bluuebunny/crossref_metadata_2025 huggingface dataset:
Revisiting the pseudo-supercritical path method: An improved formulation for the alchemical calculation of solid–liquid coexistence
Authors: Correa Gabriela B. , Zhang Yong , Abreu Charlles R. A. , Tavares Frederico W. , Maginn Edward J.
Published: September 2023

Alchemical free energy calculations via molecular dynamics have been applied to obtain thermodynamic properties related to solid–liquid equilibrium conditions, such as melting points. In recent years, the pseudo-supercritical path (PSCP) method has proved to be an important approach to melting point prediction due to its flexibility and applicability. In the present work, we propose improvements to the PSCP alchemical cycle to make it more compact and efficient through a concerted evaluation of different potential energies. The multistate Bennett acceptance ratio (MBAR) estimator was applied at all stages of the new cycle to provide greater accuracy and uniformity, which is essential concerning uncertainty calculations. In particular, for the multistate expansion stage from solid to liquid, we employed the MBAR estimator with a reduced energy function that allows affine transformations of coordinates. Free energy and mean derivative profiles were calculated at different cycle stages for argon, triazole, propenal, and the ionic liquid 1-ethyl-3-methyl-imidazolium hexafluorophosphate. Comparisons showed a better performance of the proposed method than the original PSCP cycle for systems with higher complexity, especially the ionic liquid. A detailed study of the expansion stage revealed that remapping the centers of mass of the molecules or ions is preferable to remapping the coordinates of each atom, yielding better overlap between adjacent states and improving the accuracy of the methodology.
Electron thermalization length in solid para-hydrogen at low-temperature
Authors: Borghesani A. F. , Carugno G. , Messineo G. , Pazzini J.
Published: September 2023

We report the first ever measurements of the thermalization length of low-energy electrons injected into solid para-hydrogen at a temperature T ≈ 2.8 K. The use of the pulsed Townsend photoinjection technique has allowed us to investigate the behavior of quasi-free electrons rather than of massive, slow negative charges, as reported in all previous literature. We have found an average thermalization length ⟨z0⟩ = 26.1 nm, which is three to five times longer than that in liquid helium at the same temperature.
Analysis of the distribution and orientation of oxygenated and non-oxygenated blood in a double outlet right ventricle
Authors: Collia D. , Angeli E. , Careddu L. , Pedrizzetti G.
Published: September 2023

Double outlet right ventricle (DORV) is a malformation of the fetal heart in utero that affects the ventricular chambers. It usually presents with a displacement of the aorta and more than half the circumference of both arterial valves in the right ventricle. A peculiar characteristic is given by an interventricular septal defect (VSD), which allows communication between the left ventricle and the right with consequent mixing of oxygenated and non-oxygenated blood inside the cavities. A crucial question in assessing the degree of severity of functional dysfunction concerns the percentage of oxygenated blood that is ejected into the primary circulation via the aorta, a result that depends on the details of the vortex flow pattern within the two ventricular chambers. This study analyzes a complete DORV case through the use of numerical simulations that allow to identify the concentrations of oxygenated and non-oxygenated blood passing through this geometry. Results show that the VSD presents a significant impact on the fluid dynamic performance of the two ventricles. The analysis of blood concentration allowed to quantify the presence of oxygenated blood ejected into the pulmonary artery and of non-oxygenated blood into the aortic artery. The analysis of this specific case aims to demonstrate how the fluid dynamics analysis of this rare malformation, properly coupled with imaging technology, can provide information that could not be obtained otherwise and that are relevant for a careful clinical management including timely therapeutic intervention.
A fast, dense Chebyshev solver for electronic structure on GPUs
Authors: Finkelstein Joshua , Negre Christian F. A. , Fattebert Jean-Luc
Published: September 2023

Matrix diagonalization is almost always involved in computing the density matrix needed in quantum chemistry calculations. In the case of modest matrix sizes (≲4000), performance of traditional dense diagonalization algorithms on modern GPUs is underwhelming compared to the peak performance of these devices. This motivates the exploration of alternative algorithms better suited to these types of architectures. We newly derive, and present in detail, an existing Chebyshev expansion algorithm [Liang et al., J. Chem. Phys. 119, 4117–4125 (2003)] whose number of required matrix multiplications scales with the square root of the number of terms in the expansion. Focusing on dense matrices of modest size, our implementation on GPUs results in large speed ups when compared to diagonalization. Additionally, we improve upon this existing method by capitalizing on the inherent task parallelism and concurrency in the algorithm. This improvement is implemented on GPUs by using CUDA and HIP streams via the MAGMA library and leads to a significant speed up over the serial-only approach for smaller (≲1000) matrix sizes. Finally, we apply our technique to a model system with a high density of states around the Fermi level, which typically presents significant challenges.
High impedance Josephson junction resonators in the transmission line geometry
Authors: Ranni Antti , Havir Harald , Haldar Subhomoy , Maisi Ville F.
Published: September 2023

