bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ionizing photon interactions modulate the optical properties of crystals with femtosecond scale temporal resolution
Authors: Tao Li , Coffee Ryan N , Jeong Diana , Levin Craig S 
Published: January 2021

Abstract
In this work, we continue our study of a new method for the detection of ionizing radiation with the potential for a dramatic improvement in coincidence time resolution (CTR) for time-of-flight positron emission tomography (ToF-PET) using the modulation of a material’s optical properties instead of the scintillation mechanism. Our previous work has shown that for non-scintillation materials such as bismuth silicon oxide (BSO) and cadmium telluride (CdTe), their refractive index can be modulated by annihilation photon interactions. The ultrafast nature of this process however remains unexplored. The ionizing radiation-induced charge carriers alter the local band structure in these materials, thus changing the complex refractive index. This mechanism is routinely used at the linac coherent light source (LCLS) facility of the SLAC National Accelerator Laboratory to measure x-ray pulse arrival times with femtosecond scale resolution for photon energies between 0.5 and 10 keV. The method described here follows that example by using a frequency chirped visible continuum pulse to provide a monotonic wavelength-to-time mapping by which one can measure the time-dependent refractive index modulation. In addition, we describe an interference-based measurement setup that allows for significantly improved sensitivity while preserving a timing precision of approximately 10 fs (σ) when measuring the arrival time of below 10 keV x-ray pulses with yttrium aluminum garnet (YAG) crystal. The method is presented in the context of ToF-PET application with further discussions on the potential CTR achievable if a similar detection concept is adopted for detecting 511 keV photons. Semi-empirical analysis indicates that the predicted CTR achievable is on the order of 1 ps (FWHM).
Electric field and turbulence in global Braginskii simulations across the ASDEX Upgrade edge and scrape-off layer
Authors: Zholobenko W , Body T , Manz P , Stegmeir A , Zhu B , Griener M , Conway G D , Coster D , Jenko F 
Published: January 2021

Abstract
Turbulence simulations in diverted geometry across the edge and scrape-off layer (SOL) of ASDEX Upgrade are performed with the GRILLIX code (Stegmeir et al 2019 Phys. Plasmas
26 052517). The underlying global (full-f) drift-reduced Braginskii model allows to concurrently study the self-consistent dynamics of the turbulence and the background as well as the evolution of toroidal and zonal flows. Different contributions to the radial electric field are identified. The dominant contribution on closed flux surfaces comes from the ion pressure gradient, due to the diamagnetic drift in the curved magnetic field. Large deviations can be induced, in particular, by the polarization particle flux, leading to zonal flows. The latter are driven by small-scale eddies, but do not exhibit much impact on the overall transport which is driven by ballooning modes at larger scales. Ion viscosity is found to be important in damping poloidal rotation through adjusting of the parallel velocity profile, but not via direct vorticity damping. The zonal flow drive peaks at the separatrix, where a strong shear layer forms due to the sheath-induced counter-propagating SOL flow, allowing for the formation of a transport barrier. The temperature profile across the separatrix is determined by the competition between cross-field transport and outflow in the SOL, the latter being largely controlled by the parallel heat conductivity.
ASCOT simulations of 14 MeV neutron rates in W7-X: effect of magnetic configuration
Authors: Kontula J , Koschinsky J P , Äkäslompolo S , Kurki-Suonio T 
Published: January 2021

Abstract
Neutron production rates in fusion devices are determined not only by the kinetic profiles but also the fast ion slowing-down distributions. In this work, we investigate the effect of magnetic configuration on neutron production rates in future deuterium plasmas in the Wendelstein 7-X stellarator. The neutral beam injection, beam and triton slowing-down distributions, and the fusion reactivity are simulated with the ASCOT suite of codes. The results indicate that the magnetic configuration has only a small effect on the production of 2.45 MeV neutrons from thermonuclear and beam-target fusion. The 14.1 MeV neutron production rates were found to be between 1.49 × 1012 and

1.67
×

10

12

s

−
1

, which is estimated to be sufficient for a time-resolved detection using a scintillating fiber detector, although only in high-performance discharges.
Enhancing teleportation of a single-qubit state by the unitary transformation in arbitrary decoherence rate
Authors: Chen Zun-Yi , Xu Jin-Rong , Yu Jiangying , Hou Kui 
Published: January 2021

