bluuebunny/crossref_metadata_2025 huggingface dataset:
Resolving the interlayer distance of cationic pyrene clusters embedded in superfluid helium droplets using electron diffraction
Authors: Lei Lei , Zhang Jie , Trejo Marisol , Bradford Stephen D. , Kong Wei
Published: January 2022

We report the electron diffraction of cationic pyrene (C16H10) clusters embedded in superfluid helium droplets. The diffraction profile contains a significant contribution from helium, but interferences of atomic pairs of pyrene are still recognizable. From least-squares fittings, we determine an interlayer distance of 3.0 Å for the cationic cluster, shortened from 3.5 Å in neutral clusters. The relative contributions of dimers and trimers are about 2:1, in qualitative agreement with the doping statistics. Limited by the detection range of the experimental data, we cannot distinguish further structure details. The predominant contribution of helium also prevents observations of the solvation shell of the ionic cluster. Nevertheless, the success of this experiment demonstrates the feasibility of electron diffraction from an ionic all-light-atom system, dispelling the concern over limited particle concentration of ionic species in the diffraction region, and the need of heavy atoms for diffraction intensity.
Genetic assessment of the rare freshwater shrimp
Authors: Chow Lai Him , Tsang Ling Ming , Chu Ka Hou , Ma Ka Yan
Published: January 2022

The lack of information is one of the major impediments to effective conservation of rare, endemic species. One of which concerns the freshwater atyid shrimp Caridina logemanni known only from three streams in Hong Kong, with an area of occupancy of less than 20 km2, further threatened by harvesting for aquarium trade and potential introgressive hybridisation with a ubiquitous congener C. cantonensis. Here, we delineated the genetic diversity and population structure of C. logemanni, and examined its extent of hybridisation with C. cantonensis, using one mitochondrial (COI), one nuclear (NaK intron) and six microsatellite markers. The two examined populations of C. logemanni exhibited strong genetic differentiation at a spatial scale of <1.5 km apart, and generally low genetic diversity. Historic introgressive hybridisation is evident from the sharing of COI haplotypes between species and the more extensive inter-specific microsatellite admixture than inter-population admixture, such that both C. logemanni populations were of hybrid origin. Future conservation efforts on C. logemanni should aim at (1) minimising waterway modifications to prevent potential anthropogenic hybridisation, (2) fortifying conservation legislations to stop its harvesting, and (3) conducting continuous monitoring in case of stochastic events associated with small population size and linear habitat.
Stem–loop formation drives RNA folding in mechanical unzipping experiments
Authors: Rissone Paolo , Bizarro Cristiano V. , Ritort Felix
Published: January 2022

Significance

Understanding how complementary RNA single strands anneal to form the native structure requires accurate knowledge of the energetics of hybridization and the kinetics driving the hairpin fold. The annealing dynamics are highly complex for RNA, where multiple long-lived intermediate states occur along the folding pathway. In this framework, single-molecule experiments allow us to derive the thermodynamics and kinetics of RNA folding and the characterization of the intermediates along the folding pathway. We mechanically unzip a 2-kbp RNA hairpin with optical tweezers in sodium and magnesium, deriving the 10 RNA nearest-neighbor free energies and modeling the hybridization kinetics in a barrier energy landscape of stem–loop secondary structures. Our study contributes to a better understanding of the RNA folding problem.
RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder
Authors: Oh Juntaek , Jia Tiezheng , Xu Jun , Chong Jenny , Dervan Peter B. , Wang Dong
Published: January 2022

Elongating RNA polymerase II (Pol II) can be paused or arrested by a variety of obstacles. These obstacles include DNA lesions, DNA-binding proteins, and small molecules. Hairpin pyrrole-imidazole (Py-Im) polyamides bind to the minor groove of DNA in a sequence-specific manner and induce strong transcriptional arrest. Remarkably, this Py-Im–induced Pol II transcriptional arrest is persistent and cannot be rescued by transcription factor TFIIS. In contrast, TFIIS can effectively rescue the transcriptional arrest induced by a nucleosome barrier. The structural basis of Py-Im–induced transcriptional arrest and why TFIIS cannot rescue this arrest remain elusive. Here we determined the X-ray crystal structures of four distinct Pol II elongation complexes (Pol II ECs) in complex with hairpin Py-Im polyamides as well as of the hairpin Py-Im polyamides–dsDNA complex. We observed that the Py-Im oligomer directly interacts with RNA Pol II residues, introduces compression of the downstream DNA duplex, prevents Pol II forward translocation, and induces Pol II backtracking. These results, together with biochemical studies, provide structural insight into the molecular mechanism by which Py-Im blocks transcription. Our structural study reveals why TFIIS fails to promote Pol II bypass of Py-Im–induced transcriptional arrest.
Microscopic mechanisms of cooperative communications within single nanocatalysts
Authors: Punia Bhawakshi , Chaudhury Srabanti , Kolomeisky Anatoly B.
Published: January 2022

