cssi/SciSciGPT-SciSciNet huggingface dataset:
ari: The Automated R Instructor

We present the ari package for automatically generating technology-focused educational videos. The goal of the package is to create reproducible videos, with the ability to change and update video content seamlessly. We present several examples of generating videos including using R Markdown slide decks, PowerPoint slides, or simple images as source material. We also discuss how ari can help instructors reach new audiences through programmatically translating materials into other languages.
Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function

Background The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. Such tests cannot, however, detect changes in the function of RNA molecules. Methods Here we apply a test for branch-specific oversubstitution of mutations within narrow windows of the genome without reference to the genetic code. Results We recapitulate the finding that the gene encoding Spike protein has been a target of both purifying and positive selection. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. Homology-directed modeling indicates no change in either Nsp4 or Nsp16 protein structure relative to the most recent common ancestor. These SARS-CoV-2-specific mutations may affect molecular processes mediated by the positive or negative RNA molecules, including transcription, translation, RNA stability, and evasion of the host innate immune system. Our results highlight the importance of considering mutations in viral genomes not only from the perspective of their impact on protein structure, but also how they may impact other molecular processes critical to the viral life cycle.
Notes on Growth Accounting

Growth accounting breaks down economic growth into components associated with changes in factor inputs and the Solow residual, which reflects technological progress and other elements. After a presentation of the standard model, the analysis considers dual approaches to growth accounting (which considers changes in factor prices rather than quantities), spillover effects and increasing returns, taxes, and multiple types of factor inputs. Later sections place the growth-accounting exercise within the context of two recent strands of endogenous growth theory—varieties-of-products models and quality-ladders models. Within these settings, the Solow residual can be interpreted in terms of measures of the endogenously changing level of technology.
Insurance 4.0 and Digital Transformation

This chapter aims to demonstrate, through the exploration of essential concepts related to insurance 4.0, how crucial it is, and the possible approaches to managing insurance 4.0 successfully. The digital revolution has turned the business scenario upside-down. This chapter provides definitions of the digital transformation connected with insurance 4.0, referring to the research of some scholars and finally paying attention to the real value that digital transformation can bring to organizations and customers. This rapid and ever more relevant evolution is a phenomenon that involves every organization. (Rogers, D. L. [2016]. The digital transformation playbook: Rethink your business for the digital age. New York, NY: Columbia University Press.) This chapter also presents the significance of several enabling platforms to the digitization process and the factors affecting innovation acceptance management. This chapter details a roadmap for a successful transformation to insurance 4.0.
A Magnetized, Moon-forming Giant Impact

The Moon is believed to have formed in the aftermath of a giant impact between a planetary mass body and the proto-Earth. In a typical giant impact scenario, a disk of vapor, liquid, and solid debris forms around the proto-Earth and--after possibly decades of evolution--condenses to form the Moon. Using state-of-the-art numerical simulations, we investigate the dynamical effects of magnetic fields on the Moon-forming giant impact. We show that turbulence generated by the collision itself, shear in the boundary layer between the post-impact debris field and the proto-Earth, and turbulence in the vapor component of the disk amplify the field to dynamically significant strengths. Magnetically driven turbulence promotes angular momentum transport in the protolunar disk. Debris material is accreted onto the proto-Earth, making Moon formation less efficient, while the disk is forced to spread to larger radii, cooling at its outer edge. Magnetic fields speed the evolution of the vapor component of the protolunar disk and hasten the formation of the Moon.
On the electrodynamics of moving permanent dipoles in external electromagnetic fields

The classical theory of electrodynamics is built upon Maxwell’s equations and the concepts of electromagnetic field, force, energy and momentum, which are intimately tied together by Poynting’s theorem and the Lorentz force law. Whereas Maxwell’s macroscopic equations relate the electric and magnetic fields to their material sources (i.e., charge, current, polarization and magnetization), Poynting’s theorem governs the flow of electromagnetic energy and its exchange between fields and material media, while the Lorentz law regulates the back-and-forth transfer of momentum between the media and the fields. The close association of momentum with energy thus demands that the Poynting theorem and the Lorentz law remain consistent with each other, while, at the same time, ensuring compliance with the conservation laws of energy, linear momentum, and angular momentum. This paper shows how a consistent application of the aforementioned laws of electrodynamics to moving permanent dipoles (both electric and magnetic) brings into play the rest-mass of the dipoles. The rest mass must vary in response to external electromagnetic fields if the overall energy of the system is to be conserved. The physical basis for the inferred variations of the rest-mass appears to be an interference between the internal fields of the dipoles and the externally applied fields. We use two different formulations of the classical theory in which energy and momentum relate differently to the fields, yet we find identical behavior for the restmass in both formulations.
REFINING THE CENSUS OF THE UPPER SCORPIUS ASSOCIATION WITH GAIA

