Metropolis simulations of Met-Enkephalin with solvent-accessible area parameterizations

We investigate the solvent-accessible area method by means of Metropolis simulations of the brain peptide Met-Enkephalin at 300$K$. For the energy function ECEPP/2 nine atomic solvation parameter (ASP) sets are studied. The simulations are compared with one another, with simulations with a distance dependent electrostatic permittivity $\epsilon (r)$, and with vacuum simulations ($\epsilon =2$). Parallel tempering and the biased Metropolis techniques RM$_1$ are employed and their performance is evaluated. The measured observables include energy and dihedral probability densities (pds), integrated autocorrelation times, and acceptance rates. Two of the ASP sets turn out to be unsuitable for these simulations. For all other systems selected configurations are minimized in search of the global energy minima, which are found for the vacuum and the $\epsilon(r)$ system, but for none of the ASP models. Other observables show a remarkable dependence on the ASPs. In particular, we find three ASP sets for which the autocorrelations at 300$$K are considerably smaller than for vacuum simulations.Comment: 10 pages and 8 figure

Energy dependent counting statistics in diffusive superconducting tunnel junctions

We present an investigation of the energy dependence of the full charge counting statistics in diffusive normal-insulating-normal-insulating-superconducting junctions. It is found that the current in general is transported via a correlated transfer of pairs of electrons. Only in the case of strongly asymmetric tunnel barriers or energies much larger than the Thouless energy is the pair transfer uncorrelated. The second cumulant, the noise, is found to depend strongly on the applied voltage and temperature. For a junction resistance dominated by the tunnel barrier to the normal reservoir, the differential shot noise shows a double peak feature at voltages of the order of the Thouless energy, a signature of an ensemble averaged electron-hole resonance.Comment: 8 pages, 5 figure

Energy gap and proximity effect in MgB2MgB_2 superconducting wires

Measurements of the penetration depth $\lambda (T,H)$ in the presence of a DC magnetic field were performed in $MgB_2$ wires. In as-prepared wires $\lambda (T,H<130 Oe)$ shows a strong diamagnetic downturn below $\approx 10 K$. A DC magnetic field of $130 Oe$ completely suppressed the downturn. The data are consistent with proximity coupling to a surface $Mg$ layer left during synthesis. A theory for the proximity effect in the clean limit, together with an assumed distribution of the $Mg$ layer thickness, qualitatively explains the field and temperature dependence of the data. Removal of the $Mg$ by chemical etching results in an exponential temperature dependence for $\lambda (T)$ with an energy gap of $2 \Delta (0)/T_c\approx 1.54$ ($\Delta(0) \approx 2.61 meV$), in close agreement with recent measurements on commercial powders and single crystals. This minimum gap is only 44% of the BCS weak coupling value, implying substantial anisotropy.Comment: RevTeX 4, 4 EPS figure

Functional characterization of a 28-Kilobase Catabolic Island from Pseudomonas sp. Strain M1 involved in biotransformation of β-Myrcene and related plant-derived volatiles

