bluuebunny/crossref_metadata_2025 huggingface dataset:
Solving the problem of overdetermination of quasisymmetric equilibrium solutions by near-axis expansions. II. Circular axis stellarator solutions
Authors: Rodríguez E. , Bhattacharjee A.
Published: January 2021

We apply the near-axis expansion method for quasisymmetric magnetic fields with anisotropic pressure (developed in Paper I) [E. Rodriguez and A. Bhattacharjee, Phys. Plasmas 28, 012508 (2020)] to construct numerical solutions to circular axis stellarators. The solutions are found to second order in the distance from the axis, not possible in the standard Garren–Boozer construction [D. A. Garren and A. H. Boozer, Phys. Fluids B 3, 2822 (1991)], which assumes magnetostatic equilibria with isotropic pressure. In the limit of zero anisotropy, it is shown that a subset of coefficients can be chosen to avoid the overdetermination problem.
Low field electron transport in α−Ga2O3: An ab initio approach
Authors: Sharma Ankit , Singisetti Uttam
Published: January 2021

Trigonal α−Ga2O3 is an ultrawideband semiconductor with potential applications in power electronics and ultraviolet opto-electronic devices. In this Letter, we calculate the low field electron mobility in α−Ga2O3 from first principles calculations. The effect of all the 30 phonon modes is taken into account for the transport calculation. The phonon dispersion and the Raman and Infrared spectra are calculated under the density functional perturbation theory formalism and compared with experiments. The electron–phonon interaction (EPI) elements on a dense reciprocal space grid are obtained using the Wannier function interpolation. The full energy dispersion of the phonons is included in both the polar and nonpolar EPI calculations. The electron mobility is then evaluated incorporating the effects of the polar, nonpolar, and ionized impurity scattering using Rode's iterative method. At room temperature, the low field isotropic average electron mobility is estimated to be ∼220 cm2/V s predominantly limited by the polar optical phonon scattering at a doping density of 1.0×1015 cm−3. The anisotropy in the mobility arising from the phonon scattering is also evaluated. Temperature and dopant concentration variation of mobility is also studied, which can help in optimization of the growth for transport measurements.
Enhancement of YIG|Pt spin conductance by local Joule annealing
Authors: Kohno R. , Thiery N. , An K. , Noel P. , Vila L. , Naletov V. V. , Beaulieu N. , Youssef J. Ben , de Loubens G. , Klein O.
Published: January 2021

We report that Joule heating can be used to enhance the interfacial spin conductivity between a metal and an oxide. We observe that local annealing of the interface at about 550 K, when injecting large current densities (>1012A/m2) into a pristine 7 nm thick Pt nanostrip evaporated on top of yttrium iron garnet (YIG), can improve the effective spin transmission up to a factor of 3. This result is of particular interest when interfacing ultrathin garnet films to avoid strong chemical etching of the surface. The effect is confirmed by the following methods: spin Hall magnetoresistance, spin pumping, and non-local spin transport. We use it to study the influence of the YIG|Pt coupling on the non-linear spin transport properties. We find that the crossover current from a linear to a non-linear spin transport regime is independent of this coupling.
Correlation between changes in nanoscale structural and optical properties upon swift heavy ion irradiation of SiNx thin films
Authors: Gupta Harsh , Bommali Ravi K. , Ghosh Santanu , Srivastava Himanshu , Srivastava Arvind , Srivastava Pankaj
Published: January 2021

This work reports the correlation of changes in structural and optical properties of a-SiNx:H thin films irradiated with 100 MeV Au8+ at various fluences. Cross-sectional TEM studies show the evolution of discontinuous ion tracks with a radius of 3 nm as the nanoscale structural changes in films. Spectroscopic ellipsometry was used for the extraction of different optical parameters, viz., refractive index, extinction coefficient, Urbach tail energy, and bandgap along with thickness and roughness by fitting the experimental data and modeling the dielectric function with the Cody–Lorentz model. An increase in the Si-N phase was evident, with an increase in the bandgap. Change in the Urbach energy and broadening of oscillator parameters suggest an increased disorder and introduction of defect states upon irradiation. The Wemple–Dedomenico dispersion model was used to deduce dispersion energy to establish a change in thin films' density upon irradiation. The change in the density of thin films is further correlated to the increase in the refractive index. The evolution of various parameters reveals the correlation between changes in optical properties with structural properties down to nanoscale upon swift heavy ion irradiation on a-SiNx:H thin films.
Chip-based electrostatic beam splitting of guided kiloelectron volt electrons
Authors: Seidling M. , Zimmermann R. , Hommelhoff P.
Published: January 2021

We present a beam splitter for guided electrons using an electrostatic guiding potential created above the surface of two opposing planar microstructured printed circuit boards. The electric fields acting on the electrons result in a ponderomotive potential. We show that we can smoothly transition the ponderomotive potential from a single-well into a double-well, which leads to the splitting of the electron beam. Efficient beam splitting is observed over a large range of kinetic energies starting at 200 eV up to 1700 eV. We discuss future work needed to reach adiabatic beam splitting for quantum state-selective electron optics. This will pave the way for an electron interferometer on a chip and, therefore, result in until now not possible elements for electron optics and microscopy.
Synthesis and characterization of amorphous Fe2.75Dy-oxide thin films demonstrating room-temperature semiconductor, magnetism, and optical transparency
Authors: Prasad Koirala Krishna , Deb Aniruddha , Bey Sara , Allen Tatiana , Sachan Ritesh , Prasad Sandireddy Venkatanarayana , Liu Chenze , Duscher Gerd , Penner-Hahn James , Kalyanaraman Ramki
Published: January 2021