We have refined the census of stars and brown dwarfs in the Upper Sco association (~ 10 Myr, ~145 pc) by 1) updating the selection of candidate members from our previous survey to include the high-precision astrometry from the second data release of Gaia, 2) obtaining spectra of a few hundred candidate members to measure their spectral types and verify their youth, and 3) assessing the membership (largely with Gaia astrometry) of 2020 stars toward Upper Sco that show evidence of youth in this work and previous studies. We arrive at a catalog of 1761 objects that are adopted as members of Upper Sco. The distribution of spectral types among the adopted members is similar to those in other nearby star-forming regions, indicating a similar initial mass function. In previous studies, we have compiled mid-infrared photometry from WISE and the Spitzer Space Telescope for members of Upper Sco and used those data to identify the stars that show evidence of circumstellar disks; we present the same analysis for our new catalog of members. As in earlier work, we find that the fraction of members with disks increases with lower stellar masses, ranging from ≲ 10% for > 1 M ⊙ to ~ 22% for 0.01-0.3 M ⊙. Finally, we have estimated the relative ages of Upper Sco and other young associations using their sequences of low-mass stars in M G RP versus G BP - G RP. This comparison indicates that Upper Sco is a factor of two younger than the β Pic association (21-24 Myr) according to both non-magnetic and magnetic evolutionary models.
Free Energy in the Generalized Sherrington-Kirkpatrick Mean Field Model

In [11], Talagrand gave a rigorous proof of the Parisi formula in the classical Sherrington–Kirkpatrick (SK) model. In this paper, we build upon the methodology developed in [11] and extend Talagrand's result to the class of SK type models in which the spins have arbitrary prior distribution on a bounded subset of the real line.
Coordinate-friendly structures, algorithms and applications

This paper focuses on coordinate update methods, which are useful for solving problems involving large or high-dimensional datasets. They decompose a problem into simple subproblems, where each updates one, or a small block of, variables while fixing others. These methods can deal with linear and nonlinear mappings, smooth and nonsmooth functions, as well as convex and nonconvex problems. In addition, they are easy to parallelize. The great performance of coordinate update methods depends on solving simple subproblems. To derive simple subproblems for several new classes of applications, this paper systematically studies coordinate friendly operators that perform low-cost coordinate updates. Based on the discovered coordinate friendly operators, as well as operator splitting techniques, we obtain new coordinate update algorithms for a variety of problems in machine learning, image processing, as well as sub-areas of optimization. Several problems are treated with coordinate update for the first time in history. The obtained algorithms are scalable to large instances through parallel and even asynchronous computing. We present numerical examples to illustrate how effective these algorithms are.
Acoustokinetics: Crafting force landscapes from sound waves

The acoustokinetic framework expresses the acoustic radiation force acting on a small object in terms of the amplitude and phase profiles of the incident sound wave. This formulation clarifies how to control the conservative and nonconservative forces exerted by sound and how to design structured sound waves that trap, twirl and transport objects along arbitrary paths in three dimensions. The authors illustrate the design process by crafting pseudo-standing waves, alternating picket-fence force fields, and propagation-invariant tractor beams.
A MACHINE LEARNING APPROACH FOR DYNAMICAL MASS MEASUREMENTS OF GALAXY CLUSTERS

We present a modern machine learning approach for cluster dynamical mass measurements that is a factor of two improvement over using a conventional scaling relation. Different methods are tested against a mock cluster catalog constructed using halos with mass >= 10^14 Msolar/h from Multidark's publicly-available N-body MDPL halo catalog. In the conventional method, we use a standard M(sigma_v) power law scaling relation to infer cluster mass, M, from line-of-sight (LOS) galaxy velocity dispersion, sigma_v. The resulting fractional mass error distribution is broad, with width=0.87 (68% scatter), and has extended high-error tails. The standard scaling relation can be simply enhanced by including higher-order moments of the LOS velocity distribution. Applying the kurtosis as a correction term to log(sigma_v) reduces the width of the error distribution to 0.74 (16% improvement). Machine learning can be used to take full advantage of all the information in the velocity distribution. We employ the Support Distribution Machines (SDMs) algorithm that learns from distributions of data to predict single values. SDMs trained and tested on the distribution of LOS velocities yield width=0.46 (47% improvement). Furthermore, the problematic tails of the mass error distribution are effectively eliminated. Decreasing cluster mass errors will improve measurements of the growth of structure and lead to tighter constraints on cosmological parameters.
The effect of material defects on resonant spin wave modes in a nanomagnet

