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)]

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

Complex Precipitation Pathways in Multi-Component Alloys

One usual way to strengthen a metal is to add alloying elements and to control the size and the density of the precipitates obtained. However, precipitation in multicomponent alloys can take complex pathways depending on the relative diffusivity of solute atoms and on the relative driving forces involved. In Al-Zr-Sc alloys, atomic simulations based on first-principle calculations combined with various complementary experimental approaches working at different scales reveal a strongly inhomogeneous structure of the precipitates: owing to the much faster diffusivity of Sc compared with Zr in the solid solution, and to the absence of Zr and Sc diffusion inside the precipitates, the precipitate core is mostly Sc-rich, whereas the external shell is Zr-rich. This explains previous observations of an enhanced nucleation rate in Al-Zr-Sc alloys compared with binary Al-Sc alloys, along with much higher resistance to Ostwald ripening, two features of the utmost importance in the field of light high-strength materials

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

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

Ab initio study of the modification of elastic properties of alpha-iron by hydrostatic strain and by hydrogen interstitials

The effect of hydrostatic strain and of interstitial hydrogen on the elastic properties of $\alpha$-iron is investigated using \textit{ab initio} density-functional theory calculations. We find that the cubic elastic constants and the polycrystalline elastic moduli to a good approximation decrease linearly with increasing hydrogen concentration. This net strength reduction can be partitioned into a strengthening electronic effect which is overcome by a softening volumetric effect. The calculated hydrogen-dependent elastic constants are used to determine the polycrystalline elastic moduli and anisotropic elastic shear moduli. For the key slip planes in $\alpha$-iron, $[1\bar{1}0]$ and $[11\bar{2}]$, we find a shear modulus reduction of approximately 1.6% per at.% H.Comment: Updated first part of 1009.378

Partial Resistance to Peroxisome Proliferator–Activated Receptor-α Agonists in ZDF Rats Is Associated With Defective Hepatic Mitochondrial Metabolism

OBJECTIVE—Fluxes through mitochondrial pathways are defective in insulin-resistant skeletal muscle, but it is unclear whether similar mitochondrial defects play a role in the liver during insulin resistance and/or diabetes. The purpose of this study is to determine whether abnormal mitochondrial metabolism plays a role in the dysregulation of both hepatic fat and glucose metabolism during diabetes

Longitudinal association of biomarkers of pesticide exposure with cardiovascular disease risk factors in youth with diabetes

Background: Cardiovascular disease (CVD) is the leading cause of death among individuals with diabetes, but little is known about the role of exposures to environmental chemicals such as pesticides in the early development of CVD risk in this population. Objectives: To describe changes over time in concentrations of pesticide biomarkers among youth with diabetes in the United States and to estimate the longitudinal association between these concentrations and established risk factors for CVD. Methods: Pesticide biomarkers were quantified in urine and serum samples from 87 youth with diabetes participating in the multi-center SEARCH cohort study. Samples were obtained around the time of diagnosis (baseline visit, between 2006 and 2010) and, on average, 5.4 years later (follow-up visit, between 2012 and 2015). We calculated geometric mean (95% CI) pesticide biomarker concentrations. Eight CVD risk factors were measured at these two time points: body mass index (BMI) z-score, HbA1c, insulin sensitivity, fasting C-peptide (FCP), LDL cholesterol, HDL cholesterol, total cholesterol, and triglycerides. Linear regression models were used to estimate the associations between each pesticide biomarker at baseline and each CVD risk factor at follow-up, adjusting for baseline health outcome, elapsed time between baseline and follow up, sex, age, race/ethnicity, and diabetes type. Results: Participants were, on average, 14.2 years old at their baseline visit, and most were diagnosed with type 1 diabetes (57.5%). 4-nitrophenol, 3-phenoxybenzoic acid, 2,4-dichlorophenoxyacetic acid (2,4-D), 3,5,6-trichloro-2-pyridinol, 2,2-bis(4-chlorophenyl)-1,1-dichloroethene, and hexachlorobenzene were detected in a majority of participants at both time points. Participants in the highest quartile of 2,4-D and 4-nitrophenol at baseline had HbA1c levels at follow-up that were 1.05 percentage points (95% CI: −0.40, 2.51) and 1.27 percentage points (0.22, 2.75) higher, respectively, than participants in the lowest quartile of these pesticide biomarkers at baseline. These participants also had lower log FCP levels (indicating reduced beta-cell function) compared to participants in the lowest quartile at baseline: beta (95% CI) for log FCP of −0.64 (−1.17, −0.11) for 2,4-D and −0.39 (−0.96, 0.18) for 4-nitrophenol. In other words, participants in the highest quartile of 2,4-D had a 47.3% lower FCP level compared to participants in the lowest quartile, and those in the highest quartile of 4-nitrophenol had a 32.3% lower FCP level than those in the lowest quartile. Participants with trans-nonachlor concentrations in the highest quartile at baseline had HbA1c levels that were 1.45 percentage points (−0.11, 3.01) higher and log FCP levels that were −0.28 (−0.84, 0.28) lower than participants in the lowest quartile at baseline, that is to say, participants in the highest quartile of trans-nonachlor had a 24.4% lower FCP level than those in the lowest quartile. While not all of these results were statistically significant, potentially due to the small same size, clinically, there appears to be quantitative differences. No associations were observed between any pesticide biomarker at baseline with BMI z-score or insulin sensitivity at follow-up. Conclusions: Exposure to select pesticides may be associated with impaired beta-cell function and poorer glycemic control among youth with diabetes

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

The αGal Epitope of the Histo-Blood Group Antigen Family Is a Ligand for Bovine Norovirus Newbury2 Expected to Prevent Cross-Species Transmission

Among Caliciviridae, the norovirus genus encompasses enteric viruses that infect humans as well as several animal species, causing gastroenteritis. Porcine strains are classified together with human strains within genogroup II, whilst bovine norovirus strains represent genogroup III. Various GI and GII human strains bind to carbohydrates of the histo-blood group family which may be shared among mammalian species. Genetic relatedness of human and animal strains as well as the presence of potentially shared ligands raises the possibility of norovirus cross-species transmission. In the present study, we identified a carbohydrate ligand for the prototype bovine norovirus strain Bo/Newbury2/76/UK (NB2). Attachment of virus-like particles (VLPs) of the NB2 strain to bovine gut tissue sections showed a complete match with the staining by reagents recognizing the Galα1,3 motif. Alpha-galactosidase treatment confirmed involvement of a terminal alpha-linked galactose. Specific binding of VLPs to the αGal epitope (Galα3Galβ4GlcNAcβ-R) was observed. The binding of Galα3GalαOMe to rNB2 VLPs was characterized at atomic resolution employing saturation transfer difference (STD) NMR experiments. Transfection of human cells with an α1,3galactosyltransferase cDNA allowed binding of NB2 VLPs, whilst inversely, attachment to porcine vascular endothelial cells was lost when the cells originated from an α1,3galactosyltransferase KO animal. The αGal epitope is expressed in all mammalian species with the exception of the Hominidaea family due to the inactivation of the α1,3galactosyltransferase gene (GGTA1). Accordingly, the NB2 carbohydrate ligand is absent from human tissues. Although expressed on porcine vascular endothelial cells, we observed that unlike in cows, it is not present on gut epithelial cells, suggesting that neither man nor pig could be infected by the NB2 bovine strain