Pseudomonas sp. strain M1 is able to mineralize highly hydrophobic and recalcitrant compounds, such as benzene, phenol, and their methylated/halogenated derivatives, as well as the backbone of several monoterpenes. The ability to use such a spectrum of compounds as the sole carbon source is, most probably, associated with a genetic background evolved under different environmental constraints. The outstanding performance of strain M1 regarding β-myrcene catabolism was elucidated in this work, with a focus on the biocatalytical potential of the β-myrcene-associated core code, comprised in a 28-kb genomic island (GI), predicted to be organized in 8 transcriptional units. Functional characterization of this locus with promoter probes and analytical approaches validated the genetic organization predictedin silicoand associated the β-myrcene-induced promoter activity to the production of β-myrcene derivatives. Notably, by using a whole-genome mutagenesis strategy, different genotypes of the 28-kb GI were generated, resulting in the identification of a novel putative β-myrcene hydroxylase, responsible for the initial oxidation of β-myrcene into myrcen-8-ol, and a sensor-like regulatory protein, whose inactivation abolished themyr + trait of M1 cells. Moreover, it was demonstrated that the range of monoterpene substrates of the M1 enzymatic repertoire, besides β-myrcene, also includes other acyclic (e.g., β-linalool) and cyclic [e.g.,R-(+)-limonene and (-)-β-pinene] molecules. Our findings are the cornerstone for following metabolic engineering approaches and hint at a major role of the 28-kb GI in the biotransformation of a broad monoterpene backbone spectrum for its future biotechnological applications.IMPORTANCEInformation regarding microbial systems able to biotransform monoterpenes, especially β-myrcene, is limited and focused mainly on nonsystematic metabolite identification. Complete and detailed knowledge at the genetic, protein, metabolite, and regulatory levels is essential in order to set a model organism or a catabolic system as a biotechnology tool. Moreover, molecular characterization of reported systems is scarce, almost nonexistent, limiting advances in the development of optimized cell factories with strategies based on the new generation of metabolic engineering platforms. This study provides new insights into the intricate molecular functionalities associated with β-myrcene catabolism inPseudomonas, envisaging the production of a molecular knowledge base about the underlying catalytic and regulatory mechanisms of plant-derived volatile catabolic pathways.Vectors from the Standard European Vector Architecture (SEVA) library and pBAM1 used in this work were kindly provided by Victor de Lorenzo (CNB-CSIC, Madrid, Spain). This work was supported by the strategic program UID/BIA/04050/2013 (POCI-01- 0145-FEDER-007569) funded by national funds through the FCT I.P. and by the ERDF through the COMPETE2020-Programa Operacional Competitividade e Internacionalização (POCI) and through a Ph.D. grant (grant SFRH/BD/76894/2011) to P.S.-C.info:eu-repo/semantics/publishedVersio

Shot Noise in Mesoscopic Diffusive Andreev Wires

We study shot noise in mesoscopic diffusive wires between a normal and a superconducting terminal. We particularly focus on the regime, in which the proximity-induced reentrance effect is important. We will examine the difference between a simple Boltzmann-Langevin description, which neglects induced correlations beyond the simple conductivity correction, and a full quantum calculation. In the latter approach, it turns out that two Andreev pairs propagating coherently into the normal metal are anti-correlated for E<E_c, where E_c=D/L^2 is the Thouless energy. In a fork geometry the flux-sensitive suppression of the effective charge was confirmed experimentally.Comment: 12 pages, proceedings of the NATO ARW MQO, Bled, Sloveni

Quasiclassical theory of superconductivity: a multiple interface geometry

The purpose of the paper is to suggest a new method which allows one to study multiple coherent reflection/transmissions by partially transparent interfaces (e.g. in multi-layer mesoscopic structures or grain boundaries in high-Tc's) in the framework of the quasiclassical theory of superconductivity. It is argued that typically the trajectory of the particle is a simply connected tree (no loops) with knots, i.e. the points where interface scattering events occur and ballistic pieces of the trajectory are mixed. A linear boundary condition for the 2-component trajectory "wave function" which factorizes matrix (retarded) Green's function, is formulated for an arbitrary interface, specular or diffusive. To show the usage of the method, the current response to the vector potential (the total superfluid density rho_s) of a SS' sandwich with the different signs of the order parameter in S and S', is calculated. In this model, a few percent of reflection by the SS' interface transforms the paramagnetic response (rho_s < 0) created by the zero-energy Andreev bound states near an ideal interface (see Fauchere et al. PRL, 82, 3336 (1999), cond-mat/9901112), into the usual diamagnetic one (rho_s >0).Comment: Extended abstract submitted to "Electron Transport in Mesoscopic Systems", Satellite conference to LT22, Goteborg, 12-15 August, 1999. 2 pages Minor changes + the text height problem fixe

Reflectionless tunneling in ballistic normal-metal--superconductor junctions

We investigate the phenomenon of reflectionless tunneling in ballistic normal-metal--superconductor (NS) structures, using a semiclassical formalism. It is shown that applied magnetic field and superconducting phase difference both impair the constructive interference leading to this effect, but in a qualitatively different way. This is manifested both in the conductance and in the shot noise properties of the system considered. Unlike diffusive systems, the features of the conductance are sharp, and enable fine spatial control of the current, as well as single channel manipulations. We discuss the possibility of conducting experiments in ballistic semiconductor-superconductor structures with smooth interfaces and some of the phenomena, specific to such structures, that could be measured. A general criterion for the barrier at NS interfaces, though large, to be effectively transparent to pair current is obtained.Comment: published versio