In this article, we present an experimental study of microwave resonators made out of Josephson junctions. The junctions are embedded in a transmission line geometry so that they increase the inductance per length for the line. By comparing two devices with different input/output coupling strengths, we show that the coupling capacitors, however, add a significant amount to the total capacitance of the resonator. This makes the resonators with high coupling capacitance to act rather as lumped element resonators with inductance from the junctions and capacitance from the end sections. Based on a circuit analysis, we show that the input and output couplings of the resonator are limited to a maximum value of ωrZ0/4Zr, where ωr is the resonance frequency and Z0 and Zr are the characteristic impedances of the input/output lines and the resonator, respectively.
Atomistic simulations of calcium aluminosilicate interfaced with liquid water
Authors: Vuković F. , Garcia N. A. , Perera S. , Turchi M. , Andersson M. P. , Solvang M. , Raiteri P. , Walsh T. R.
Published: September 2023

The dissolution behavior of calcium aluminosilicate based glass fibers, such as stone wool fibers, is an important consideration in mineral wool applications for both the longevity of the mineral wool products in humid environments and limiting the health impacts of released and inhaled fibers from the mineral wool product. Balancing these factors requires a molecular-level understanding of calcium aluminosilicate glass dissolution mechanisms, details that are challenging to resolve with experiment alone. Molecular dynamics simulations are a powerful tool capable of providing complementary atomistic insights regarding dissolution; however, they require force fields capable of describing not-only the calcium aluminosilicate surface structure but also the interactions relevant to dissolution phenomena. Here, a new force field capable of describing amorphous calcium aluminosilicate surfaces interfaced with liquid water is developed by fitting parameters to experimental and first principles simulation data of the relevant oxide-water interfaces, including ab initio molecular dynamics simulations performed for this work for the wüstite and periclase interfaces. Simulations of a calcium aluminosilicate surface interfaced with liquid water were used to test this new force field, suggesting moderate ingress of water into the porous glass interface. This design of the force field opens a new avenue for the further study of calcium and network-modifier dissolution phenomena in calcium aluminosilicate glasses and stone wool fibers at liquid water interfaces.
III–V microdisk lasers coupled to planar waveguides
Authors: Kryzhanovskaya N. V. , Ivanov K. A. , Fominykh N. A. , Komarov S. D. , Makhov I. S. , Moiseev E. I. , Guseva J. A. , Kulagina M. M. , Mintairov S. A. , Kalyuzhnyy N. A. , Lihachev A. I. , Khabibullin R. A. , Galiev R. R. , Pavlov A. Yu. , Tomosh K. N. , Maximov M. V. , Zhukov A. E.
Published: September 2023

We report on InGaAs/GaAs quantum dot injection microdisk lasers laterally connected with a bus waveguide fabricated by planar technology from the same epi-structure. Various coupling schemes of microlaser with waveguide are studied including a microlaser attached to a waveguide (zero gap), a 100 nm gap for evanescence light outcoupling, and with a waveguide surrounding the resonator. The modes outcoupling and microlaser's loss (Q-factor) are analyzed by simulation of the lasers. A strong decrease in the number of the microdisk resonance lines associated with an increase in loss in the resonator due to the coupling with waveguide is observed in modeling and experimentally. We study the spectral and lasing parameters of the microdisk lasers, as well as characteristics of the outcoupled emission, and demonstrate efficient light outcoupling for 30 and 40 μm diameter continuous wave operating microdisk laser up to 96 °C.
A comparative study of the correlation between the structure and the dynamics for systems interacting via attractive and repulsive potentials
Authors: Sharma Mohit , Nandi Manoj Kumar , Maitra Bhattacharyya Sarika
Published: September 2023

We present the study of the structure–dynamics correlation for systems interacting via attractive Lennard-Jones (LJ) and its repulsive counterpart, the Weeks–Chandler–Andersen (WCA) potentials. The structural order parameter (SOP) is related to the microscopic mean-field caging potential. At a particle level, the SOP shows a distribution. Although the two systems have similar pair structures, their average SOP differs. However, this difference alone is insufficient to explain the well known slowing down of the dynamics in the LJ system at low temperatures. The slowing down can be explained in terms of a stronger coupling between the SOP and the dynamics. To understand the origin of this system specific coupling, we study the difference in the microscopic structure between the hard and soft particles. We find that for the LJ system, the structural differences of the hard and soft particles are more significant and have a much stronger temperature dependence compared to the WCA system. Thus, the study suggests that attractive interaction creates more structurally different communities. This broader difference in the structural communities is probably responsible for stronger coupling between the structure and dynamics. Thus, the system specific structure–dynamics correlation, which also leads to a faster slowing down in the dynamics, appears to have a structural origin. A comparison of the predictive power of our SOP with the local energy and two body excess entropy in determining the dynamics shows that in the LJ system, the enthalpy plays a dominant role and in the WCA system, the entropy plays a dominant role, and our SOP can capture both these contributions.
High mobility hydrogen-terminated diamond FET with h-BN gate dielectric using pickup method
Authors: Huang Yan , Xiao Junfeng , Tao Ran , Liu Zhi , Mo Yiran , Yu Xinxin , Cao Zhengyi , Wu Yun , Li Zhonghui , Wang Haolin , Wang Lei
Published: September 2023

