Molecular dynamics simulation of the behaviour of water in nano-confined ionic liquid-water mixtures.

This work describes the behaviour of water molecules in 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid under nanoconfinement, between graphene sheets. By means of molecular dynamics simulations, the adsorption of water molecules at the graphene surface is studied. A depletion of water molecules in the vicinity of the neutral and negatively charged graphene surfaces, and their adsorption at the positively charged surface are observed in line with the preferential hydration of the ionic liquid anions. The findings are appropriately described using a two-level statistical model. The confinement effect on the structure and dynamics of the mixtures is thoroughly analyzed using the density and the potential of mean force profiles, as well as by the vibrational densities of the states of water molecules near the graphene surface. The orientation of water molecules and the water-induced structural transitions in the layer closest to the graphene surface are also discussed.We acknowledge the supercomputing support from the EPSRC funded ARCHIE-WeSt HighPerformance Computer centre (www.archie-west.ac.uk, EPSRC grant no. EP/K000586/1) and the Galician Supercomputing Centre (CESGA). The financial support of the Estonian Materials Technology Program Project SLOKT12180T, Project of European Structure Funds SLOKT12026T, Estonian Institutional Research Project IUT20-013, Estonian Personal Research Project PUT1107, and Estonian Centres of Excellence in Science Project: High-technology Materials for Sustainable Development TK117 is highly appreciated. The financial support of the Spanish Ministry of Economy and Competitiveness MAT2014-57943-C3-1-P and MAT2014- 57943-C3-3-P is gratefully acknowledged. Moreover, this work was funded by the Spanish Ministry of Economy and Competitiveness (FIS2012-33126) and by the Xunta de Galicia (AGRUP2015/11). All these research projects were partially supported by FEDER. Funding from the European Union (COST Action CM 1206) and by the Galician Network on Ionic Liquids, REGALIs (CN 2014/015) is also acknowledged

CAR-T cell. the long and winding road to solid tumors

Adoptive cell therapy of solid tumors with reprogrammed T cells can be considered the "next generation" of cancer hallmarks. CAR-T cells fail to be as effective as in liquid tumors for the inability to reach and survive in the microenvironment surrounding the neoplastic foci. The intricate net of cross-interactions occurring between tumor components, stromal and immune cells leads to an ineffective anergic status favoring the evasion from the host's defenses. Our goal is hereby to trace the road imposed by solid tumors to CAR-T cells, highlighting pitfalls and strategies to be developed and refined to possibly overcome these hurdles

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns

On-chip generation of high-dimensional entangled quantum states and their coherent control

Optical quantum states based on entangled photons are essential for solving questions in fundamental physics and are at the heart of quantum information science1. Specifically, the realization of high-dimensional states (D-level quantum systems, that is, qudits, with D > 2) and their control are necessary for fundamental investigations of quantum mechanics2, for increasing the sensitivity of quantum imaging schemes3, for improving the robustness and key rate of quantum communication protocols4, for enabling a richer variety of quantum simulations5, and for achieving more efficient and error-tolerant quantum computation6. Integrated photonics has recently become a leading platform for the compact, cost-efficient, and stable generation and processing of non-classical optical states7. However, so far, integrated entangled quantum sources have been limited to qubits (D = 2)8, 9, 10, 11. Here we demonstrate on-chip generation of entangled qudit states, where the photons are created in a coherent superposition of multiple high-purity frequency modes. In particular, we confirm the realization of a quantum system with at least one hundred dimensions, formed by two entangled qudits with D = 10. Furthermore, using state-of-the-art, yet off-the-shelf telecommunications components, we introduce a coherent manipulation platform with which to control frequency-entangled states, capable of performing deterministic high-dimensional gate operations. We validate this platform by measuring Bell inequality violations and performing quantum state tomography. Our work enables the generation and processing of high-dimensional quantum states in a single spatial mode

Quasistationary Stabilization of the Decay of a Weakly-Bound Level and Its Breakdown in a Strong Laser Field

Although it was pointed out about 10 years ago that an atomic decay rate might decrease as the intensity of a high-frequency laser field increases, there still does not exist any complete understanding of either the physical origin of this interesting nonlinear phenomenon or its dependence on the atomic and field parameters. Essentially, the problem consists in that the phenomenon requires a major modification of the standard picture of photoeffect in a strong laser field. In Reference #1 the origin of this stabilization is related to a particular distortion of an atomic potential by an intense monochromatic high-frequency field. This phenomenon is called adiabatic or quasistationary stabilization (QS). For the case of Rydberg levels, another (interference) mechanism of QS was suggested. Both theories predict an unlimited decrease of the decay rate (or of the width Γ of an atomic level, i.e., of the imaginary part of the complex quasienergy, ε = Re ε – iΓ/2 ) as the laser field amplitude increases. In recent years the idea of “dynamic stabilization” (DS) has become popular. It originates from the pulse form of a laser field rather than from any intrinsic property of the atom in a strong monochromatic field. Within this model the numerous simulations point also to the possibility of a breakdown of stabilization for the case of superintense short laser pulses. However, a recent paper, using the quasistationary quasienergy states (QQES) as an adiabatic basis for the laser pulse has shown that DS has the same (quasistationary) origin as QS. Finally, a number of authors deny the existence of stabilization, in particular, of QS for ionization from a short-range potential and of DS in pulsed fields. Obviously, these controversies and ambiguities are caused by the complexity of the numerical solution of the Cauchy problem for the time-dependent Schrödinger equation in a strong field and by the absence of analyses for exactly solvable analytical models. We analyze the exactly solvable problem of an electron in a three-dimensional, short-range potential and consider the two questions: does a QS-like behavior of the decay rate exist for this model, and, if so, is there an upper intensity limit of the QS regime

