for the events ultimately leading to DNA fragmentation. Such findings impact the early stages of damage recognition and signalling by specialised proteins, also implying that the identification and counting of DSBs by different experimental methods is non-unique.
9 citations
TL;DR: In this article, the thermal conductivity of cylindrical and smooth silicon nanowires is systematically studied as a function of diameter and length by fully atomistic simulations, and a transient thermal regime is created and monitored by molecular dynamics.
Abstract: The thermal conductivity of cylindrical and smooth silicon nanowires is systematically studied as a function of diameter and length by fully atomistic simulations. A transient thermal regime is created and monitored by molecular dynamics. This approach-to-equilibrium methodology, already proven to be very efficient for bulk systems, is here applied to nanowires of length up to 1.2 micron, and diameter in the range 1 to 14 nm. It is shown that the temperature profile along the nanowire axis and its temporal evolution comply with the heat equation. A one-dimensional thermal conductivity is extracted from the characteristic decay time according to the time-dependent solution of the heat equation. Like for the bulk using the same method, the thermal conductivity exhibits a length dependence due to the slowly growing cumulative distribution of the phonon mean free paths. Unlike the bulk, the infinite-length saturation of the conductivity value can be observed in our simulations, thanks to a reduction of the phonon mean free path in the nanowires, estimated to be a few hundred nanometers. A finite thermal conductivity can be extracted for each diameter, and no divergence at long length is observed.
9 citations
TL;DR: The apparent Young's and shear moduli of a dense nanostructure, composed of a triangular arrangement of identical MUDA-decorated Au nanoparticles, are found to be smaller than estimates indirectly deduced by atomic-force experiments but quite close to previous computer simulations of molecular monolayers on flat surfaces and of bulk nanoparticle assemblies.
Abstract: The localized deformation of molecular monolayers constrained between the spherical surfaces of Au nanoparticles is studied by means of molecular dynamics simulations. Alkyl or polyethylene glycol long-chain molecules were homogeneously distributed over the curved Au surface, pushed against each other by repeated cycles of force relaxation and constant-volume equilibration at temperatures increasing from 50 to 300 K before being slowly quenched to near-zero temperature. Plots of minimum configurational energy can be obtained as a function of the nanoparticle distance, according to different directions of approach; therefore, such simulations describe a range of deformations, from perfectly uniaxial compression to a combination of compression and shear. Despite the relative rigidity of molecular backbones, the deformation is always found to be localized at the interface between the opposing molecular monolayers. We find that shorter ligands can be more densely packed on the surface but do no interdigitate ...
4 citations