Hydrogen-terminated diamond surfaces, emerging as a promising two-dimensional (2D) electron platform with great thermal and electronic properties, hold great potential for the next-generation high power and high frequency field effect transistor (FET). However, ideal gate dielectrics with high crystallinity and defect-free surfaces are still largely elusive. In this work, using the contamination-free pickup transfer method, hexagonal boron nitride (h-BN) flakes were fabricated on top of the hydrogen-terminated diamond surface to serve as a gate material and the passivation layer. The morphological and optical characterizations revealed the formation of homogeneous and intimate interface between h-BN and diamond. Benefiting from the h-BN gate dielectric layer, the maximum drain current density, subthreshold swing, and on/off ratio of diamond FET are measured to be −210.3 mA mm−1, 161 mV/dec, and 106, respectively. Especially, the transport measurement shows an almost constant Hall mobility of around 260 cm2 V−1 s−1 in the hole density range of 2 − 6 × 1012 cm−2, suggesting the excellent gate controllability of h-BN. Our results indicate that h-BN could form high-quality interface with hydrogen-terminated diamond, paving the way for the development of diamond-based electronic applications.
Promising cathode material MnO2/CoO2 heterostructure for the Li and Na ion battery: A computational study
Authors: Sahoo Shubham , Kumari Puja , Jyoti Ray Soumya
Published: September 2023

Although two-dimensional (2D) transition metal oxide monolayers have shown potential for applications in metal-ion batteries, the heterostructures of this family are yet to be studied in details for energy storage applications. In this work, we have made the heterostructure by taking half-metallic ferromagnetic 2D transition metal oxide CoO2 and semiconducting MnO2 monolayers and demonstrated its potential application as a cathode material in lithium and sodium-ion batteries by performing first-principles calculations using density functional theory approach. We have systematically studied the electronic structure and stability of the MnO2/CoO2 heterostructure. We have carefully examined the adsorption and diffusion behavior of metal ions (lithium and sodium). Our structure has offered a maximum adsorption energy of −3.84 eV, which is greater than the adsorption energy of individual monolayers. We found that the lowest diffusion barrier is 0.4 eV for lithium ion and 0.32 eV for sodium ion. Also, our system has shown a maximum open circuit voltage of 2.18 V for lithium ion battery and 0.32 V for Na-ion battery. The specific capacity is found to be 584 mAh g−1 for lithium ion and 529 mAh g−1 for sodium ion battery. These findings can serve as a proof that the MnO2/CoO2 heterostructure should be considered as a potential cathode for lithium- and sodium-ion batteries.
Mass and shape determination of optically levitated nanoparticles
Authors: Schellenberg Bart , Behbahani Mina Morshed , Balasubramanian Nithesh , Fikkers Ties H. , Hoekstra Steven
Published: September 2023

When introducing a nanoparticle into an optical trap, its mass and shape are not immediately apparent. We combine a charge-based mass measurement with a shape determination method based on light scattering and an analysis of the damping rate anisotropy, all on the same set of silica nanoparticles, trapped using optical tweezers in vacuum. These methods have previously only been used separately, and the mass determination method has not been applied to asymmetric particles before. We demonstrate that the combination of these classification techniques is required to distinguish particles with similar mass but different shape, and vice versa. The ability to identify these parameters is a key step for a range of experiments on precision measurements and sensing using optically levitated nanoparticles.
Ferromagnetism in Ni quantum dots anchored graphdiyne
Authors: Zheng Yongping , Kang Huifang , Gao Peiyan , Xu Lanqing , Li Jiaxin , Lin Yingbin , Huang Zhigao
Published: September 2023

Achieving ferromagnetic ordering in two-dimensional carbon semiconductors like graphdiyne remains a challenge in spintronics. We synthesized Ni-doped graphdiyne (Ni-GDY) using an electrochemical method and found that adjusting the Ni atom concentration allows for a transition from paramagnetism to ferromagnetism, with a high Curie temperature of 175 K. Our density functional theory calculations revealed that the magnetic moment in Ni-GDY arises from Ni quantum dots. At low concentrations, the distant quantum dots result in paramagnetism, while at high concentrations, the formation of bound polarons and long-range exchange coupling through carbon p orbitals leads to ferromagnetism. This study clarifies the contradiction in magnetism observed in various transition metal-doped graphdiyne materials and highlights the potential applications of Ni-doped graphdiyne in electronic devices.
Coexistence of natural and forced vortex dislocations in step cylinder flow
Authors: Tian Cai , Zhu Jianxun , Holmedal Lars Erik
Published: September 2023

The wake behind a step cylinder [consisting of a small diameter cylinder (d) and a large diameter cylinder (D)] with diameter ratio D/d=2 at Reynolds number ReD = 200 (the mode A* regime) is simulated by direct numerical simulations. New detailed information of the interaction between natural vortex dislocations and forced vortex dislocations is described. In the large cylinder wake, the forced and natural vortex dislocations coexist. The regular formation of forced vortex dislocation is found to be delayed under the effect of natural vortex dislocations. The occurrence of natural vortex dislocations is suppressed in the large cylinder wake close to the small cylinder. Moreover, the effect of vortex dislocations on structural loads is described. The results of this paper provide a more thorough understanding of the formation and interaction between the natural and forced vortex dislocations.
Singlet–triplet dephasing in radical pairs in avian cryptochromes leads to time-dependent magnetic field effects
Authors: Golesworthy Matthew J. , Zollitsch Tilo , Luo Jiate , Selby Dan , Jarocha Lauren E. , Henbest Kevin B. , Paré-Labrosse Olivier , Bartölke Rabea , Schmidt Jessica , Xu Jingjing , Mouritsen Henrik , Hore P. J. , Timmel Christiane R. , Mackenzie Stuart R.
Published: September 2023