Generic Algorithm to Predict the Speed of Translational Elongation: Implications for Protein Biogenesis

Synonymous codon usage and variations in the level of isoaccepting tRNAs exert a powerful selective force on translation fidelity. We have developed an algorithm to evaluate the relative rate of translation which allows large-scale comparisons of the non-uniform translation rate on the protein biogenesis. Using the complete genomes of Escherichia coli and Bacillus subtilis we show that stretches of codons pairing to minor tRNAs form putative sites to locally attenuate translation; thereby the tendency is to cluster in near proximity whereas long contiguous stretches of slow-translating triplets are avoided. The presence of slow-translating segments positively correlates with the protein length irrespective of the protein abundance. The slow-translating clusters are predominantly located down-stream of the domain boundaries presumably to fine-tune translational accuracy with the folding fidelity of multidomain proteins. Translation attenuation patterns at highly structurally and functionally conserved domains are preserved across the species suggesting a concerted selective pressure on the codon selection and species-specific tRNA abundance in these regions

Large Scale Comparative Codon-Pair Context Analysis Unveils General Rules that Fine-Tune Evolution of mRNA Primary Structure

BACKGROUND: Codon usage and codon-pair context are important gene primary structure features that influence mRNA decoding fidelity. In order to identify general rules that shape codon-pair context and minimize mRNA decoding error, we have carried out a large scale comparative codon-pair context analysis of 119 fully sequenced genomes. METHODOLOGIES/PRINCIPAL FINDINGS: We have developed mathematical and software tools for large scale comparative codon-pair context analysis. These methodologies unveiled general and species specific codon-pair context rules that govern evolution of mRNAs in the 3 domains of life. We show that evolution of bacterial and archeal mRNA primary structure is mainly dependent on constraints imposed by the translational machinery, while in eukaryotes DNA methylation and tri-nucleotide repeats impose strong biases on codon-pair context. CONCLUSIONS: The data highlight fundamental differences between prokaryotic and eukaryotic mRNA decoding rules, which are partially independent of codon usage

Differential Inhibitor Sensitivity between Human Kinases VRK1 and VRK2

Human vaccinia-related kinases (VRK1 and VRK2) are atypical active Ser-Thr kinases implicated in control of cell cycle entry, apoptosis and autophagy, and affect signalling by mitogen activated protein kinases (MAPK). The specific structural differences in VRK catalytic sites make them suitable candidates for development of specific inhibitors. In this work we have determined the sensitivity of VRK1 and VRK2 to kinase inhibitors, currently used in biological assays or in preclinical studies, in order to discriminate between the two proteins as well as with respect to the vaccinia virus B1R kinase. Both VRK proteins and vaccinia B1R are poorly inhibited by inhibitors of different types targeting Src, MEK1, B-Raf, JNK, p38, CK1, ATM, CHK1/2 and DNA-PK, and most of them have no effect even at 100 µM. Despite their low sensitivity, some of these inhibitors in the low micromolar range are able to discriminate between VRK1, VRK2 and B1R. VRK1 is more sensitive to staurosporine, RO-31-8220 and TDZD8. VRK2 is more sensitive to roscovitine, RO 31–8220, Cdk1 inhibitor, AZD7762, and IC261. Vaccinia virus B1R is more sensitive to staurosporine, KU55933, and RO 31–8220, but not to IC261. Thus, the three kinases present a different pattern of sensitivity to kinase inhibitors. This differential response to known inhibitors can provide a structural framework for VRK1 or VRK2 specific inhibitors with low or no cross-inhibition. The development of highly specific VRK1 inhibitors might be of potential clinical use in those cancers where these kinases identify a clinical subtype with a poorer prognosis, as is the case of VRK1 in breast cancer

Plant growth-promoting actinobacteria: a new strategy for enhancing sustainable production and protection of grain legumes

Grain legumes are a cost-effective alternative for the animal protein in improving the diets of the poor in South-East Asia and Africa. Legumes, through symbiotic nitrogen fixation, meet a major part of their own N demand and partially benefit the following crops of the system by enriching soil. In realization of this sustainability advantage and to promote pulse production, United Nations had declared 2016 as the “International Year of pulses”. Grain legumes are frequently subjected to both abiotic and biotic stresses resulting in severe yield losses. Global yields of legumes have been stagnant for the past five decades in spite of adopting various conventional and molecular breeding approaches. Furthermore, the increasing costs and negative effects of pesticides and fertilizers for crop production necessitate the use of biological options of crop production and protection. The use of plant growth-promoting (PGP) bacteria for improving soil and plant health has become one of the attractive strategies for developing sustainable agricultural systems due to their eco-friendliness, low production cost and minimizing consumption of non-renewable resources. This review emphasizes on how the PGP actinobacteria and their metabolites can be used effectively in enhancing the yield and controlling the pests and pathogens of grain legumes