Recently, amorphous/disordered oxide thin films made from Fe and lanthanides like Dy and Tb have been reported to have a rich set of magnetic, optical, and electronic properties, as well as room-temperature magneto-electric coupling with multiferroics [A. Malasi et al., Sci. Rep. 5, 18157 (2015); H. Taz et al., Sci. Rep. 6, 27869 (2016); and H. Taz et al., Sci. Rep. 10, 1–10 (2020)]. Here, we report the synthesis and detailed characterization of Fe2.75Dy-oxide thin films prepared on various substrates using electron beam co-evaporation. The structure, chemistry, electric, magnetic, and optical properties were studied for the as-prepared and annealed (373 K, in air, 1 h) films of thickness 40 nm. High resolution transmission electron microscopy and electron diffraction study showed that the films were amorphous in both the as-prepared and annealed states. The electron energy-loss spectroscopy studies quantified that metal oxygen stoichiometry changed from Fe2.75Dy-O1.5 to Fe2.75Dy-O1.7 upon annealing. Synchrotron-based x-ray absorption spectroscopy investigation confirmed that the as-prepared films were highly disordered with predominantly metallic Fe and Dy states that became slightly oxidized with annealing in air. The as-prepared amorphous films demonstrated significantly high value of ordinary (∼10 cm2/V s) and anomalous (∼102 cm2/V s) Hall mobility and high electrical conductivity of ∼103 S/cm at room temperature. The cryogenic magnetic property measurement shows two-step magnetization below 200 K, suggesting exchange-spring magnetic interaction. The nature of the field cooled and zero-field cooled curves suggested a spin-glass like transition between 78 K and 80 K, with a characteristic broad peak. The Tauc plot analysis from optical transmission spectra confirms the existence of an optical bandgap of ∼2.42 eV that increased slightly to ∼2.48 eV upon annealing. This rich set of transport, optical, and magnetic properties in these thin films is very exciting and points to potential applicability in low-cost multifunctional devices requiring a combination of transparent, semiconducting, and magnetic responses, such as in spintronics.
A modal wave-packet model for the multi-mode Richtmyer–Meshkov instability
Authors: Dimonte Guy
Published: January 2021

A model for multimode perturbations subject to the Richtmyer–Meshkov (RM) instability is presented and compared with simulations and experiments for conditions relevant to inertial confinement fusion. The model utilizes the single mode response to the RM impulse whereby its amplitude h(k, t) first grows with an initial velocity V0 ∝ kh(k, 0) that eventually decays in time as 1/kV0t. Both the growth and saturation stages are subject to nonlinearities since they depend explicitly on the initial amplitude. However, rather than using the individual mode amplitude h(k, t), nonlinearity is taken to occur when the root-mean-square amplitude hrms(k, t) of a wave-packet within wavenumbers k ± δk becomes comparable to 1/k. This is done because nearby sidebands can act in unison for an auto-correlation distance 1/δk beyond nonlinearity as observed in the beam-plasma instability. Thus, the nonlinear saturation amplitude for each mode is reduced from the usual 1/k by a phase space factor that depends on the physical dimensionality, as in the Haan model for the Rayleigh–Taylor instability. In addition, for RM, the average value of khrms for the initial spectrum is used to calculate a nonlinear factor FNL that reduces V0, as observed for single modes. For broadband perturbations, the model describes self-similar growth ∝tθ as successively longer wavelength modes reach saturation. The growing and saturated modes must be discerned because only the former promote θ and are enhanced by reshock and spherical convergence. All of these flows are described here by the model in good agreement with simulations and experiments.
The Raspberry Pi auto-aligner: Machine learning for automated alignment of laser beams
Authors: Mathew Renju S. , O’Donnell Roshan , Pizzey Danielle , Hughes Ifan G.
Published: January 2021

We present a novel solution to automated beam alignment optimization. This device is based on a Raspberry Pi computer, stepper motors, commercial optomechanics and electronic devices, and the open-source machine learning algorithm M-LOOP. We provide schematic drawings for the custom hardware necessary to operate the device and discuss diagnostic techniques to determine the performance. The beam auto-aligning device has been used to improve the alignment of a laser beam into a single-mode optical fiber from manually optimized fiber alignment, with an iteration time of typically 20 minutes. We present example data of one such measurement to illustrate device performance.
Examining the self-assembly of patchy alkane-grafted silica nanoparticles using molecular simulation
Authors: Craven Nicholas C. , Gilmer Justin B. , Spindel Caroline J. , Summers Andrew Z. , Iacovella Christopher R. , McCabe Clare
Published: January 2021

In this work, molecular dynamics simulations are used to examine the self-assembly of anisotropically coated “patchy” nanoparticles. Specifically, we use a coarse-grained model to examine silica nanoparticles coated with alkane chains, where the poles of the grafted nanoparticle are bare, resulting in strongly attractive patches. Through a systematic screening process, the patchy nanoparticles are found to form dispersed, string-like, and aggregated phases, dependent on the combination of alkane chain length, coating chain density, and the fractional coated surface area. Correlation analysis is used to identify the ability of various particle descriptors to predict bulk phase behavior from more computationally efficient single grafted nanoparticle simulations and demonstrates that the solvent-accessible surface area of the nanoparticle core is a key predictor of bulk phase behavior. The results of this work enhance our knowledge of the phase space of patchy nanoparticles and provide a powerful approach for future screening of these materials.
Large anomalous Hall angle in a topological semimetal candidate TbPtBi
Authors: Chen Jie , Li Hang , Ding Bei , Zhang Hongwei , Liu Enke , Wang Wenhong
Published: January 2021