Cryptochrome 4a (Cry4a) has been proposed as the sensor at the heart of the magnetic compass in migratory songbirds. Blue-light excitation of this protein produces magnetically sensitive flavin–tryptophan radical pairs whose properties suggest that Cry4a could indeed be suitable as a magnetoreceptor. Here, we use cavity ring-down spectroscopy to measure magnetic field effects on the kinetics of these radical pairs in modified Cry4a proteins from the migratory European robin and from nonmigratory pigeon and chicken. B1/2, a parameter that characterizes the magnetic field-dependence of the reactions, was found to be larger than expected on the basis of hyperfine interactions and to increase with the delay between pump and probe laser pulses. Semiclassical spin dynamics simulations show that this behavior is consistent with a singlet–triplet dephasing (STD) relaxation mechanism. Analysis of the experimental data gives dephasing rate constants, rSTD, in the range 3–6 × 107 s−1. A simple “toy” model due to Maeda, Miura, and Arai [Mol. Phys. 104, 1779–1788 (2006)] is used to shed light on the origin of the time-dependence and the nature of the STD mechanism. Under the conditions of the experiments, STD results in an exponential approach to spin equilibrium at a rate considerably slower than rSTD. We attribute the loss of singlet–triplet coherence to electron hopping between the second and third tryptophans of the electron transfer chain and comment on whether this process could explain differences in the magnetic sensitivity of robin, chicken, and pigeon Cry4a’s.
Photodissociation dynamics of the ethyl radical via the Ã2A′(3s) state: H-atom product channels and ethylene product vibrational state distribution
Authors: Sun Ge , Zheng Xianfeng , Song Yu , Zhou Weidong , Zhang Jingsong
Published: September 2023

The photodissociation dynamics of jet-cooled ethyl radical (C2H5) via the Ã2A′(3s) states are studied in the wavelength region of 230–260 nm using the high-n Rydberg H-atom time-of-flight (TOF) technique. The H + C2H4 product channels are reexamined using the H-atom TOF spectra and photofragment translational spectroscopy. A prompt H + C2H4(X̃1Ag) product channel is characterized by a repulsive translational energy release, anisotropic product angular distribution, and partially resolved vibrational state distribution of the C2H4(X̃1Ag) product. This fast dissociation is initiated from the 3s Rydberg state and proceeds via a H-bridged configuration directly to the H + C2H4(X̃1Ag) products. A statistical-like H + C2H4(X̃1Ag) product channel via unimolecular dissociation of the hot electronic ground-state ethyl (X̃2A′) after internal conversion from the 3s Rydberg state is also examined, showing a modest translational energy release and isotropic angular distribution. An adiabatic H + excited triplet C2H4(ã3B1u) product channel (a minor channel) is identified by energy-dependent product angular distribution, showing a small translational energy release, anisotropic angular distribution, and significant internal excitation in the C2H4(ã3B1u) product. The dissociation times of the different product channels are evaluated using energy-dependent product angular distribution and pump–probe delay measurements. The prompt H + C2H4(X̃1Ag) product channel has a dissociation time scale of <10 ps, and the upper bound of the dissociation time scale of the statistical-like H + C2H4(X̃1Ag) product channel is <5 ns.
Edge detection in gradient ghost imaging through complex media
Authors: Zhou Lina , Xiao Yin , Chen Wen
Published: September 2023

In this Letter, we report on high-contrast gradient ghost imaging (GGI) through dynamic and complex scattering media for edge detection. By introducing a reference beam in the designed setup to correct dynamic change of scaling factors induced by dynamic and complex scattering media, the mismatches between illumination patterns and single-pixel intensity measurements can be corrected. Then, edge information of a sample can be obtained through dynamic and complex scattering media with dual single-pixel detections. The proposed scheme can implement direct edge detection without any postprocessing. It is experimentally verified that the proposed method can realize high-contrast GGI of unknown objects through various dynamic and complex scattering media where conventional schemes cannot work. Our experimental results suggest that the proposed method broadens and deepens the GGI, offering a potential for edge detection in diverse applications.
In-plane tunnel spectroscopy of cuprate superconductors with nano-scale Josephson junctions
Authors: LeFebvre Jay C. , Cho Ethan Y. , Cybart Shane A.
Published: September 2023

Superconducting tunnel spectroscopy has been used for decades to gather valuable information about the electronic density of states and the energy gap in superconductors. For thin film materials, this has, for the most part, only been possible in directions perpendicular to the substrate. For anisotropic materials like the cuprate superconductors, this has hindered knowledge about the density of states in the a–b plane of the film where superconductivity is strongest. The advent of helium ion beam fabricated planar Josephson junctions has fundamentally changed how we can perform tunnel spectroscopy. In this work, we utilize nanoscale Josephson tunnel junctions orientated along different crystalline directions and report the anisotropy of the superconducting energy gap of cuprates at both the micro- and nanoscale. The smaller nanoelectrodes exhibit more variation that roughly correlates with the granularity of the film. We also observe that the gap energy is inversely proportional to the material's conductivity in the voltage state.
Analysis of droplet behavior and breakup mechanisms on wet solid surfaces
Authors: Shiri Yousef , Sabour Seyed Mohammad Javad Seyed
Published: September 2023