Significance

Catalysis is an experimental approach to accelerate chemical reactions. It plays a critical role in modern industries. Recent experimental studies uncovered striking observations of cooperative communications for reactions on nanocatalysts. In these experiments, it was shown that the chemical reactions observed at specific active sites might effectively stimulate the same reactions at the neighboring sites. We developed a theoretical model to investigate the microscopic mechanisms of these phenomena. Our idea is that the catalytic communication is the result of the complex dynamics of charged holes. Explicit calculations are able to quantitatively explain all experimental observations, clarifying the molecular origin of cooperative communications. The presented theoretical framework might be utilized for developing efficient catalytic systems with better control over chemical reactions.
Expanding quasiperiodicity in soft matter: Supramolecular decagonal quasicrystals by binary giant molecule blends
Authors: Liu Yuchu , Liu Tong , Yan Xiao-Yun , Guo Qing-Yun , Lei Huanyu , Huang Zongwu , Zhang Rui , Wang Yu , Wang Jing , Liu Feng , Bian Feng-Gang , Meijer E.W. , Aida Takuzo , Huang Mingjun , Cheng Stephen Z.D.
Published: January 2022

Significance

As the formation of quasicrystalline ordering in both metal alloys and soft matters reinforces the scale-invariance principle, however, it remains unknown that why metallic quasicrystals prefer decagonal quasicrystalline (DQC, 10-fold) ordering, and the condensed soft maters only exhibit dodecagonal quasicrystalline (DDQC, 12-fold) ordering. By tuning the self-sorting ability in a pair of giant molecules, the well-mixed binary blends generate a metastable DQC phase and corresponding unprecedent phase sequence (DQC → DDQC → Frank–Kasper σ) during thermal annealing. These peculiar assembling behaviors result from interplays of submesoatomic and mesoatomic packings. Reducing the self-sorting strength has induced an extra complexity in the sub-mesoatomic packings of giant molecules, which further influences the clustering on the mesoatomic level.
SNX27 suppresses SARS-CoV-2 infection by inhibiting viral lysosome/late endosome entry
Authors: Yang Bo , Jia Yuanyuan , Meng Yumin , Xue Ying , Liu Kefang , Li Yan , Liu Shichao , Li Xiaoxiong , Cui Kaige , Shang Lina , Cheng Tianyou , Zhang Zhichao , Hou Yingxiang , Yang Xiaozhu , Yan Hong , Duan Liqiang , Tong Zhou , Wu Changxin , Liu Zhida , Gao Shan , Zhuo Shu , Huang Weijin , Gao George Fu , Qi Jianxun , Shang Guijun
Published: January 2022

Significance

We here established the interaction between PDZ binding motif (PBM) at the C terminal of ACE2 and PDZ domain of sorting nexin 27 (SNX27) and solved the crystal structure of ACE2-PBM/SNX27-PDZ complex. Together with retromer complex, SNX27 was found to regulate the homeostasis of cell surface ACE2 under physiological conditions. When endocytic pathway was used during SARS-CoV-2 infection, SNX27-retromer sorts ACE2/SARS-CoV-2 complex at early endosome and prevents it from entering lysosome/late endosome, inhibiting the cell entry of the virus. These findings add substantially to the current understanding of the important role of cytosolic tail of ACE2 during the invasion of SARS-CoV-2, and it could be used as a new therapeutic target for drug development.
Grammar and variation in the classroom
Authors: Dovalil Vít , Hanulíková Adriana
Published: January 2022

Grammar is the structural foundation of successful communication, language use, and literacy development. Grammar is therefore sometimes viewed as the heart of language with an important place in language teaching. In a classroom setting, regulation of grammar knowledge through teachers is strongly influenced by teachers’ linguistic competence and beliefs. In this paper, we will first show the diversity in this knowledge by means of teacher interviews and speeded grammatical-acceptability data from pupils and students. We will then sketch a socio- and psycholinguistic perspective on several selected morphosyntactic variables in German. These will be discussed with reference to social forces that determine what is standard in a language (language norm authorities, language experts, model texts, and codifiers). Finally, we will draw a roadmap for teachers, language practitioners and editors looking for a qualified solution to grammatical cases of doubt in contemporary German and provide practical examples by drawing upon the German reference corpus.
Trametes versicolor
. [Descriptions of Fungi and Bacteria].
Authors: Minter D. W. , Soliman G. S.
Published: January 2022

