Kinetics of martensitic transitions in Cu-Al-Mn under thermal cycling: Analysis at multiple length scales

In this paper we study the evolution of the kinetic features of the martensitic transition in a Cu-Al-Mn single crystal under thermal cycling. The use of several experimental techniques including optical microscopy, calorimetry, and acoustic emission, has enabled us to perform an analysis at multiple scales. In particular, we have focused on the analysis of avalanche events (associated with the nucleation and growth of martensitic domains), which occur during the transition. There are significant differences between the kinetics at large and small length scales. On the one hand, at small length scales, small avalanche events tend to sum to give new larger events in subsequent loops. On the other hand, at large length scales the large domains tend to split into smaller ones on thermal cycling. We suggest that such different behavior is the necessary ingredient that leads the system to the final critical state corresponding to a power-law distribution of avalanches.

The circadian clock coordinates ribosome biogenesis.

Biological rhythms play a fundamental role in the physiology and behavior of most living organisms. Rhythmic circadian expression of clock-controlled genes is orchestrated by a molecular clock that relies on interconnected negative feedback loops of transcription regulators. Here we show that the circadian clock exerts its function also through the regulation of mRNA translation. Namely, the circadian clock influences the temporal translation of a subset of mRNAs involved in ribosome biogenesis by controlling the transcription of translation initiation factors as well as the clock-dependent rhythmic activation of signaling pathways involved in their regulation. Moreover, the circadian oscillator directly regulates the transcription of ribosomal protein mRNAs and ribosomal RNAs. Thus the circadian clock exerts a major role in coordinating transcription and translation steps underlying ribosome biogenesis.

Diluted three-dimensional random field Ising model at zero temperature with metastable dynamics.

The influence of vacancy concentration on the behavior of the three-dimensional random field Ising model with metastable dynamics is studied. We have focused our analysis on the number of spanning avalanches which allows us a clear determination of the critical line where the hysteresis loops change from continuous to discontinuous. By a detailed finite-size scaling analysis we determine the phase diagram and numerically estimate the critical exponents along the whole critical line. Finally, we discuss the origin of the curvature of the critical line at high vacancy concentration.

Influence of the driving mechanism on the response of systems with athermal dynamics: The example of the random-field Ising model

We investigate the influence of the driving mechanism on the hysteretic response of systems with athermal dynamics. In the framework of local mean-field theory at finite temperature (but neglecting thermally activated processes), we compare the rate-independent hysteresis loops obtained in the random field Ising model when controlling either the external magnetic field H or the extensive magnetization M. Two distinct behaviors are observed, depending on disorder strength. At large disorder, the H-driven and M-driven protocols yield identical hysteresis loops in the thermodynamic limit. At low disorder, when the H-driven magnetization curve is discontinuous (due to the presence of a macroscopic avalanche), the M-driven loop is reentrant while the induced field exhibits strong intermittent fluctuations and is only weakly self-averaging. The relevance of these results to the experimental observations in ferromagnetic materials, shape memory alloys, and other disordered systems is discussed.

Hysteresis in a system driven by either generalized force or displacement variables: martensitic phase transition in single-crystalline Cu-Zn-Al

We report on experiments aimed at comparing the hysteretic response of a Cu-Zn-Al single crystal undergoing a martensitic transition under strain-driven and stress-driven conditions. Strain-driven experiments were performed using a conventional tensile machine while a special device was designed to perform stress-driven experiments. Significant differences in the hysteresis loops were found. The strain-driven curves show reentrant behavior yield point which is not observed in the stress-driven case. The dissipated energy in the stress-driven curves is larger than in the strain-driven ones. Results from recently proposed models qualitatively agree with experiments.

Helium in polygonal nanopores at zero temperature: Density functional theory calculations

We investigate adsorption of helium in nanoscopic polygonal pores at zero temperature using a finite-range density functional theory. The adsorption potential is computed by means of a technique denoted as the elementary source method. We analyze a rhombic pore with Cs walls, where we show the existence of multiple interfacial configurations at some linear densities, which correspond to metastable states. Shape transitions and hysterectic loops appear in patterns which are richer and more complex than in a cylindrical tube with the same transverse area.

Unique spectrum of activity of prosimian TRIM5alpha against exogenous and endogenous retroviruses.