The behavior and dynamics of droplet spreading are pivotal phenomena that exert a profound influence on numerous scientific disciplines, technological advancements, and natural processes. This study was conducted with the aim to investigate factors influencing the shape and geometry of a liquid droplet on a solid surface using the lattice Boltzmann method (LBM). LBM as a mesoscale numerical fluid simulation has gained increasing popularity among the most favorable numerical methods for simulating multi-phase/multi-component fluid flow in complex geometries. Accordingly, parameters dependency, surface tension, two-phase diagram, and wettability were evaluated in the LBM, and stable and calibrated forms were used for the droplet simulations. Also, an equation was obtained to determine the contact angle in the LBM system with a determination coefficient of 0.988. Then, droplet behavior was examined for its dependency on wettability, interfacial tension, and line tension. The results showed droplets breakup in a certain interfacial tension at high adhesive force. These breakups were due to the force balance in the triple line. They were not monotonic and first decreased and then increased the volume of the droplets.
Photomultiplication type quasi-planar all-polymer photodetectors with tunable response range
Authors: Zhang Haolan , Liu Ming , Zhao Xingchao , Ma Xiaoling , Yuan Guangcai , Li Junming , Zhang Fujun
Published: September 2023

Photomultiplication type quasi-planar all-polymer photodetectors (PM-QAPDs) are fabricated with P3HT/PY-IT as active layers by employing a sequential spin-coating method. The part of PY-IT can penetrate into a P3HT layer to emerge isolated electron-traps formed with PY-IT surrounded by P3HT. The trapped electron distribution near an Al electrode will determine the spectral response range of PM-QAPDs. Broadband PM-QAPDs can be achieved with a 0.25 μm thick P3HT layer and a ultra-thin PY-IT layer prepared from 1 mg/ml solution, exhibiting a broad response from 320 to 870 nm. An external quantum efficiency (EQE) value of optimal PM-QAPDs approaches 16 000% at 360 nm under −12 V bias. When the thickness of the P3HT layer is increased to 2.4 μm, the PM-QAPDs exhibit a narrowband response from 630 to 870 nm, which can be well explained according to the Beer–Lambert law. The work may provide a smart strategy to adjust response range of PM-QAPDs by alerting the thickness of the donor layer.
Lattice structure dependence of laser-induced ultrafast magnetization switching in ferrimagnets
Authors: Vélez J. A. , Otxoa R. M. , Atxitia U.
Published: September 2023

The experimental discovery of single-pulse ultrafast magnetization switching in ferrimagnetic alloys, such as GdFeCo and MnRuGa, opened the door to a promising route toward faster and more energy efficient data storage. A recent semi-phenomenological theory has proposed that a fast, laser-induced demagnetization below a threshold value puts the system into a dynamical regime where angular momentum transfer between sublattices dominates. Notably, this threshold scales inversely proportional to the number of exchange-coupled nearest neighbors considered in the model, which in the simplest case is directly linked to the underlying lattice structure. In this work, we study the role of the lattice structure on the laser-induced ultrafast magnetization switching in ferrimagnets by complementing the phenomenological theory with atomistic spin dynamics computer simulations. We consider a spin model of the ferrimagnetic GdFeCo alloy with increasing number of exchange-coupled neighbors. Within this model, we demonstrate that the laser-induced magnetization dynamics and switching depend on the lattice structure. Furthermore, we determine that the critical laser energy for switching reduces for decreasing number of exchange-coupled neighbors.
Development of a novel and more holistic approach for assessing impact in health and medical research: the Research Impact Assessment Framework
Authors: Ward Robyn L. , Nutbeam Don , Mijnhardt Wilfred , Nelson Philip , Todd Angela , Rees Mark I. , Richards Janine , Khan Nadia N. , Ho Isaac , Chung Sean
Published: September 2023

Considered investment in health and medical research (HMR) is critical for fostering a healthcare system that is sustainable, effective, responsive, and innovative. While several tools exist to measure the impact of research, few assess the research environment that nurtures and supports impactful research and the strategic alignment of research with societal needs. This perspective article discusses the limitations of existing assessment tools and presents a novel Research Impact Assessment Framework designed to enable more strategic and targeted investment towards HMR, having the potential for significant public benefit.
BrRD20 improves abiotic stress resistance in chrysanthemum
Authors: Xue Zhao , Zhang Jierui , Li Xin , Qian Xuelei , Yan Haifang
Published: September 2023

