bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrodynamics of random-organizing hyperuniform fluids
Authors: Lei Qun-Li , Ni Ran 
Published: October 2019

Significance
Recently, an exotic hyperuniform fluid state was found in a number of nonequilibrium systems, which shows the promise for fabrication of novel lifelike functional materials capable of self-healing and self-adapting. However, the general mechanism of fluidic hyperuniformity (HU) and its fundamental difference from equilibrium fluids remain unclear, which hinders the rational design of nonequilibrium hyperuniform fluids. In this work, we propose a nonequilibrium hard-sphere model of hyperuniform fluids and formulate a full hydrodynamic description based on the generalized Navier–Stokes equations. Our theory reveals the mechanism of fluidic HU in a simple and intuitive way, which is confirmed by simulating a realistic active spinner system.
Single-nucleotide control of tRNA folding cooperativity under near-cellular conditions
Authors: Leamy Kathleen A. , Yamagami Ryota , Yennawar Neela H. , Bevilacqua Philip C. 
Published: October 2019

Significance
RNA structures control many essential functions of life, including gene expression, protein synthesis, and development. To perform these functions, RNAs often adopt complex tertiary folds. Here, we study the thermodynamics of late-transcriptional folding of eukaryotic and prokaryotic tRNAs. In near-cellular conditions, tRNAs gain folding cooperativity only when nearly all nucleotides in the acceptor stem are transcribed. Furthermore, the native 5′ and 3′ extensions in the precursor do not affect the folding pathway. Therefore, tRNA folding cooperativity is controlled by a single nucleotide under near-cellular conditions.
Molecular doping of blue phosphorene: a first-principles investigation
Authors: Sun Minglei , Tang Wencheng , Li Song , Chou Jyh-Pin , Hu Alice , Schwingenschlögl Udo 
Published: October 2019

Abstract
Using first-principles calculations, we show that p-doped blue phosphorene can be obtained by molecular doping with 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4-TCNQ) and 1,3,4,5,7,8-hexafluorotetracyanonaphthoquinodimethane (F6-TNAP), whereas n-doped blue phosphorene can be realized by doping with tetrathiafulvalene (TTF) and cyclooctadecanonaene (CCO). Moreover, the doping gap can be effectively modulated in each case by applying an external perpendicular electric field. The optical absorption of blue phosphorene can be considerably enhanced in a broad spectral range through the adsorption of CCO, F4-TCNQ, and F6-TNAP molecules, suggesting potential of the doped materials in the field of renewable energy.
Dosimetric performance of the Elekta Unity MR-linac system: 2D and 3D dosimetry in anthropomorphic inhomogeneous geometry
Authors: Pappas E , Kalaitzakis G , Boursianis T , Zoros E , Zourari K , Pappas E P , Makris D , Seimenis I , Efstathopoulos E , Maris T G 
Published: October 2019

Abstract
Following the clinical introduction of the Elekta Unity MR-linac, there is an urgent need for development of dosimetry protocols and tools, not affected by the presence of a magnetic field. This work presents a benchmarking methodology comprising 2D/3D passive dosimetry and involving on-couch adaptive treatment planning, a unique step in MR-linac workflows.
Two identical commercially available 3D-printed head phantoms (featuring realistic bone anatomy and MR/CT contrast) were employed. One phantom incorporated a film dosimetry insert, while the second was filled with polymer gel. Gel dose-response characteristics were evaluated under the Unity irradiation and read-out conditions, using vials and a cubic container filled with gel from the same batch.
Treatment plan for the head phantoms involved a hypothetical large C-shape brain lesion, partly surrounding the brainstem. An IMRT step-and-shoot 7-beam plan was employed. Pre-treatment on-couch MR-images were acquired in order for the treatment planning system to calculate the virtual couch shifts and perform adaptive planning. Absolute 2D and relative 3D measurements were compared against calculations related to both adapted and original plans. Real-time dose accumulation monitoring in the gel-filled phantom was also performed.
Results from the vials and cubic container suggest that gel dose-response is linear in the dose range investigated and signal integrity is mature at the read-out timings considered. Head phantom 2D and 3D measurements agreed well with calculations with 3D gamma index passing rates above 90% in all cases, even with the most stringent criteria used (2 mm/2%). By exploiting the 3D information provided by the gel, comparison also involved DVHs, dose-volume and plan quality metrics, which also reflected the agreement between adapted and delivered plans within  ±4%. No considerable discrepancies were detected between adapted and original plans.
A novel methodology was developed and implemented, suitable for QA procedures in Unity. TPS calculations were validated within the experimental uncertainties involved.
Interactions of magnetized plasma flows in pulsed-power driven experiments
Authors: Suttle L G , Burdiak G C , Cheung C L , Clayson T , Halliday J W D , Hare J D , Rusli S , Russell D R , Tubman E R , Ciardi A , Loureiro N F , Li J , Frank A , Lebedev S V 
Published: October 2019