A description is provided for
Trametes versicolor
. Some information on morphological characteristics, its associated organisms and substrata, habitats, economic impacts, dispersal and transmission, conservation status is given, along with details of its geographical distribution (Africa (Benin, Burundi, Cameroon, Democratic Republic of the Congo, Ethiopia, Kenya, Libya, Malawi, Morocco, Nigeria, Rwanda, Sierra Leone, South Africa, Tanzania, Uganda, Zimbabwe.), Antarctica, Asia (Armenia, Azerbaijan, China, Anhui, Gansu, Guangdong, Guanxi, Guizhou, Hainan, Hebei, Heilongjang, Henan, Hong Kong, Hubei, Hunan, Jiangsu, Jiangxi, Jilin, Liaoning, Nei Mongol Autonomous Region, Qinghai, Shandong, Shanxi, Sichuan, Xinjiang, Yunnan, Zhejiang, Cyprus, Georgia, India, Assam, Goa, Himachal Pradesh, Jammu and Kashmir, Karnataka, Kerala, Madhya Pradesh, Maharashtra, Meghalaya, Punjab, Rajasthan, Sikkim, Tamil Nadu, Uttarakhand, West Bengal, Indonesia, Iran, Iraq, Japan, Kazakhstan (Almaty), Kyrgyzstan, Laos, Malaysia, Mongolia, Myanmar, Nepal, Pakistan, Philippines, Russia, Singapore, South Korea, Sri Lanka, Taiwan, Tajikistan, Thailand, Turkey, Turkmenistan, Uzbekistan, Vietnam, Atlantic Ocean (Bermuda), Australasia (Australia, Australian Capital Territory, New South Wales, Queensland, South Australia, Tasmania, Victoria, Western Australia, New Zealand), Caribbean (Cuba, Dominican Republic, Haiti, Jamaica, Puerto Rico), Central America (Belize, Costa Rica, El Salvador, Guatemala, Nicaragua, Panama), Europe (Andorra, Austria, Belarus, Belgium, Bosnia and Herzegovina, Bulgaria, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Ireland, Isle of Man, Italy, Kosovo, Latvia, Lithuania, Luxembourg, Moldova, Netherlands, Norway, Poland, Portugal, Romania, Russia, Serbia, Slovakia, Slovenia, Spain, Sweden, Switzerland, Ukraine, UK), Indian Ocean (Réunion), North America (Canada, Alberta, British Columbia, Manitoba, New Brunswick, Newfoundland and Labrador, Northwest Territories, Nova Scotia, Ontario, Prince Edward Island, Quebec, Saskatchewan, Yukon, Mexico, USA, Alabama, Alaska, Arizona, Arkansas, California, Colorado, Connecticut, Delaware, District of Columbia, Florida, Georgia, Idaho, Illinois, Indiana, Iowa, Kansas, Kentucky, Louisiana, Maine, Maryland, Massachusetts, Michigan, Minnesota, Mississippi, Missouri, Montana, Nebraska, Nevada, New Hampshire, New Jersey, New Mexico, New York, North Carolina, North Dakota, Ohio, Oklahoma, Oregon, Pennsylvania, Rhode Island, South Carolina, South Dakota, Tennessee, Texas, Utah, Vermont, Virginia, Washington, West Virginia, Wisconsin, Wyoming), Pacific Ocean (USA, Hawaii), South America (Argentina, Bolivia, Brazil, Acre, Amazonas, Bahia, Distrito Federal, Espírito Santo, Mato Grosso do Sul, Minas Gerais, Pará, Paraná, Pernambuco, Rio Grande do Sul, Rio de Janeiro, Rondônia, Roraima, Santa Catarina São Paulo, Chile, Colombia, Ecuador, Paraguay, Peru, Suriname, Uruguay, Venezuela))).
T-independent antigen induces humoral memory through germinal centers
Authors: Liu Xin , Zhao Yongshan , Qi Hai
Published: January 2022

T-dependent humoral responses generate long-lived memory B cells and plasma cells (PCs) predominantly through germinal center (GC) reaction. In human and mouse, memory B cells and long-lived PCs are also generated during immune responses to T-independent antigen, including bacterial polysaccharides, although the underlying mechanism for such T-independent humoral memory is not clear. While T-independent antigen can induce GCs, they are transient and thought to be nonproductive. Unexpectedly, by genetic fate-mapping, we find that these GCs actually output memory B cells and PCs. Using a conditional BCL6 deletion approach, we show memory B cells and PCs fail to last when T-independent GCs are precluded, suggesting that the GC experience per se is important for programming longevity of T-independent memory B cells and PCs. Consistent with the fact that infants cannot mount long-lived humoral memory to T-independent antigen, B cells from young animals intrinsically fail to form T-independent GCs. Our results suggest that T-independent GCs support humoral memory, and GC induction may be key to effective vaccines with T-independent antigen.
Goldilocks and the three TILs
Authors: Dada Hannah , Dustin Michael L.
Published: January 2022

In this issue of JEM, Shakiba et al. (2021. J. Exp. Med. https://doi.org/10.1084/jem.20201966) tell a tale of three tumor infiltrating lymphocytes (TILs). The first TIL was too strong and became exhausted. The second TIL was too weak and became inert. The third TIL lost CD8, and this made it just right.
Ultrafast manipulation of magnetic anisotropy in a uniaxial intermetallic heterostructure TbCo2/FeCo
Authors: Ovcharenko Sergei , Gaponov Mikhail , Klimov Alexey , Tiercelin Nicolas , Pernod Philippe , Mishina Elena , Sigov Alexander , Preobrazhensky Vladimir
Published: January 2022

We study experimentally and theoretically the dynamics of spin relaxation motion excited by a femtosecond pulse in the TbCo2/FeCo multilayer structures with different ratios of TbCo2 to FeCo thicknesses

r
d

=

d

T
b
C

o
2

/

d

F
e
C
o

. The main attribute of the structure is in-plane magnetic anisotropy that is artificially induced during sputtering under a DC magnetic field. The optical pump-probe method revealed strongly damped high-frequency oscillations of the dynamical Kerr rotation angle, followed by its slow relaxation to the initial state. Modeling experimental results using the Landau–Lifshitz-Gilbert (LLG) equation showed that the observed entire dynamics is due to destruction and restoration of magnetic anisotropy rather than to demagnetization. For the pumping fluence of 7 mJ cm−2, the maximal photo-induced disruption of the anisotropy field is about 14% for the sample with

r
d

=
1

and decreases when r

d
increases. The anisotropy relaxation is a three-stage process: the ultrafast one occurs within several picoseconds, and the slow one occurs on a nanosecond time scale. The Gilbert damping in the multilayers is found to be one order of magnitude higher than that in the constituent monolayers.
Cross-free in both lateral and axial directions for Fourier-domain full-field optical coherence tomography
Authors: Li Jinxi , Zhang Jason , Zhang Luozhi , Bai Xing , Yu Zhan , Yang Zhongzhuo , Wang Yujie , Chen Xingyu , Zhou Xin
Published: January 2022