RESPONSIVE TO DESSICATION 20 (RD20) is a member of the caleosin family, which is involved in plant growth and development, signal transduction, abiotic stress and plant immunity. However, the molecular mechanism of the biological function of RD20 in turnip is still largely unknown. This study aimed to characterise the roles of BrRD20 during abiotic stress resistance and their responses in various abiotic stresses by isolating BrRD20 (MK896873) from ‘Tsuda’ turnip. Quantitative polymerase chain reaction analysis showed that the highest expression levels of BrRD20 occurred in the petal, followed by the leaf, bud and red root epidermis, with tissue specificity. The transcript level of BrRD20 was much higher under natural light than under dark conditions in 0–5-day-old turnip seedlings. BrRD20 was also induced to be regulated by abiotic stresses such as high or low temperature, dehydration, osmotic hormone salt and alkali stresses. BrRD20 overexpression (BrRD20-OE) in Chrysanthemum presented an enhanced tolerance to low temperature, dehydration and salt stress compared with the wild type. The BrRD20 gene was induced to be regulated by abiotic stresses such as high or low temperature, dehydration, osmotic and salt stresses. The BrRD20 gene also improved abiotic stress resistance in chrysanthemum. The above results suggested that BrRD20 plays a crucial role in abiotic stress resistance.
Trophic resources use pathways between two coexisting freshwater shrimp (Palaemon argentinus and Macrobrachium borellii)
Authors: Viozzi M. Florencia , Williner Verónica
Published: September 2023

Context A better understanding of the use of different trophic pathways as a mechanism for adjusting interactions between coexisting omnivorous decapod species may help define the extent of their influence on energy flows in freshwater ecosystems. Aims Analyse the patterns of use of the benthic and littoral pathways by Macrobrachium borellii and Palaemon argentinus during a hydrological cycle in lakes of the middle Paraná River. Methods The study was conducted during one high-water (HW) and one low-water (LW) period in three lakes permanently connected to the middle Paraná River. We calculated the relative contributions of potential basal resources (benthic and littoral) to each species for each lake and hydrological period using mixing models. Key results It was observed that M. borellii feeds more in the littoral pathway and P. argentinus in the benthic pathway, especially in low water where we observed that the partitioning of resources was more pronounced. Conclusion The more aggessive species, M. borelli, during HW period quickly utilises the bioavailable material. Trophic dynamics and resource use are part of the coexistence mechanisms of both decapod species. Implications This may have important consequences in the aquatic trophic webs in which these organisms participate, because when segregating the use of resources, they intervene in different energetic pathways.
Modelling the management of an invasive species at landscape scale: are oral contraceptives the missing ingredient for success?
Authors: Croft S. , Massei G.
Published: September 2023

Context Invasive non-native species are on the rise worldwide, exacerbating already significant environmental and economic impacts. Concurrently, public attitudes towards methods of controlling these species are changing, with greater demand for non-lethal solutions. This has fostered research into developing new, effective technologies and strategies for wildlife management. Aims On the basis of a case study focusing on the eastern grey squirrel (Sciurus carolinensis) in the UK, this study aimed to understand the potential for population management, using either live trapping or oral contraception. First, assuming completely coordinated landscape-scale control, and then, coordinated control only on parts of the landscape, accounting for the potential that landowners’ attitudes towards alternative methods may differ and reflect those of the wider public. Methods We used an existing spatially explicit individual-based modelling approach applying various parameterisations to define management. We varied the density of traps or hoppers delivering contraceptives, the duration of deployment, contraceptive efficacy, initial population size, and the probability of landowner participation. The latter was based on a previous public survey, suggesting that 40% of the respondents were open to management using trapping and 64% to using contraception. Key results With complete coordinated control, trapping was generally faster and more cost-effective than was contraception. However, when differences in social acceptance were considered, reducing participation and, consequently, the spatial coverage of management, contraception was found to maintain greater population reductions than was trapping with similar effort, assuming a contraceptive efficacy of 75% or higher. Conclusions This study added another layer of complexity to managing invasive non-native species, namely the potential effect that landowners’ attitudes to different methods of population management might have on the level of coordinated control at landscape scale. In a situation such as the one modelled by this study, where management is not a legal requirement, this human dimension must be considered alongside cost-effectiveness, to develop successful control in line with management goals. Implications Further work is required to establish the actual attitudes of landowners, and in different contexts (e.g. urban, rural areas), how this may change as new approaches become available, and then how spatial variation (clustering) in the resulting wildlife population control may affect outcomes.
Virtual blebbistatin: A robust and rapid software approach to motion artifact removal in optical mapping of cardiomyocytes
Authors: Woodhams Louis G. , Guo Jingxuan , Schuftan David , Boyle John J. , Pryse Kenneth M. , Elson Elliot L. , Huebsch Nathaniel , Genin Guy M.
Published: September 2023

Fluorescent reporters of cardiac electrophysiology provide valuable information on heart cell and tissue function. However, motion artifacts caused by cardiac muscle contraction interfere with accurate measurement of fluorescence signals. Although drugs such as blebbistatin can be applied to stop cardiac tissue from contracting by uncoupling calcium-contraction, their usage prevents the study of excitation–contraction coupling and, as we show, impacts cellular structure. We therefore developed a robust method to remove motion computationally from images of contracting cardiac muscle and to map fluorescent reporters of cardiac electrophysiological activity onto images of undeformed tissue. When validated on cardiomyocytes derived from human induced pluripotent stem cells (iPSCs), in both monolayers and engineered tissues, the method enabled efficient and robust reduction of motion artifact. As with pharmacologic approaches using blebbistatin for motion removal, our algorithm improved the accuracy of optical mapping, as demonstrated by spatial maps of calcium transient decay. However, unlike pharmacologic motion removal, our computational approach allowed direct analysis of calcium-contraction coupling. Results revealed calcium-contraction coupling to be more uniform across cells within engineered tissues than across cells in monolayer culture. The algorithm shows promise as a robust and accurate tool for optical mapping studies of excitation–contraction coupling in heart tissue.
Crystal structure and activity of a de novo enzyme, ferric enterobactin esterase Syn-F4
Authors: Kurihara Kodai , Umezawa Koji , Donnelly Ann E. , Sperling Brendan , Liao Guanyu , Hecht Michael H. , Arai Ryoichi
Published: September 2023