Abstract
A supersonic flow of magnetized plasma is produced by the application of a 1 MA-peak, 500 ns current pulse to a cylindrical arrangement of parallel wires, known as an inverse wire array. The plasma flow is produced by the J × B acceleration of the ablated wire material, and a magnetic field of several Tesla is embedded at source by the driving current. This setup has been used for a variety of experiments investigating the interactions of magnetized plasma flows. In experiments designed to investigate magnetic reconnection, the collision of counter-streaming flows, carrying oppositely directed magnetic fields, leads to the formation of a reconnection layer in which we observe ions reaching temperatures much greater than predicted by classical heating mechanisms. The breakup of this layer under the plasmoid instability is dependent on the properties of the inflowing plasma, which can be controlled by the choice of the wire array material. In other experiments, magnetized shocks were formed by placing obstacles in the path of the magnetized plasma flow. The pile-up of magnetic flux in front of a conducting obstacle produces a magnetic precursor acting on upstream electrons at the distance of the ion inertial length. This precursor subsequently develops into a steep density transition via ion-electron fluid decoupling. Obstacles which possess a strong private magnetic field affect the upstream flow over a much greater distance, providing an extended bow shock structure. In the region surrounding the obstacle the magnetic pressure holds off the flow, forming a void of plasma material, analogous to the magnetopause around planetary bodies with self-generated magnetic fields.
Cosmology data analysis challenges and opportunities in the LSST sky survey
Authors: Anthony Tyson J 
Published: October 2019

Abstract
Fueled by advances in software, microelectronics, and large optics fabrication, a new type of sky survey will soon begin. In a relentless campaign of 15 second exposures with a 3 gigapixel camera, the Large Synoptic Survey Telescope will cover the sky deeply every week for ten years. LSST will chart billions of remote galaxies, providing multiple probes of the mysterious Dark Matter and Dark Energy. Multiple probes of the effects of dark energy over an unprecedented volume of the universe will allow us to measure how dark energy behaves over time to high precision. Hundreds of petabytes of high dimensional complex data will be mined and compared with Exascale simulations. After reviewing the LSST project, I will describe some of the computational challenges and opportunities.
Principal component analysis of the magnetic transition in the three-dimensional Fermi-Hubbard model
Authors: Khatami Ehsan 
Published: October 2019

Abstract
Machine learning techniques have been widely used in the study of strongly correlated systems in recent years. Here, we review some applications to classical and quantum many-body systems and present results from an unsupervised machine learning technique, the principal component analysis, employed to identify the finite-temperature phase transition of the three-dimensional Fermi-Hubbard model to the antiferromagnetically ordered state. We find that this linear method can capture the phase transition as well as other more complicated and nonlinear counterparts.
Learning Materials Properties from Orbital Interactions
Authors: Pham Tien-Lam , Dang Tran-Thai , Nguyen Van-Doan , Kino Hiori , Miyake Takashi , Dam Hieu-Chi 
Published: October 2019