We have theoretically studied how resonant spin wave modes in an elliptical nanomagnet are affected by fabrication defects, such as small local thickness variations. Our results indicate that defects of this nature, which can easily result from the fabrication process, or are sometimes deliberately introduced during the fabrication process, will significantly alter the frequencies, magnetic field dependence of the frequencies, and the power and phase profiles of the resonant spin wave modes. They can also spawn new resonant modes and quench existing ones. All this has important ramifications for multi-device circuits based on spin waves, such as phase locked oscillators for neuromorphic computing, where the device-to-device variability caused by defects can be inhibitory.
Reheating in two-sector cosmology

We analyze reheating scenarios where a hidden sector is populated during reheating along with the sector containing the Standard Model. We numerically solve the Boltzmann equations describing perturbative reheating of the two sectors, including the full dependence on quantum statistics, and study how quantum statistical effects during reheating as well as the non-equilibrium inflaton-mediated energy transfer between the two sectors affects the temperature evolution of the two radiation baths. We obtain new power laws describing the temperature evolution of fermions and bosons when quantum statistics are important during reheating. We show that inflaton-mediated scattering is generically most important at radiation temperatures T ∼ Mϕ/4, and build on this observation to obtain analytic estimates for the temperature asymmetry produced by asymmetric reheating. We find that for reheating temperatures Trh ≪ Mϕ/4, classical perturbative reheating provides an excellent approximation to the final temperature asymmetry, while for Trh ≫ Mϕ/4, inflaton-mediated scattering dominates the population of the colder sector and thus the final temperature asymmetry. We additionally present new techniques to calculate energy transfer rates between two relativistic species at different temperatures.
Symbolic Execution + Model Counting + Entropy Maximization = Automatic Search Synthesis

We present a method of automatically synthesizing steps to solve search problems. Given a specification of a search problem, our approach uses symbolic execution to analyze the specification in order to extract a set of constraints which model the problem. These constraints are used in a process called model counting, which is leveraged to compute probability distributions relating search steps to predicates about an unknown target. The probability distribution functions determine an information gain objective function based on Shannon entropy, which, when maximized, yields the next optimal step of the search. We prove that our algorithm converges to a correct solution, and discuss computational complexity issues. We implemented a domain specific language in which to write search problem specifications, enabling our static analysis phase. Our experiments demonstrate the effectiveness of our approach on a set of search problem case studies inspired by the domains of software security, computational geometry, AI for games, and user preference ranking.
Observed Effect of Magnetic Fields on the Propagation of Magnetoacoustic Waves in the Lower Solar Atmosphere

We study Hinode/SOT-FG observations of intensity fluctuations in Ca ii H-line and G-band image sequences and their relation to simultaneous and co-spatial magnetic field measurements. We explore the G-band and H-line intensity oscillation spectra both separately and comparatively via their relative phase differences, time delays and cross-coherences. In the non-magnetic situations, both sets of fluctuations show strong oscillatory power in the 3 – 7 mHz band centered at 4.5 mHz, but this is suppressed as magnetic field increases. A relative phase analysis gives a time delay of H-line after G-band of 20±1 s in non-magnetic situations implying a mean effective height difference of 140 km. The maximum coherence is at 4 – 7 mHz. Under strong magnetic influence the measured delay time shrinks to 11 s with the peak coherence near 4 mHz. A second coherence maximum appears between 7.5 – 10 mHz. Investigation of the locations of this doubled-frequency coherence locates it in diffuse rings outside photospheric magnetic structures. Some possible interpretations of these results are offered.
Theory of chemical kinetics and charge transfer based on nonequilibrium thermodynamics.

Advances in the fields of catalysis and electrochemical energy conversion often involve nanoparticles, which can have kinetics surprisingly different from the bulk material. Classical theories of chemical kinetics assume independent reactions in dilute solutions, whose rates are determined by mean concentrations. In condensed matter, strong interactions alter chemical activities and create variations that can dramatically affect the reaction rate. The extreme case is that of a reaction coupled to a phase transformation, whose kinetics must depend not only on the order parameter but also on its gradients at phase boundaries. Reaction-driven phase transformations are common in electrochemistry, when charge transfer is accompanied by ion intercalation or deposition in a solid phase. Examples abound in Li-ion, metal–air, and lead–acid batteries, as well as metal electrodeposition–dissolution. Despite complex thermodynamics, however, the standard kinetic model is the Butler–Volmer equation, based on a dilute s...
Instability and dynamics of volatile thin films

Volatile viscous fluids on partially-wetting solid substrates can exhibit interesting dynamics and interfacial instabilities. A study of vapor condensation and fluid evaporation in a one-sided lubrication model incorporating surface tension, intermolecular effects, and evaporative fluxes is presented.
Absence of Physical walls in hot gauge theories

This paper shows that there are no physical walls in the deconfined, high-temperature phase of Z(2) lattice gauge theory. In a Hamiltonian formulation, the interface in the Wilson lines is not physical. The line interface and its energy are interpreted in terms of physical variables. They are associated with a difference between two partition functions. One includes only the configurations with even flux across the interface. The other is restricted to odd flux.
Resolvent Methods for Quantum Walks with an Application to a Thue–Morse Quantum Walk