Abstract
The proposal of the quantum teleportation(QT) is to transfer an unknown quantum state from one place to another through local operations and classical communication. However, the efficiency of standard QT will be significantly reduced due to the influence of the inevitable noise in environments. In this work, we propose two schemes to improve the efficiency of the QT protocol when quantum channel is subjected to bit-flip or phase-flip noise. We find that the so-called more entanglement means low efficiency in the performance of the standard teleportation protocol, and the optimal fidelity is obtained only by using the appropriate unitary operation. Specially, we show that the optimal averaged fidelity to our schemes is always more than the best classically achievable fidelity 2/3. We also provide a physical explanation of the obtained conclusions and our results will be helpful for improving quantum communication with real implementation.
Guided assembly of cancer ellipsoid on suspended hydrogel microfibers estimates multi-cellular traction force
Authors: Lee Cheng-Tai , Gill Elisabeth L , Wang Wenyu , Gerigk Magda , Terentjev Eugene M , Shery Huang Yan Yan 
Published: January 2021

Abstract
Three-dimensional (3D) multi-cellular aggregates hold important applications in tissue engineering and in vitro biological modeling. Probing the intrinsic forces generated during the aggregation process, could open up new possibilities in advancing the discovery of tissue mechanics-based biomarkers. We use individually suspended, and tethered gelatin hydrogel microfibers to guide multicellular aggregation of brain cancer cells (glioblastoma cell line, U87), forming characteristic cancer ‘ellipsoids’. Over a culture period of up to 13 days, U87 aggregates evolve from a flexible cell string with cell coverage following the relaxed and curly fiber contour; to a distinct ellipsoid-on-string morphology, where the fiber segment connecting the ellipsoid poles become taut. Fluorescence imaging revealed the fiber segment embedded within the ellipsoidal aggregate to exhibit a morphological transition analogous to filament buckling under a compressive force. By treating the multicellular aggregate as an effective elastic medium where the microfiber is embedded, we applied a filament post-buckling theory to model the fiber morphology, deducing the apparent elasticity of the cancer ellipsoid medium, as well as the collective traction force inherent in the aggregation process.
Edge effect and interface confinement modulated strain distribution and interface adhesion energy in graphene/Si system
Authors: Huang Ying-Di , Xie Jia-Ting , Hu Su-Mei , He Yan 
Published: January 2021

Abstract
In order to clarify the edge and interface effect on the adhesion energy between graphene (Gr) and its substrate, a theoretical model is proposed to study the interaction and strain distribution of Gr/Si system in terms of continuum medium mechanics and nanothermodynamics. We find that the interface separation and adhesion energy are determined by the thickness of Gr and substrate. The disturbed interaction and redistributed strain in the Gr/Si system induced by the effect of surface and interface can make the interface adhesion energy decrease with increasing thickness of Gr and diminishing thickness of Si. Moreover, our results show that the smaller area of Gr is more likely to adhere to the substrate since the edge effect improves the active energy and strain energy. Our predictions can be expected to be a guide for designing high performance of Gr-based electronic devices.
Three-dimensional cytoplasmic calcium propagation with boundaries
Authors: Jiang Han-Yu , He Jun 
Published: January 2021

Abstract
Ca2+ plays an important role in cell signal transduction. Its intracellular propagation is the most basic process of Ca2+ signaling, such as calcium wave and double messenger system. In this work, with both numerical simulation and mean field ansatz, the three-dimensional probability distribution of Ca2+, which is read out by phosphorylation, is studied in two scenarios with boundaries. The coverage of distribution of Ca2+ is found at an order of magnitude of μm, which is consistent with experimental observed calcium spike and wave. Our results suggest that the double messenger system may occur in the ER-PM junction to acquire great efficiency. The buffer effect of kinase is also discussed by calculating the average position of phosphorylations and free Ca2+. The results are helpful to understand the mechanism of Ca2+ signaling.
Fast-ion pressure dominating the mass dependence of the core heat transport in ASDEX Upgrade H-modes
Authors: Schneider P.A. , Bonanomi N. , Angioni C. , Weiland M. , Cavedon M. , David P. , Fischer R. , Hennequin P. , Hobirk J. , Kappatou A. , Kurzan B. , McDermott R.M. , Plank U. , Pütterich T. , Ryter F. , Willensdorfer M. , the ASDEX Upgrade Team  , and the EUROfusion MST1 Team  
Published: January 2021