In this study, the magnetotransport properties of antiferromagnetic half-Heusler single crystals of TbPtBi, a magnetic field-induced topological semimetal with a simple band structure, were investigated. We found a nonmonotonic dependence of the anomalous Hall resistivity on the magnetic field in a strong magnetic field (B > 7 T), which comes from the change in the band structure caused by the Zeeman-like splitting when an external magnetic field is applied. The experimental results show that credible anomalous Hall resistivity and conductivity reach up to 0.68 mΩ cm and 125 Ω−1 cm−1, respectively. A large anomalous Hall angle up to 33% is achieved in TbPtBi, which is comparable to a typical ferromagnetic Weyl semimetal. The analysis of the results shows that this should be attributed to the topological band around EF and low carrier density.
How to deform an egg yolk? On the study of soft matter deformation in a liquid environment
Authors: Lang Ji , Nathan Rungun , Wu Qianhong
Published: January 2021

In this paper, we report a novel experimental study to examine the response of a soft capsule bathed in a liquid environment to sudden external impacts. Taking an egg yolk as an example, we found that the soft matter is not sensitive to translational impacts but is very sensitive to rotational, especially decelerating-rotational, impacts, during which the centrifugal force and the shape of the membrane together play a critical role in causing the deformation of the soft object. This finding, as the first study of its kind, reveals the fundamental physics behind the motion and deformation of a membrane-bound soft object, e.g., egg yolk, cells, and soft brain matter, in response to external impacts.
Impact of vacancies and impurities on ferroelectricity in PVD- and ALD-grown HfO2 films
Authors: Baumgarten Lutz , Szyjka Thomas , Mittmann Terence , Materano Monica , Matveyev Yury , Schlueter Christoph , Mikolajick Thomas , Schroeder Uwe , Müller Martina
Published: January 2021

We investigate the emerging chemical states of TiN/HfO2/TiN capacitors and focus especially on the identification of vacancies and impurities in the ferroelectric HfO2 layers, which are produced either by physical vapor deposition (PVD) or atomic layer deposition (ALD). Depending on the specific growth conditions, we identify different mechanisms of oxygen vacancy formation. Corresponding spectral features are consistently observed for all HfO2- and TiN-related core levels by hard x-ray photoelectron spectroscopy (HAXPES). In ALD-grown samples, we find spectral signatures for the electronic interaction between oxygen vacancies and nitrogen impurities. By linking the HAXPES results to electric field cycling experiments on the TiN/HfO2/TiN capacitors, we discuss possible formation mechanisms and stabilization of the ferroelectric HfO2 phase directly related to specific PVD or ALD conditions.
Impact of the interplay of piezoelectric strain and current-induced heating on the field-like spin–orbit torque in perpendicularly magnetized Ta/Co20Fe60B20/Ta/MgO film
Authors: Filianina M. , Wang Z. , Baldrati L. , Lee K. , Vafaee M. , Jakob G. , Kläui M.
Published: January 2021

Spin–orbit torques (SOTs) are known to be the most efficient way to manipulate the magnetization direction by electrical currents. While, conventionally, one symmetry component of the SOTs, namely, the damping-like torque, was considered to play a primary role, recently, the significance of the other component, the field-like torque, has been revised, owing to the non-trivial dynamics it can induce in heavy metal/ferromagnet multilayers. In this work, we first discuss the unusual behavior of the field-like SOT in a Ta/CoFeB/Ta/MgO multilayer system with a reduced magnetic anisotropy and demonstrate an energy-efficient approach to manipulate the magnitude of the SOT effective fields. Finally, our results show a possibility to engineer the anisotropy of the field-like SOTs by piezoelectric strain, which can be potentially attractive for application in spintronics.
Long-range correlation of intra-molecular and inter-molecular vibration in liquid CCl4
Authors: Shelton David P.
Published: January 2021

Experiments measuring the polarization dependence of hyper-Raman light scattering reveal long-range correlation of molecular vibrations in liquid CCl4. The ν3 and ν1 + ν4 intra-molecular vibrations at about 770 cm−1 are strongly polarized transverse to the scattering wavevector. Weaker transverse polarization is exhibited by the ν1, ν2, and ν4 intra-molecular vibrations and by the inter-molecular collision-induced band around 0 cm−1. The observed polarization dependence is due to the correlation of the vibrations on molecules separated by about 200 nm. The strength of the observed correlation increases with the transition dipole moment for the vibration mode and is consistent with dipole–dipole coupling.
Thermoelectric properties of
α
-In2Se3 monolayer
Authors: Nian Taojie , Wang Zhenhai , Dong Baojuan
Published: January 2021

Thermoelectric (TE) properties of monolayered α-In2Se3 are investigated using the first-principles calculations based on the density functional theory and Boltzmann transport theory. The results show that monolayered α-In2Se3 is a great candidate for high-performance thermoelectric materials with the power factor PF and the figure of merit ZT as high as 0.02 W/mK2 and 2.18 at room temperature, respectively. We attribute such great TE performance to the large electrical conductivity and low lattice thermal conductivity, which originate from unique band structures of group III chalcogenides and anharmonic scattering. Furthermore, we prove that the quantum confinement effect can realize up to an order of magnitude enhancement in the PF. Our findings may open up new possibilities for two-dimensional thermoelectric materials in practical applications.
Monitoring damage of self-assembled monolayers using metastable excited helium atoms
Authors: Stratis Georgios , Zesch Jordan D. , Pan Henry S. , Webb Lauren J. , Raizen Mark G.
Published: January 2021