In this expository note, we discuss spatially inhomogeneous quantum walks in one dimension and describe a genre of mathematical methods that enables one to translate information about the time-independent eigenvalue equation for the unitary generator into dynamical estimates for the corresponding quantum walk. To illustrate the general methods, we show how to apply them to a 1D coined quantum walk whose coins are distributed according to an element of the Thue--Morse subshift.
Machine-learning-based interatomic potential for phonon transport in perfect crystalline Si and crystalline Si with vacancies

We report that the single interatomic potential, developed using Gaussian regression of data from density functional theory calculations, has high accuracy and flexibility to describe phonon transport with ab initio accuracy in two different atomistic configurations: perfect crystalline Si and crystalline Si with vacancies. The high accuracies of second- and third-order force constants from the Gaussian approximation potential (GAP) are demonstrated with phonon dispersion, Gr\"uneisen parameter, three-phonon scattering rate, phonon-vacancy scattering rate, and thermal conductivity, all of which are very close to the results from density functional theory calculations. We also show that the widely used empirical potentials (Stillinger-Weber and Tersoff) produce much larger errors compared to the GAP. The computational cost of GAP is higher than the two empirical potentials, but five orders of magnitude lower than density functional theory calculations. Our work shows that GAP can provide a new opportunity for studying phonon transport in partially disordered crystalline phases with the high predictive power of ab initio calculation but at a feasible computational cost.
A POLYNOMIAL INVARIANT FOR LINKS IN LENS SPACES

We prove the existence of a polynomial invariant that satisfies the HOMFLY skein relation for links in a lens space. In the process we also develop a skein theory of toroidal grid diagrams in a lens space.
On Reliability of Underwater Magnetic Induction Communications with Tri-Axis Coils

Underwater magnetic induction communication (UWMIC) provides a low-power and high-throughput solution for autonomous underwater vehicles (AUVs). UWMIC with tri-axis coils increases the reliability of wireless channel by exploring the coil orientation diversity. However, the UWMIC channel is different from typical fading channels and the mutual inductance information (MII) is not always available. It is not clear the performance of the tri-axis coil MIMO without MII. Also, its performances with multiple users have not been investigated. In this paper, we analyze the reliability and multiplexing gain of UWMIC with tri-axis coils by using coil selection. We optimally select the transmit and receive coils to reduce the computation complexity and power consumption and explore the diversity for multiple users. We find that without using all the coils and MII, we can still achieve reliability. Also, the multiplexing gain of UWMIC without MII is 5 dB smaller than typical terrestrial fading channels. The results of this paper provide a more power-efficient way to use UWMIC with tri-axis coils.
The centered dual and the maximal injectivity radius of hyperbolic surfaces

We give sharp upper bounds on the maximal injectivity radius of finite-area hyperbolic surfaces and use them, for each g 2, to identify a constant rg 1;2 such that the set of closed genus-g hyperbolic surfaces with maximal injectivity radius at least r is compact if and only if r > rg 1;2 . The main tool is a version of the centered dual complex that we introduced earlier, a coarsening of the Delaunay complex. In particular, we bound the area of a compact centered dual two-cell below given lower bounds on its side lengths. 52C15, 57M50 This paper analyzes the centered dual complex of a locally finite subset S of H 2 , first introduced in our prior preprint [6], and applies it to describe the maximal injectivity radius of hyperbolic surfaces. The centered dual complex is a cell decomposition with vertex set S and totally geodesic edges. Its underlying space contains that of the geometric dual to the Voronoi tessellation. We regard it as a tool for understanding the geometry of packings. The rough idea behind the construction is that geometric dual 2‐cells that are not centered (see Definition 0.2) are hard to analyze individually but naturally group into larger cells that can be treated as units. Our first main theorem bears the fruit of this approach, turning a lower bound on edge lengths into a good lower bound on area for centered dual 2‐cells.
REMEDIAL EDUCATION AND STUDENT ACHIEVEMENT: A REGRESSION-DISCONTINUITY ANALYSIS

As standards and accountability have become increasingly prominent features of the educational landscape, educators have relied more on remedial programs such as summer school and grade retention to help low-achieving students meet minimum academic standards. Yet the evidence on the effectiveness of such programs is mixed, and prior research suffers from selection bias. However, recent school reform efforts in Chicago provide an opportunity to examine the causal impact of these remedial education programs. In 1996, the Chicago Public Schools instituted an accountability policy that tied summer school and promotional decisions to performance on standardized tests, which resulted in a highly nonlinear relationship between current achievement and the probability of attending summer school or being retained. Using a regression discontinuity design, we find that the net effect of these programs was to substantially increase academic achievement among third-graders, but not sixth-graders. In addition, contrary ...
Scale Transformations on the Noncommutative Plane and the Seiberg-Witten Map

