bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlation between domain wall creep parameters of thin ferromagnetic films
Authors: Quinteros C. P. , Bustingorry S. , Curiale J. , Granada M.
Published: June 2018

Designing magnetic materials for potential applications based on domain wall motion requires the knowledge of the relationship between physical properties and phenomenological parameters characterizing domain wall dynamics. We address in this work the study of magnetic-field-driven domain wall motion within the creep regime on a prototypical metallic Pt/Co/Pt stack with perpendicular magnetic anisotropy. By controlling the deposition characteristics, different magnetic properties are achieved, giving rise to different creep parameters. Those phenomenological parameters are found to collapse in a single linear dependence for all samples based on the same material. Moreover, using data in the literature, we show that the same behavior is observed in Au/Co/Au and Tb/Fe based samples. We therefore obtain a pair of global parameters that fully characterize the family of domain wall velocity-field curves within the creep regime for each group of samples, which can be used as input for the optimization of materials.
A 4 K FT-ICR cell for infrared ion spectroscopy
Authors: Fritsche Lukas , Bach Andreas , Miloglyadova Larisa , Tsybizova Alexandra , Chen Peter
Published: June 2018

We present the design of the newly constructed cryogenic Fourier-transform ion cyclotron resonance (FT-ICR) ion trap for infrared ion spectroscopy. Trapped ions are collisionally cooled by the pulsed introduction of buffer gas into the cell. Using different buffer gases and cell temperatures, we record action spectra of weakly bound neutral gas-analyte complexes with an IR laser source. We show for the first time that ion-He complexes can be observed in an ICR cell at temperatures around 4 K. We compare the experimental vibrational spectra of Ag(PPh3)2+ obtained by tagging with different neutral gases: He, Ne, Ar, H2, and N2 to computed vibrational spectra. Furthermore, the conditions necessary for the formation of neutral tags within an ICR ion trap are studied.
A mixed alchemical and equilibrium dynamics to simulate heterogeneous dense fluids: Illustrations for Lennard-Jones mixtures and phospholipid membranes
Authors: Fathizadeh Arman , Elber Ron
Published: June 2018

An algorithm to efficiently simulate multi-component fluids is proposed and illustrated. The focus is on biological membranes that are heterogeneous and challenging to investigate quantitatively. To achieve rapid equilibration of spatially inhomogeneous fluids, we mix conventional molecular dynamics simulations with alchemical trajectories. The alchemical trajectory switches the positions of randomly selected pairs of molecules and plays the role of an efficient Monte Carlo move. It assists in accomplishing rapid spatial de-correlations. Examples of phase separation and mixing are given in two-dimensional binary Lennard-Jones fluid and a DOPC-POPC membrane. The performance of the algorithm is analyzed, and tools to maximize its efficiency are provided. It is concluded that the algorithm is vastly superior to conventional molecular dynamics for the equilibrium study of biological membranes.
Vascular-targeted particle binding efficacy in the presence of rigid red blood cells: Implications for performance in diseased blood
Authors: Gutierrez Mario , Ojeda Lauro Sebastian , Eniola-Adefeso Omolola
Published: June 2018

The field of drug delivery has taken an interest in combating numerous blood and heart diseases via the use of injectable vascular-targeted carriers (VTCs). However, VTC technology has encountered limited efficacy due to a variety of challenges associated with the immense complexity of the in vivo blood flow environment, including the hemodynamic interactions of blood cells, which impact their margination and adhesion to the vascular wall. Red blood cell (RBC) physiology, i.e., size, shape, and deformability, drive cellular distribution in blood flow and has been shown to impact VTC margination to the vessel wall significantly. The RBC shape and deformability are known to be altered in certain human diseases, yet little experimental work has been conducted towards understanding the effect of these alterations, specifically RBC rigidity, on VTC dynamics in physiological blood flow. In this work, we investigate the impact of RBCs of varying stiffnesses on the adhesion efficacy of particles of various sizes, moduli, and shapes onto an inflamed endothelial layer in a human vasculature-inspired, in vitro blood flow model. The blood rigid RBC compositions and degrees of RBC stiffness evaluated are analogous to conditions in diseases such as sickle cell disease. We find that particles of different sizes, moduli, and shapes yield drastically different adhesion patterns in blood flow in the presence of rigid RBCs when compared to 100% healthy RBCs. Specifically, up to 50% reduction in the localization and adhesion of non-deformable 2 μm particles to the vessel wall was observed in the presence of rigid RBCs. Interestingly, deformable 2 μm particles showed enhanced vessel wall localization and adhesion, by up to 85%, depending on the rigidity of RBCs evaluated. Ultimately, this work experimentally clarifies the importance of considering RBC rigidity in the intelligent design of particle therapeutics and highlights possible implications for a wide range of diseases relating to RBC deformability.
Highly sensitive wearable strain sensor based on ultra-violet/ozone cracked carbon nanotube/elastomer
Authors: Li Q. , Wang K. , Gao Y. , Tan J. P. , Wu R. Y. , Xuan F. Z.
Published: June 2018