The breaking of molecular bonds during exposure to ionizing radiation and electron beams creates irreversible damage in the molecular structure. In some cases, such as lithography, controlled damage of a molecular resist is a desirable process and is the basis for the entire semiconductor industry. In other cases, such as environmental exposure or probing of the molecular structure, the induced damage is a major problem that has limited advances in science and technology. We report here the use of an in situ probe that is minimally invasive to detect real-time damage induced in organic materials. Specifically, we use metastable excited helium atoms in the 3S1 state to characterize the damage caused by a low-energy electron beam ∼30 eV on an organic self-assembled monolayer of 11-bromo-1-undecanethiol on a gold substrate. We were able to monitor the damage caused by the electron beam without introducing any additional observed damage by the probing metastable atoms.
Parity-controlled spin-wave excitations in synthetic antiferromagnets
Authors: Sud A. , Koike Y. , Iihama S. , Zollitsch C. , Mizukami S. , Kurebayashi H.
Published: January 2021

We report in this study the current-induced-torque excitation of acoustic and optical modes in Ta/NiFe/Ru/NiFe/Ta synthetic antiferromagnet stacks grown on SiO2/Si substrates. The two Ta layers serve as spin torque sources with the opposite polarizations in both spin currents and Oersted fields acting on their adjacent NiFe layers. This can create the odd symmetry of spatial spin torque distribution across the growth direction, allowing us to observe different spin-wave excitation efficiency from synthetic antiferromagnets excited by homogeneous torques. We analyze the torque symmetry by the in-plane angular dependence of symmetric and anti-symmetric line shape amplitudes for their resonance and confirm the parallel (perpendicular) pumping nature for the acoustic (optical) modes in our devices, which is in stark contrast to the modes excited by spatially homogeneous torques. We also present our macrospin model for this particular spin-torque excitation geometry, which excellently supports our experimental observation. Our results offer capability of controlling spin-wave excitations by local spin-torque sources, and we can explore further spin-wave control schemes based on this concept.
Coherent vortex in a spatially restricted two-dimensional turbulent flow in absence of bottom friction
Authors: Doludenko A. N. , Fortova S. V. , Kolokolov I. V. , Lebedev V. V.
Published: January 2021

We investigate the coherent vortex produced by two-dimensional turbulence excited in a finite box. We establish analytically the mean velocity profile of the vortex for the case where the bottom friction is negligible and express its characteristics via the parameters of pumping. Our theoretical predictions are verified and confirmed by direct numerical simulations in the framework of two-dimensional weakly compressible hydrodynamics with zero boundary conditions.
On the formation of van der Waals complexes through three-body recombination
Authors: Mirahmadi Marjan , Pérez-Ríos Jesús
Published: January 2021

In this work, we show that van der Waals molecules X–RG (where RG is the rare gas atom) may be created through direct three-body recombination collisions, i.e., X + RG + RG → X–RG + RG. In particular, the three-body recombination rate at temperatures relevant for buffer gas cell experiments is calculated via a classical trajectory method in hyperspherical coordinates [Pérez-Ríos et al., J. Chem. Phys. 140, 044307 (2014)]. As a result, it is found that the formation of van der Waals molecules in buffer gas cells (1 K ≲ T ≲ 10 K) is dominated by the long-range tail (distances larger than the LeRoy radius) of the X–RG interaction. For higher temperatures, the short-range region of the potential becomes more significant. Moreover, we notice that the rate of formation of van der Walls molecules is of the same order of the magnitude independent of the chemical properties of X. As a consequence, almost any X–RG molecule may be created and observed in a buffer gas cell under proper conditions.
Plantastic!
Authors: Clowes Catherine , Gyan Rachel
Published: January 2021

Did you know that there are plants that eat insects? Plants whose seeds spread in poo? Plants that move when you touch them? And plants that grow on other plants?

Plantastic! presents 26 of Australia's most unique and incredible native plants. Discover and identify native plants found in your local park, bushland, or even in your very own backyard.

With its perfect balance of fun facts, activities, adventurous ideas and gorgeous illustrations, Plantastic! will prove just how fantastic Australia's native plants really are!
Using data-driven approaches to improve delivery of animal health care interventions for public health
Authors: Mazeri Stella , Burdon Bailey Jordana L. , Mayer Dagmar , Chikungwa Patrick , Chulu Julius , Grossman Paul Orion , Lohr Frederic , Gibson Andrew D. , Handel Ian G. , Bronsvoort Barend M. deC. , Gamble Luke , Mellanby Richard J.
Published: January 2021

Significance

Rabies is arguably the exemplar of the One Health Agenda in which preventative health care in one species can improve health of other species. Interrogation of large epidemiology datasets offers the potential to deliver health care initiatives in a more efficient and cost-effective manner. However, real-life examples demonstrating this potential are limited. Here, we report a real-time, data-driven approach to improve cost effectiveness of dog vaccination campaigns in urban sub-Saharan African settings, which eliminates the need of expensive door-to-door vaccination by replacing them with strategically positioned fixed and roaming static points (SPs). This approach has the potential to act as a template for future successful and sustainable urban SP-only dog vaccination campaigns.
Pervasive cropland in protected areas highlight trade-offs between conservation and food security
Authors: Vijay Varsha , Armsworth Paul R.
Published: January 2021