We write down three kinds of scale transformations (i)–(iii) on the noncommutative plane. Transformation (i) is the analogue of standard dilations on the plane, transformation (ii) is a rescaling of the noncommutative parameter θ, and transformation (iii) is a combination of the previous two, whereby the defining relations for the noncommutative plane are preserved. The action of the three transformations is defined on gauge fields evaluated at fixed coordinates and θ. The transformations are obtained only up to terms which transform covariantly under gauge transformations. We give possible constraints on these terms. We show how the transformations (i) and (ii) depend on the choice of star product, and show the relation of (ii) to Seiberg–Witten transformations. Because transformation (iii) preserves the fundamental commutation relations it is a symmetry of the algebra. One has the possibility of implementing it as a symmetry of the dynamics, as well, in noncommutative field theories where θ is not fixed.
CLASSICAL AND VIRTUAL PSEUDODIAGRAM THEORY AND NEW BOUNDS ON UNKNOTTING NUMBERS AND GENUS

A pseudodiagram is a diagram of a knot with some crossing information missing. We review and expand the theory of pseudodiagrams introduced by Hanaki. We then extend this theory to the realm of virtual knots, a generalization of knots. In particular, we analyze the trivializing number of a pseudodiagram, i.e. the minimum number of crossings that must be resolved to produce the unknot. We consider how much crossing information is needed in a virtual pseudodiagram to identify a non-trivial knot, a classical knot, or a non-classical knot. We then apply pseudodiagram theory to develop new upper bounds on unknotting number, virtual unknotting number, and genus.
Optimal regulation of protein degradation to schedule cellular events with precision

An important event in many cellular contexts is the crossing of a prescribed threshold by a regulatory protein. The timing of such events is stochastic as a consequence of the innate randomness in gene expression. A question of interest is to understand how gene expression is regulated to achieve precision in event timing. To address this, we model event timing using a first-passage time framework. The protein evolution is described via a simple stochastic model of gene expression. Moreover, feedback regulation of the protein degradation is considered to be a possible noise control mechanism employed to achieve the precision. Exact analytical formulas are developed for the distribution and moments of the first-passage time. Using these expressions, we investigate for the optimal feedback strategy such that noise (coefficient of variation squared) in event timing is minimized around a given fixed mean time. Our results show that the minimum noise is achieved when the protein degradation rate is zero for all protein levels. Lastly, the implications of this finding are discussed.
Early-time spectra of supernovae and their precursor winds. The luminous blue variable/yellow hypergiant progenitor of SN 2013cu

We present the first quantitative spectroscopic modeling of an early-time supernova (SN) that interacts with its progenitor wind. Using the radiative transfer code CMFGEN, we investigate the recently reported 15.5 h post-explosion spectrum of the type IIb SN 2013cu. We are able to directly measure the chemical abundances of a SN progenitor and find a relatively H-rich wind, with H and He abundances (by mass) of X = 0.46 ± 0.2 and Y = 0.52 ± 0.2, respectively. The wind is enhanced in N and depleted in C relative to solar values (mass fractions of 8.2 × 10-3 and 1.0 × 10-5 , respectively). We obtain that a slow, dense wind or circumstellar medium surrounds the precursor at the pre-SN stage, with a wind terminal velocity v wind ≲ 100 km s-1 and mass-loss rate of Ṁ ≃ 3 × 10-3 (v wind / 100 km s-1 ) M ⊙ yr-1 . These values are lower than previous analytical estimates, although Ṁ /υ ∞ is consistent with previous work. We also compute a CMFGEN model to constrain the progenitor spectral type; the high Ṁ and low v wind imply that the star had an effective temperature of ≃ 8000 K immediately before the SN explosion. Our models suggest that the progenitor was either an unstable luminous blue variable or a yellow hypergiant undergoing an eruptive phase, and rule out a Wolf-Rayet star. We classify the post-explosion spectra at 15.5 h as XWN5(h) and advocate for the use of the prefix “X” (eXplosion) to avoid confusion between post-explosion, non-stellar spectra, and those of massive stars. We show that the XWN spectrum results from the ionization of the progenitor wind after the SN, and that the progenitor spectral type is significantly different from the early post-explosion spectral type owing to the huge differences in the ionization structure before and after the SN event. We find the following temporal evolution: LBV/YHG → XWN5(h) → SN IIb. Future early-time spectroscopy in the UV will further constrain the properties of SN precursors, such as their metallicities.
Self-consistent Ion Cyclotron Anisotropy-Beta Relation for Solar Wind Protons

