Near-Equilibrium Dynamics of Crystalline Interfaces with Long-Range Interactions in 1+1 Dimensional Systems

The dynamics of a one-dimensional crystalline interface model with long-range interactions is investigated. In the absence of randomness, the linear response mobility decreases to zero when the temperature approaches the roughening transition from above, in contrast to a finite jump at the critical point in the Kosterlitz-Thouless (KT) transition. In the presence of substrate disorder, there exists a phase transition into a low-temperature pinning phase with a continuously varying dynamic exponent $z>1$. The expressions for the non-linear response mobility of a crystalline interface in both cases are also derived.Comment: 14 Pages, Revtex3.0, accepted to be published in Phys. Rev. E Rapid Communicatio

Commensurability oscillations in the rf conductivity of unidirectional lateral superlattices: measurement of anisotropic conductivity by coplanar waveguide

We have measured the rf magnetoconductivity of unidirectional lateral superlattices (ULSLs) by detecting the attenuation of microwave through a coplanar waveguide placed on the surface. ULSL samples with the principal axis of the modulation perpendicular (S_perp) and parallel (S_||) to the microwave electric field are examined. For low microwave power, we observe expected anisotropic behavior of the commensurability oscillations (CO), with CO in samples S_perp and S_|| dominated by the diffusion and the collisional contributions, respectively. Amplitude modulation of the Shubnikov-de Haas oscillations is observed to be more prominent in sample S_||. The difference between the two samples is washed out with the increase of the microwave power, letting the diffusion contribution govern the CO in both samples. The failure of the intended directional selectivity in the conductivity measured with high microwave power is interpreted in terms of large-angle electron-phonon scattering.Comment: 8 pages, 5 figure

Finite-size and correlation-induced effects in Mean-field Dynamics

The brain's activity is characterized by the interaction of a very large number of neurons that are strongly affected by noise. However, signals often arise at macroscopic scales integrating the effect of many neurons into a reliable pattern of activity. In order to study such large neuronal assemblies, one is often led to derive mean-field limits summarizing the effect of the interaction of a large number of neurons into an effective signal. Classical mean-field approaches consider the evolution of a deterministic variable, the mean activity, thus neglecting the stochastic nature of neural behavior. In this article, we build upon two recent approaches that include correlations and higher order moments in mean-field equations, and study how these stochastic effects influence the solutions of the mean-field equations, both in the limit of an infinite number of neurons and for large yet finite networks. We introduce a new model, the infinite model, which arises from both equations by a rescaling of the variables and, which is invertible for finite-size networks, and hence, provides equivalent equations to those previously derived models. The study of this model allows us to understand qualitative behavior of such large-scale networks. We show that, though the solutions of the deterministic mean-field equation constitute uncorrelated solutions of the new mean-field equations, the stability properties of limit cycles are modified by the presence of correlations, and additional non-trivial behaviors including periodic orbits appear when there were none in the mean field. The origin of all these behaviors is then explored in finite-size networks where interesting mesoscopic scale effects appear. This study leads us to show that the infinite-size system appears as a singular limit of the network equations, and for any finite network, the system will differ from the infinite system

The modulation of topoisomerase I-mediated DNA cleavage and the induction of DNA–topoisomerase I crosslinks by crotonaldehyde-derived DNA adducts

Crotonaldehyde is a representative α,β-unsaturated aldehyde endowed of mutagenic and carcinogenic properties related to its propensity to react with DNA. Cyclic crotonaldehyde-derived deoxyguanosine (CrA-PdG) adducts can undergo ring opening in duplex DNA to yield a highly reactive aldehydic moiety. Here, we demonstrate that site-specifically modified DNA oligonucleotides containing a single CrA-PdG adduct can form crosslinks with topoisomerase I (Top1), both directly and indirectly. Direct covalent complex formation between the CrA-PdG adduct and Top1 is detectable after reduction with sodium cyanoborohydride, which is consistent with the formation of a Schiff base between Top1 and the ring open aldehyde form of the adduct. In addition, we show that the CrA-PdG adduct alters the cleavage and religation activities of Top1. It suppresses Top1 cleavage complexes at the adduct site and induces both reversible and irreversible cleavage complexes adjacent to the CrA-PdG adduct. The formation of stable DNA–Top1 crosslinks and the induction of Top1 cleavage complexes by CrA-PdG are mutually exclusive. Lastly, we found that crotonaldehyde induces the formation of DNA–Top1 complexes in mammalian cells, which suggests a potential relationship between formation of DNA–Top1 crosslinks and the mutagenic and carcinogenic properties of crotonaldehyde

Minkowski Tensors of Anisotropic Spatial Structure

This article describes the theoretical foundation of and explicit algorithms for a novel approach to morphology and anisotropy analysis of complex spatial structure using tensor-valued Minkowski functionals, the so-called Minkowski tensors. Minkowski tensors are generalisations of the well-known scalar Minkowski functionals and are explicitly sensitive to anisotropic aspects of morphology, relevant for example for elastic moduli or permeability of microstructured materials. Here we derive explicit linear-time algorithms to compute these tensorial measures for three-dimensional shapes. These apply to representations of any object that can be represented by a triangulation of its bounding surface; their application is illustrated for the polyhedral Voronoi cellular complexes of jammed sphere configurations, and for triangulations of a biopolymer fibre network obtained by confocal microscopy. The article further bridges the substantial notational and conceptual gap between the different but equivalent approaches to scalar or tensorial Minkowski functionals in mathematics and in physics, hence making the mathematical measure theoretic method more readily accessible for future application in the physical sciences

Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight

Indexación: Web of Science; PubMedBackground Berry size is considered as one of the main selection criteria in table grape breeding programs. However, this is a quantitative and polygenic trait, and its genetic determination is still poorly understood. Considering its economic importance, it is relevant to determine its genetic architecture and elucidate the mechanisms involved in its expression. To approach this issue, an RNA-Seq experiment based on Illumina platform was performed (14 libraries), including seedless segregants with contrasting phenotypes for berry weight at fruit setting (FST) and 6–8 mm berries (B68) phenological stages. Results A group of 526 differentially expressed (DE) genes were identified, by comparing seedless segregants with contrasting phenotypes for berry weight: 101 genes from the FST stage and 463 from the B68 stage. Also, we integrated differential expression, principal components analysis (PCA), correlations and network co-expression analyses to characterize the transcriptome profiling observed in segregants with contrasting phenotypes for berry weight. After this, 68 DE genes were selected as candidate genes, and seven candidate genes were validated by real time-PCR, confirming their expression profiles. Conclusions We have carried out the first transcriptome analysis focused on table grape seedless segregants with contrasting phenotypes for berry weight. Our findings contributed to the understanding of the mechanisms involved in berry weight determination. Also, this comparative transcriptome profiling revealed candidate genes for berry weight which could be evaluated as selection tools in table grape breeding programs.http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-016-0789-

Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories

Formalin-fixed paraffin-embedded (FFPE) tissues are a valuable resource for retrospective clinical studies. Here, we evaluate the feasibility of (phospho-)proteomics on FFPE lung tissue regarding protein extraction, quantification, pre-analytics, and sample size. After comparing protein extraction protocols, we use the best-performing protocol for the acquisition of deep (phospho-)proteomes from lung squamous cell and adenocarcinoma with >8,000 quantified proteins and >14,000 phosphosites with a tandem mass tag (TMT) approach. With a microscaled approach, we quantify 7,000 phosphosites, enabling the analysis of FFPE biopsies with limited tissue amounts. We also investigate the influence of pre-analytical variables including fixation time and heat-assisted de-crosslinking on protein extraction efficiency and proteome coverage. Our improved workflows provide quantitative information on protein abundance and phosphosite regulation for the most relevant oncogenes, tumor suppressors, and signaling pathways in lung cancer. Finally, we present general guidelines to which methods are best suited for different applications, highlighting TMT methods for comprehensive (phospho-)proteome profiling for focused clinical studies and label-free methods for large cohorts

Velocity-force characteristics of an interface driven through a periodic potential

We study the creep dynamics of a two-dimensional interface driven through a periodic potential using dynamical renormalization group methods. We find that the nature of weak-drive transport depends qualitatively on whether the temperature $T$ is above or below the equilibrium roughening transition temperature $T_c$. Above $T_c$, the velocity-force characteristics is Ohmic, with linear mobility exhibiting a jump discontinuity across the transition. For $T \le T_c$, the transport is highly nonlinear, exhibiting an interesting crossover in temperature and weak external force $F$. For intermediate drive, $F>F_*$, we find near $T_c^{-}$ a power-law velocity-force characteristics $v(F)\sim F^\sigma$, with $\sigma-1\propto \tilde{t}$, and well-below $T_c$, $v(F)\sim e^{-(F_*/F)^{2\tilde{t}}}$, with $\tilde{t}=(1-T/T_c)$. In the limit of vanishing drive ($F\ll F_*$) the velocity-force characteristics crosses over to $v(F)\sim e^{-(F_0/F)}$, and is controlled by soliton nucleation.Comment: 18 pages, submitted to Phys. Rev.

Shedding light on the 239Pu fission source term with new high-precision experiments and advanced fission modeling

In the last decade, there has been a renaissance of fission research resulting in new high-precision experiments and advanced fission modeling. For instance, the Chi-Nu and CEA teams supplied, for the first time, the 239Pu prompt fission neutron spectrum (PFNS) for broad ranges of incident and outgoing neutron energies. The CEA team also measured 239Pu average prompt neutron multiplicities, ν̄p, with lower statistical uncertainties and a technique significantly different than the one used in the past. The NIFFTE collaboration provided 239Pu(n,f)/235U(n,f) cross section shape ratios with uncertainties below 1% utilizing a novel detector type. Advanced fission event generators were developed, among them CGMF, FIFRELIN, FREYA, and GEF, which calculate post-scission fission observables in a correlated manner. These new experimental data and more consistent fission models change the evaluated PFNS, ν̄p, and (n,f) cross sections, some only modestly, compared to ENDF/B-VIII.0. In turn, the individual new nuclear data distinctly change simulated effective neutron multiplication factors of fast critical assemblies, but their combined impact is small, while affecting the prediction of LLNL pulsed sphere neutron leakage spectra and reaction rates only within experimental uncertainties. Also, the parameters obtained from fitting to ν̄p reproduce various post-scission fission observables within the uncertainties of experimental data. This indicates that new differential experiments and consistent fission modeling reduce compensating errors present in ENDF/B-VIII.0