To simultaneously achieve high sensitivities (gauge factor > 100) and large stretchability (>50%) is still a grand challenge in developing the wearable strain sensors. In this study, a strain sensor with a high sensitivity up to 1020.2 and a large stretchability of 100% was developed based on ultra-violet/ozone (UV/O3) cracked carbon nanotubes/elastomers. The high sensitivity is ascribed to the widening of the cut-through cracks generated by the UV/O3 surface engineering process. The UV/O3-cracked strain sensors show potential applications in electronic skins to detect various human motion signals such as bending of the wrist, pulsing, and eye blinking.
Theoretical study of (e, 2e) triple differential cross sections of tetrahydrofuran using multicenter distorted-wave method
Authors: Xu Xiaojie , Gong Maomao , Li Xingyu , Zhang Song Bin , Chen Xiangjun
Published: June 2018

We present in this work a theoretical study of the triple differential cross sections for electron-impact single ionization of 12a′ and 9b orbitals of a tetrahydrofuran molecule. The calculations are performed by the multicenter distorted-wave (MCDW) method in coplanar asymmetric kinematics with an incident electron energy of 250 eV, where previous (e, 2e) experiments and theories are available for comparison. The present calculations reproduce the experimental measurements satisfactorily, indicating that the MCDW method can be easily extended to study biomolecules with sufficiently high calculation efficiency.
Predissociation of the B Σu−3 state of S2: A coupled-channel model
Authors: Lewis B. R. , Gibson S. T. , Stark G. , Heays A. N.
Published: June 2018

A coupled-channel Schrödinger equation model of predissociation in the B Σu−3 state of S2 is developed and optimized by comparison with recent photoabsorption spectra of the B Σu−3−X Σg−3(v,0) bands for 11 ≤ v ≤ 27, covering the energy range 35 800–41 500 cm−1. All bands in this range exhibit varying degrees of diffuseness, with corresponding predissociation linewidths Γ ≈ 4–60 cm−1 full-width at half-maximum. Model comparisons with both low-temperature (T = 370 K) and high-temperature (T = 823 K) spectra indicate, for many bands, significant dependence of the linewidth on both the rotational quantum number J and the fine-structure component Fi. Just as in the analogous case of O2, the B(v)-state predissociation in S2 is caused principally by spin-orbit interaction with 3Πu, 1Πu, 5Πu, and Σu+3 states. The inner-limb crossing with B″3Πu is responsible for the predissociation of B(v = 11) and provides a significant slowly varying contribution for B(v ≥ 12). The outer crossings with the 1Πu, 5Πu, and 2 Σu+3 states are responsible for oscillatory contributions to the predissociation widths, with first peaks at v = 13, 20, and 24, respectively, and the 5Πu contribution dominant. Prior to the photodissociation imaging study of Frederix et al. [J. Phys. Chem. A 113, 14995 (2009)], which redefined the dissociation energy of S2, the prevailing paradigm was that only the 1Πu interaction was responsible for the B(v = 11–16) predissociation: this view is not supported by our model.
Diffuse phase transition of BST thin films in the microwave domain
Authors: Nadaud Kevin , Borderon Caroline , Renoud Raphaël , Ghalem Areski , Crunteanu Aurelian , Huitema Laure , Dumas-Bouchiat Frédéric , Marchet Pascal , Champeaux Corinne , Gundel Hartmut W.
Published: June 2018

Ferroelectric materials are widely used in the paraelectric phase in order to realize tunable capacitors with reduced losses and a low hysteresis effect. Nevertheless, for polycrystalline thin films, the ferro-/para-electric phase transition can be diffuse and some crystallites can exhibit a ferroelectric nature even if the sample seems to be globally in a paraelectric phase. In this case, domain wall motions are responsible for the sensitivity of the dielectric properties to the driving field and are very dissipative phenomena. In this paper, we evaluate, in the high-frequency band, the impact of ferroelectricity on the properties of Ba2/3Sr1/3TiO3 thin films near the phase transition, by measuring the film's dielectric properties as a function of the incident RF power and for different temperatures.
Wafer-scale, stretchable nanomeshes from an ultrathin-support-layer assisted transfer
Authors: Seo Kyung Jin , Han Xun , Qiang Yi , Zhao Xuanyi , Zhong Yiding , Shi Zhan , Fang Hui
Published: June 2018

Metal nanomeshes possess unique electrical and mechanical properties for next-generation stretchable electronics. However, a critical unmet need lies in producing stretchable conductive nanomeshes at large scale with high uniformity and intactness. Here, we present a wafer-scale nondestructive transfer method by utilizing an ultrathin polyimide layer. This polyimide support layer allows etchant vapor to transmit through to etch the sacrificial layer underneath, while being continuous to support the nanomeshes during transfer before being removed completely after the transfer. From this simple yet effective method, we developed 4-in.-wafer-scale gold nanomeshes with low sheet resistance of 8.35 Ω/◻, good transparency of 65% at 550 nm, and stretchability of 70%. Detailed vapor transmission studies reveal that etchant vapor indeed transmitted through the support layer, with realistic sacrificial etching time needed for transfer. Together, these results provide a practical pathway towards fabricating large-scale nanomesh based stretchable electronics, with applications ranging from on-skin electronics to implantable biomedical devices. We also expect this ultrathin support layer approach to be generally applicable to the processing of many other nanomaterials at large scale.
Experimental characterization of impact ionization coefficients for electrons and holes in GaN grown on bulk GaN substrates
Authors: Cao Lina , Wang Jingshan , Harden Galen , Ye Hansheng , Stillwell Roy , Hoffman Anthony J. , Fay Patrick
Published: June 2018