We derive a set of self-consistent marginally stable states for a system of ion-cyclotron waves propagating parallel to the large-scale magnetic field through a homogeneous proton-electron plasma. The proton distributions and the wave dispersions are related through the condition that no further ion-cyclotron resonant particle scattering or wave growth/damping may take place. The thermal anisotropy of the protons in these states therefore defines the threshold value for triggering the proton-cyclotron anisotropy instability. A number of recent papers have noted that the anisotropy of solar wind protons at 1 AU does not seem to be limited by the proton-cyclotron anisotropy threshold, even at low plasma beta. However, this puzzle seems to be due solely to the estimation of this anisotropy threshold under the assumption that the protons have a bi-Maxwellian distribution. We note that bi-Maxwellian distributions are never marginally stable to the resonant cyclotron interaction, so these estimates do not represent physically valid thresholds. The threshold anisotropies obtained from our marginally stable states are much larger, as a function of proton parallel beta, than the bi-Maxwellian estimates, and we show that the measured data remains below these more rigorous thresholds. Thus, the results of this paper resolve the apparent contradiction presented by the solar wind anisotropy observations at 1 AU: the bi-Maxwellian anisotropies are not rigorous thresholds, and so do not limit the proton distributions in the solar wind.
Towards Run Time Estimation of the Gaussian Chemistry Code for SEAGrid Science Gateway

Accurate estimation of the run time of computational codes has a number of significant advantages for scientific computing. It is required information for optimal resource allocation, improving turnaround times and utilization of science gateways. Furthermore, it allows users to better plan and schedule their research, streamlining workflows and improving the overall productivity of cyberinfrastructure. Predicting run time is challenging, however. The inputs to scientific codes can be complex and high dimensional. Their relationship to the run time may be highly non-linear, and, in the most general case is completely arbitrary and thus unpredictable (i.e., simply a random mapping from inputs to run time). Most codes are not so arbitrary, however, and there has been significant prior research on predicting the run time of applications and workloads. Such predictions are generally application-specific, however. In this paper, we focus on the Gaussian computational chemistry code. We characterize a data set of runs from the SEAGrid science gateway with a number of different studies. We also explore a number of different potential regression methods and present promising future directions.
Inspecting the Higgs for new weakly interacting particles

We explore new physics scenarios which are optimally probed through precision Higgs measurements rather than direct collider searches. Such theories consist of additional electroweak charged or singlet states which couple directly to or mix with the Higgs boson; particles of this kind may be weakly constrained by direct limits due to their meager production rates and soft decay products. We present a simplified framework which characterizes the effects of these states on Higgs physics by way of tree level mixing (with neutral scalars) and loop level modifications (from electrically charged states), all expressed in terms of three mixing angles and three loop parameters, respectively. The theory parameters are constrained and in some cases even fixed by ratios of Higgs production and decay rates. Our setup is simpler than a general effective operator analysis, in that we discard parameters irrelevant to Higgs observables while retaining complex correlations among measurements that arise due to the underlying mixing and radiative effects. We show that certain correlated observations are forbidden, e.g. a depleted ratio of Higgs production from gluon fusion versus vector boson fusion together with a depleted ratio of Higgs decays to bb[over-bar] versus WW. Moreover, we study the strong correlation between the Higgs decay rate to γγ and WW and how it can be violated in the presence of additional electrically charged particles. Our formalism maps straightforwardly onto a variety of new physics models, such as the NMSSM. We show, for example, that with a Higgsino of mass m_(χ ± 1) ≳ 100 GeV and a singlet-Higgs coupling of λ = 0.7, the photon signal strength can deviate from the vector signal strength by up to ∼ 40 − 60% while depleting the vector signal strength by only 5 − 15% relative to the Standard Model.
Indefinite Morse 2-functions; broken fibrations and generalizations

A Morse 2–function is a generic smooth map from a smooth manifold to a surface. In the absence of definite folds (in which case we say that the Morse 2–function is indefinite), these are natural generalizations of broken (Lefschetz) fibrations. We prove existence and uniqueness results for indefinite Morse 2–functions mapping to arbitrary compact, oriented surfaces. “Uniqueness” means there is a set of moves which are sufficient to go between two homotopic indefinite Morse 2–functions while remaining indefinite throughout. We extend the existence and uniqueness results to indefinite, Morse 2–functions with connected fibers.
The volume of the past light-cone and the Paneitz operator

We study a conjecture involving the invariant volume of the past light-cone from an arbitrary observation point back to a fixed initial value surface. The conjecture is that a fourth order differential operator which occurs in the theory of conformal anomalies gives 8π when acted upon the invariant volume of the past light-cone. We show that an extended version of the conjecture is valid for an arbitrary homogeneous and isotropic geometry. First order perturbation theory about flat spacetime reveals a violation of the conjecture which, however, vanishes for any vacuum solution of the Einstein equation. These results may be significant for constructing quantum gravitational observables, for quantifying the back-reaction on spacetime expansion and for alternate gravity models which feature a timelike vector field.
STATISTICAL ANALYSIS OF CURRENT SHEETS IN THREE-DIMENSIONAL MAGNETOHYDRODYNAMIC TURBULENCE