Producing novel enzymes that are catalytically active in vitro and biologically functional in vivo is a key goal of synthetic biology. Previously, we reported Syn-F4, the first de novo protein that meets both criteria. Syn-F4 hydrolyzed the siderophore ferric enterobactin, and expression of Syn-F4 allowed an inviable strain of
Escherichia coli
(Δ
fes
) to grow in iron-limited medium. Here, we describe the crystal structure of Syn-F4. Syn-F4 forms a dimeric 4-helix bundle. Each monomer comprises two long α-helices, and the loops of the Syn-F4 dimer are on the same end of the bundle (
syn
topology). Interestingly, there is a penetrated hole in the central region of the Syn-F4 structure. Extensive mutagenesis experiments in a previous study showed that five residues (Glu26, His74, Arg77, Lys78, and Arg85) were essential for enzymatic activity in vivo. All these residues are located around the hole in the central region of the Syn-F4 structure, suggesting a putative active site with a catalytic dyad (Glu26–His74). The complete inactivity of purified proteins with mutations at the five residues supports the putative active site and reaction mechanism. Molecular dynamics and docking simulations of the ferric enterobactin siderophore binding to the Syn-F4 structure demonstrate the dynamic property of the putative active site. The structure and active site of Syn-F4 are completely different from native enterobactin esterase enzymes, thereby demonstrating that proteins designed de novo can provide life-sustaining catalytic activities using structures and mechanisms dramatically different from those that arose in nature.
A synergistic future for AI and ecology
Authors: Han Barbara A. , Varshney Kush R. , LaDeau Shannon , Subramaniam Ajit , Weathers Kathleen C. , Zwart Jacob
Published: September 2023

Research in both ecology and AI strives for predictive understanding of complex systems, where nonlinearities arise from multidimensional interactions and feedbacks across multiple scales. After a century of independent, asynchronous advances in computational and ecological research, we foresee a critical need for intentional synergy to meet current societal challenges against the backdrop of global change. These challenges include understanding the unpredictability of systems-level phenomena and resilience dynamics on a rapidly changing planet. Here, we spotlight both the promise and the urgency of a convergence research paradigm between ecology and AI. Ecological systems are a challenge to fully and holistically model, even using the most prominent AI technique today: deep neural networks. Moreover, ecological systems have emergent and resilient behaviors that may inspire new, robust AI architectures and methodologies. We share examples of how challenges in ecological systems modeling would benefit from advances in AI techniques that are themselves inspired by the systems they seek to model. Both fields have inspired each other, albeit indirectly, in an evolution toward this convergence. We emphasize the need for more purposeful synergy to accelerate the understanding of ecological resilience whilst building the resilience currently lacking in modern AI systems, which have been shown to fail at times because of poor generalization in different contexts. Persistent epistemic barriers would benefit from attention in both disciplines. The implications of a successful convergence go beyond advancing ecological disciplines or achieving an artificial general intelligence—they are critical for both persisting and thriving in an uncertain future.
Targeted glycan degradation potentiates cellular immunotherapy for solid tumors
Authors: Wu Jicheng , Wang Xudong , Huang Yuqiao , Zhang Yunjing , Su Siyu , Shou Hao , Wang Haoran , Zhang Jin , Wang Ben
Published: September 2023

Immune cell–based cancer therapies, such as chimeric antigen receptor T (CAR-T)-cell immunotherapy, have demonstrated impressive potency against hematological tumors. However, the efficacy of CAR-T cells against solid tumors remains limited. Herein, we designed tumor-targeting molecule–sialidase conjugates that potently and selectively stripped different sialoglycans from a variety of cancer cells. Desialylation enhanced induced pluripotent stem cell–derived chimeric antigen receptor–macrophage (CAR-iMac) infiltration and activation. Furthermore, the combination of cancer cell desialylation and CAR-iMac adoptive cellular therapy exerted a dramatic therapeutic effect on solid tumors and significantly prolonged the survival of tumor-bearing mice; these effects were mainly dependent on blockade of the checkpoint composed of sialic acid–binding immunoglobulin-like lectin (Siglec)-5 and Siglec-10 on the macrophages, and knockout of the glycoimmune checkpoint receptors could construct a CAR-iMac cell with stronger anticancer activity. This strategy that reverts the immune escape state (“cold tumor”) to a sensitive recognition state (“hot tumor”) has great significance for enhancing the effect of cellular immunotherapy on solid tumors. Therefore, desialylation combined with CAR-iMac cellular immunotherapy is a promising approach to enhance treatment with cellular immunotherapy and expand the valid indications among solid tumors, which provides inspiration for the development of cellular immunotherapies with glycoimmune checkpoint inhibition for the treatment of human cancer.
Visualization of
trans
homophilic interaction of clustered protocadherin in neurons
Authors: Hoshino Natsumi , Kanadome Takashi , Takasugi Tomomi , Itoh Mizuho , Kaneko Ryosuke , Inoue Yukiko U. , Inoue Takayoshi , Hirabayashi Takahiro , Watanabe Masahiko , Matsuda Tomoki , Nagai Takeharu , Tarusawa Etsuko , Yagi Takeshi
Published: September 2023