Epitaxial p-i-n structures grown on native GaN substrates have been fabricated and used to extract the impact ionization coefficients in GaN. The photomultiplication method has been used to experimentally determine the impact ionization coefficients; avalanche dominated breakdown is confirmed by variable-temperature breakdown measurements. To facilitate photomultiplication measurements of both electrons and holes, the structures include a thin pseudomorphic In0.07Ga0.93N layer on the cathode side of the drift layer. Illumination with 193 nm and 390 nm UV light has been performed on diodes with different intrinsic layer thicknesses. From the measured multiplication characteristics, the impact ionization coefficients of electrons (α) and holes (β) were determined for GaN over the electric field range from 2 MV/cm to 3.7 MV/cm. The results show that for transport along the c-axis, holes dominate the impact ionization process at lower electric field strengths; the impact ionization coefficient of electrons becomes comparable to that of holes (β/α<5) for electric field strengths above 3.3 MV/cm.
Room temperature WGM resonances in the red spectral range from Ho3+ activated ZnO micro-spherical cavities
Authors: Fabitha K. , Nagasaki F. , Fujiwara Y. , Wakiyama Y. , Nakamura D. , Ramachandra Rao M. S.
Published: June 2018

Highly crystalline and smooth 1% Ho3+ doped ZnO microspheres with diameters ranging from 0.5 to 15 μm were synthesized using laser ablation technique. Near band edge whispering gallery mode (WGM) resonances from Ho:ZnO microspheres with a single oscillation route in the UV range are observed with 355 nm excitation. Apart from the significantly enhanced visible WGM resonances associated with intrinsic oxygen vacancy defects by Ho3+ doping, the visible range WGM resonances associated with the Ho3+ 5F5 → 5I8 emission at 629–690 nm are also observed with a 488 nm excitation. The WGMs of Ho3+ f-f emission possess lower threshold and high Q-factor values.
Proximity effect induced enhanced spin pumping in Py/Gd at room temperature
Authors: Bansal Rajni , Chowdhury Niru , Muduli P. K.
Published: June 2018

We report on ferromagnetic resonance spectroscopy studies of Py/Gd system by varying thickness of Gd layer. We found that a portion of the Gd layer at the interface becomes ferromagnetically ordered at room temperature and become antiferromagnetic coupled to the Py due to the magnetic proximity effect, as evidenced by a Gd-thickness dependent shift in the resonance field and exchange bias field. We show a large increase in the effective Gilbert damping of the Py layer when the thickness of the adjacent Gd layer is increased. We argue that a major contribution of this increase is due to the spin pumping effect into the ordered ferromagnetic Gd layer.
A simulation method for the phase diagram of complex fluid mixtures
Authors: Jung Hyuntae , Yethiraj Arun
Published: June 2018

The phase behavior of complex fluid mixtures is of continuing interest, but obtaining the phase diagram from computer simulations can be challenging. In the Gibbs ensemble method, for example, each of the coexisting phases is simulated in a different cell, and ensuring the equality of chemical potentials of all components requires the transfer of molecules from one cell to the other. For complex fluids such as polymers, successful insertions are rare. An alternative method is to simulate both coexisting phases in a single simulation cell, with an interface between them. The challenge here is that the interface position moves during the simulation, making it difficult to determine the concentration profile and coexisting concentrations. In this work, we propose a new method for single cell simulations that uses a spatial concentration autocorrelation function to (spatially) align instantaneous concentration profiles from different snapshots. This allows one to obtain average concentration profiles and hence the coexisting concentrations. We test the method by calculating the phase diagrams of two systems: the Widom-Rowlinson model and the symmetric blends of freely jointed polymer molecules for which phase diagrams from conventional methods are available. Excellent agreement is found, except in the neighborhood of the critical point where the interface is broad and finite size effects are important. The method is easy to implement and readily applied to any mixture of complex fluids.
Oxidation states and thermoelectric properties of BiCuSeO bulks fabricated under Bi or Se deficiencies in the nominal composition
Authors: Ishizawa Mamoru , Yasuzato Yuki , Fujishiro Hiroyuki , Naito Tomoyuki , Katsui Hirokazu , Goto Takashi
Published: June 2018

We have fabricated the BiCuSeO bulks using raw materials with Bi or Se deficiencies in the nominal composition and investigated crystallographic, chemical compositional, and thermoelectric properties. Owing to the Bi or Se deficiencies in the starting composition, excessive elements and related compounds were deposited as impurity phases and the matrix phase is nearly the stoichiometric BiCuSeO phase. The electrical resistivity, ρ(T), of the bulks decreases and thermoelectric power, S(T), also decreases with increasing the contents of Bi or Se deficiencies in the starting composition in spite of the stoichiometric matrix phase. These results strongly suggest that, from the X-ray photoelectron spectroscopy measurements, the actual oxidation states of Bi and Cu deviate from the formal valences of stoichiometric Bi3+Cu1+Se2−O2−. The introduction of a small amount of Bi and Se vacancies is also suggested. As a result, mobile carriers are introduced and the ρ and S values are changed. The maximum thermoelectric dimensionless figure of merit of ZT = 0.60 was achieved at 773 K for the Bi1-xCuSeO samples (x = 0.025 and 0.05) in the starting composition. These results are in clear contrast with the reported results for the Cu deficiency bulks. Using these results, we propose charge valence equations and the origin of the carriers in the present BiCuSeO bulks and discuss the influence of created carriers on the thermoelectric properties.
Band alignment of AlN/β-Ga2O3 heterojunction interface measured by x-ray photoelectron spectroscopy
Authors: Chen Jin-Xin , Tao Jia-Jia , Ma Hong-Ping , Zhang Hao , Feng Ji-Jun , Liu Wen-Jun , Xia Changtai , Lu Hong-Liang , Zhang David Wei
Published: June 2018