We develop a framework for studying the statistical properties of current sheets in numerical simulations of magnetohydrodynamic (MHD) turbulence with a strong guide field, as modeled by reduced MHD. We describe an algorithm that identifies current sheets in a simulation snapshot and then determines their geometrical properties (including length, width, and thickness) and intensities (peak current density and total energy dissipation rate). We then apply this procedure to simulations of reduced MHD and perform a statistical analysis on the obtained population of current sheets. We evaluate the role of reconnection by separately studying the populations of current sheets which contain magnetic X-points and those which do not. We find that the statistical properties of the two populations are different in general. We compare the scaling of these properties to phenomenological predictions obtained for the inertial range of MHD turbulence. Finally, we test whether the reconnecting current sheets are consistent with the Sweet-Parker model.
A Puzzle about Further Facts

In metaphysics, there are a number of distinct but related questions about the existence of “further facts”—facts that are contingent relative to the physical structure of the universe. These include further facts about qualia, personal identity, and time. In this article I provide a sequence of examples involving computer simulations, ranging from one in which the protagonist can clearly conclude such further facts exist to one that describes our own condition. This raises the question of where along the sequence (if at all) the protagonist stops being able to soundly conclude that further facts exist.
Transient Trapping into Metastable States in Systems with Competing Orders

A difference in the relaxation timescales of competing orders in a system allows one to drive the system into metastable states not accessible in equilibrium.
Consequences of a dark disk for the Fermi and PAMELA signals in theories with a Sommerfeld enhancement

Much attention has been given to dark matter explanations of the PAMELA positron fraction and Fermi electronic excesses. For those theories with a TeV-scale WIMP annihilating through a light force-carrier, the associated Sommerfeld enhancement provides a natural explanation of the large boost factor needed to explain the signals, and the light force-carrier naturally gives rise to hard cosmic ray spectra without excess π0-gamma rays or anti-protons. The Sommerfeld enhancement of the annihilation rate, which at low relative velocities vrel scales as 1/vrel, relies on the comparatively low velocity dispersion of the dark matter particles in the smooth halo. Dark matter substructures in which the velocity dispersion is smaller than in the smooth halo have even larger annihilation rates. N-body simulations containing only dark matter predict the existence of such structures, for example subhalos and caustics, and the effects of these substructures on dark matter indirect detection signals have been studied extensively. The addition of baryons into cosmological simulations of disk-dominated galaxies gives rise to an additional substructure component, a dark disk. The disk has a lower velocity dispersion than the spherical halo component by a factor ~ 6, so the contributions to dark matter signals from the disk can be more significant in Sommerfeld models than for WIMPs without such low-velocity ehancements. We consider the consequences of a dark disk on the observed signals of e+e−, p and γ-rays as measured by Fermi and PAMELA in models where the WIMP annihilations are into a light boson. We find that both the PAMELA and Fermi results are easily accomodated by scenarios in which a disk signal is included with the standard spherical halo signal. If contributions from the dark disk are important, limits from extrapolations to the center of the galaxy contain significant uncertainties beyond those from the spherical halo profile alone.
Accurate force field for molybdenum by machine learning large materials data

In this work, we present a highly accurate spectral neighbor analysis potential (SNAP) model for molybdenum (Mo) developed through the rigorous application of machine learning techniques on large materials data sets. Despite Mo's importance as a structural metal, existing force fields for Mo based on the embedded atom and modified embedded atom methods do not provide satisfactory accuracy on many properties. We will show that by fitting to the energies, forces, and stress tensors of a large density functional theory (DFT)-computed dataset on a diverse set of Mo structures, a Mo SNAP model can be developed that achieves close to DFT accuracy in the prediction of a broad range of properties, including elastic constants, melting point, phonon spectra, surface energies, grain boundary energies, etc. We will outline a systematic model development process, which includes a rigorous approach to structural selection based on principal component analysis, as well as a differential evolution algorithm for optimizing the hyperparameters in the model fitting so that both the model error and the property prediction error can be simultaneously lowered. We expect that this newly developed Mo SNAP model will find broad applications in large and long-time scale simulations.
Diskoseismology and QPOs Confront Black Hole Spin

We compare the determinations of the angular momentum of stellar mass black holes via the continuum and line methods with those from diskoseismology. The assumption that is being tested is that one of the quasi-periodic oscillations (QPOs) in each binary X-ray source is produced by the fundamental g-mode. This should be the most robust and visible normal mode of oscillation of the accretion disk, and therefore its absence should rule out diskoseismology as the origin of QPOs. The comparisons are consistent with the second highest frequency QPO being produced by this g-mode, but are not consistent with models in which one QPO frequency is that of the innermost stable circular orbit.
A simple adaptive estimator of the integrated square of a density

