CSM-427: Coarse Graining in an Evolutionary Algorithm with Recombination, Duplication and Inversion

A generalised form of recombination, wherein an offspring can be formed from any of the genetic material of the parents, is analysed in the context of a two-locus recombinative GA. A complete, exact solution, is derived, showing how the dynamical behaviour is radically different to that of homologous crossover. Inversion is shown to potentially introduce oscillations in the dynamics, while gene duplication leads to an asymmetry between homogeneous and heterogeneous strings. All non-homologous operators lead to allele ?diffusion? along the chromosome. We discuss how inferences from the two-locus results extend to the case of a recombinative GA with selection and more than two loci

CSM-426: Theoretical Analysis of Generalised Recombination

In this paper we propose, model theoretically and study a general notion of recombination for fixed-length strings where homologous crossover, inversion, gene duplication, gene deletion, diploidy and more are just special cases. The analysis of the model reveals similarities and differences between genetic systems based on these operations. It also reveals that the notion of schema emerges naturally from the model?s equations even for the strangest of recombination operations. The study provides a variety of fixed points for the case where recombination is used alone, which generalise Geiringer?s theorem

The Drosophila simulans Y chromosome interacts with the autosomes to influence male fitness.

This is the author's accepted manuscriptThe final version is available from Wiley via the DOI in this recordThe Y chromosome should degenerate because it cannot recombine. However, male limited transmission increases selection efficiency for male benefit alleles on the Y, and therefore Y-chromosomes should contribute significantly to variation in male-fitness. This means that although the Drosophila Y chromosome is small and gene-poor, Y-linked genes are vital for male fertility in D. melanogaster and the Y chromosome has large male-fitness effects. It is unclear if the same pattern is seen in the closely related D. simulans. We backcrossed Y chromosomes from 3 geographic locations into 5 genetic backgrounds and found strong Y and genetic background effects on male fertility. There was a significant Y-background interaction, indicating substantial epistasis between the Y and autosomal genes affecting male fertility. This supports accumulating evidence that interactions between the Y chromosome and the autosomes are key determinants of male fitness. This article is protected by copyright. All rights reserved.DJH was funded by The Leverhulme Trust

Complementarity Endures: No Firewall for an Infalling Observer

We argue that the complementarity picture, as interpreted as a reference frame change represented in quantum gravitational Hilbert space, does not suffer from the "firewall paradox" recently discussed by Almheiri, Marolf, Polchinski, and Sully. A quantum state described by a distant observer evolves unitarily, with the evolution law well approximated by semi-classical field equations in the region away from the (stretched) horizon. And yet, a classical infalling observer does not see a violation of the equivalence principle, and thus a firewall, at the horizon. The resolution of the paradox lies in careful considerations on how a (semi-)classical world arises in unitary quantum mechanics describing the whole universe/multiverse.Comment: 11 pages, 1 figure; clarifications and minor revisions; v3: a small calculation added for clarification; v4: some corrections, conclusion unchange

The hidden horizon and black hole unitarity

We motivate through a detailed analysis of the Hawking radiation in a Schwarzschild background a scheme in accordance with quantum unitarity. In this scheme the semi-classical approximation of the unitary quantum - horizonless - black hole S-matrix leads to the conventional description of the Hawking radiation from a classical black hole endowed with an event horizon. Unitarity is borne out by the detailed exclusive S-matrix amplitudes. There, the fixing of generic out-states, in addition to the in-state, yields in asymptotic Minkowski space-time saddle-point contributions which are dominated by Planckian metric fluctuations when approaching the Schwarzschild radius. We argue that these prevent the corresponding macroscopic "exclusive backgrounds" to develop an event horizon. However, if no out-state is selected, a distinct saddle-point geometry can be defined, in which Planckian fluctuations are tamed. Such "inclusive background" presents an event horizon and constitutes a coarse-grained average over the aforementioned exclusive ones. The classical event horizon appears as a coarse-grained structure, sustaining the thermodynamic significance of the Bekenstein-Hawking entropy. This is reminiscent of the tentative fuzzball description of extremal black holes: the role of microstates is played here by a complete set of out-states. Although the computations of unitary amplitudes would require a detailed theory of quantum gravity, the proposed scheme itself, which appeals to the metric description of gravity only in the vicinity of stationary points, does not.Comment: 29 pages, 4 figures. Typos corrected. Two footnotes added (footnotes 3 and 5