Fourier-domain full-field optical coherence tomography has the advantages of high resolution and parallel detection. However, using parallel detection can result in optical crosstalk. Toward minimizing crosstalk, we implemented a very fast deformable membrane (DM) that introduces random phase illumination, which can effectively reduce the crosstalk by washing out fringes originating from multiply scattered light. However, although the application of DM has reduced the crosstalk problem in parallel detection to a certain extent, there will still be a lot of background noise, which may come from the circadian rhythm of the sample and multiple scattered photons. The problem could be solved by employing adaptive singular value decomposition (SVD) filtering. We also combined SVD with the cumulative sum method, which can significanlty improve image resolution. Also, the random phase introduced by DM in the spectral domain will cause axial crosstalk after an inverse Fourier transform. As far as we know, we are the first team to notice axial crosstalk and propose that this problem can be solved by controlling the deformation range of DM. We have carried out a theoretical analysis of the above methods and verified its feasibility by simulation.
A dual-ended 400 km OFDR for vibration detection
Authors: Qin Zujun , Hu Yiwei , Yue Yaoli , Tan Chao
Published: January 2022

Optical frequency-domain reflectometer (OFDR) has been widely used in vibration detection because of its unique advantages of simple configuration and high spatial resolution. Based on remote fiber amplification, an unrepeated OFDR is experimentally investigated for vibration detection. To locate the vibration, we present an algorithm by calculating segmental cross-correlation between the beating signals with and without disturbances over the sensing fiber. It is shown that the OFDR demonstrates the ability of detecting the vibration over 222 km testing distance (112 km + 110 km). After sensing the first spool fiber of 112 km, the remnant laser is amplified by a remote-pumped erbium-doped fiber amplifier before proceeding to probe the vibration in the second spool one of 110 km. To be specific, the piezoelectric ceramic transducer-induced vibrations positioned at z = 110.9 km and z = 220.9 km are detected, respectively. More importantly, the OFDR system can be extended to operate in bi-directional sensing mode for the purpose of doubling the detection range, i.e. 400 km.
Robust phase unwrapping algorithm based on Zernike polynomial fitting and Swin-Transformer network
Authors: Zhao Zixin , Zhou Menghang , Du Yijun , Li Junxiang , Fan Chen , Zhang Xuchao , Wei Xiang , Zhao Hong
Published: January 2022

Phase unwrapping plays an important role in optical phase measurements. In particular, phase unwrapping under heavy noise conditions remains an open issue. In this paper, a deep learning-based method is proposed to conduct the phase unwrapping task by combining Zernike polynomial fitting and a Swin-Transformer network. In this proposed method, phase unwrapping is regarded as a regression problem, and the Swin-Transformer network is used to map the relationship between the wrapped phase data and the Zernike polynomial coefficients. Because of the self-attention mechanism of the transformer network, the fitting coefficients can be estimated accurately even under extremely harsh noise conditions. Simulation and experimental results are presented to demonstrate the outperformance of the proposed method over the other two polynomial fitting-based methods. This is a promising phase unwrapping method in optical metrology, especially in electronic speckle pattern interferometry.
Controlled release of metal phenolic network protected phage for treating bacterial infection
Authors: Sun Weilun , Xu Jingjing , Liu Bo , Zhao Yuan-Di , Yu Ling , Chen Wei
Published: January 2022

Phage is a promising therapeutic agent for treating antibiotic resistant bacteria. However, in the process of treatment, phage may be cleared by the immune system and cleaved by protease, which could affect the efficacy of phage. In order to solve the above problems, phage encapsulation is usually adopted. In this study, we employed metal phenolic network (MPN) for efficient phage encapsulation which could protect phage from the cleavage of protease, and keep cytotoxicity weak. In the model of skin wound infection, the encapsulated phage could be released in response to pH change to achieve good antibacterial effect. Furthermore, the MPN encapsulation could prolong the T4 phage residence time at the wound. Our findings suggest that MPN can be a promising material for phage encapsulation.
Electrical impedance tomography: a potential tool for intraoperative imaging of the tongue base
Authors: Brazey B , Haddab Y , Koebel L , Zemiti N
Published: January 2022

Background. The presence of a tumor in the tongue is a pathology that requires surgical intervention from a certain stage. This type of surgery is difficult to perform because of the limited space available around the base of the tongue for the insertion of surgical tools. During the procedure, the surgeon has to stretch and then fix the tongue firmly in order to optimize the available space and prevent tissue movement. As a result, the preoperative images of the inside of the tongue no longer give a reliable indication of the position and shape of the cancerous tissue due to the deformation of the overall tissue in the area. Thus, new images are needed during the operation, but are very difficult to obtain using conventional techniques due to the presence of surgical tools. Objective. Electrical Impedance Tomography (EIT) is an imaging technique that maps the resistivity or difference of resistivity of biological tissues from electrical signals. The small size of the electrodes makes it a potentially interesting tool to obtain intraoperative images of the inside of the tongue. In this paper, the objective is to study the possibility of using EIT for this purpose is investigated. Main results. A detection method is proposed, including an original configuration of the electrodes, consistent with the anatomical specificities of the tongue. The proposed method is studied in simulation and then a proof of concept is obtained experimentally on a 3D printed test tank filled with saline solution and plant tissue.
Beta-induced Alfvén eigenmodes and geodesic acoustic modes in the presence of strong tearing activity during the current ramp-down on JET
Authors: Pucella G , Alessi E , Auriemma F , Buratti P , Falessi M V , Giovannozzi E , Zonca F , Baruzzo M , Challis C D , Dumont R , Frigione D , Garzotti L , Hobirk J , Kappatou A , Keeling D L , King D , Kiptily V G , Lerche E , Lomas P J , Maslov M , Nunes I , Rimini F , Sirén P , Sozzi C , Stamp M F , Stancar Z , Sun H , Van Eester D , Zerbini M
Published: January 2022