Abstract
H-mode plasmas in ASDEX Upgrade (AUG) using different hydrogen isotopes are analysed with respect to their core transport properties. The experimental results are discussed and we present gyrokinetic simulations which are able to reproduce the experimental observations. A novel strategy allows us to disentangle core and pedestal physics by mitigating the isotopic dependence of pedestal properties while keeping the heat and particle sources the same. Matched pedestal profiles are obtained between hydrogen (H) and deuterium (D) plasmas when increasing the triangularity in H plasmas with respect to D plasmas. In the core of these plasmas little isotopic dependence is observed when the fast-ion content is low W
fast/W
th < 1/3. Quasi-linear modelling with TGLF reproduces the experimental trends under these conditions. For larger fast-ion fractions an isotope dependence is observed in the core heat transport. This is related to a difference in fast-ion stabilization of turbulent transport. The fast-ion pressure in H and D plasmas is different due to the mass dependence in the fast-ion slowing down time as well as to operational restrictions when heating with H neutral beam injection (H-NBI) or D-NBI. Typically, W
fast,H < 1/2W
fast,D for comparable NBI heating powers in AUG. The gyrokinetic analysis shows that linear growth rates of ITG modes do not show a pure gyro-Bohm mass dependence, but follow the experimentally observed mass dependence when taking collisions, EM-effects and fast ions into account. Non-linear gyrokinetic simulations reproduce the experimental heat fluxes for different isotopes when fast ions are included. This highlights the role of the fast-ion pressure as a key element to explain the observed differences in the core of H and D plasmas.
Ballistic propagation of a local impact in the one-dimensional XY model
Authors: Yoshinaga Atsuki 
Published: January 2021

Abstract
Light-cone-like propagation of information is a universal phenomenon of nonequilibrium dynamics of integrable spin systems. In this paper, we investigate propagation of a local impact in the one-dimensional XY model with the anisotropy γ in a magnetic field h by calculating the magnetization profile. Applying a local and instantaneous unitary operation to the ground state, which we refer to as the local-impact protocol, we numerically observe various types of light-cone-like propagation in the parameter region 0 ⩽ γ ⩽ 1 and 0 ⩽ h ⩽ 2 of the model. By combining numerical integration with an asymptotic analysis, we find the following: (i) for |h| ⩾ |1 − γ
2| except for the case on the line h = 1 with

0
<
γ
<

3

/
2

, a wave front propagates with the maximum group velocity of quasiparticles, except for the case γ = 1 and 0 < h < 1, in which there is no clear wave front; (ii) for |h| < |1 − γ
2| as well as on the line h = 1 with

0
<
γ
<

3

/
2

, a second wave front appears owing to multiple local extrema of the group velocity; (iii) for |h| = |1 − γ
2|, edges of the second wave front collapses at the origin, and as a result, the magnetization profile exhibits a ridge at the impacted site. Furthermore, we find by an asymptotic analysis that the height of the wave front decays in a power law in time t with various exponents depending on the model parameters: the wave fronts exhibit a power-law decay t
−2/3 except for the line h = 1, on which the decay can be given by either ∼t
−3/5 or ∼t
−1; the ridge at the impacted site for |h| = |1 − γ
2| shows the decay t
−1/2 as opposed to the decay t
−1 in other cases.
Stationary properties of a non-Markovian Brownian gyrator
Authors: Nascimento Eduardo dos S , Morgado Welles A M 
Published: January 2021

Abstract
We investigate the stochastic behavior of a non-Markovian version of an elementary Brownian gyrator. The model is defined by overdamped Langevin-like dynamics with a two-dimensional harmonic potential that presents distinct principal axes and is coupled to heat baths at different temperatures. The thermal noises are assumed to be Gaussian, and are related to friction forces through a dissipation memory kernel. The stationary states present rotational motion with non-trivial average torques due to harmonic, friction and fluctuating thermal forces. However, the Markovian limit of the system exhibits a zero average torque produced by fluctuating thermal forces. For the case of stochastic torque exerted by harmonic force, the cumulant-generating function is calculated exactly. We also study the average heat fluxes in the steady-state regime, where a memory-dependent behavior is observed.
The open XXZ chain at Δ = −1/2 and the boundary quantum Knizhnik–Zamolodchikov equations
Authors: Hagendorf Christian , Liénardy Jean 
Published: January 2021