Lentiviruses, the genus of retrovirus that includes HIV-1, rarely endogenize. Some lemurs uniquely possess an endogenous lentivirus called PSIV ("prosimian immunodeficiency virus"). Thus, lemurs provide the opportunity to study the activity of host defense factors, such as TRIM5α, in the setting of germ line invasion. We characterized the activities of TRIM5α proteins from two distant lemurs against exogenous retroviruses and a chimeric PSIV. TRIM5α from gray mouse lemur, which carries PSIV in its genome, exhibited the narrowest restriction activity. One allelic variant of gray mouse lemur TRIM5α restricted only N-tropic murine leukemia virus (N-MLV), while a second variant restricted N-MLV and, uniquely, B-tropic MLV (B-MLV); both variants poorly blocked PSIV. In contrast, TRIM5α from ring-tailed lemur, which does not contain PSIV in its genome, revealed one of the broadest antiviral activities reported to date against lentiviruses, including PSIV. Investigation into the antiviral specificity of ring-tailed lemur TRIM5α demonstrated a major contribution of a 32-amino-acid expansion in variable region 2 (v2) of the B30.2/SPRY domain to the breadth of restriction. Data on lemur TRIM5α and the prediction of ancestral simian sequences hint at an evolutionary scenario where antiretroviral specificity is prominently defined by the lineage-specific expansion of the variable loops of B30.2/SPRY.

The QCD Potential at O(1/m2): Complete spin-dependent and spin-independent result

Within an effective field theory framework, we obtain an expression, with O(1/m2) accuracy, for the energies of the gluonic excitations between heavy quarks, which holds beyond perturbation theory. For the singlet heavy-quarkantiquark energy, in particular, we also obtain an expression in terms of Wilson loops. This provides, twenty years after the seminal work of Eichten and Feinberg, the first complete expression for the heavy quarkonium potential up to O(1/m2) for pure gluodynamics. Several errors present in the previous literature (also in the work of Eichten and Feinberg) have been corrected. We also briefly discuss the power counting of NRQCD in the nonperturbative regime.

Novel calmodulin mutations associated with congenital arrhythmia susceptibility.

BACKGROUND: Genetic predisposition to life-threatening cardiac arrhythmias such as congenital long-QT syndrome (LQTS) and catecholaminergic polymorphic ventricular tachycardia (CPVT) represent treatable causes of sudden cardiac death in young adults and children. Recently, mutations in calmodulin (CALM1, CALM2) have been associated with severe forms of LQTS and CPVT, with life-threatening arrhythmias occurring very early in life. Additional mutation-positive cases are needed to discern genotype-phenotype correlations associated with calmodulin mutations. METHODS AND RESULTS: We used conventional and next-generation sequencing approaches, including exome analysis, in genotype-negative LQTS probands. We identified 5 novel de novo missense mutations in CALM2 in 3 subjects with LQTS (p.N98S, p.N98I, p.D134H) and 2 subjects with clinical features of both LQTS and CPVT (p.D132E, p.Q136P). Age of onset of major symptoms (syncope or cardiac arrest) ranged from 1 to 9 years. Three of 5 probands had cardiac arrest and 1 of these subjects did not survive. The clinical severity among subjects in this series was generally less than that originally reported for CALM1 and CALM2 associated with recurrent cardiac arrest during infancy. Four of 5 probands responded to β-blocker therapy, whereas 1 subject with mutation p.Q136P died suddenly during exertion despite this treatment. Mutations affect conserved residues located within Ca(2+)-binding loops III (p.N98S, p.N98I) or IV (p.D132E, p.D134H, p.Q136P) and caused reduced Ca(2+)-binding affinity. CONCLUSIONS: CALM2 mutations can be associated with LQTS and with overlapping features of LQTS and CPVT.

Dynamics of the two-dimensional gonihedric spin model

In this paper, we study dynamical aspects of the two-dimensional (2D) gonihedric spin model using both numerical and analytical methods. This spin model has vanishing microscopic surface tension and it actually describes an ensemble of loops living on a 2D surface. The self-avoidance of loops is parametrized by a parameter ¿. The ¿=0 model can be mapped to one of the six-vertex models discussed by Baxter, and it does not have critical behavior. We have found that allowing for ¿¿0 does not lead to critical behavior either. Finite-size effects are rather severe, and in order to understand these effects, a finite-volume calculation for non-self-avoiding loops is presented. This model, like his 3D counterpart, exhibits very slow dynamics, but a careful analysis of dynamical observables reveals nonglassy evolution (unlike its 3D counterpart). We find, also in this ¿=0 case, the law that governs the long-time, low-temperature evolution of the system, through a dual description in terms of defects. A power, rather than logarithmic, law for the approach to equilibrium has been found.

TCRep 3D: an automated in silico approach to study the structural properties of TCR repertoires.