The energy band alignment of AlN/β-Ga2O3 heterostructures was investigated by X-ray photoelectron spectroscopy. The valence band offsets were estimated to be −0.09 ± 0.1 eV (type II alignment) for AlN grown by plasma enhanced atomic layer deposition (PEALD) on β-Ga2O3 and 0.72 ± 0.1 eV (type I alignment) for AlN prepared by thermal atomic layer deposition (T-ALD) on β-Ga2O3, which gives the conduction band offsets of 1.39 ± 0.1 eV for PEALD AlN and 0.58 ± 0.1 eV for T-ALD AlN. The large difference in the band alignment for the AlN/β-Ga2O3 heterostructures is dominated by different levels of oxygen incorporation into the AlN films as a result of different deposition techniques. The determination of the band alignment of the AlN/β-Ga2O3 heterostructure has significant implications for the design of electronic and optical devices based on AlN/β-Ga2O3 heterojunctions.
Impact of surface states and bulk doping level on hybrid inorganic/organic semiconductor interface energy levels
Authors: Schultz T. , Niederhausen J. , Schlesinger R. , Sadofev S. , Koch N.
Published: June 2018

In applications, surface states and bulk doping concentration are important parameters of inorganic semiconductors, as they determine the bulk properties and substantially influence the properties of interfaces in devices, foremost the electron energy level alignment. In this work, we provide a qualitative model to describe the influence of surface state density and bulk donor concentration on the work function increase upon deposition of strong organic molecular acceptors onto the surface of n-doped inorganic semiconductors. This work function increase due to electron transfer to the molecular layer has two contributions: the formation of an interface dipole and a change of the near-surface space charge region inside the inorganic semiconductor, referred to as surface band bending. By using different surface preparation methods, we show how the surface state density limits the surface band bending change and enhances the interface dipole, both measured independently by photoelectron spectroscopy. In addition, we show that bulk donor concentration variation of the inorganic semiconductor has minor influence on the ratio of the two contributions to the work function change, at least for low to moderate donor concentrations up to 1019 cm−3.
Characterization of the lid-driven cavity magnetohydrodynamic flow at finite magnetic Reynolds numbers using far-field magnetic boundary conditions
Authors: Kawczynski Charles , Smolentsev Sergey , Abdou Mohamed
Published: June 2018

The lid-driven cavity (LDC) flow is a canonic hydrodynamic problem. Here, a 3D LDC flow of electrically conducting, incompressible fluid is studied numerically in the presence of a strong magnetic field, which is applied parallel to the lid plane and perpendicular to the direction of the lid motion. The cavity has electrically conducting walls of finite thickness and an infinitely thin moving lid. The problem is characterized by three dimensionless parameters: the Reynolds number (Re), the Hartmann number (Ha), and the magnetic Reynolds number (Rem). The primary research focus is on the effect of Rem, which was changed in the study from Rem ≪ 1 to the maximal Rem = 2000 at which dynamo action may be expected, while Ha = 100 and Re = 2000. The computational approach is based on the utilization of far-field magnetic boundary conditions by solving the full magnetohydrodynamic (MHD) flow problem at finite Rem for a multi-material domain composed of the inner conducting liquid, conducting walls, and sufficiently large insulating outer domain called “vacuum” (the induced magnetic field vanishes at the vacuum boundaries) using a fractional-step method. The computed results show many interesting features with regard to the effect of Rem on the MHD boundary layer and the bulk flow, generation of a magnetic field and its penetration into vacuum, energy balance, tendency of the magnetic field to become frozen in the fluid and associated magnetic flux expulsion, transition to unsteady flows, and self-excitation of the magnetic field and the associated dynamo-type action at high Rem.
An efficient water force field calibrated against intermolecular THz and Raman spectra
Authors: Sidler David , Meuwly Markus , Hamm Peter
Published: June 2018

A polarizable water model is presented which has been calibrated against experimental THz and Raman spectra of bulk water. These low-frequency spectra directly probe the dynamics, and thereby intermolecular interactions, on time scales relevant to molecular motions. The model is based on the TL4P force field developed recently by Tavan and co-workers [J. Phys. Chem. B 117, 9486 (2013)], which has been designed to be transferable between different environments; in particular, to correctly describe the electrostatic properties of both the isolated water molecule in the gas-phase and the liquid water at ambient conditions. Following this design philosophy, TL4P was amended with charge transfer across hydrogen-bonded dimers as well as an anisotropic polarizability in order to correctly reproduce the THz and Raman spectra. The thermodynamic and structural properties of the new model are of equal quality as those of TL4P, and at the same time, an almost quantitative agreement with the spectroscopic data could be achieved. Since TL4P is a rigid model with a single polarizable site, it is computationally very efficient, while the numerical overhead for the addition of charge transfer and the anisotropic polarizability is minor. Overall, the model is expected to be well suited for, e.g., large scale simulations of 2D-Raman-THz spectra or biomolecular simulations.
Multimillimeter-sized cubic boron arsenide grown by chemical vapor transport via a tellurium tetraiodide transport agent
Authors: Xing Jie , Chen Xi , Zhou Yuanyuan , Culbertson James. C. , Freitas Jaime A. , Glaser Evan R. , Zhou Jianshi , Shi Li , Ni Ni
Published: June 2018