The analysis of the current ramp-down phase of JET plasmas has revealed the occurrence of additional magnetic oscillations in pulses characterized by large magnetic islands. The frequencies of these oscillations range from 5 to

20
 

kHz

, being well below the toroidal gap in the Alfvén continuum and of the same order as the low-frequency gap opened by plasma compressibility. The additional oscillations only appear when the magnetic island width exceeds a critical threshold, suggesting that the oscillations could tap their energy from the tearing mode (TM) by a non-linear coupling mechanism. A possible role of fast ions in the excitation process can be excluded, being the pulse phase considered in the observations characterized by very low additional heating. The calculation of the coupled Alfvén–acoustic continuum in toroidal geometry suggests the possibility of beta-induced Alfvén eigenmodes (BAEs) rather than beta-induced Alfvén–acoustic eigenmodes. As a main novelty compared to previous work, the analysis of the electron temperature profiles from electron cyclotron emission has shown the simultaneous presence of magnetic islands on different rational surfaces in pulses with multiple magnetic oscillations in the low-frequency gap of the Alfvén continuum. This observation supports the hypothesis of different BAE with toroidal mode number n = 1 associated with different magnetic islands. As another novelty, the observation of magnetic oscillations with n = 2 in the BAE range is reported for the first time in this work. Some pulses, characterized by slowly rotating magnetic islands, exhibit additional oscillations with n = 0, likely associated with geodesic acoustic modes (GAMs), and a cross-spectral bicoherence analysis has confirmed a non-linear interaction between TM, BAE and GAM, with the novelty of the observation of multiple triplets (twin BAEs plus GAM), due to the simultaneous presence of several magnetic islands in the plasma.
Characterization of ultra-intense laser in radiation damping regime using ponderomotive scattering
Authors: Holkundkar Amol R , Mackenroth Felix
Published: January 2022

We present a novel approach to analyzing phase-space distributions of electrons ponderomotively scattered off an ultra-intense laser pulse and comment on the implications for the thus conceivable in-situ laser-characterization schemes. To this end, we present fully relativistic test particle simulations of electrons scattered from an ultra-intense, counter-propagating laser pulse. The simulations unveil non-trivial scalings of the scattered electron distribution with the laser intensity, pulse duration, beam waist, and energy of the electron bunch. We quantify the found scalings by means of an analytical expression for the scattering angle of an electron bunch ponderomotively scattered from a counter-propagating, ultra-intense laser pulse, also accounting for radiation reaction (RR) through the Landau–Lifshitz (LL) model. For various laser and bunch parameters, the derived formula is in excellent quantitative agreement with the simulations. We also demonstrate how, in the radiation-dominated regime, a simple re-scaling of our model’s input parameter yields quantitative agreement with numerical simulations based on the LL model.
A nonlinear piezoelectric shunt absorber with 2:1 internal resonance: experimental proof of concept
Authors: Shami Zein Alabidin , Giraud-Audine Christophe , Thomas Olivier
Published: January 2022

An experimental proof of concept of a new semi-passive nonlinear piezoelectric shunt absorber, introduced theoretically in a companion article, is presented in this work. This absorber is obtained by connecting, through a piezoelectric transducer, an elastic structure to a resonant circuit that includes a quadratic nonlinearity. This nonlinearity is obtained by including in the circuit a voltage source proportional to the square of the voltage across the piezoelectric transducer, thanks to an analog multiplier circuit. Then, by tuning the electric resonance of the circuit to half the value of one of the resonances of the elastic structure, a two-to-one internal resonance is at hand. As a result, a strong energy transfer occurs from the mechanical mode to be attenuated to the electrical mode of the shunt, leading to two essential features: a nonlinear antiresonance in place of the mechanical resonance and an amplitude saturation. Namely, the amplitude of the elastic structure oscillations at the antiresonance becomes, above a given threshold, independent of the forcing level, contrary to a classical linear resonant shunt. This paper presents the experimental setup, the designed nonlinear shunt circuit and the main experimental results.
Measurement and data-assisted simulation of bit error rate in RQL circuits
Authors: Herr Quentin , Braun Alex , Brownfield Andrew , Rudman Ed , Dosch Dan , Josephsen Trent , Herr Anna
Published: January 2022

