205 research outputs found
Dislocation Core Energies and Core Fields from First Principles
Ab initio calculations in bcc iron show that a screw dislocation
induces a short-range dilatation field in addition to the Volterra elastic
field. This core field is modeled in anisotropic elastic theory using force
dipoles. The elastic modeling thus better reproduces the atom displacements
observed in ab initio calculations. Including this core field in the
computation of the elastic energy allows deriving a core energy which converges
faster with the cell size, thus leading to a result which does not depend on
the geometry of the dislocation array used for the simulation.Comment: DOI: 10.1103/PhysRevLett.102.05550
Predicting dislocation climb: Classical modeling versus atomistic simulations
The classical modeling of dislocation climb based on a continuous description
of vacancy diffusion is compared to recent atomistic simulations of dislocation
climb in body-centered cubic iron under vacancy supersaturation [Phys. Rev.
Lett. 105 095501 (2010)]. A quantitative agreement is obtained, showing the
ability of the classical approach to describe dislocation climb. The analytical
model is then used to extrapolate dislocation climb velocities to lower
dislocation densities, in the range corresponding to experiments. This allows
testing of the validity of the pure climb creep model proposed by Kabir et al.
[Phys. Rev. Lett. 105 095501 (2010)]
Dislocation core field. II. Screw dislocation in iron
The dislocation core field, which comes in addition to the Volterra elastic
field, is studied for the screw dislocation in alpha-iron. This core
field, evidenced and characterized using ab initio calculations, corresponds to
a biaxial dilatation, which we modeled within the anisotropic linear
elasticity. We show that this core field needs to be considered when extracting
quantitative information from atomistic simulations, such as dislocation core
energies. Finally, we look at how dislocation properties are modified by this
core field, by studying the interaction between two dislocations composing a
dipole, as well as the interaction of a screw dislocation with a carbon atom
Screw dislocation in zirconium: An ab initio study
Plasticity in zirconium is controlled by 1/3 screw dislocations
gliding in the prism planes of the hexagonal close-packed structure. This
prismatic and not basal glide is observed for a given set of transition metals
like zirconium and is known to be related to the number of valence electrons in
the d band. We use ab initio calculations based on the density functional
theory to study the core structure of screw dislocations in zirconium.
Dislocations are found to dissociate in the prism plane in two partial
dislocations, each with a pure screw character. Ab initio calculations also
show that the dissociation in the basal plane is unstable. We calculate then
the Peierls barrier for a screw dislocation gliding in the prism plane and
obtain a small barrier. The Peierls stress deduced from this barrier is lower
than 21 MPa, which is in agreement with experimental data. The ability of an
empirical potential relying on the embedded atom method (EAM) to model
dislocations in zirconium is also tested against these ab initio calculations
Time reversal methods in acousto-elastodynamics
The aim of the article is to solve an inverse problem in order to determine the presence and some properties of an elastic “inclusion” (an unknown object, characterized by elastic properties discriminant from the surrounding medium) from partial observa- tions of acoustic waves, scattered by the inclusion. The method will require developing techniques based on Time Reversal methods. A finite element method based on varia- tional acousto-elastodynamics formulation will be derived and used to solve to solve the forward, and then, the time reversed problem. A criterion, derived from the reverse time migration framework, is introduced, to help use to construct images of the inclusions to be determined. Our approach will be applied to configurations modeling breast cancer detection, using simulated ultrasound waves
Nucleation of Al3Zr and Al3Sc in aluminum alloys: from kinetic Monte Carlo simulations to classical theory
Zr and Sc precipitate in aluminum alloys to form the compounds Al3Zr and
Al3Sc which for low supersaturations of the solid solution have the L12
structure. The aim of the present study is to model at an atomic scale this
kinetics of precipitation and to build a mesoscopic model based on classical
nucleation theory so as to extend the field of supersaturations and annealing
times that can be simulated. We use some ab-initio calculations and
experimental data to fit an Ising model describing thermodynamics of the Al-Zr
and Al-Sc systems. Kinetic behavior is described by means of an atom-vacancy
exchange mechanism. This allows us to simulate with a kinetic Monte Carlo
algorithm kinetics of precipitation of Al3Zr and Al3Sc. These kinetics are then
used to test the classical nucleation theory. In this purpose, we deduce from
our atomic model an isotropic interface free energy which is consistent with
the one deduced from experimental kinetics and a nucleation free energy. We
test di erent mean-field approximations (Bragg-Williams approximation as well
as Cluster Variation Method) for these parameters. The classical nucleation
theory is coherent with the kinetic Monte Carlo simulations only when CVM is
used: it manages to reproduce the cluster size distribution in the metastable
solid solution and its evolution as well as the steady-state nucleation rate.