Abstract
The open XXZ spin chain with the anisotropy parameter

Δ
=
−

1

2

and diagonal boundary magnetic fields that depend on a parameter x is studied. For real x > 0, the exact finite-size ground-state eigenvalue of the spin-chain Hamiltonian is explicitly computed. In a suitable normalisation, the ground-state components are characterised as polynomials in x with integer coefficients. Linear sum rules and special components of this eigenvector are explicitly computed in terms of determinant formulas. These results follow from the construction of a contour-integral solution to the boundary quantum Knizhnik–Zamolodchikov equations associated with the R-matrix and diagonal K-matrices of the six-vertex model. A relation between this solution and a weighted enumeration of totally-symmetric alternating sign matrices is conjectured.
Backward bifurcation arises from the smoking transmission model considering media campaign
Authors: Fatimah M. , Aldila D. , Handari B. D. 
Published: January 2021

AbstractIn this paper, we present and analyze a smoking cessation model with intervention from media campaigns. In our model, we consider potential smokers choosing not to smoke because of media campaign interventions. From the mathematical analysis, we obtain a threshold value of the model, called the basic reproduction number, which is the threshold condition for the smoking-free and endemic equilibrium stability. Next, it is shown that two endemic equilibrium may exist when the threshold basic reproduction number less than unity, and a unique endemic equilibrium exists if the threshold basic reproduction number exceeds unity. Using the center-manifold theory, we show that a backward bifurcation may occur when the value of the basic reproduction number equal to unity. This result implies that the classical epidemiological requirement of making basic reproduction number less than unity is no longer sufficient, although necessary, for effectively controlling the spread of smoking in a population. The numerical simulation was conducted for several scenarios to support and visualize our analytical results.
Applications of cuckoo search and ant lion optimization for analyzing protein-protein interaction through regularized Markov clustering on coronavirus
Authors: Rizki A , Bustamam A , Sarwinda D 
Published: January 2021

Abstract
All living viruses have important structures such as protein. Proteins can interact with each other forming large networks of Protein-Protein Interaction (PPI). In order to facilitate the study of these PPI networks, there needs to be clustering analysis of the PPI. In this research, we use PPI network datasets from SARS-CoV-2 and humans. The interactions of the PPI network will then be formed into graphs. Regularized Markov Clustering (RMCL) is used to perform graph clustering. RMCL consists of three main steps which are regularization, inflation, and pruning. The RMCL algorithm is a variant of Markov Clustering (MCL). However, the inflation parameter in RMCL must be inputted manually by the user to obtain the best results. To solve the limitations of RMCL, we developed a new method by combining each Cuckoo Search (CS) and Ant Lion Optimization (ALO) with the original RMCL algorithm. The optimizers are used to optimize the inflation parameter in RMCL. CS and ALO are a part of swarm intelligence which is inspired by the behaviour of cuckoo birds and antlions in nature. The results show that the interactions formed from CS-RMCL vary from 1401 to 1402. It is more stable than the interactions formed from ALO-RMCL which ranges from 1408 to 3641. The difference between the best elite in each iteration of ALO-RMCL is very influential to the interaction compared to the best nest from the CS-RMCL.
Enhanced proliferation and angiogenic phenotype of endothelial cells via negatively-charged alginate and chondroitin sulfate microsphere hydrogels
Authors: Xiong Xiong , Xiao Wen , Zhou Sijie , Cui Rongwei , Xu Hockin H K , Qu Shuxin 
Published: January 2021