Significance

Biodiversity conservation strategies emphasize protected area expansion to mitigate species losses by safeguarding habitat. However, demand for land for food production is also increasing. We establish a baseline estimate of where and why cropland occurs in protected areas. Our estimates would indicate cropland represents around 18% of all human impacts inside protected areas. Cropland will not be effective in conserving many species, particularly habitat specialists, rare, and threatened species. This suggests a reexamination of the effectiveness of area-based protected area planning is needed. The success of post-2020 biodiversity management depends on addressing trade-offs with food production by creating opportunities to integrate ecosystem conservation and restoration with programs for hunger and malnutrition.
Positive epistasis between disease-causing missense mutations and silent polymorphism with effect on mRNA translation velocity
Authors: Rauscher Robert , Bampi Giovana B. , Guevara-Ferrer Marta , Santos Leonardo A. , Joshi Disha , Mark David , Strug Lisa J. , Rommens Johanna M. , Ballmann Manfred , Sorscher Eric J. , Oliver Kathryn E. , Ignatova Zoya
Published: January 2021

Significance

The same mutation can have different effects among individuals, and one reason for this is the presence of additional mutations, a relationship known as epistasis. Epistatic effects are difficult to predict. We report a rare example of positive epistasis between a silent mutation (that changes nucleotide but not the encoded amino acid) and missense mutation(s) (that change amino acid and cause cystic fibrosis disease). Individually, each mutation has a detrimental effect, but they are beneficial when present together. The underlying molecular effect is in their ability to markedly modulate the ribosomal speed on mRNA in a synergistic fashion. In a broader setting of human diseases, our results suggest that epistasis with silent mutation broadens the spectrum of disease outcome.
Evolution and demise of passive margins through grain mixing and damage
Authors: Bercovici David , Mulyukova Elvira
Published: January 2021

Significance

Subduction of sea floor into the Earth’s mantle is the engine of plate tectonics. Yet, how subduction initiates remains a mystery. Subduction often occurs along trenches at the ocean–continent margin, which implies they formed there, when the margin was once immobile or passive, but then collapsed. Margin collapse occurs when near-surface mantle, the lithosphere, gets cold and heavy and founders. That cold lithosphere, however, should be too stiff to sink. Grain damage in mantle rocks, whereby mineral grains under stress diminish in size, weakens the lithosphere and mostly occurs where minerals mix with each other. Horizontal compressive stresses in a passive margin induce mixing and damage and generate weak bands in the lithosphere that facilitate subduction initiation.
Distinct electrophysiological signatures of task-unrelated and dynamic thoughts
Authors: Kam Julia W. Y. , Irving Zachary C. , Mills Caitlin , Patel Shawn , Gopnik Alison , Knight Robert T.
Published: January 2021

Significance

Our minds rarely stay still when left alone. Such trains of thought, however, may unfold in vastly different ways. Here, we combined electrophysiological recording with thought sampling to assess four types of thoughts: task-unrelated, freely moving, deliberately constrained, and automatically constrained. Parietal P3 was larger for task-related relative to task-unrelated thoughts, whereas frontal P3 was increased for deliberately constrained compared with unconstrained thoughts. Enhanced frontal alpha power was observed during freely moving thoughts compared with non-freely moving thoughts. Alpha-power variability was increased for task-unrelated, freely moving, and unconstrained thoughts. Our findings indicate these thought types have distinct electrophysiological signatures, suggesting that they capture the heterogeneity of our ongoing thoughts.
Autoinhibitory elements of the Chd1 remodeler block initiation of twist defects by destabilizing the ATPase motor on the nucleosome
Authors: Nodelman Ilana M. , Shen Zhongtian , Levendosky Robert F. , Bowman Gregory D.
Published: January 2021

Significance

Nucleosomes, the fundamental packaging unit of eukaryotic chromosomes, affect gene expression profiles based on their positioning. By shifting nucleosomes along genomic DNA, chromatin remodelers are key reorganizing factors that are often mutated in cancers and developmental disorders. Here, we demonstrate how one remodeler class, called Chd1, uses autoinhibitory elements to control the direction of nucleosome sliding. We show that, through positioning of its DNA-binding domain, the autoinhibitory elements of Chd1 can block an initial stage of DNA distortion required for sliding. This interference by autoinhibitory domains weakens remodeler–nucleosome interactions, transiently preventing subsequent binding and hydrolysis of ATP from ratcheting nucleosomes along DNA.
Quantum phases of Rydberg atoms on a kagome lattice
Authors: Samajdar Rhine , Ho Wen Wei , Pichler Hannes , Lukin Mikhail D. , Sachdev Subir
Published: January 2021

Significance

Programmable quantum simulators based on Rydberg atom arrays have recently emerged as versatile platforms for exploring exotic many-body phases and quantum dynamics of strongly correlated systems. In this work, we theoretically investigate the quantum phases that can be realized by arranging such Rydberg atoms on a kagome lattice. Along with an extensive analysis of the states which break lattice symmetries due to classical correlations, we identify an intriguing regime that constitutes a promising candidate for hosting a phase with long-range quantum entanglement and topological order. Our results provide a route to experimentally realizing and probing highly entangled quantum matter.
Structure and assembly of the diiron cofactor in the heme-oxygenase–like domain of the
N
-nitrosourea–producing enzyme SznF
Authors: McBride Molly J. , Pope Sarah R. , Hu Kai , Okafor C. Denise , Balskus Emily P. , Bollinger J. Martin , Boal Amie K.
Published: January 2021

