Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.

/pdf/landscape-of-transcription-in-human-cells-2s40xrm8iy.pdf

Landscape of transcription in human cells

On September 14, 2015 at 09:50:45 UTC the two detectors of the Laser Interferometer Gravitational-Wave Observatory simultaneously observed a transient gravitational-wave signal. The signal sweeps upwards in frequency from 35 to 250 Hz with a peak gravitational-wave strain of 1.0×10(-21). It matches the waveform predicted by general relativity for the inspiral and merger of a pair of black holes and the ringdown of the resulting single black hole. The signal was observed with a matched-filter signal-to-noise ratio of 24 and a false alarm rate estimated to be less than 1 event per 203,000 years, equivalent to a significance greater than 5.1σ. The source lies at a luminosity distance of 410(-180)(+160)  Mpc corresponding to a redshift z=0.09(-0.04)(+0.03). In the source frame, the initial black hole masses are 36(-4)(+5)M⊙ and 29(-4)(+4)M⊙, and the final black hole mass is 62(-4)(+4)M⊙, with 3.0(-0.5)(+0.5)M⊙c(2) radiated in gravitational waves. All uncertainties define 90% credible intervals. These observations demonstrate the existence of binary stellar-mass black hole systems. This is the first direct detection of gravitational waves and the first observation of a binary black hole merger.

/pdf/the-observation-of-gravitational-waves-from-a-binary-black-58srpupgg9.pdf

The Observation of Gravitational Waves from a Binary Black Hole Merger

The status of experimental tests of general relativity and of theoretical frameworks for analyzing them is reviewed and updated. Einstein’s equivalence principle (EEP) is well supported by experiments such as the Eotvos experiment, tests of local Lorentz invariance and clock experiments. Ongoing tests of EEP and of the inverse square law are searching for new interactions arising from unification or quantum gravity. Tests of general relativity at the post-Newtonian level have reached high precision, including the light deflection, the Shapiro time delay, the perihelion advance of Mercury, the Nordtvedt effect in lunar motion, and frame-dragging. Gravitational wave damping has been detected in an amount that agrees with general relativity to better than half a percent using the Hulse-Taylor binary pulsar, and a growing family of other binary pulsar systems is yielding new tests, especially of strong-field effects. Current and future tests of relativity will center on strong gravity and gravitational waves.

/pdf/the-confrontation-between-general-relativity-and-experiment-5dqdube5p9.pdf

The Confrontation Between General Relativity and Experiment

This is a review of the physics and cosmology of the cosmological constant. Focusing on recent developments, I present a pedagogical overview of cosmology in the presence of a cosmological constant, observational constraints on its magnitude, and the physics of a small (and potentially nonzero) vacuum energy.

/pdf/the-cosmological-constant-4ljm1nl1cq.pdf

The Cosmological Constant

Using a two-dimensional hydrodynamics code (PROMETHEUS), we explore the continued evolution of rotating helium stars, Mα 10 M☉, in which iron-core collapse does not produce a successful outgoing shock but instead forms a black hole of 2-3 M☉. The model explored in greatest detail is the 14 M☉ helium core of a 35 M☉ main-sequence star. The outcome is sensitive to the angular momentum. For j16 ≡ j/(1016 cm2 s-1) 3, material falls into the black hole almost uninhibited. No outflows are expected. For j16 20, the infalling matter is halted by centrifugal force outside 1000 km where neutrino losses are negligible. The equatorial accretion rate is very low, and explosive oxygen burning may power a weak equatorial explosion. For 3 j16 20, however, a reasonable value for such stars, a compact disk forms at a radius at which the gravitational binding energy can be efficiently radiated as neutrinos or converted to beamed outflow by magnetohydrodynamical (MHD) processes. These are the best candidates for producing gamma-ray bursts (GRBs). Here we study the formation of such a disk, the associated flow patterns, and the accretion rate for disk viscosity parameter α ≈ 0.001 and 0.1. Infall along the rotational axis is initially uninhibited, and an evacuated channel opens during the first few seconds. Meanwhile the black hole is spun up by the accretion (to a ≈ 0.9), and energy is dissipated in the disk by MHD processes and radiated by neutrinos. For the α = 0.1 model, appreciable energetic outflows develop between polar angles of 30° and 45°. These outflows, powered by viscous dissipation in the disk, have an energy of up to a few times 1051 ergs and a mass ~1 M☉ and are rich in 56Ni. They constitute a supernova-like explosion by themselves. Meanwhile accretion through the disk is maintained for approximately 10-20 s but is time variable (±30%) because of hydrodynamical instabilities at the outer edge in a region where nuclei are experiencing photodisintegration. Because the efficiency of neutrino energy deposition is sensitive to the accretion rate, this instability leads to highly variable energy deposition in the polar regions. Some of this variability, which has significant power at 50 ms and overtones, may persist in the time structure of the burst. During the time followed, the average accretion rate for the standard α = 0.1 and j16 = 10 model is 0.07 M☉ s-1. The total energy deposited along the rotational axes by neutrino annihilation is (1-14) × 1051 ergs, depending upon the evolution of the Kerr parameter and uncertain neutrino efficiencies. Simulated deposition of energy in the polar regions, at a constant rate of 5 × 1050 ergs s-1 per pole, results in strong relativistic outflow jets beamed to about 1% of the sky. These jets may be additionally modulated by instabilities in the sides of the "nozzle" through which they flow. The jets blow aside the accreting material, remain highly focused, and are capable of penetrating the star in ~10 s. After the jet breaks through the surface of the star, highly relativistic flow can emerge. Because of the sensitivity of the mass ejection and jets to accretion rate, angular momentum, and disk viscosity, and the variation of observational consequences with viewing angle, a large range of outcomes is possible, ranging from bright GRBs like GRB 971214 to faint GRB-supernovae like SN 1998bw. X-ray precursors are also possible as the jet first breaks out of the star. While only a small fraction of supernovae make GRBs, we predict that collapsars will always make supernovae similar to SN 1998bw. However, hard, energetic GRBs shorter than a few seconds will be difficult to produce in this model and may require merging neutron stars and black holes for their explanation.