Cubic boron arsenide (c-BAs) has been predicted to exhibit thermal conductivity values around 1400 W/m-K at room temperature by first-principles calculations and, thus, shows promise to be one of the solutions for the thermal management challenge faced by the semiconductor industry. However, the size of single crystals of c-BAs in reported growth efforts is still less than 1 mm. In addition, the measured thermal conductivity is well below the predicted value due to the presence of defects in the grown crystal. Here we report the growth of c-BAs single crystals up to a few mm by the chemical vapor transport technique based on a TeI4 transport agent under gas pressures up to 8 atm. Raman spectroscopy revealed a sharp P1 phonon mode, suggesting good crystalline quality. High-angle annular dark-field scanning transmission electron microscopy revealed the AsB (As-atom on B) and BAs (B-atom on As) antisite pairs. A bulk thermal conductivity value of 133 ± 17 W/m-K at 300 K was obtained using steady-state comparative measurements. Although the bulk thermal conductivity is still one order of magnitude lower than the calculation, the ability to increase the size of the crystal is an important step toward the synthesis of high quality bulk c-BAs crystals.
Distribution of label spacings for genome mapping in nanochannels
Authors: Ödman D. , Werner E. , Dorfman K. D. , Doering C. R. , Mehlig B.
Published: June 2018

In genome mapping experiments, long DNA molecules are stretched by confining them to very narrow channels, so that the locations of sequence-specific fluorescent labels along the channel axis provide large-scale genomic information. It is difficult, however, to make the channels narrow enough so that the DNA molecule is fully stretched. In practice, its conformations may form hairpins that change the spacings between internal segments of the DNA molecule, and thus the label locations along the channel axis. Here, we describe a theory for the distribution of label spacings that explains the heavy tails observed in distributions of label spacings in genome mapping experiments.
Enhancement of optical emission and ion currents in a laser produced silicon plasma by femtosecond laser-induced periodic surface structuring
Authors: Anoop K. K. , Verma Nancy , Joy Nithin , Harilal S. S. , Philip Reji
Published: June 2018

Laser-induced periodic surface structuring is a powerful technique for modifying the surface properties of solids. Using ultrashort pulses from a Ti:sapphire laser (800 nm, 100 fs), we have fabricated nanoscale order laser-induced periodic surface structures (LIPSSs) on a silicon (100) surface. The LIPSS patterns are found to be strongly dependent on the laser pulse energy, state of polarization, number of shots delivered on the target, and the ambient pressure. The role of laser wavelength is studied by using the second harmonic output (400 nm) also for fabrication. Large area (5 × 4 mm2) surface structuring has been carried out at atmospheric pressure after optimizing the laser parameters at 800 nm. The patterned silicon surface shows a substantial reduction in the reflection of incident light over a wide range of wavelengths, in comparison to plain silicon. Moreover, when used for laser induced breakdown spectroscopy experiments, enhanced optical emission and ion current have been observed from the patterned surface. This indicates that the coupling of laser energy to the surface is enhanced in the case of patterned silicon. While spectral lines emitted by doubly ionized silicon have been observed from the patterned surface, the plain surface gives lines from singly ionized silicon only. A discernible enhancement has been measured in both optical (50%–90%) and electrical (34%) signals from the plasma generated on the patterned surface. These results confirm that LIPSS is a versatile method for enhancing the coupling of laser energy onto irradiated solid surfaces.
An improved discrete velocity method (DVM) for efficient simulation of flows in all flow regimes
Authors: Yang L. M. , Shu C. , Yang W. M. , Chen Z. , Dong H.
Published: June 2018

In this paper, an improved discrete velocity method (DVM) is developed for efficient simulation of fluid problems in all flow regimes. Compared with the conventional explicit DVM, the present scheme could effectively remove its drawbacks of low accuracy and efficiency in continuum flow regime with no deterioration of its performance in rarefied flow regime. One of the novel strategies adopted in the new method is to introduce a prediction step for solving the macroscopic governing equation. By using the prediction step, the equilibrium state is first estimated before solving the discrete velocity Boltzmann equation (DVBE). As a result, the collision term in the DVBE can be discretized implicitly to improve the stability and efficiency of the conventional explicit DVM. Another contribution of the new method is to physically reconstruct numerical flux at the cell interface by incorporating the collision effect into the process. To maintain simplicity and efficiency of the conventional DVM, in the present scheme, the collision effect in the flux reconstruction at the cell interface is considered through the solution of the macroscopic governing equation. This can effectively control the effect of numerical dissipation in the process of updating the macroscopic flow variables in the continuum flow regime. Analyses indicate that the prediction step does not contribute to the evolution of distribution functions in the highly rarefied flow regime while dominating the solutions in the continuum flow regime. Accordingly, the improved scheme automatically converges toward the conventional explicit DVM in the free molecular flow regime and approaches the Navier-Stokes solver in the continuum flow regime.
Computer simulations of Jupiter’s deep internal dynamics help interpret what Juno sees
Authors: Glatzmaier Gary A.
Published: June 2018