A circuit-simulation-based method is used to determine the thermally-induced bit error rate of superconducting Single Flux Quantum logic circuits. Simulations are used to evaluate the multidimensional Gaussian integral across noise current sources attached to the active devices. The method is data-assisted and has predictive power. Measurement determines the value of a single parameter, effective noise bandwidth, for each error mechanism. The errors in the distributed networks of comparator-free Reciprocal Quantum Logic nucleate across multiple Josephson junctions, so the effective critical current is about three times that of the individual devices. The effective noise bandwidth is only 6%–23% of the junction plasma frequency at a modest clock rate of 3.4 GHz, which is 1% of the plasma frequency. This analysis shows the ways measured bit error rate comes out so much lower than simplistic estimates based on isolated devices.
Effects of defects and surface roughness on the vortex penetration and vortex dynamics in superconductor–insulator–superconductor multilayer structures exposed to RF magnetic fields: numerical simulations within TDGL theory
Authors: Wang Qing-Yu , Xue Cun , Dong Chao , Zhou You-He
Published: January 2022

Vortex penetration and vortex dynamics are significantly important to superconducting devices, for example, the superconducting cavities, since vortex motions will create substantial dissipation. In experiments, different kinds of defects as well as different degrees of surface roughness were observed. By considering these in superconductor–insulator–superconductor (SIS) structures, vortex penetration and vortex dynamics are very complex due to their interactions with defects and the influence of surface roughness, especially for radio-frequency (RF) magnetic fields, which are quite different from ideal defect-free SIS multilayer structures. In this paper, within the Ginzburg–Landau theory, we perform numerical simulations to study the effects of nanoscale defects, surface roughness, and cracks in the coating layer on the vortex penetration and superheating field in Nb3Sn–I–Nb multilayer structures exposed to a quasi-static magnetic field. The validation of the numerical simulations is verified by good consistency with previous theoretical results in ideal defect-free SIS multilayer and single Nb structures. Furthermore, we explore the vortex dynamics and induced voltages in SIS multilayer structures exposed to RF magnetic fields for both ideal defect-free structures and real situations that include surface roughness. Our numerical simulations indicate that, unlike the quasi-static case, the advantage of SIS multilayer structures over a single Nb structure depends on the degree of surface roughness as well as the frequency and amplitude of the RF magnetic field. The results of this paper provide deep insight to evaluate the actual performance-limiting characteristics of next-generation superconducting RF cavities with different proposed candidate materials, which are quite susceptible to nonideal surfaces.
Experimental estimates of the photon background in a potential light-by-light scattering study
Authors: Doyle L , Khademi P , Hilz P , Sävert A , Schäfer G , Schreiber J , Zepf M
Published: January 2022

High power short pulse lasers provide a promising route to study the strong field effects of the quantum vacuum, for example by direct photon–photon scattering in the all-optical regime. Theoretical predictions based on realistic laser parameters achievable today or in the near future predict scattering of a few photons with colliding Petawatt laser pulses, requiring single photon sensitive detection schemes and very good spatio-temporal filtering and background suppression. In this article, we present experimental investigations of this photon background by employing only a single high power laser pulse tightly focused in residual gas of a vacuum chamber. The focal region was imaged onto a single-photon sensitive, time gated camera. As no detectable quantum vacuum signature was expected in our case, the setup allowed for characterization and first mitigation of background contributions. For the setup employed, scattering off surfaces of imperfect optics dominated below residual gas pressures of 1 × 10−4 mbar. Extrapolation of the findings to intensities relevant for photon–photon scattering studies is discussed.
Analysis of hydrogen fueling, recycling, and confinement at Wendelstein 7-X via a single-reservoir particle balance
Authors: Kremeyer Thierry , König R. , Brezinsek S. , Schmitz O. , Feng Y. , Winters V. , Rudischhauser L. , Buttenschön B. , Brunner K.J. , Drewelow P. , Flom E. , Fuchert G. , Gao Y. , Geiger J. , Jakubowski M. , Killer C. , Knauer J. , Krychowiak M. , Lazerson S. , Reimold F. , Schlisio G. , Viebke H. , the W7-X Team
Published: January 2022

A single-reservoir particle balance for the main plasma species hydrogen has been established for W7-X. This has enabled the quantitative characterization of the particle sources in the standard island divertor configuration for the first time. Findings from attached scenarios with two different island sizes with a boronized wall and turbo molecular pumping are presented. Fueling efficiencies, particle flows and source locations were measured and used to infer the total particle confinement time τ
p. Perturbative gas injection experiments served to measure the effective particle confinement time

τ

p

*

. Combining both confinement times provides access to the global recycling coefficient

R

¯

. Hydrogen particle inventories have been addressed and the knowledge of particle sources and sinks reveals the core fueling distribution and provides insight into the capability of the magnetic islands to control exhaust features. Measurements of hydrogen fueling efficiencies were sensitive to the precise fueling location and measured between 12% and 31% with the recycling fueling at the strike line modeled at only 6%, due to much higher densities. 15% of the total 5.2 × 1022 a/s recycling flow ionizes far away from the recycling surfaces in the main chamber. It was shown that 60% of recycled particles ionize above the horizontal and 18% above the vertical divertor target, while the remainder of the recycling flow ionizes above the baffle (7%). Combining these source terms with their individual fueling efficiencies resolves the core fueling distribution. Due to the higher fueling efficiency in the main chamber, up to 51% of the total 5.1 × 1021 s−1 core fueling particles are entering the confined plasma from the main chamber. τ
p values in the range of 260 ms were extracted for these discharges. Together with τ
p, the global recycling coefficient

R

¯

was resolved for every

τ

p

*

measurement and a typical value close to unity was obtained. An increase of the island size, resulted in no change of τ
p, but doubled