Significance

The enzyme SznF assembles the
N
-nitrosourea pharmacophore of the drug streptozotocin. Its
N
-oxygenase domain resembles heme-oxygenase (HO) and belongs to an emerging superfamily of HO-like diiron enzymes (HDOs) with unstable metallocofactors that have resisted structural characterization. Insight into cofactor dynamics from our prior investigation of SznF’s
N
-oxygenation reactions suggested an approach that has yielded a structure of a functionally assigned HDO with its diiron cofactor intact. Conformational changes accompanying cofactor (dis)assembly explain its instability, and the observation of an unanticipated glutamate ligand that is conserved in only a subset of HDO sequences provides a potential basis for top-level assignment of enzymatic function. Our results thus provide a roadmap for structural and functional characterization of novel HDOs.
Discrete TrkB-expressing neurons of the dorsomedial hypothalamus regulate feeding and thermogenesis
Authors: Houtz Jessica , Liao Guey-Ying , An Juan Ji , Xu Baoji
Published: January 2021

Significance

Neurons in the dorsomedial hypothalamus that express TrkB (DMH
TrkB
) have been implicated in the regulation of appetite; however, their relevance to energy expenditure is less clear. This study reveals that activation of DMH
TrkB
neurons potently induce thermogenesis and locomotor activity. Notably, increased energy expenditure mediated by DMH
TrkB
neurons is not accompanied by increased heart rate or blood pressure, which have traditionally complicated weight loss therapies that target thermogenesis. Furthermore, our results reveal separate populations of DMH
TrkB
neurons that form diverging neurocircuits to either the raphe pallidus or the paraventricular hypothalamus and preoptic area to independently regulate thermogenesis or feeding, respectively. These findings support a mechanism whereby DMH
TrkB
neurons act through multiple pathways to promote weight loss without adverse cardiovascular consequences.
Multiple cannabinoid signaling cascades powerfully suppress recurrent excitation in the hippocampus
Authors: Jensen Kyle R. , Berthoux Coralie , Nasrallah Kaoutsar , Castillo Pablo E.
Published: January 2021

Significance

In the hippocampus, the recurrent excitatory circuit established by reciprocal connections between dentate granule cells and mossy cells is dynamically regulated by activity and has been implicated in pattern separation and epilepsy. The extensive projections of mossy cells make this recurrent circuit particularly prone to runaway activity. Here, we identified multiple mechanisms by which activation of cannabinoid receptors, which are highly expressed in mossy cell axons, powerfully dampen the activity of this circuit by selectively suppressing both mossy cell to granule cell basal synaptic transmission and LTP induction. These inhibitory actions likely contribute to a sparse network of quiet granule cells, which is critical to pattern separation, precludes epilepsy, and may explain some of the marijuana-mediated effects in hippocampal-dependent memory.
Native American fire management at an ancient wildland–urban interface in the Southwest United States
Authors: Roos Christopher I. , Swetnam Thomas W. , Ferguson T. J. , Liebmann Matthew J. , Loehman Rachel A. , Welch John R. , Margolis Ellis Q. , Guiterman Christopher H. , Hockaday William C. , Aiuvalasit Michael J. , Battillo Jenna , Farella Joshua , Kiahtipes Christopher A.
Published: January 2021

Significance

As residential development continues into flammable landscapes, wildfires increasingly threaten homes, lives, and livelihoods in the so-called “wildland–urban interface,” or WUI. Although this problem seems distinctly modern, Native American communities have lived in WUI contexts for centuries. When carefully considered, the past offers valuable lessons for coexisting with wildfire, climate change, and related challenges. Here we show that ancestors of Native Americans from Jemez Pueblo used ecologically savvy intensive burning and wood collection to make their ancient WUI resistant to climate variability and extreme fire behavior. Learning from the past offers modern WUI communities more options for addressing contemporary fire challenges. Public/private–tribal partnerships for wood and fire management can offer paths forward to restore fire-resilient WUI communities.
Synaptotagmin-1–, Munc18-1–, and Munc13-1–dependent liposome fusion with a few neuronal SNAREs
Authors: Stepien Karolina P. , Rizo Josep
Published: January 2021

Significance

Neurotransmitter release is crucial for neuronal communication. Reproducing the steps that lead to neuronal exocytosis with lipid vesicles and purified proteins provides a powerful strategy to elucidate the molecular mechanisms underlying release. Previous studies showed that reconstitution experiments including Munc18-1, Munc13-1, NSF, α-SNAP, and the SNARE proteins synaptobrevin, syntaxin-1, and SNAP-25, all of which are critical for neurotransmitter release, led to highly efficient vesicle fusion. However, synaptotagmin-1, the Ca
2+
sensor that triggers release, did not have detectable effects in these fusion assays. We now show that, when the amounts of synaptobrevin and syntaxin-1 are lowered in otherwise analogous reconstitution experiments, vesicle fusion is strongly dependent on synaptotagmin-1, exhibiting several features that parallel those of neurotransmitter release in neurons.
Growth hormone-releasing hormone agonists ameliorate chronic kidney disease-induced heart failure with preserved ejection fraction
Authors: Rieger Angela C. , Bagno Luiza L. , Salerno Alessandro , Florea Victoria , Rodriguez Jose , Rosado Marcos , Turner Darren , Dulce Raul A. , Takeuchi Lauro M. , Kanashiro-Takeuchi Rosemeire M. , Buchwald Peter , Wanschel Amarylis C. B. A. , Balkan Wayne , Schulman Ivonne H. , Schally Andrew V. , Hare Joshua M.
Published: January 2021

