Gauge drivers for the generalized harmonic Einstein equations

The generalized harmonic representation of Einstein's equations is manifestly hyperbolic for a large class of gauge conditions. Unfortunately most of the useful gauges developed over the past several decades by the numerical relativity community are incompatible with the hyperbolicity of the equations in this form. This paper presents a new method of imposing gauge conditions that preserves hyperbolicity for a much wider class of conditions, including as special cases many of the standard ones used in numerical relativity: e.g., K freezing, Gamma freezing, Bona-Massó slicing, conformal Gamma drivers, etc. Analytical and numerical results are presented which test the stability and the effectiveness of this new gauge-driver evolution system

Visualizing Spacetime Curvature via Frame-Drag Vortexes and Tidal Tendexes II. Stationary Black Holes

When one splits spacetime into space plus time, the Weyl curvature tensor (which equals the Riemann tensor in vacuum) splits into two spatial, symmetric, traceless tensors: the tidal field $E$, which produces tidal forces, and the frame-drag field $B$, which produces differential frame dragging. In recent papers, we and colleagues have introduced ways to visualize these two fields: tidal tendex lines (integral curves of the three eigenvector fields of $E$) and their tendicities (eigenvalues of these eigenvector fields); and the corresponding entities for the frame-drag field: frame-drag vortex lines and their vorticities. These entities fully characterize the vacuum Riemann tensor. In this paper, we compute and depict the tendex and vortex lines, and their tendicities and vorticities, outside the horizons of stationary (Schwarzschild and Kerr) black holes; and we introduce and depict the black holes' horizon tendicity and vorticity (the normal-normal components of $E$ and $B$ on the horizon). For Schwarzschild and Kerr black holes, the horizon tendicity is proportional to the horizon's intrinsic scalar curvature, and the horizon vorticity is proportional to an extrinsic scalar curvature. We show that, for horizon-penetrating time slices, all these entities ($E$, $B$, the tendex lines and vortex lines, the lines' tendicities and vorticities, and the horizon tendicities and vorticities) are affected only weakly by changes of slicing and changes of spatial coordinates, within those slicing and coordinate choices that are commonly used for black holes. [Abstract is abbreviated.]Comment: 19 pages, 7 figures, v2: Changed to reflect published version (changes made to color scales in Figs 5, 6, and 7 for consistent conventions). v3: Fixed Ref

High-accuracy waveforms for binary black hole inspiral, merger, and ringdown

The first spectral numerical simulations of 16 orbits, merger, and ringdown of an equal-mass non-spinning binary black hole system are presented. Gravitational waveforms from these simulations have accumulated numerical phase errors through ringdown of ~0.1 radian when measured from the beginning of the simulation, and ~0.02 radian when waveforms are time and phase shifted to agree at the peak amplitude. The waveform seen by an observer at infinity is determined from waveforms computed at finite radii by an extrapolation process accurate to ~0.01 radian in phase. The phase difference between this waveform at infinity and the waveform measured at a finite radius of r=100M is about half a radian. The ratio of final mass to initial mass is M_f/M = 0.95162 +- 0.00002, and the final black hole spin is S_f/M_f^2=0.68646 +- 0.00004.Comment: 15 pages, 11 figures; New figure added, text edited to improve clarity, waveform made availabl

Single-cell transcriptomic analysis of bloodstream Trypanosoma brucei reconstructs cell cycle progression and developmental quorum sensing

Developmental steps in the trypanosome life-cycle involve transition between replicative and non-replicative forms specialised for survival in, and transmission between, mammalian and tsetse fly hosts. Here, using oligopeptide-induced differentiation in vitro, we model the progressive development of replicative ‘slender’ to transmissible ‘stumpy’ bloodstream form Trypanosoma brucei and capture the transcriptomes of 8,599 parasites using single cell transcriptomics (scRNA-seq). Using this framework, we detail the relative order of biological events during asynchronous development, profile dynamic gene expression patterns and identify putative regulators. We additionally map the cell cycle of proliferating parasites and position stumpy cell-cycle exit at early G1 before progression to a distinct G0 state. A null mutant for one transiently elevated developmental regulator, ZC3H20 is further analysed by scRNA-seq, identifying its point of failure in the developmental atlas. This approach provides a paradigm for the dissection of differentiation events in parasites, relevant to diverse transitions in pathogen biology

Visualizing Spacetime Curvature via Frame-Drag Vortexes and Tidal Tendexes III. Quasinormal Pulsations of Schwarzschild and Kerr Black Holes

In recent papers, we and colleagues have introduced a way to visualize the full vacuum Riemann curvature tensor using frame-drag vortex lines and their vorticities, and tidal tendex lines and their tendicities. We have also introduced the concepts of horizon vortexes and tendexes and 3-D vortexes and tendexes (regions where vorticities or tendicities are large). Using these concepts, we discover a number of previously unknown features of quasinormal modes of Schwarzschild and Kerr black holes. These modes can be classified by mode indexes (n,l,m), and parity, which can be electric [(-1)^l] or magnetic [(-1)^(l+1)]. Among our discoveries are these: (i) There is a near duality between modes of the same (n,l,m): a duality in which the tendex and vortex structures of electric-parity modes are interchanged with the vortex and tendex structures (respectively) of magnetic-parity modes. (ii) This near duality is perfect for the modes' complex eigenfrequencies (which are well known to be identical) and perfect on the horizon; it is slightly broken in the equatorial plane of a non-spinning hole, and the breaking becomes greater out of the equatorial plane, and greater as the hole is spun up; but even out of the plane for fast-spinning holes, the duality is surprisingly good. (iii) Electric-parity modes can be regarded as generated by 3-D tendexes that stick radially out of the horizon. As these "longitudinal," near-zone tendexes rotate or oscillate, they generate longitudinal-transverse near-zone vortexes and tendexes, and outgoing and ingoing gravitational waves. The ingoing waves act back on the longitudinal tendexes, driving them to slide off the horizon, which results in decay of the mode's strength. (iv) By duality, magnetic-parity modes are driven in this same manner by longitudinal, near-zone vortexes that stick out of the horizon. [Abstract abridged.]Comment: 53 pages with an overview of major results in the first 11 pages, 26 figures. v2: Very minor changes to reflect published version. v3: Fixed Ref