Abstract
Orbital field matrix (OFM) descriptors were developed with an emphasis on atomic orbitals for representing material structures in datasets of multi-element compounds. The descriptors were based on atomic valence shell electrons and their coordination. In addition to original OFM and OFM1 which is OFM with a column representing information on the center atom, in this work, we present another version, named OFM0, which is OFM1 without information on atomic distances, for predicting the properties of unoptimized structures. We focus on formation energy and phase stability of crystalline systems, while the atomization energy is examined for molecules. With the emphasis on the ability to identify materials with similar properties, here, the applicabilities of OFM, OFM1, and OFM0 are systematically examined with decision tree (DT) regression, random forest (RF) regression, and kernel ridge regression (KRR). We show that the family of OFM descriptors are highly capable to build predictive models for the properties of solids and molecules. The accuracy of a DT and a forest of trees (RF) is comparable to that of the KRR models. The KRR with a Laplacian kernel estimated by OFM1 yields the most accurate predictions, with the formation energy, phase stability, and atomization energy having mean absolute errors (MAEs) of 0.072 eV/atom, 0.059 eV/atom, and 6.74 kcal/mol, respectively. The OFM0 without atomic distances also yields acceptable predictions with respective MAEs of 0.090 eV/atom, 0.069 eV/atom, and 7.77 kcal/mol. The results imply that our descriptors are highly useful to find similar materials.
A Comparison of Medium-Sized Basis Sets for the Prediction of Geometries, Vibrational Frequencies, Infrared Intensities and Raman Activities for Water
Authors: Ferrari Brian C. , Bennett Chris J. 
Published: October 2019

AbstractOptimized geometries, vibrational frequencies, as well as infrared intensities and Raman activities were calculated for water (H2O) utilizing popular quantum mechanical approaches. Here, density functional theory (DFT) calculations were performed using the B3LYP (Becke, three-parameter, Lee-Yang-Parr) functional, as well asab initiocalculations using second-order Møller-Plesset (MP2) perturbation theory and coupled-cluster with single, double and perturbative triple excitations [CCSD(T)] levels of theory were used. We assess and benchmark the performance of 69 different atomic orbital basis sets including various popular families of medium-sized basis sets typically of two to four zeta quality and differing levels of augmentation by polar and diffuse functions. The basis sets range from the commonly adopted Pople-style (6-31G & 6-311G), Dunning’s correlation consistent (cc-pV(n+d)Z & aug-cc-pV(n+d)Z, as well as Truhlar’s calendar variations, Jensen’s polarization consistent (pc-n & aug-pc-n), Ahlrichs (def2-…), Sapporo’s and Karlsruches as well as atomic natural orbitals (ANOs) such as NASA Ames (ANOn), Neese-style, and Roos-style. We also compare several basis sets specifically designed to calculate vibrational and electronic properties, including the Sadlej-pVTZ (and LPol-X families), as well as SNS families of Barone. The results are compared to experimental values where available, or calculations performed with 5 or 6 zeta-level (e.g., cc-pV6Z). The performance of each family of basis sets is discussed in terms of their accuracy (and pitfalls), as well as computational resource scaling and efficiency. The Def2 basis family performs very well overall, yielding more accurate results with lower runtimes than traditional basis sets. ‘May’ basis sets also provide accurate predictions of vibrational frequencies at significantly lower costs. Raman activities can be accurately calculated using MP2 under harmonic approximation with several ‘spectroscopic’ families performing well.
A Brief History of Strukturbericht Symbols and Other Crystallographic Classification Schemes
Authors: Mehl Michael J. 
Published: October 2019

Abstract
In 1913, x-ray crystallography was first used to determine the crystal structure of diamond. Since that time hundreds of thousands, if not millions, of crystal structures have been determined. Published structures require critical review and indexing to make them easily available to other researchers. One of the first systems for doing this was Strukturbericht (Structure Reports), published in Germany from 1931-1943 and covering research from 1913-1939, and now best known for the Strukturbericht symbols which label common crystal structures. A comprehensive history of Strukturbericht has not been written. This brief report sketches the early history of Strukturbericht, as well as its post-World War II successor publications, handbooks, and online resources.
DCA++ project: Sustainable and scalable development of a high-performance research code
Authors: Hähner U R , Balduzzi G , Doak P W , Maier T A , Solcà R , Schulthess T C 
Published: October 2019