https://iopscience.iop.org/article/10.1086/307790/pdf

Collapsars: Gamma-ray bursts and explosions in 'failed supernovae'

The physics of black holes is explored in terms of a membrane paradigm which treats the event horizon as a two-dimensional membrane embedded in three-dimensional space. A 3+1 formalism is used to split Schwarzschild space-time and the laws of physics outside a nonrotating hole, which permits treatment of the atmosphere in terms of the physical properties of thin slices. The model is applied to perturbed slowly or rapidly rotating and nonrotating holes, and to quantify the electric and magnetic fields and eddy currents passing through a membrane surface which represents a stretched horizon. Features of tidal gravitational fields in the vicinity of the horizon, quasars and active galalctic nuclei, the alignment of jets perpendicular to accretion disks, and the effects of black holes at the center of ellipsoidal star clusters are investigated. Attention is also given to a black hole in a binary system and the interactions of black holes with matter that is either near or very far from the event horizon. Finally, a statistical mechanics treatment is used to derive a second law of thermodynamics for a perfectly thermal atmosphere of a black hole.

Black holes: The membrane paradigm

Nonspherical Perturbations of Relativistic Gravitational Collapse. I. Scalar and Gravitational Perturbations

We study the power-law tails in the evolution of massless fields around a fixed background geometry corresponding to a black hole. We give analytical arguments for their existence at ${\mathrm{scri}}_{+}$, at the future horizon, and at future timelike infinity. We confirm their existence with numerical integrations of the curved spacetime wave equation on the background of a Schwarzschild and a Reissner-Nordstr\"om black hole. These results are relevant to studies of mass inflation and the instability of Cauchy horizons. The analytic arguments also suggest the behavior of the full nonlinear dynamics, which we study numerically in a companion paper.

Late-time behavior of stellar collapse and explosions. I. Linearized perturbations.

This paper derives the ‘‘membrane formalism’’ for black holes. The membrane formalism rewrites the standard mathematical theory of black holes in a language and notation which (we hope) will facilitate research in black-hole astrophysics: The horizon of a black hole is replaced by a surrogate ‘‘stretched horizon,’’ which is viewed as a 2-dimensional membrane that resides in 3-dimensional space and evolves in response to driving forces from the external universe. This membrane, following ideas of Damour and Znajek, is regarded as made from a 2-dimensional viscous fluid that is electrically charged and electrically conducting and has finite entropy and temperature, but cannot conduct heat. The interaction of the stretched horizon with the external universe is described in terms of familiar laws for the horizon’s fluid, e.g., the Navier-Stokes equation, Ohm’s law, a tidal-force equation, and the first and second laws of thermodynamics. Because these laws have familiar forms, they are likely to help astrophysicists understand intuitively and compute quantitatively the behaviors of black holes in complex external environments. Previous papers have developed and elucidated electromagnetic aspects of the membrane formalism for time-independent rotating holes. This paper derives the full formalism for dynamical, evolving holes, with one exception: In its present form the formalism is not equipped to handle horizon caustics, where new generators attach themselves to the horizon.

/pdf/membrane-viewpoint-on-black-holes-properties-and-evolution-2uopt56o0t.pdf

Richard H. Price

Papers

Black holes: The membrane paradigm

Black holes: The membrane paradigm

Nonspherical Perturbations of Relativistic Gravitational Collapse. I. Scalar and Gravitational Perturbations

Late-time behavior of stellar collapse and explosions. I. Linearized perturbations.

Membrane viewpoint on black holes: Properties and evolution of the stretched horizon