Application of single cell transcriptomics to kinetoplastid research

Kinetoplastid parasites are responsible for both human and animal diseases across the globe where they have a great impact on health and economic well-being. Many species and life cycle stages are difficult to study due to limitations in isolation and culture, as well as to their existence as heterogeneous populations in hosts and vectors. Single-cell transcriptomics (scRNA-seq) has the capacity to overcome many of these difficulties, and can be leveraged to disentangle heterogeneous populations, highlight genes crucial for propagation through the life cycle, and enable detailed analysis of host–parasite interactions. Here, we provide a review of studies that have applied scRNA-seq to protozoan parasites so far. In addition, we provide an overview of sample preparation and technology choice considerations when planning scRNA-seq experiments, as well as challenges faced when analysing the large amounts of data generated. Finally, we highlight areas of kinetoplastid research that could benefit from scRNA-seq technologies

An Adaptive Optics Survey of Stellar Variability at the Galactic Center

We present a $\approx 11.5$ year adaptive optics (AO) study of stellar variability and search for eclipsing binaries in the central $\sim 0.4$ pc ($\sim 10''$) of the Milky Way nuclear star cluster. We measure the photometry of 563 stars using the Keck II NIRC2 imager ($K'$-band, $\lambda_0 = 2.124 \text{ } \mu \text{m}$). We achieve a photometric uncertainty floor of $\Delta m_{K'} \sim 0.03$ ($\approx 3\%$), comparable to the highest precision achieved in other AO studies. Approximately half of our sample ($50 \pm 2 \%$) shows variability. $52 \pm 5\%$ of known early-type young stars and $43 \pm 4 \%$ of known late-type giants are variable. These variability fractions are higher than those of other young, massive star populations or late-type giants in globular clusters, and can be largely explained by two factors. First, our experiment time baseline is sensitive to long-term intrinsic stellar variability. Second, the proper motion of stars behind spatial inhomogeneities in the foreground extinction screen can lead to variability. We recover the two known Galactic center eclipsing binary systems: IRS 16SW and S4-258 (E60). We constrain the Galactic center eclipsing binary fraction of known early-type stars to be at least $2.4 \pm 1.7\%$. We find no evidence of an eclipsing binary among the young S-stars nor among the young stellar disk members. These results are consistent with the local OB eclipsing binary fraction. We identify a new periodic variable, S2-36, with a 39.43 day period. Further observations are necessary to determine the nature of this source.Comment: 69 pages, 28 figures, 12 tables. Accepted for publication in The Astrophysical Journa

Modeling the transmission and thermal emission in a pupil image behind the Keck II adaptive optics system

The design and performance of astronomical instruments depend critically on the total system throughput as well as the background emission from the sky and instrumental sources. In designing a pupil stop for background- limited imaging, one seeks to balance throughput and background rejection to optimize measurement signal-to-noise ratios. Many sources affect transmission and emission in infrared imaging behind the Keck Observatory’s adaptive optics systems, such as telescope segments, segment gaps, secondary support structure, and AO bench optics. Here we describe an experiment, using the pupil-viewing mode of NIRC2, to image the pupil plane as a function of wavelength. We are developing an empirical model of throughput and background emission as a function of position in the pupil plane. This model will be used in part to inform the optimal design of cold pupils in future instruments, such as the new imaging camera for OSIRIS

Momentum flow in black-hole binaries: II. Numerical simulations of equal-mass, head-on mergers with antiparallel spins

Research on extracting science from binary-black-hole (BBH) simulations has often adopted a "scattering matrix" perspective: given the binary's initial parameters, what are the final hole's parameters and the emitted gravitational waveform? In contrast, we are using BBH simulations to explore the nonlinear dynamics of curved spacetime. Focusing on the head-on plunge, merger, and ringdown of a BBH with transverse, antiparallel spins, we explore numerically the momentum flow between the holes and the surrounding spacetime. We use the Landau-Lifshitz field-theory-in-flat-spacetime formulation of general relativity to define and compute the density of field energy and field momentum outside horizons and the energy and momentum contained within horizons, and we define the effective velocity of each apparent and event horizon as the ratio of its enclosed momentum to its enclosed mass-energy. We find surprisingly good agreement between the horizons' effective and coordinate velocities. To investigate the gauge dependence of our results, we compare pseudospectral and moving-puncture evolutions of physically similar initial data; although spectral and puncture simulations use different gauge conditions, we find remarkably good agreement for our results in these two cases. We also compare our simulations with the post-Newtonian trajectories and near-field energy-momentum. [Abstract abbreviated; full abstract also mentions additional results.]Comment: Submitted to Phys. Rev.