TCRep 3D is an automated systematic approach for TCR-peptide-MHC class I structure prediction, based on homology and ab initio modeling. It has been considerably generalized from former studies to be applicable to large repertoires of TCR. First, the location of the complementary determining regions of the target sequences are automatically identified by a sequence alignment strategy against a database of TCR Vα and Vβ chains. A structure-based alignment ensures automated identification of CDR3 loops. The CDR are then modeled in the environment of the complex, in an ab initio approach based on a simulated annealing protocol. During this step, dihedral restraints are applied to drive the CDR1 and CDR2 loops towards their canonical conformations, described by Al-Lazikani et. al. We developed a new automated algorithm that determines additional restraints to iteratively converge towards TCR conformations making frequent hydrogen bonds with the pMHC. We demonstrated that our approach outperforms popular scoring methods (Anolea, Dope and Modeller) in predicting relevant CDR conformations. Finally, this modeling approach has been successfully applied to experimentally determined sequences of TCR that recognize the NY-ESO-1 cancer testis antigen. This analysis revealed a mechanism of selection of TCR through the presence of a single conserved amino acid in all CDR3β sequences. The important structural modifications predicted in silico and the associated dramatic loss of experimental binding affinity upon mutation of this amino acid show the good correspondence between the predicted structures and their biological activities. To our knowledge, this is the first systematic approach that was developed for large TCR repertoire structural modeling.

Regulated exocytosis from astrocytes physiological and pathological related aspects.

Astrocytes have traditionally been considered ancillary, satellite cells of the nervous system. However, it is a very recent acquisition that glial cells generate signaling loops which are integral to the brain circuitry and participate, interactively with neuronal networks, in the processing of information. Such a conceptual breakthrough makes this field of investigation one of the hottest in neuroscience, as it calls for a revision of past theories of brain function as well as for new strategies of experimental exploration of brain function. Glial cells are electrically not excitable, and it was only the use of optical recording techniques together with calcium sensitive dyes, that allowed the chemical excitability of glial cells to become apparent. Studies using these new techniques have shown for the first time that glial cells are activated by surrounding synaptic activity and translate neuronal signals into their own calcium code. Intracellular calcium concentration([Ca2+]i) elevations in glial cells have then shown to underlie spatial transfer of information in the glial network, accompanied by release of chemical transmitters (gliotransmitters) such as glutamate and back-signaling to neurons. As a consequence, optical imaging techniques applied to cell cultures or intact tissue have become a state-of-the-art technology for studying glial cell signaling. The molecular mechanisms leading to release of "gliotransmitters," especially glutamate, from glia are under debate. Accumulating evidence clearly indicates that astrocytes secrete numerous transmitters by Ca(2+)-dependent exocytosis. This review will discuss the mechanisms underlying the release of chemical transmitters from astrocytes with a particular emphasis to the regulated exocytosis processes.

SrRuO3/SrTiO3/SrRuO3 heterostructures for magnetic tunnel junctions

We report on the growth and characterization of SrRuO3 single layers and SrRuO3/SrTiO3/SrRuO3 heterostructures grown on SrTiO3(100) substrates. The thickness dependence of the coercivity was determined for these single layers. Heterostructures with barrier thickness tb=1, 2.5, and 4 nm were fabricated, with electrodes having thickness ranging from 10 to 100 nm. The hysteresis loops of heterostructures with tb=2.5¿nm, 4 nm reveal uncoupled magnetic switching of the electrodes. Therefore, these heterostructures can be used for the fabrication of magnetic tunneling junctions.

Kerr measurements on single-domain SrRuO3 thin films

We report on the magneto-optical measurements of an epitaxial SrRuO3 film grown on SrTiO3 (0 0 1), which previously was determined to be single domain orientated by x-ray diffraction and Raman spectroscopy techniques. Our experiments reveal a large Kerr rotation, which reaches a maximum value of about 0.5° at low temperature. By measuring magnetic hysteresis loops at different temperatures, we determined the temperature dependence of the Kerr rotation in the polar configuration. Values of the anisotropic magnetoresistance ~ 20% have been measured. These values are remarkably higher than those of other metallic oxides such as manganites. This striking difference can be attributed to the strong spin-orbit interaction of the Ru 4d ion in the SrRuO3 compound.

Influence of the dipolar interactions in the magnetization reversal asymmetry of hard-soft magnetic ribbons

Partial crystallization of the metallic glass Co66Si16B12Fe4Mo2 was performed by annealing at temperatures between 500 and 540°C for 10-20 min, resulting in crystallite volume fractions of (0.7-5)×10¿3 and sizes of 50-100 nm. This two-phase alloy presents a remarkable feature: a hysteresis loop shift that can be tailored by simply premagnetizing the sample in the adequate magnetic field. Shifts as large as five times the coercive field have been obtained which make them interesting for application as magnetic cores in dc pulse transformers. The asymetrical magnetic reversal is explained in terms of the magnetic dipolar field interaction and the observed hysteresis loops have been satisfactorily simulated by a modification of Stoner-Wohlfarth¿s model of coherent rotations.