Given an i.i.d. sample $X_1, …, X_n$ with common bounded density $f_0$ belonging to a Sobolev space of order $α$ over the real line, estimation of the quadratic functional $∫_ℝf_0^2(x) \mathrm{d}x$ is considered. It is shown that the simplest kernel-based plug-in estimator $$\frac{2}{n(n-1)h_{n}} \sum_{1\leq i 1/4$ and rate-optimal if $α≤1/4$. A data-driven rule to choose the bandwidth $h_n$ is then proposed, which does not depend on prior knowledge of $α$, so that the corresponding estimator is rate-adaptive for $α≤1/4$ and asymptotically efficient if $α>1/4$.
Simplifying complex software assembly: the component retrieval language and implementation

Assembling simulation software along with the associated tools and utilities is a challenging endeavor, particularly when the components are distributed across multiple source code versioning systems. It is problematic for researchers compiling and running the software across many different supercomputers, as well as for novices in a field who are often presented with a bewildering list of software to collect and install.In this paper, we describe a language (CRL) for specifying software components with the details needed to obtain them from source code repositories. The language supports public and private access. We describe a tool called Get Components which implements CRL and can be used to assemble software.We demonstrate the tool for application scenarios with the Cactus Framework on the NSF TeraGrid resources. The tool itself is distributed with an open source license and freely available from our web page.
Currents and moduli in the (4,0) theory

We consider black strings in five dimensions and their description as a (4,0) CFT. The CFT moduli space is described explicitly, including its subtle global structure. BPS conditions and global symmetries determine the spectrum of charged excitations, leading to an entropy formula for near-extreme black holes in four dimensions with arbitrary charge vector. In the BPS limit, this formula reduces to the quartic E7(7) invariant. The prospects for a description of the (4,0) theory as a solvable CFT are explored.
From few- to many-body quantum systems

This work was funded by the American National Science Foundation (NSF) Grant No. DMR-1603418
State and Parameter Estimation for Natural Gas Pipeline Networks Using Transient State Data

We formulate two estimation problems for pipeline systems in which measurements of the compressible gas flowing through a network of pipes are affected by time-varying injections, withdrawals, and compression. We consider a state estimation problem that is then extended to a joint state and parameter estimation problem that can be used for data assimilation. In both formulations, the flow dynamics are described on each pipe by space- and time-dependent densities and mass flux which evolve according to a system of coupled partial differential equations, in which momentum dissipation is modeled using the Darcy–Wiesbach friction approximation. These dynamics are first spatially discretized to obtain a system of nonlinear ordinary differential equations on which state and parameter estimation formulations are given as nonlinear least squares problems. A rapid, scalable computational method for performing a nonlinear least squares estimation is developed. Extensive simulations and computational experiments on multiple pipeline test networks demonstrate the effectiveness of the formulations in obtaining state and parameter estimates in the presence of measurement and process noise.
MAGNETOHYDRODYNAMIC SIMULATIONS OF HOT JUPITER UPPER ATMOSPHERES

Two-dimensional simulations of hot Jupiter upper atmospheres including the planet's magnetic field are presented. The goal is to explore magnetic effects on the layer of the atmosphere that is ionized and heated by stellar EUV radiation, and the imprint of these effects on the Lyα transmission spectrum. The simulations are axisymmetric, isothermal, and include both rotation and azimuth-averaged stellar tides. Mass density is converted to atomic hydrogen density through the assumption of ionization equilibrium. The three-zone structure—polar dead zone (DZ), mid-latitude wind zone (WZ), and equatorial DZ—found in previous analytic calculations is confirmed. For a magnetic field comparable to that of Jupiter, the equatorial DZ, which is confined by the magnetic field and corotates with the planet, contributes at least half of the transit signal. For even stronger fields, the gas escaping in the mid-latitude WZ is found to have a smaller contribution to the transit depth than the equatorial DZ. Transmission spectra computed from the simulations are compared to Hubble Space Telescope Space Telescope Imaging Spectrograph and Advanced Camera for Surveys data for HD 209458b and HD 189733b, and the range of model parameters consistent with the data is found. The central result of this paper is that themore » transit depth increases strongly with magnetic field strength when the hydrogen ionization layer is magnetically dominated, for dipole magnetic field B {sub 0} ≳ 10 G. Hence transit depth is sensitive to magnetic field strength, in addition to standard quantities such as the ratio of thermal to gravitational binding energies. Another effect of the magnetic field is that the planet loses angular momentum orders of magnitude faster than in the non-magnetic case, because the magnetic field greatly increases the lever arm for wind braking of the planet's rotation. Spin-down timescales for magnetized models of HD 209458b that agree with the observed transit depth can be as short as ≅ 30 Myr, which is much shorter than the age of the system.« less