Significance

This randomized, blinded study used rigorous hemodynamic tools to test the efficacy of a synthetic growth hormone-releasing hormone agonist (GHRH‐A) on the restoration of diastolic function in a large animal model of chronic kidney disease (CKD)-induced heart failure with preserved ejection fraction (HFpEF). CKD was produced in Yorkshire swine by performing a 5/6 nephrectomy via catheter-based renal artery embolization. HFpEF was evident at 12 wk postembolization. Daily injection of GHRH-A improved cardiac diastolic hemodynamics, including end-diastolic pressure, end-diastolic pressure–volume ratio, and stroke work, compared to placebo. Development of this swine model and therapeutic approach has important implications because of the high prevalence of CKD-induced HFpEF and cardiorenal syndromes, lack of effective therapies, and few large-animal models available for investigation.
A short ORF-encoded transcriptional regulator
Authors: Koh Minseob , Ahmad Insha , Ko Yeonjin , Zhang Yuxiang , Martinez Thomas F. , Diedrich Jolene K. , Chu Qian , Moresco James J. , Erb Michael A. , Saghatelian Alan , Schultz Peter G. , Bollong Michael J.
Published: January 2021

Significance

The small size of short ORF-encoded peptides (SEPs) has made it difficult to identify their cellular binding partners using standard methods. Here, we show that the photo-crosslinking amino acid AbK can be incorporated into overexpressed, epitope-tagged SEP transgenes, allowing covalent bond formation between SEPs and their interactors in live cells. From an AP-MS–based screen of conserved mammalian SEPs, we identified short ORF-encoded histone binding protein (SEBHP), a micropeptide which acts as a transcriptional regulator, capable of modulating more than 15% of the active transcriptome. The methodology described herein will likely be of broad utility in annotating the essential physiological roles of SEPs.
Long-range structural defects by pathogenic mutations in most severe glucose-6-phosphate dehydrogenase deficiency
Authors: Horikoshi Naoki , Hwang Sunhee , Gati Cornelius , Matsui Tsutomu , Castillo-Orellana Carlos , Raub Andrew G. , Garcia Adriana A. , Jabbarpour Fatemeh , Batyuk Alexander , Broweleit Joshua , Xiang Xinyu , Chiang Andrew , Broweleit Rachel , Vöhringer-Martinez Esteban , Mochly-Rosen Daria , Wakatsuki Soichi
Published: January 2021

Significance

Mechanism of the loss of activity of the most severe patient-derived mutants of glucose-6-phosphate dehydrogenase (G6PD) deficiency has remained elusive despite the availability of the G6PD structures for decades. Structural and biophysical investigations have revealed a common mechanism and dynamics of how these mutations hinder the substrate-binding site, reducing enzymatic activity. These are triggered by a long-distance propagation of structural defects at the dimer interface and the binding site of the noncatalytic cofactor. These structural distortions are found among all of the class I mutants investigated, providing critical clues for drug design to address G6PD deficiency by correcting the structural defects.
Rag GTPases and phosphatidylinositol 3-phosphate mediate recruitment of the AP-5/SPG11/SPG15 complex
Authors: Hirst Jennifer , Hesketh Geoffrey G. , Gingras Anne-Claude , Robinson Margaret S.
Published: January 2021

Adaptor protein complex 5 (AP-5) and its partners, SPG11 and SPG15, are recruited onto late endosomes and lysosomes. Here we show that recruitment of AP-5/SPG11/SPG15 is enhanced in starved cells and occurs by coincidence detection, requiring both phosphatidylinositol 3-phosphate (PI3P) and Rag GTPases. PI3P binding is via the SPG15 FYVE domain, which, on its own, localizes to early endosomes. GDP-locked RagC promotes recruitment of AP-5/SPG11/SPG15, while GTP-locked RagA prevents its recruitment. Our results uncover an interplay between AP-5/SPG11/SPG15 and the mTORC1 pathway and help to explain the phenotype of AP-5/SPG11/SPG15 deficiency in patients, including the defect in autophagic lysosome reformation.
High-content imaging-based pooled CRISPR screens in mammalian cells
Authors: Yan Xiaowei , Stuurman Nico , Ribeiro Susana A. , Tanenbaum Marvin E. , Horlbeck Max A. , Liem Christina R. , Jost Marco , Weissman Jonathan S. , Vale Ronald D.
Published: January 2021