Significance

NASA’s Juno spacecraft is currently orbiting Jupiter, collecting high-fidelity measurements of its near surface. The resulting patterns of magnetic and gravity fields above Jupiter’s surface have already started providing insight into the type of winds in Jupiter’s deep interior. In addition, by monitoring cloud motions on Jupiter’s surface, Juno may detect a particular type of wave with properties that could tell us the size of Jupiter’s small rocky core. Here, we describe 3D time-dependent computer simulations of thermal convection and magnetic field generation in Jupiter’s deep interior that will help interpret and explain the maintenance of these global near-surface patterns that Juno continues to measure.
Fatty acid metabolism complements glycolysis in the selective regulatory T cell expansion during tumor growth
Authors: Pacella Ilenia , Procaccini Claudio , Focaccetti Chiara , Miacci Stefano , Timperi Eleonora , Faicchia Deriggio , Severa Martina , Rizzo Fabiana , Coccia Eliana Marina , Bonacina Fabrizia , Mitro Nico , Norata Giuseppe Danilo , Rossetti Grazisa , Ranzani Valeria , Pagani Massimiliano , Giorda Ezio , Wei Yu , Matarese Giuseppe , Barnaba Vincenzo , Piconese Silvia
Published: June 2018

Significance

Recent studies have established that metabolic restrains, such as glucose restriction, impair the activities of effector T cells in the tumor microenvironment. In the same context, a huge expansion of activated Treg cells in tumor tissues has been described in mice and humans, contributing to the suppression of protective antitumor immunity. Our data demonstrate that Tregs are committed to survive and proliferate in such a hostile milieu thanks to a metabolic advantage based on the combination of glycolysis and fatty acid synthesis and oxidation. This allows Tregs to prevail over conventional T cells that rely primarily on the glycolytic pathway for their metabolic demands. Awareness of the metabolic dynamics of Tregs in tumor could provide a means for cancer immunotherapy.
Multigenome analysis implicates miniature inverted-repeat transposable elements (MITEs) in metabolic diversification in eudicots
Authors: Boutanaev Alexander M. , Osbourn Anne E.
Published: June 2018

Significance

Recently discovered biosynthetic gene clusters in plants are a striking example of the nonrandom complex structure of eukaryotic genomes. The mechanisms underpinning the formation of these clustered pathways are not understood. Here we carry out a systematic analysis of transposable elements associated with clustered terpene biosynthetic genes in plant genomes, and find evidence to suggest a role for miniature inverted-repeat transposable elements in cluster formation in eudicots. Our analyses provide insights into potential mechanisms of cluster assembly. They also shed light on the emergence of a “block” mechanism for the foundation of new terpene clusters in the eudicots in which microsyntenic blocks of terpene synthase and cytochrome P450 gene pairs duplicate, providing templates for the evolution of new pathways.
Enhancement of Ebola virus infection by seminal amyloid fibrils
Authors: Bart Stephen M. , Cohen Courtney , Dye John M. , Shorter James , Bates Paul
Published: June 2018

Significance

During the 2014–2016 Ebola outbreak, multiple instances of male-to-female sexual transmission of Ebola virus (EBOV) were reported. While relatively uncommon, EBOV sexual transmission presents a major public health concern, as these transmission events occurred months after recovery. Further, sexual transmission was linked to a resurgence of EBOV disease in Guinea, which had previously been declared Ebola-free. However, the role of host factors involved in sexual transmission remains unknown. We find that seminal amyloids and semen greatly enhance EBOV infection and alter the virion physical properties, stabilizing viral infectivity and protecting the virus from drying. These results promote seminal amyloids as possible targets for intervention to prevent EBOV sexual transmission and seeding new infection chains that reignite an outbreak.
Mouse maternal protein restriction during preimplantation alone permanently alters brain neuron proportion and adult short-term memory
Authors: Gould Joanna M. , Smith Phoebe J. , Airey Chris J. , Mort Emily J. , Airey Lauren E. , Warricker Frazer D. M. , Pearson-Farr Jennifer E. , Weston Eleanor C. , Gould Philippa J. W. , Semmence Oliver G. , Restall Katie L. , Watts Jennifer A. , McHugh Patrick C. , Smith Stephanie J. , Dewing Jennifer M. , Fleming Tom P. , Willaime-Morawek Sandrine
Published: June 2018

Significance

Maternal protein malnutrition during pregnancy and lactation compromises brain development, with lasting consequences for motor and cognitive function. However, the importance of nutrition on early brain development is unknown. We have previously shown that maternal low-protein diet confined to the preimplantation period (Emb-LPD) in mice, with normal nutrition thereafter, is sufficient to induce cardiometabolic and locomotor behavioral abnormalities in adult offspring. Here, we report that Emb-LPD and sustained LPD reduce neural stem cells (NSCs) in the fetal brain. Moreover, Emb-LPD causes remaining NSCs to upregulate neuronal differentiation in compensation beyond control levels and increase cortex thickness and neuron ratio, leading to adult memory deficits. These data demonstrate that poor maternal nutrition from conception adversely affects brain development and adult memory.
Degradation of unmethylated miRNA/miRNA*s by a DEDDy-type 3′ to 5′ exoribonuclease Atrimmer 2 in
Arabidopsis
Authors: Wang Xiaoyan , Wang Yuan , Dou Yongchao , Chen Lu , Wang Junli , Jiang Ning , Guo Chunce , Yao Qingqing , Wang Chizao , Liu Lin , Yu Bin , Zheng Binglian , Chekanova Julia A. , Ma Jinbiao , Ren Guodong
Published: June 2018