τ

p

*

, indicating the feasibility of the control coils as an actuator to control exhaust features without affecting core confinement properties.
Influence of low-Z impurity on the stabilization of m/n
= 2/1 tearing/locked modes in EAST
Authors: Xu Ming , Liang Yunfeng , Wei Lai , Duan Yanmin , Shi Tonghui , Zhao Hailin , Xu Liqing , Zhou Ruijie , Zhang Ling , Gu Shuai , Gao Wei , Zhang Yang , Wang Zhengxiong , Zang Qing , Liu Haiqing , Sun Youwen , Zhang Shoubiao , Hu Liqun , Gong Xianzu , Xu Guosheng , Hu Jiansen , Wan Baonian , the EAST Team
Published: January 2022

The impact of the low-Z impurity concentration on mode stabilization has been investigated in the EAST tokamak. A series of tearing modes (TMs) with multiple helicities are excited by the low-Z (carbon) impurity concentration, and the dominant mode structure features m/n = 2/1 magnetic islands that propagate in the electron diamagnetic drift direction (m and n are poloidal and toroidal mode numbers, respectively). The m/n = 2/1 locked modes (LMs) can be formed by the redistribution of low-Z impurity concentration, and are unlocked spontaneously due to the decrease in the impurity concentration, where the width of the magnetic islands can reach w ≈ 5 cm (w/a ≈ 0.1, a is the minor radius). The increase in the electromagnetic brake torque is the primary reason for the mode locking, and the ‘O’-point of the m/n = 2/1 magnetic islands is locked by the tungsten protector limiter (toroidal position: −0.4π ⩽ ϕ ⩽ −0.3π) with separation of Δϕ ≈ 0. The 3D asymmetric structure of the m/n = 2/1 magnetic islands is formed for the interaction with the tungsten protector limiter, and the electromagnetic interaction decreases dramatically for the separation of Δϕ ⩾ 0.2π. The mode excitation and locking mechanisms can be illustrated by the ‘hysteresis effect’ between the low-Z impurity concentration and the width of the m/n = 2/1 magnetic islands; namely, the growth of magnetic islands is modulated by the low-Z impurity concentration, and the rotation velocity is decelerated accordingly. However, the intrinsic mechanism for the unlocking of m/n = 2/1 LMs is complicated by considering the concentration of the low-Z impurity, and the possible unlocking mechanism is discussed. Therefore, understanding the relationship between the impurities and magnetic islands is more important for optimization of the control techniques (resonant magnetic perturbations → LMs, electron cyclotron resonant heating (ECRH) → neoclassical tearing mode (NTM), impurity seeding → major collapse, etc).
Evaluation of ambipolar potential barrier in the gas dynamic trap by Doppler spectroscopy
Authors: Lizunov Andrej , Maximov Vladimir , Sandomirsky Andrey
Published: January 2022

The recently developed Doppler spectroscopy diagnostic has been used to evaluate the height of the ambipolar potential barrier forming in the gas dynamic trap (GDT) plasma between the central cell and the region with a large magnetic expansion ratio beyond the mirror. The diagnostic technique based on the gas jet charge exchange target, allowed to measure the potential profile along the line of sight covering the radial range from the axis to the limiter. The on-axis potential drop was found to be 2.6 ÷ 3.1 in units of the central plane electron temperature, which supports the existing theoretical understanding of suppression of electron thermal conductivity in the GDT expander.
Effects of homophily and heterophily on preferred-degree networks: mean-field analysis and overwhelming transition
Authors: Li Xiang , Mobilia Mauro , Rucklidge Alastair M , Zia R K P
Published: January 2022

We investigate the long-time properties of a dynamic, out-of-equilibrium network of individuals holding one of two opinions in a population consisting of two communities of different sizes. Here, while the agents’ opinions are fixed, they have a preferred degree which leads them to endlessly create and delete links. Our evolving network is shaped by homophily/heterophily, a form of social interaction by which individuals tend to establish links with others having similar/dissimilar opinions. Using Monte Carlo simulations and a detailed mean-field analysis, we investigate how the sizes of the communities and the degree of homophily/heterophily affect the network structure. In particular, we show that when the network is subject to enough heterophily, an ‘overwhelming transition’ occurs: individuals of the smaller community are overwhelmed by links from the larger group, and their mean degree greatly exceeds the preferred degree. This and related phenomena are characterized by the network’s total and joint degree distributions, as well as the fraction of links across both communities and that of agents having fewer edges than the preferred degree. We use our mean-field theory to discuss the network’s polarization when the group sizes and level of homophily vary.
Comment on ‘Out-of-equilibrium Frenkel–Kontorova model’ (Imparato A 2021 J. Stat. Mech.
013214)
Authors: Quapp W , Bofill J M
Published: January 2022

We explain the ‘phases’ of a Frenkel–Kontorova chain of atoms in a different way to the commented article. We reject the decision of states of the chain into commensurate and incommensurate states introduced by Aubry.
Steady-state thermodynamics for population dynamics in fluctuating environments with side information
Authors: Miyahara Hideyuki
Published: January 2022

Steady-state thermodynamics (SST) is a relatively newly emerging subfield of physics, which deals with transitions between steady states. In this paper, we find an SST-like structure in population dynamics of organisms that can sense their fluctuating environments. As heat is divided into two parts in SST, we decompose population growth into two parts: housekeeping growth and excess growth. Then, we derive the Clausius equality and inequality for excess growth. Using numerical simulations, we demonstrate how the Clausius inequality behaves depending on the magnitude of noise and strategies that organisms employ. Finally, we discuss the novelty of our findings and compare them with a previous study.
A 25 Gbps VCSEL driving ASIC: an attempt for ultra-high-speed front-end readout applications
Authors: Zhao C. , Guo D. , Chen Q. , Fang N. , Gan Y. , Guo Z. , Sun X. , Yi L.
Published: January 2022