Clustered protocadherin (Pcdh) functions as a cell recognition molecule through the homophilic interaction in the central nervous system. However, its interactions have not yet been visualized in neurons. We previously reported PcdhγB2-Förster resonance energy transfer (FRET) probes to be applicable only to cell lines. Herein, we designed γB2-FRET probes by fusing FRET donor and acceptor fluorescent proteins to a single γB2 molecule and succeeded in visualizing γB2 homophilic interaction in cultured hippocampal neurons. The γB2-FRET probe localized in the soma and neurites, and FRET signals, which were observed at contact sites between neurites, eliminated by ethylene glycol tetraacetic acid (EGTA) addition. Live imaging revealed that the FRET-negative γB2 signals rapidly moved along neurites and soma, whereas the FRET-positive signals remained in place. We observed that the γB2 proteins at synapses rarely interact homophilically. The γB2-FRET probe might allow us to elucidate the function of the homophilic interaction and the cell recognition mechanism.
Truncated mass divergence in a Mott metal
Authors: Semeniuk Konstantin , Chang Hui , Baglo Jordan , Friedemann Sven , Tozer Stanley W. , Coniglio William A. , Gamża Monika B. , Reiss Pascal , Alireza Patricia , Leermakers Inge , McCollam Alix , Grockowiak Audrey D. , Grosche F. Malte
Published: September 2023

The Mott metal–insulator transition represents one of the most fundamental phenomena in condensed matter physics. Yet, basic tenets of the canonical Brinkman-Rice picture of Mott localization remain to be tested experimentally by quantum oscillation measurements that directly probe the quasiparticle Fermi surface and effective mass. By extending this technique to high pressure, we have examined the metallic state on the threshold of Mott localization in clean, undoped crystals of NiS
2
. We find that i) on approaching Mott localization, the quasiparticle mass is strongly enhanced, whereas the Fermi surface remains essentially unchanged; ii) the quasiparticle mass closely follows the divergent form predicted theoretically, establishing charge carrier slowdown as the driver for the metal–insulator transition; iii) this mass divergence is truncated by the metal–insulator transition, placing the Mott critical point inside the insulating section of the phase diagram. The inaccessibility of the Mott critical point in NiS
2
parallels findings at the threshold of ferromagnetism in clean metallic systems, in which criticality at low temperature is almost universally interrupted by first-order transitions or novel emergent phases such as incommensurate magnetic order or unconventional superconductivity.
US and Chinese preschoolers normalize household labor inequality
Authors: Midgette Allegra J. , Ma Danyang , Stowe Lucy M. , Chernyak Nadia
Published: September 2023

Across many cultural contexts, the majority of women conduct the majority of their household labor. This gendered distribution of labor is often unequal, and thus represents one of the most frequently experienced forms of daily inequality because it occurs within one’s own home. Young children are often passive observers of their family’s distribution of labor, and yet little is known about the developmental onset of their perceptions of it. By the preschool age, children also show strong normative feelings about both equal resource distribution and gender stereotypes. To investigate the developmental onset of children’s recognition of the (in)equality of household labor, we interviewed 3 to 10-y-old children in two distinct cultural contexts (US and China) and surveyed their caregivers about who does more household labor across a variety of tasks. Even at the youngest ages and in both cultural contexts, children’s reports largely matched their parents’, with both populations reporting that mothers do the majority of household labor. Both children and parents judged this to be generally fair, suggesting that children are observant of the gendered distribution of labor within their households, and show normalization of inequality from a young age. Our results point to preschool age as a critical developmental time period during which it is important to have parent-child discussions about structural constraints surrounding gender norms and household labor.
Noise properties of adaptation-conferring biochemical control modules
Authors: Kell Brayden , Ripsman Ryan , Hilfinger Andreas
Published: September 2023

A key goal of synthetic biology is to develop functional biochemical modules with network-independent properties. Antithetic integral feedback (AIF) is a recently developed control module in which two control species perfectly annihilate each other’s biological activity. The AIF module confers robust perfect adaptation to the steady-state average level of a controlled intracellular component when subjected to sustained perturbations. Recent work has suggested that such robustness comes at the unavoidable price of increased stochastic fluctuations around average levels. We present theoretical results that support and quantify this trade-off for the commonly analyzed AIF variant in the idealized limit with perfect annihilation. However, we also show that this trade-off is a singular limit of the control module: Even minute deviations from perfect adaptation allow systems to achieve effective noise suppression as long as cells can pay the corresponding energetic cost. We further show that a variant of the AIF control module can achieve significant noise suppression even in the idealized limit with perfect adaptation. This atypical configuration may thus be preferable in synthetic biology applications.