Abstract
Scientific discoveries across all fields, from physics to biology, are increasingly driven by computer simulations. At the same time, the computational demand of many problems necessitates large-scale calculations on high-performance supercomputers. Developing and maintaining the underlying codes, however, has become a challenging task due to a combination of factors. Leadership computer systems require massive parallelism, while their architectures are diversifying. New sophisticated algorithms are continuously developed and have to be implemented efficiently for such complex systems. Finally, the multidisciplinary nature of modern science involves large, changing teams to work on a given codebase. Using the example of the DCA++ project, a highly scalable and efficient research code to solve quantum many-body problems, we explore how computational science can overcome these challenges by adopting modern software engineering approaches. We present our principles for scientific software development and describe concrete practices to meet them, adapted from agile software development frameworks.
Free energy profiles of lipid translocation across pure POPC and POPC/CHOL bilayer: all-atom molecular dynamics study
Authors: Saito Hiroaki , Morishita Tetsuya , Mizukami Taku , Nishiyama Ken-ichi , Kawaguchi Kazutomo , Nagao Hidemi 
Published: October 2019

Abstract
All-atom molecular dynamics (MD) simulations of pure 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer and POPC bilayer containing cholesterol (POPC/CHOL) with CHARMM36 force field were carried out to investigate the effects of CHOL on structure and lipid translocation across the membranes. We calculated the potential mean force (PMF) profiles for translocation of POPC and CHOL along the pure POPC and the POPC/CHOL bilayer normal by umbrella sampling method. The obtained PMF profile of the POPC translocation was in good agreement with that of the previous MD study, showing that the estimated PMF profiles with the CHARMM36 force field should be reasonable. We found that the PMF peak appears slightly beyond the bilayer center. The CHOL effects on the PMF profile of POPC translocation were clearly observed; the free energy barrier for the flip-flop of lipid increased and, the energy for the desorption of lipid decreased. These changes in the PMF profile should be responsible for the tight packing of the POPC/CHOL bilayer. The PMF profiles for the CHOL translocation showed that the free energy barriers at the bilayer center were sufficiently smaller than those of POPC translocation, indicating that the CHOL can easily flip over compared to the POPC in the membrane. In the case of PMF of CHOL translocation in the POPC/CHOL system, while the PMF energy in the hydrophobic core region was higher than that of the pure POPC bilayer, the free energy difference at bilayer center was small.
On the carbuncle instability of the HLLE-type solvers
Authors: Shen Zhijun , Ren Jian , Cui Xia 
Published: October 2019

Abstract
The carbuncle phenomenon is a numerical instability that affects the numerical capturing of shock waves when low-dissipative upwind scheme is used. This paper investigates shock instabilities of the HLLE-type methods for the Euler equations under the strong shock interaction, where the HLLE-type methods include the HLLE, HLLC, HLLEM, HLLCM and HLLEC Riemann solvers with specific wavespeed estimates. Based on a matrix stability analysis for two dimensional steady shocks, a new factor to influence carbuncle phenomenon is pointed out and the choice of the signal velocity plays an important role. A numerical flux function with wave velocity estimates which can crisply resolve shocks seems to be vulnerable to the shock anomalies even if the numerical fluxes to be regarded to be free from the carbuncle phenomenon. A suggestion to the choice of the wave speed is proposed when calculating strong shock wave problems.
On the geometric structures in evolutionary games on square and triangular lattices
Authors: Burovski Evgeni , Malyutin Aleksandr , Shchur Lev 
Published: October 2019

Abstract
We study a model of a spatial evolutionary game, based on the Prisoner’s dilemma for two regular arrangements of players, on a square lattice and on a triangular lattice. We analyze steady state distributions of players which evolve from irregular, random initial configurations. We find significant differences between the square and triangular lattice, and we characterize the geometric structures which emerge on the triangular lattice.
A Brief Review on Canonical Loop Quantum Gravity: The Kinematical Part
Authors: Zen Freddy Permana , Ariwahjoedi Seramika 
Published: October 2019

Abstract
In this article, we briefly review the kinematical part of canonical loop quantum gravity. This article starts with tetradic formulation of gravity both in the covariant approach and canonical approach. The next step is to introduce Ashtekar new variables and to apply the Dirac canonical quantization procedure of gravity. By the holonomy representation, one obtains the loop representation of quantum gravity.
Matter perturbation in coupled scalar field cosmology
Authors: Mulki F A M , Wulandari H 
Published: October 2019