CRISPR (clustered regularly interspaced short palindromic repeats)-based gene inactivation provides a powerful means for linking genes to particular cellular phenotypes. CRISPR-based screening typically uses large genomic pools of single guide RNAs (sgRNAs). However, this approach is limited to phenotypes that can be enriched by chemical selection or FACS sorting. Here, we developed a microscopy-based approach, which we name optical enrichment, to select cells displaying a particular CRISPR-induced phenotype by automated imaging-based computation, mark them by photoactivation of an expressed photoactivatable fluorescent protein, and then isolate the fluorescent cells using fluorescence-activated cell sorting (FACS). A plugin was developed for the open source software μManager to automate the phenotypic identification and photoactivation of cells, allowing ∼1.5 million individual cells to be screened in 8 h. We used this approach to screen 6,092 sgRNAs targeting 544 genes for their effects on nuclear size regulation and identified 14 bona fide hits. These results present a scalable approach to facilitate imaging-based pooled CRISPR screens.
Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation
Authors: Wong Gerard C L , Antani Jyot D , Lele Pushkar P , Chen Jing , Nan Beiyan , Kühn Marco J , Persat Alexandre , Bru Jean-Louis , Høyland-Kroghsbo Nina Molin , Siryaporn Albert , Conrad Jacinta C , Carrara Francesco , Yawata Yutaka , Stocker Roman , V Brun Yves , Whitfield Gregory B , Lee Calvin K , de Anda Jaime , Schmidt William C , Golestanian Ramin , O’Toole George A , Floyd Kyle A , Yildiz Fitnat H , Yang Shuai , Jin Fan , Toyofuku Masanori , Eberl Leo , Nomura Nobuhiko , Zacharoff Lori A , El-Naggar Mohamed Y , Yalcin Sibel Ebru , Malvankar Nikhil S , Rojas-Andrade Mauricio D , Hochbaum Allon I , Yan Jing , Stone Howard A , Wingreen Ned S , Bassler Bonnie L , Wu Yilin , Xu Haoran , Drescher Knut , Dunkel Jörn
Published: January 2021

Bacterial biofilms are communities of bacteria that exist as aggregates that can adhere to surfaces or be free-standing. This complex, social mode of cellular organization is fundamental to the physiology of microbes and often exhibits surprising behavior. Bacterial biofilms are more than the sum of their parts: single-cell behavior has a complex relation to collective community behavior, in a manner perhaps cognate to the complex relation between atomic physics and condensed matter physics. Biofilm microbiology is a relatively young field by biology standards, but it has already attracted intense attention from physicists. Sometimes, this attention takes the form of seeing biofilms as inspiration for new physics. In this roadmap, we highlight the work of those who have taken the opposite strategy: we highlight the work of physicists and physical scientists who use physics to engage fundamental concepts in bacterial biofilm microbiology, including adhesion, sensing, motility, signaling, memory, energy flow, community formation and cooperativity. These contributions are juxtaposed with microbiologists who have made recent important discoveries on bacterial biofilms using state-of-the-art physical methods. The contributions to this roadmap exemplify how well physics and biology can be combined to achieve a new synthesis, rather than just a division of labor.
Weakening connections in heterogeneous mean-field models
Authors: Dias C , Hase M O
Published: January 2021

Two versions of the susceptible-infected-susceptible epidemic model, which have different transmission rules, are analysed. Both models are considered on a weighted network to simulate a mitigation in the connection between the individuals. The analysis is performed through a heterogeneous mean-field approach on a scale-free network. For a suitable choice of the parameters, both models exhibit a positive infection threshold, when they share the same critical exponents associated with the behaviour of the prevalence against the infection rate. Nevertheless, when the infection threshold vanishes, the prevalence of these models display different algebraic decays to zero for low values of the infection rate.
Infection process near criticality: influence of the initial condition
Authors: Krapivsky P L
Published: January 2021

We investigate how the initial number of infected individuals affects the behavior of the critical susceptible-infected-recovered process. We analyze the outbreak size distribution, duration of the outbreaks, and the role of fluctuations.
An IoT Based diabetic patient Monitoring System Using Machine Learning and Node MCU
Authors: Rghioui Amine , Naja Assia , Mauri Jaime Lloret , Oumnad Abedlmajid
Published: January 2021

Diabetic patient monitoring is a systematic method that provides us with detailed information about the diabetic patient. Diabetic patient monitoring systems play a significant role in monitoring the patient's health, especially with the use of Internet of Things (IoT) devices. Diabetic patient monitoring systems are able basically to monitor diabetic patients and save some data about blood glucose level, body temperature, and location. The role of this system is not limited to patients monitoring, it can also classify data using machine learning techniques. Predictive analytic for diabetic patients is very important due to its ability to help diabetic patients, their families, doctors, and medical researchers to make decisions on diabetic patient treatment based on big data. This paper describes a new system for monitoring diabetic patients and discusses predictive analytics using four different machine-learning algorithms. The performance and accuracy of the applied algorithms are discussed and compared to choose the best one in terms of several parameters.
Simulation and Functional Mechanism of Tuna Median Fins on Yaw Mobility in Unsteady Flow
Authors: Li Xiaohu , Weng Lei , Gao Ji
Published: January 2021

Tuna keeps its median fins erect in searching and feeding behaviors. During the process of these behaviors, tuna probably needs to yaw frequently in the wake of a shoal of small fish. This paper aims to clarify the functional mechanism of the erected median fins on yaw mobility in unsteady flow. Firstly, the CAD simulation models with two morphing states of the median fins are constructed by scanning and measuring the physical prototype of real yellowfin tuna. Secondly, the wake environment of the fish school is created by swinging a tuna model back and forth. Lastly, the hydrodynamic analysis of different morphing states of tuna median fins in unsteady flow is carried out. The results show that the lift forces of the median fins increases in the erection state to a certain extent, which is beneficial to the tuna’s yaw motions. Moreover, the hydrodynamics of the tuna’s body also rise due to the interaction between the body and the median fins. This further improves the yaw mobility of the tuna in unsteady flow.