Significance

The steady-state levels of miRNAs are under sophisticated control to ensure their proper functions such as development and responses to environmental stimuli. Nevertheless, enzymes responsible for the degradation of various forms of unmethylated miRNAs remain enigmatic, which largely impedes our understanding of miRNA homeostasis and active turnover. Here we report a 3′ to 5′ exoribonuclease Atrimmer 2 that may degrade unmethylated miRNAs in their miRNA/miRNA* duplex status, at places distinct from their production sites (i.e., Dicing bodies). Our study not only increases the complexity of miRNA surveillance, but also provides clues into how nascent miRNA/miRNA* duplexes undergo methylation and RNA-induced silencing complex loading, which is a big challenge in the plant small RNA field.
F-actin homeostasis through transcriptional regulation and proteasome-mediated proteolysis
Authors: Onishi Masayuki , Pecani Kresti , Jones Taylor , Pringle John R. , Cross Frederick R.
Published: June 2018

Significance

Cytoskeletal actin microfilaments have roles in cell-shape determination, motility, membrane trafficking, and cell division. Actin filaments respond dynamically to environmental changes and shifting cellular needs, and functionally different actin subtypes may play important roles in such responses. The alga
Chlamydomonas
has two actins: IDA5, an actin of conventional sequence that is expressed in normal growing cells, and NAP1, a divergent actin that is normally not expressed. Disruption of IDA5 filaments results in rapid transcriptional induction of
NAP1
and hundreds of other genes, rapidly replacing all IDA5 filaments with NAP1 filaments, in part by proteasome-mediated degradation of IDA5. This system allows resistance of
Chlamydomonas
to actin-depolymerizing drugs and probably also compensates for other, diverse actin cytoskeletal perturbations, whether intrinsic or induced.
Staphylococcus aureus
biofilms release leukocidins to elicit extracellular trap formation and evade neutrophil-mediated killing
Authors: Bhattacharya Mohini , Berends Evelien T. M. , Chan Rita , Schwab Elizabeth , Roy Sashwati , Sen Chandan K. , Torres Victor J. , Wozniak Daniel J.
Published: June 2018

Significance

Methicillin-resistant
Staphylococcus aureus
(MRSA) infections are responsible for approximately 11,285 deaths per year in the United States. With the ability to acquire antibiotic resistance and counteract host immunity, there is an emergent need for novel therapeutic agents for these infections. Biofilms persist in chronic infections and can tolerate significantly higher antimicrobial concentrations than single cells, greatly complicating the prognosis of MRSA infections. Our knowledge of the persistence mechanisms associated with these infections is limited. This report describes some major strategies used by MRSA biofilms to evade the host innate immune response and shows that
S. aureus
utilizes the combined activity of leukocidins to persist during chronic infections. Host cells efficiently cleared biofilms that were unable to express leukocidins, presenting an exciting avenue for antiinfection therapeutic agents.
Ionic liquids for oral insulin delivery
Authors: Banerjee Amrita , Ibsen Kelly , Brown Tyler , Chen Renwei , Agatemor Christian , Mitragotri Samir
Published: June 2018

Significance

Insulin is currently available as an injectable formulation, but an oral product would enjoy higher patient compliance and would significantly improve the quality of life of diabetic patients worldwide. However, oral delivery of proteins such as insulin is challenging due to various gastrointestinal barriers to oral absorption of macromolecules. We have developed a safe and highly effective ionic liquid-based oral insulin formulation that significantly enhanced oral insulin absorption by efficiently circumventing the gastrointestinal barriers. Besides, the formulation demonstrated good stability at room temperature and under refrigeration. Evidence from cell and animal studies supports a promising prospect of development of the formulation into a clinical product.
Kinetics teach that electronic coupling lowers the free-energy change that accompanies electron transfer
Authors: Sampaio Renato N. , Piechota Eric J. , Troian-Gautier Ludovic , Maurer Andrew B. , Hu Ke , Schauer Phil A. , Blair Amber D. , Berlinguette Curtis P. , Meyer Gerald J.
Published: June 2018

Significance

Nature’s use of electronic coupling (H
DA
) and free-energy (ΔG
o
) gradients to vectorially control electron transport provides inspiration for artificial photosynthesis. Theoretical predictions indicate that H
DA
and ΔG
o
are not independent parameters, and are instead linked. Reported here is a broadly applicable kinetic approach that was utilized to demonstrate such behavior for four acceptor–bridge–donor compounds. When the electronic coupling was large and electron transfer was adiabatic, the free energy of the reaction |ΔG
o
| was less than that for nonadiabatic transfer. This finding should be taken into account in the design of hybrid materials for solar energy conversion and has broad implications to the many classes of electron-transfer reactions in biology and chemistry.
Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales
Authors: Borton Mikayla A. , Hoyt David W. , Roux Simon , Daly Rebecca A. , Welch Susan A. , Nicora Carrie D. , Purvine Samuel , Eder Elizabeth K. , Hanson Andrea J. , Sheets Julie M. , Morgan David M. , Wolfe Richard A. , Sharma Shikha , Carr Timothy R. , Cole David R. , Mouser Paula J. , Lipton Mary S. , Wilkins Michael J. , Wrighton Kelly C.
Published: June 2018