Abstract
A universe containing a coupled scalar field would have different dynamical evolution compared to uncoupled cases. Significant differences are expected to emerge during matter dominated era, where scalar field density mimics how matter density evolves, by becoming subdominant. Analysis of the dynamics was investigated both analytically and numerically through phase plane method, and we obtained two attractor solutions which are compatible to a late time cosmic acceleration as the ending of matter dominated era. Ordinary scalar field triggers an acceleration with stable attractor solution which converges to ωϕ
= ωeff
≈ −1. Whereas, phantom scalar field allows negative values for its own energy (ωeff
˂ −1 and Ωϕ ˂ 0); however this is not stable, therefore it will be caught by attractor solution which is stable to ωϕ
= ωeff
≈ −1. In addition, we found cosmological parameters generated from both analytical and numerical calculations, i.e. ωϕ
, Ωϕ and ωeff
, by assuming a flat universe. The existence of a coupling constant Q between scalar field and matter induces different structure growth compared to uncoupled cases and standard cold dark matter (CDM) model. During matter dominated era, ordinary scalar field induces growth of structures so that it becomes faster than the standard model does, whereas phantom scalar field slows down the growth of structures. During scalar field dominated era (far in the future), we obtained that formed structures or density contrasts will decay in a similar way as in uncoupled cases, whereas following phantom scenario, the decay of formed structures occurs faster and more significant. This result is associated to background dynamics which shows that big rip will be the relevant fate of our universe.
Multiwavelength analysis of nearby ultraluminous x-ray sources (ULXs) and their environment
Authors: Vierdayanti K , Khairunnisa S A , Wulandari H 
Published: October 2019

Abstract
Ultraluminous X-ray sources (ULXs) are known as extragalactic point-like X-ray sources with luminosities considerably in excess of the maximum luminosity of a 10 solar mass accreting black hole. X-ray spectra of ULXs have been investigated in many previous studies. However, sparse observations render it more difficult to convincingly distinguish between two competing scenarios, i.e. sub-critical accreting intermediate-mass black hole and super-critical accreting stellar remnant black hole. Here, we report our investigation of a sample of nearby ULXs, as well as their host galaxies, in order to get a more complete understanding of their nature. Multiwavelength analysis was applied to study these ULXs. From X-ray study, we found that most ULXs in our sample do exhibit spectral variability in which higher energy X-ray predominates the spectra as the source becomes brighter. We also compiled some properties of the host galaxies, as a proxy of ULX environment. We found that ULXs in our sample can neither be exclusively associated with a certain type of morphology, nor with high nuclear activity. We also found that 12 out of 19 ULXs reside in host galaxies with star formation rate of less than 1 solar mass per year.
Low Energy Theorem for Kaon Photoproduction
Authors: Sakinah S. , Clymton S. , Mart T. 
Published: October 2019

Abstract
We study the Low Energy Theorem (LET) for kaon photoproduction at threshold region. To this end we expand the transition amplitude in terms of the kaon mass and the averaged mass of nucleon and Λ-hyperon. The background amplitudes are obtained from the appropriate Feynman diagrams. The amplitudes have been so far expanded up to the 3th order.
Theoretical Study of Unconventional Plasmon Generation by Solving Finite-Size 3D Hubbard Model within Mean Field Approximation
Authors: Prakasa Dedi , Majidi Muhammad Aziz 
Published: October 2019

Abstract
Recent experimental study on Strontium Niobate Oxide system has revealed unconventional plasmons generated due to confinement by oxygen planes. A phenomenological model accompanied the experimental data on that report has suggested that the confined electrons behave as harmonic oscillators. These motivate us to further study the effect of space confinement to the electrons on the formation of unconventional plasmons theoretically. For this purpose, we propose a method of modeling the generation of the unconventional plasmons in a finite system. The dynamics of correlated electrons in this confined system is described using finite-size 3D Hubbard model that is solved within mean field approximation. We study a hypothetical cubic system that consists of 5x5x5 single-orbital atoms. The calculation is done with and without incorporating the on-site Coulomb repulsion. We also consider both restricted and unrestricted mean field treatments to the calculation. Our dielectric function results show that for restricted mean field with U = 0 eV and unrestricted mean field with U ≤ 2 eV, the system is metal and only two and four unconventional plasmons found respectively. While, for U > 2 eV, it becomes insulator and shows more emergence of unconventional plasmons.