Entropy bounds in terms of the w parameter

In a pair of recent articles [PRL 105 (2010) 041302 - arXiv:1005.1132; JHEP 1103 (2011) 056 - arXiv:1012.2867] two of the current authors have developed an entropy bound for equilibrium uncollapsed matter using only classical general relativity, basic thermodynamics, and the Unruh effect. An odd feature of that bound, S <= A/2, was that the proportionality constant, 1/2, was weaker than that expected from black hole thermodynamics, 1/4. In the current article we strengthen the previous results by obtaining a bound involving the (suitably averaged) w parameter. Simple causality arguments restrict this averaged parameter to be <= 1. When equality holds, the entropy bound saturates at the value expected based on black hole thermodynamics. We also add some clarifying comments regarding the (net) positivity of the chemical potential. Overall, we find that even in the absence of any black hole region, we can nevertheless get arbitrarily close to the Bekenstein entropy.Comment: V1: 14 pages. V2: One reference added. V3: This version accepted for publication in JHE

The Stokes Phenomenon and Quantum Tunneling for de Sitter Radiation in Nonstationary Coordinates

We study quantum tunneling for the de Sitter radiation in the planar coordinates and global coordinates, which are nonstationary coordinates and describe the expanding geometry. Using the phase-integral approximation for the Hamilton-Jacobi action in the complex plane of time, we obtain the particle-production rate in both coordinates and derive the additional sinusoidal factor depending on the dimensionality of spacetime and the quantum number for spherical harmonics in the global coordinates. This approach resolves the factor of two problem in the tunneling method.Comment: LaTex 10 pages, no figur

The transcriptional repressor protein NsrR senses nitric oxide directly via a [2Fe-2S] cluster

The regulatory protein NsrR, a member of the Rrf2 family of transcription repressors, is specifically dedicated to sensing nitric oxide (NO) in a variety of pathogenic and non-pathogenic bacteria. It has been proposed that NO directly modulates NsrR activity by interacting with a predicted [Fe-S] cluster in the NsrR protein, but no experimental evidence has been published to support this hypothesis. Here we report the purification of NsrR from the obligate aerobe Streptomyces coelicolor. We demonstrate using UV-visible, near UV CD and EPR spectroscopy that the protein contains an NO-sensitive [2Fe-2S] cluster when purified from E. coli. Upon exposure of NsrR to NO, the cluster is nitrosylated, which results in the loss of DNA binding activity as detected by bandshift assays. Removal of the [2Fe-2S] cluster to generate apo-NsrR also resulted in loss of DNA binding activity. This is the first demonstration that NsrR contains an NO-sensitive [2Fe-2S] cluster that is required for DNA binding activity

An optically stimulated superconducting-like phase in K3C60 far above equilibrium Tc

The control of non-equilibrium phenomena in complex solids is an important research frontier, encompassing new effects like light induced superconductivity. Here, we show that coherent optical excitation of molecular vibrations in the organic conductor K3C60 can induce a non-equilibrium state with the optical properties of a superconductor. A transient gap in the real part of the optical conductivity and a low-frequency divergence of the imaginary part are measured for base temperatures far above equilibrium Tc=20 K. These findings underscore the role of coherent light fields in inducing emergent order.Comment: 40 pages, 23 figure

Dual-gated bilayer graphene hot electron bolometer

Detection of infrared light is central to diverse applications in security, medicine, astronomy, materials science, and biology. Often different materials and detection mechanisms are employed to optimize performance in different spectral ranges. Graphene is a unique material with strong, nearly frequency-independent light-matter interaction from far infrared to ultraviolet, with potential for broadband photonics applications. Moreover, graphene's small electron-phonon coupling suggests that hot-electron effects may be exploited at relatively high temperatures for fast and highly sensitive detectors in which light energy heats only the small-specific-heat electronic system. Here we demonstrate such a hot-electron bolometer using bilayer graphene that is dual-gated to create a tunable bandgap and electron-temperature-dependent conductivity. The measured large electron-phonon heat resistance is in good agreement with theoretical estimates in magnitude and temperature dependence, and enables our graphene bolometer operating at a temperature of 5 K to have a low noise equivalent power (33 fW/Hz1/2). We employ a pump-probe technique to directly measure the intrinsic speed of our device, >1 GHz at 10 K.Comment: 5 figure