Abstract
Sodium alginate-based hydrogel was the one of the most used polymers for cell delivery. However, the adsorption of extracellular matrix and proteins was inhibited due to the formation of a hydrated surface layer of these hydrogels. In this study, a novel cell delivery system, negatively-charged alginate and chondroitin sulfate microsphere hydrogel (nCACSMH), was fabricated with excellent permeability and biocompatibility in the action of a high voltage direct-current electric field. Negative charge was introduced to the surface of nCACSMH to obtain the expanded network and enhanced permeability. Additionally, the increasing content of chondroitin sulfate in nCACSMH could give rise to the charge density and its asymmetric structure, thus the uneven, plicate and expanded surface of nCACSMH which was favorable to cell proliferation was developed. Moreover, chondroitin sulfate was released with the degradation of nCACSMH, which played a crucial role in maintaining the normal physiological functions of cells. Thus the proliferation of human umbilical vein endothelial cells (HUVECs) was further accelerated and the angiogenesis related genes expression in endothelial cells was continuously and dramatically up-regulated. After 4 d, the proliferation and viability of HUVECs were significantly improved, the cells were distributed evenly in nCACSMH. The novel nCACSMH has the potential to be used as cell delivery, three-dimensional (3D) cell cultures for cell therapy, 3D bioprinting, high-throughput screening for drugs, and disease model for regeneration and constructing of tissue engineering.
Electro-deposition synthesis of tube-like collagen–chitosan hydrogels and their biological performance
Authors: Li Ping , He Lang , Liu Xueling , Fan Shengxuan , Yuan Yifan , Zhang Juntao , Wang Haibo , Li Sheng 
Published: January 2021

Abstract
Electro-deposition is a smart, safe and efficient method for biomaterial manufacturing. Collagen, a functional protein with excellent biocompatibility and biosafety, is a promising candidate for tissue engineering and biomedical applications. However, there are few reports on electro-deposition of biomaterials using collagen without electrically or magnetically active nanoparticles. In this study, electro-deposition was employed to swiftly fabricate tube-like collagen–chitosan hydrogels in a mild environment. Fourier transform infrared spectroscopy was employed to analyze the ingredients of the tube-like hydrogels. The result showed that the hydrogels contained both collagen and chitosan. The distribution and content of collagen in the hydrogels was further measured by hematoxylin–eosin staining and hydroxyproline titration. Collagen was distributed homogeneously and its content was related to the initial collagen:chitosan ratio. The tension resistance of the composite gels and the thermal stability of collagen in the composites were obviously enhanced by the chitosan doping. Meanwhile, the tube-like hydrogels retained a good ability to promote cell proliferation of collagen. This method offers a convenient approach to the design and fabrication of collagen-based materials, which could effectively retain the bioactivity and biosafety of collagen and furnish a new way to enhance the stability of collagen and the tensile strength of collagen-based materials.
Symmetric discrete AKP and BKP equations
Authors: Li Shangshuai , Nijhoff Frank W , Sun Ying-ying , Zhang Da-jun 
Published: January 2021

Abstract
We show that when KP (Kadomtsev–Petviashvili) τ functions allow special symmetries, the discrete BKP equation can be expressed as a linear combination of the discrete AKP equation and its reflected symmetric forms. Thus the discrete AKP and BKP equations can share the same τ functions with these symmetries. Such a connection is extended to 4 dimensional (i.e. higher order) discrete AKP and BKP equations in the corresponding discrete hierarchies. Various explicit forms of such τ functions, including Hirota’s form, Gramian, Casoratian and polynomial, are given. Symmetric τ functions of Cauchy matrix form that are composed of Weierstrass σ functions are investigated. As a result we obtain a discrete BKP equation with elliptic coefficients.
Efficiency of the introduction of different Ca levels in broiler chicken diets as part of dietary fiber extrudates
Authors: Kholodilina T N 
Published: January 2021

Abstract
One of the main tasks of industrial poultry farming is the introduction of new technologies that reduce the cost of obtaining products through the use of non-traditional feed components. The aim of the research is to study the effectiveness of the technology of extrusion processing of feed components at the stage of interaction with the biome of the poultry digestive system. It was found that the inclusion of extruded bran in the diet is accompanied by a significant increase in the number of Lactobacillus. Moreover, the most significant growth was observed in the intestines of a bird receiving an extrudate with an input of 20 % calcium. This group was also characterized by a maximum growth of Escherichia 7.3 times in comparison with the control. The introduction of an extrudate with a content of 10 % calcium is associated with a decrease in the number of E. coli in the cecum of chickens. Thus, pretreatment of non-starch polysaccharides together with calcium in the extruder stimulates abdominal digestion of chickens, which indicates the possibility of their use in industrial production.