Effect of Early High-Dose Recombinant Human Erythropoietin on Behavior and Quality of Life in Children Aged 5 Years Born Very Preterm: Secondary Analysis of a Randomized Clinical Trial

IMPORTANCE In light of the promising neuroprotective properties of recombinant human erythropoietin (RHEpo), the Swiss EPO Neuroprotection Trial was started to investigate its effect on neurodevelopment in very preterm infants. The results of the primary and secondary outcome analysis did not show any effect of RHEpo on cognitive performance, neuromotor outcomes, or somatic growth of the study participants at ages 2 or 5 years. OBJECTIVE To investigate whether early high-dose RHEpo improves behavioral outcomes and health-related quality of life (HRQoL) at age 5 years. DESIGN, SETTING, AND PARTICIPANTS This was a prespecified secondary analysis of the double-blind, placebo-controlled, multicenter Swiss EPO Neuroprotection randomized clinical trial, which was conducted at 5 level-III perinatal centers in Switzerland. Infants born between 26 weeks 0 days' and 31 weeks 6 days' gestation were recruited between 2005 and 2012 and followed-up until age 5 years (last follow-up in 2018). Data were analyzed from January 6 to December 31, 2021. INTERVENTIONS Infants were assigned to receive either RHEpo (3000 IU/kg) or placebo (saline, 0.9%) intravenously 3 times within the first 42 hours after birth. MAIN OUTCOMES AND MEASURES The prespecified parent-reported measures of behavioral outcomes and health-related quality of life (HRQoL) of their children at the age of 5 years were assessed by two standardized questionnaires: the Strengths and Difficulties Questionnaire (behavioral outcomes) and the KIDSCREEN-27 (HRQoL). RESULTS Among 448 randomized infants, 228 infants were assigned to the RHEpo group and 220 infants were assigned to the placebo group. Questionnaire data were available for 317 children (71%) at a mean (SD) age of 5.8 (0.4) years (mean [SD] gestational age at birth, 29.3 [1.6] weeks; mean [SD] birth weight 1220 [340] grams; 128 [40%] female infants). At the age 5 years follow-up, the mean (SD) total difficulties score in the RHEpo group (8.41 [5.60] points) was similar to that of the placebo group (7.76 [4.81]) (P = .37). There were no statistically significant differences between the groups in any other outcome measures. CONCLUSIONS AND RELEVANCE This secondary analysis of a randomized clinical trial showed no evidence for an effect of early high-dose RHEpo administration on behavioral outcomes or HRQoL in children born very preterm at early school age. TRIAL REGISTRATION - ClinicalTrials.gov Identifier: NCT00413946

Inhibition abilities and functional brain connectivity in school-aged term-born and preterm-born children

Background Inhibition abilities are known to have impact on self-regulation, behavior, and academic success, and they are frequently impaired in children born preterm. We investigated the possible contributions of resting-state functional brain connectivity to inhibition following preterm birth. Methods Forty-four preterm and 59 term-born participants aged 8–13 years were administered two inhibition tasks and resting-state functional MRI was performed. Functional connectivity (FC) networks were compared between groups using network-based statistics. Associations of FCNs and inhibition abilities were investigated through multivariate linear regression models accounting for the interaction between birth status and inhibition. Results NBS revealed weaker FC in children born preterm compared to term-born peers in connections between motor and supplementary motor regions, frontal lobe, precuneus, and insula. Irrespective of birth status, connections between the cerebellum, frontal, and occipital lobes and inter-lobar, subcortical, intra-hemispheric long-range connections were positively correlated with one of the two inhibition tasks. Conclusions Preterm birth results in long-term alterations of FC at network level but these FCN alterations do not specifically account for inhibition problems in children born very preterm. Impact Irrespective of birth status, significant associations were found between the subdomain of response inhibition and functional connectivity in some subnetworks. A group comparisons of functional brain connectivity measured by rsfMRI in school-aged children born very preterm and at term. The investigation of network-level functional connectivity at rest does not appear adequate to explain differences in inhibition abilities between children born very preterm and at term, hence other imaging techniques might be more suited to explore the underlying neural mechanisms of inhibition abilities in school-aged children born very preterm