This paper presents the design and the test results of a 25 Gbps VCSEL driving ASIC fabricated in a 55 nm CMOS technology as an attempt for the future very high-speed optical links. The VCSEL driving ASIC is composed of an input equalizer stage, a pre-driver stage and a novel output driver stage. To achieve high bandwidth, the pre-driver stage combines the inductor-shared peaking structure and the active-feedback technique. A novel output driver stage uses the pseudo differential CML driver structure and the adjustable FFE pre-emphasis technique to improve the bandwidth. This VCSEL driver has been integrated in a customized optical module with a VCSEL array. Both the electrical function and optical performance have been fully evaluated. The output optical eye diagram has passed the eye mask test at the data rate of 25 Gbps. The peak-to-peak jitter of 25 Gbps optical eye is 19.5 ps and the RMS jitter is 2.9 ps.
Design of MIRA, a low-noise pixelated ASIC for the readout of micro-channel plates
Authors: Fabbrica E. , Carminati M. , Butta D. , Uslenghi M. , Fiorini M. , Corso A.J. , Pelizzo M.G. , Fiorini C.
Published: January 2022

We present the design of the first prototype of MIRA (MIcro-channel plate Readout ASIC) that has been designed to read out Micro-Channel Plates (MCP), in particular for UV spectroscopy. MIRA will be able to detect the cloud of electrons generated by each photon interacting with the MCP, sustaining high local and global count rates to fully exploit the MCP intrinsic dynamic range with low dead time. The main rationale that guided the electronics design is the reduction of the input Equivalent Noise Charge (ENC) in order to allow operations with lower MCP gain, thus improving its lifetime, crucial aspect for long missions in space. MIRA features two selectable analog processing times, 133 ns or 280 ns (i.e. fast mode or slow mode), granting a count rate per pixel of 100 kcps. Moreover, it shows an Equivalent Noise Charge ENC

=
17

e

r
m
s

−

. A spatial resolution of 35 μm and an operation with zero dead time, due to the readout, are targeted. The low noise, high count rate and high spatial resolution requirements are expected by keeping a compact pixel size (35 μm × 35 μm) for a total of 32 × 32 pixels in a 2 mm × 2 mm ASIC area. In this work, the ASIC design is described.
Environmental concentrations as ratios of random variables
Authors: Perri Saverio , Porporato Amilcare
Published: January 2022

Human-induced environmental change increasingly threatens the stability of socio-ecological systems. Careful statistical characterization of environmental concentrations is critical to quantify and predict the consequences of such changes on human and ecosystems conditions. However, while concentrations are naturally defined as the ratio between solute mass and solvent volume, they have rarely been treated as such, typically limiting the analysis to familiar distributions generically used for any other environmental variable. To address this gap, we propose a more general framework that leverages their definition explicitly as ratios of random variables. We show that the resulting models accurately describe the behavior of nitrate plus nitrite in US rivers and salt concentration in estuaries in the Everglades by accounting for heavy tails potentially emerging when the water volume fluctuates around low values. Models that preclude the presence of heavy tails and the related high probability of extreme concentrations could significantly undermine the accuracy of diagnostic frameworks and the effectiveness of mitigation interventions, especially for soil contamination characterized by a water volume (i.e. soil moisture) frequently approaching zero.
Unifying polar and nematic active matter: emergence and co-existence of half-integer and full-integer topological defects
Authors: Amiri Aboutaleb , Mueller Romain , Doostmohammadi Amin
Published: January 2022

The presence and significance of active topological defects is increasingly realised in diverse biological and biomimetic systems. We introduce a continuum model of polar active matter, based on conservation laws and symmetry arguments, that recapitulates both polar and apolar (nematic) features of topological defects in active turbulence. Using numerical simulations of the continuum model, we demonstrate the emergence of both half- and full-integer topological defects in polar active matter. Interestingly, we find that crossover from active turbulence with half-to full-integer defects can emerge with the coexistence region characterized by both defect types. These results put forward a minimal, generic framework for studying topological defect patterns in active matter which is capable of explaining the emergence of half-integer defects in polar systems such as bacteria and cell monolayers, as well as predicting the emergence of coexisting defect states in active matter.
Minimum entropy production, detailed balance and Wasserstein distance for continuous-time Markov processes
Authors: Dechant Andreas
Published: January 2022

We investigate the problem of minimizing the entropy production for a physical process that can be described in terms of a Markov jump dynamics. We show that, without any further constraints, a given time-evolution may be realized at arbitrarily small entropy production, yet at the expense of diverging activity. For a fixed activity, we find that the dynamics that minimizes the entropy production is driven by conservative forces. The value of the minimum entropy production is expressed in terms of the graph-distance based Wasserstein distance between the initial and final configuration. This yields a new kind of speed limit relating dissipation, the average number of transitions and the Wasserstein distance. It also allows us to formulate the optimal transport problem on a graph via continuous-time interpolating dynamics, in complete analogy to the continuous space setting. We demonstrate our findings for simple state networks, a time-dependent pump and for spin flips in the Ising model.