Significance

Microorganisms persisting in hydraulically fractured shales must maintain osmotic balance in hypersaline fluids, gain energy in the absence of electron acceptors, and acquire carbon and nitrogen to synthesize cell building blocks. We provide evidence that that cofermentation of amino acids (Stickland reaction) meets all of these organismal needs, thus functioning as a keystone metabolism in enriched and natural microbial communities from hydraulically fractured shales. This amino acid-based metabolic network can be rationally designed to optimize biogenic methane yields and minimize undesirable chemistries in this engineered ecosystem. Our proposed ecological framework extends to the human gut and other protein-rich ecosystems, where the role of Stickland fermentations and their derived syntrophies play unrecognized roles in carbon and nitrogen turnover.
Fisheries bycatch risk to marine megafauna is intensified in Lagrangian coherent structures
Authors: Scales Kylie L. , Hazen Elliott L. , Jacox Michael G. , Castruccio Frederic , Maxwell Sara M. , Lewison Rebecca L. , Bograd Steven J.
Published: June 2018

Significance

Marine capture fisheries provide a valuable source of protein and are economically important in coastal communities. However, fisheries sustainability is impacted by incidental capture of nontarget species (bycatch), which remains a major global threat to marine megafauna such as sharks, sea turtles, seals, cetaceans, and seabirds. Understanding where and when bycatch events take place can guide fisheries sustainability solutions. Here, we model how dynamic structures in the ocean such as fronts and eddies influence fisheries effort, catch, and bycatch likelihood. We find that bycatch of a diverse range of species is more likely in attracting Lagrangian coherent structures, in which water masses meet and aggregate prey, predators, and fishers into hotspots of risk.
ZNF281 inhibits neuronal differentiation and is a prognostic marker for neuroblastoma
Authors: Pieraccioli Marco , Nicolai Sara , Pitolli Consuelo , Agostini Massimiliano , Antonov Alexey , Malewicz Michal , Knight Richard A. , Raschellà Giuseppe , Melino Gerry
Published: June 2018

Significance

High-risk neuroblastomas (NBs) show undifferentiated/poorly differentiated morphology as a distinctive feature. We have identified the transcription factor ZNF281 as a factor that can counteract the neuronal differentiation of primary neurons in culture and NB cells. The expression of ZNF281 is inhibited by TAp73 and promoted by MYCN. In turn, ZNF281 inhibits the expression of GDNF and NRP2, two proteins associated with neuronal differentiation. In patients with NB, the expression of ZNF281 is higher in high-risk patients and is associated with worse prognosis. Understanding the molecular mechanisms that regulate neuronal differentiation is relevant for the identification of defects in this process that underlie the development of tumors such as NB, in which an aberrant differentiation arrest has occurred.
Mutational and transcriptional landscape of spontaneous gene duplications and deletions in
Caenorhabditis elegans
Authors: Konrad Anke , Flibotte Stephane , Taylor Jon , Waterston Robert H. , Moerman Donald G. , Bergthorsson Ulfar , Katju Vaishali
Published: June 2018

Significance

Copy-number variants are ubiquitous in nature, yet their immediate functional consequences are obscure. We conducted a spontaneous mutation accumulation experiment at varying sizes in
Caenorhabditis elegans
, thereby enabling the simultaneous investigation of the mutational input and strength of selection on the evolution of copy-number changes. Whole-genome sequencing reveals the highest genome-wide rate of gene duplication for any species thus far. Our transcriptome analysis further demonstrates that gene duplication frequently results in a greater than two-fold change in transcription. Despite the adaptive role of duplication as the primary source of novel genes, we find duplications and deletions of highly transcribed genes to be more detrimental to fitness and evidence for selection against increase in transcript abundance.
Structure of the Lassa virus glycan shield provides a model for immunological resistance
Authors: Watanabe Yasunori , Raghwani Jayna , Allen Joel D. , Seabright Gemma E. , Li Sai , Moser Felipe , Huiskonen Juha T. , Strecker Thomas , Bowden Thomas A. , Crispin Max
Published: June 2018

Significance

Lassa virus is a highly pathogenic arenavirus that causes severe hemorrhagic fever in humans. Currently, there are no efficacious vaccines or treatments available to combat this pathogen. An important component of any vaccine candidate against Lassa virus will likely include the highly glycosylated glycoprotein complex presented on the virion surface. Here, we determine the composition of the Lassa virus glycome, revealing that the virus presents an abundance of glycans that are not biosynthetically processed to full maturity. Such underprocessed glycans form spatially distinct clusters, which shield the proteinous surface of the Lassa virus glycoprotein spike from the humoral immune response. These data are integral for the development of humoral-based vaccines that mimic the mature Lassa virion.
Direct cell–cell contact activates SigM to express the ESX-4 secretion system inMycobacterium smegmatis
Authors: Clark Ryan R. , Judd Julius , Lasek-Nesselquist Erica , Montgomery Sarah A. , Hoffmann Jennifer G. , Derbyshire Keith M. , Gray Todd A.
Published: June 2018

Significance

A conjugation model of mycobacterial interaction recently revealed that intercellular communication occurs between donors and recipients. This communication links two ESAT-6 (ESX) (type VII) secretion systems that are both required for conjugation. Functionally distinct ESX secretion systems are found in all mycobacteria, and they serve important virulence functions in pathogenic mycobacteria. We demonstrate that SigM, an extracytoplasmic transcription factor, activates ESX-4. Direct donor-recipient cell contact triggers the recipient cell to release membrane-sequestered SigM, which rapidly induces an ESX-4-focused regulon. The conservation of SigM and ESX-4 throughout mycobacteria suggests that this interaction-response network is intact and active in pathogens. Contact-dependent responses similar to those identified in our model system may therefore also mediate communal processes within infectious mycobacterial populations.