We also find that the capillary approximation used in the classical nucleation
theory works surprisingly well when compared to a direct calculation of the
free energy of formation for small L12 clusters.Comment: submitted to Physical Review B (2004
Statistical inversion from reflections of spherical waves by a randomly layered medium
Involvement of microsomal vesicles in part of the sensitivity of carnitine palmitoyltransferase I to malonyl-CoA inhibition in mitochondrial fractions of rat liver
The Influence of the effect of solute on the thermodynamic driving force on grain refinement of Al alloys
Grain refinement is known to be strongly affected by the solute in cast alloys. Addition of some solute can reduce grain size considerably while others have a limited effect. This is usually attributed to the constitutional supercooling which is quantified by the growth restriction factor, Q. However, one factor that has not been considered is whether different solutes have differing effects on the thermodynamic driving force for solidification. This paper reveals that addition of solute reduces the driving force for solidification for a given undercooling, and that for a particular Q value, it is reduced more substantially when adding eutectic-forming solutes than peritectic-forming elements. Therefore, compared with the eutectic-forming solutes, addition of peritectic-forming solutes into Al alloys not only possesses a higher initial nucleation rate resulted from the larger thermodynamic driving force for solidification, but also promotes nucleation within the constitutionally supercooled zone during growth. As subsequent nucleation can occur at smaller constitutional supercoolings for peritectic-forming elements, a smaller grain size is thus produced. The very small constitutional supercooling required to trigger subsequent nucleation in alloys containing Ti is considered as a major contributor to its extraordinary grain refining efficiency in cast Al alloys even without the deliberate addition of inoculants.The Australian Research Council (ARC DP10955737)
Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi
<p>Abstract</p> <p>Background</p> <p>Noncoding RNA (ncRNA) has been recognized as an important regulator of gene expression networks in Bacteria and Eucaryota. Little is known about ncRNA in thermococcal archaea except for the eukaryotic-like C/D and H/ACA modification guide RNAs.</p> <p>Results</p> <p>Using a combination of <it>in silico </it>and experimental approaches, we identified and characterized novel <it>P</it>. <it>abyssi </it>ncRNAs transcribed from 12 intergenic regions, ten of which are conserved throughout the Thermococcales. Several of them accumulate in the late-exponential phase of growth. Analysis of the genomic context and sequence conservation amongst related thermococcal species revealed two novel <it>P</it>. <it>abyssi </it>ncRNA families. The CRISPR family is comprised of crRNAs expressed from two of the four <it>P</it>. <it>abyssi </it>CRISPR cassettes. The 5'UTR derived family includes four conserved ncRNAs, two of which have features similar to known bacterial riboswitches. Several of the novel ncRNAs have sequence similarities to orphan OrfB transposase elements. Based on RNA secondary structure predictions and experimental results, we show that three of the twelve ncRNAs include Kink-turn RNA motifs, arguing for a biological role of these ncRNAs in the cell. Furthermore, our results show that several of the ncRNAs are subjected to processing events by enzymes that remain to be identified and characterized.</p> <p>Conclusions</p> <p>This work proposes a revised annotation of CRISPR loci in <it>P</it>. <it>abyssi </it>and expands our knowledge of ncRNAs in the Thermococcales, thus providing a starting point for studies needed to elucidate their biological function.</p
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