A survey of spinning test particle orbits in Kerr spacetime

We investigate the dynamics of the Papapetrou equations in Kerr spacetime. These equations provide a model for the motion of a relativistic spinning test particle orbiting a rotating (Kerr) black hole. We perform a thorough parameter space search for signs of chaotic dynamics by calculating the Lyapunov exponents for a large variety of initial conditions. We find that the Papapetrou equations admit many chaotic solutions, with the strongest chaos occurring in the case of eccentric orbits with pericenters close to the limit of stability against plunge into a maximally spinning Kerr black hole. Despite the presence of these chaotic solutions, we show that physically realistic solutions to the Papapetrou equations are not chaotic; in all cases, the chaotic solutions either do not correspond to realistic astrophysical systems, or involve a breakdown of the test-particle approximation leading to the Papapetrou equations (or both). As a result, the gravitational radiation from bodies spiraling into much more massive black holes (as detectable, for example, by LISA, the Laser Interferometer Space Antenna) should not exhibit any signs of chaos.Comment: Submitted to Phys. Rev. D. Follow-up to gr-qc/0210042. Figures are low-resolution in order to satisfy archive size constraints; a high-resolution version is available at http://www.michaelhartl.com/papers

Widely-tunable mid-IR frequency comb source based on difference frequency generation

We report on a mid-infrared frequency comb source of unprecedented tunability covering the entire 3-10 {\mu}m molecular fingerprint region. The system is based on difference frequency generation in a GaSe crystal pumped by a 151 MHz Yb:fiber frequency comb. The process was seeded with Raman shifted solitons generated in a highly nonlinear suspended-core fiber with the same source. Average powers up to 1.5 mW were achieved at 4.7 {\mu}m wavelength.Comment: 3 pages, 3 figure

Orbital evolution of a particle around a black hole: II. Comparison of contributions of spin-orbit coupling and the self force

We consider the evolution of the orbit of a spinning compact object in a quasi-circular, planar orbit around a Schwarzschild black hole in the extreme mass ratio limit. We compare the contributions to the orbital evolution of both spin-orbit coupling and the local self force. Making assumptions on the behavior of the forces, we suggest that the decay of the orbit is dominated by radiation reaction, and that the conservative effect is typically dominated by the spin force. We propose that a reasonable approximation for the gravitational waveform can be obtained by ignoring the local self force, for adjusted values of the parameters of the system. We argue that this approximation will only introduce small errors in the astronomical determination of these parameters.Comment: 11 pages, 7 figure

Error threshold in the evolution of diploid organisms

The effects of error propagation in the reproduction of diploid organisms are studied within the populational genetics framework of the quasispecies model. The dependence of the error threshold on the dominance parameter is fully investigated. In particular, it is shown that dominance can protect the wild-type alleles from the error catastrophe. The analysis is restricted to a diploid analogue of the single-peaked landscape.Comment: 9 pages, 4 Postscript figures. Submitted to J. Phy. A: Mat. and Ge

Failure of RQC machinery causes protein aggregation and proteotoxic stress

Translation of messenger RNAs lacking a stop codon results in the addition of a carboxy-terminal poly-lysine tract to the nascent polypeptide, causing ribosome stalling. Non-stop proteins and other stalled nascent chains are recognized by the ribosome quality control (RQC) machinery and targeted for proteasomal degradation. Failure of this process leads to neurodegeneration by unknown mechanisms. Here we show that deletion of the E3 ubiquitin ligase Ltn1p in yeast, a key RQC component, causes stalled proteins to form detergent-resistant aggregates and inclusions. Aggregation is dependent on a C-terminal alanine/threonine tail that is added to stalled polypeptides by the RQC component, Rqc2p. Formation of inclusions additionally requires the poly-lysine tract present in non-stop proteins. The aggregates sequester multiple cytosolic chaperones and thereby interfere with general protein quality control pathways. These findings can explain the proteotoxicity of ribosome-stalled polypeptides and demonstrate the essential role of the RQC in maintaining proteostasis

Temporal and dimensional effects in evolutionary graph theory

The spread in time of a mutation through a population is studied analytically and computationally in fully-connected networks and on spatial lattices. The time, t_*, for a favourable mutation to dominate scales with population size N as N^{(D+1)/D} in D-dimensional hypercubic lattices and as N ln N in fully-connected graphs. It is shown that the surface of the interface between mutants and non-mutants is crucial in predicting the dynamics of the system. Network topology has a significant effect on the equilibrium fitness of a simple population model incorporating multiple mutations and sexual reproduction. Includes supplementary information.Comment: 6 pages, 4 figures Replaced after final round of peer revie

On a Conjecture of Rapoport and Zink

In their book Rapoport and Zink constructed rigid analytic period spaces $F^{wa}$ for Fontaine's filtered isocrystals, and period morphisms from PEL moduli spaces of $p$-divisible groups to some of these period spaces. They conjectured the existence of an \'etale bijective morphism $F^a \to F^{wa}$ of rigid analytic spaces and of a universal local system of $Q_p$-vector spaces on $F^a$. For Hodge-Tate weights $n-1$ and $n$ we construct in this article an intrinsic Berkovich open subspace $F^0$ of $F^{wa}$ and the universal local system on $F^0$. We conjecture that the rigid-analytic space associated with $F^0$ is the maximal possible $F^a$, and that $F^0$ is connected. We give evidence for these conjectures and we show that for those period spaces possessing PEL period morphisms, $F^0$ equals the image of the period morphism. Then our local system is the rational Tate module of the universal $p$-divisible group and enjoys additional functoriality properties. We show that only in exceptional cases $F^0$ equals all of $F^{wa}$ and when the Shimura group is $GL_n$ we determine all these cases.Comment: v2: 48 pages; many new results added, v3: final version that will appear in Inventiones Mathematica

SMaSH: A Benchmarking Toolkit for Human Genome Variant Calling

Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call variants from human sequencing data disagree on many of their predictions, and current methods to evaluate accuracy and computational performance are ad-hoc and incomplete. Agreement on benchmarking variant calling methods would stimulate development of genomic processing tools and facilitate communication among researchers. Results: We propose SMaSH, a benchmarking methodology for evaluating human genome variant calling algorithms. We generate synthetic datasets, organize and interpret a wide range of existing benchmarking data for real genomes, and propose a set of accuracy and computational performance metrics for evaluating variant calling methods on this benchmarking data. Moreover, we illustrate the utility of SMaSH to evaluate the performance of some leading single nucleotide polymorphism (SNP), indel, and structural variant calling algorithms. Availability: We provide free and open access online to the SMaSH toolkit, along with detailed documentation, at smash.cs.berkeley.edu

An aperture masking mode for the MICADO instrument

MICADO is a near-IR camera for the Europea ELT, featuring an extended field (75" diameter) for imaging, and also spectrographic and high contrast imaging capabilities. It has been chosen by ESO as one of the two first-light instruments. Although it is ultimately aimed at being fed by the MCAO module called MAORY, MICADO will come with an internal SCAO system that will be complementary to it and will deliver a high performance on axis correction, suitable for coronagraphic and pupil masking applications. The basis of the pupil masking approach is to ensure the stability of the optical transfer function, even in the case of residual errors after AO correction (due to non common path errors and quasi-static aberrations). Preliminary designs of pupil masks are presented. Trade-offs and technical choices, especially regarding redundancy and pupil tracking, are explained.Comment: SPIE 2014 Proceeding -- Montrea