Turing jumps through provability

Fixing some computably enumerable theory $T$, the Friedman-Goldfarb-Harrington (FGH) theorem says that over elementary arithmetic, each $\Sigma_1$ formula is equivalent to some formula of the form $\Box_T \varphi$ provided that $T$ is consistent. In this paper we give various generalizations of the FGH theorem. In particular, for $n>1$ we relate $\Sigma_{n}$ formulas to provability statements $[n]_T^{\sf True}\varphi$ which are a formalization of "provable in $T$ together with all true $\Sigma_{n+1}$ sentences". As a corollary we conclude that each $[n]_T^{\sf True}$ is $\Sigma_{n+1}$-complete. This observation yields us to consider a recursively defined hierarchy of provability predicates $[n+1]^\Box_T$ which look a lot like $[n+1]_T^{\sf True}$ except that where $[n+1]_T^{\sf True}$ calls upon the oracle of all true $\Sigma_{n+2}$ sentences, the $[n+1]^\Box_T$ recursively calls upon the oracle of all true sentences of the form $\langle n \rangle_T^\Box\phi$. As such we obtain a `syntax-light' characterization of $\Sigma_{n+1}$ definability whence of Turing jumps which is readily extended beyond the finite. Moreover, we observe that the corresponding provability predicates $[n+1]_T^\Box$ are well behaved in that together they provide a sound interpretation of the polymodal provability logic ${\sf GLP}_\omega$

Tolman wormholes violate the strong energy condition

For an arbitrary Tolman wormhole, unconstrained by symmetry, we shall define the bounce in terms of a three-dimensional edgeless achronal spacelike hypersurface of minimal volume. (Zero trace for the extrinsic curvature plus a "flare-out" condition.) This enables us to severely constrain the geometry of spacetime at and near the bounce and to derive general theorems regarding violations of the energy conditions--theorems that do not involve geodesic averaging but nevertheless apply to situations much more general than the highly symmetric FRW-based subclass of Tolman wormholes. [For example: even under the mildest of hypotheses, the strong energy condition (SEC) must be violated.] Alternatively, one can dispense with the minimal volume condition and define a generic bounce entirely in terms of the motion of test particles (future-pointing timelike geodesics), by looking at the expansion of their timelike geodesic congruences. One re-confirms that the SEC must be violated at or near the bounce. In contrast, it is easy to arrange for all the other standard energy conditions to be satisfied.Comment: 8 pages, ReV-TeX 3.

Time-resolved FRET fluorescence spectroscopy of visible fluorescent protein pairs

Förster resonance energy transfer (FRET) is a powerful method for obtaining information about small-scale lengths between biomacromolecules. Visible fluorescent proteins (VFPs) are widely used as spectrally different FRET pairs, where one VFP acts as a donor and another VFP as an acceptor. The VFPs are usually fused to the proteins of interest, and this fusion product is genetically encoded in cells. FRET between VFPs can be determined by analysis of either the fluorescence decay properties of the donor molecule or the rise time of acceptor fluorescence. Time-resolved fluorescence spectroscopy is the technique of choice to perform these measurements. FRET can be measured not only in solution, but also in living cells by the technique of fluorescence lifetime imaging microscopy (FLIM), where fluorescence lifetimes are determined with the spatial resolution of an optical microscope. Here we focus attention on time-resolved fluorescence spectroscopy of purified, selected VFPs (both single VFPs and FRET pairs of VFPs) in cuvette-type experiments. For quantitative interpretation of FRET–FLIM experiments in cellular systems, details of the molecular fluorescence are needed that can be obtained from experiments with isolated VFPs. For analysis of the time-resolved fluorescence experiments of VFPs, we have utilised the maximum entropy method procedure to obtain a distribution of fluorescence lifetimes. Distributed lifetime patterns turn out to have diagnostic value, for instance, in observing populations of VFP pairs that are FRET-inactiv

Production and decay of evolving horizons

We consider a simple physical model for an evolving horizon that is strongly interacting with its environment, exchanging arbitrarily large quantities of matter with its environment in the form of both infalling material and outgoing Hawking radiation. We permit fluxes of both lightlike and timelike particles to cross the horizon, and ask how the horizon grows and shrinks in response to such flows. We place a premium on providing a clear and straightforward exposition with simple formulae. To be able to handle such a highly dynamical situation in a simple manner we make one significant physical restriction, that of spherical symmetry, and two technical mathematical restrictions: (1) We choose to slice the spacetime in such a way that the space-time foliations (and hence the horizons) are always spherically symmetric. (2) Furthermore we adopt Painleve-Gullstrand coordinates (which are well suited to the problem because they are nonsingular at the horizon) in order to simplify the relevant calculations. We find particularly simple forms for surface gravity, and for the first and second law of black hole thermodynamics, in this general evolving horizon situation. Furthermore we relate our results to Hawking's apparent horizon, Ashtekar et al's isolated and dynamical horizons, and Hayward's trapping horizons. The evolving black hole model discussed here will be of interest, both from an astrophysical viewpoint in terms of discussing growing black holes, and from a purely theoretical viewpoint in discussing black hole evaporation via Hawking radiation.Comment: 25 pages, uses iopart.cls V2: 5 references added; minor typos; V3: some additional clarifications, additional references, additional appendix on the Viadya spacetime. This version published in Classical and Quiantum Gravit

Signature change events: A challenge for quantum gravity?

Within the framework of either Euclidian (functional-integral) quantum gravity or canonical general relativity the signature of the manifold is a priori unconstrained. Furthermore, recent developments in the emergent spacetime programme have led to a physically feasible implementation of signature change events. This suggests that it is time to revisit the sometimes controversial topic of signature change in general relativity. Specifically, we shall focus on the behaviour of a quantum field subjected to a manifold containing regions of different signature. We emphasise that, regardless of the underlying classical theory, there are severe problems associated with any quantum field theory residing on a signature-changing background. (Such as the production of what is naively an infinite number of particles, with an infinite energy density.) From the viewpoint of quantum gravity phenomenology, we discuss possible consequences of an effective Lorentz symmetry breaking scale. To more fully understand the physics of quantum fields exposed to finite regions of Euclidean-signature (Riemannian) geometry, we show its similarities with the quantum barrier penetration problem, and the super-Hubble horizon modes encountered in cosmology. Finally we raise the question as to whether signature change transitions could be fully understood and dynamically generated within (modified) classical general relativity, or whether they require the knowledge of a full theory of quantum gravity.Comment: 33 pages. 4 figures; V2: 3 references added, no physics changes; V3: now 24 pages - significantly shortened - argument simplified and more focused - no physics changes - this version accepted for publication in Classical and Quantum Gravit

Energy conditions in f(R) gravity and Brans-Dicke theories

The equivalence between f(R) gravity and scalar-tensor theories is invoked to study the null, strong, weak and dominant energy conditions in Brans-Dicke theory. We consider the validity of the energy conditions in Brans-Dicke theory by invoking the energy conditions derived from a generic f(R) theory. The parameters involved are shown to be consistent with an accelerated expanding universe.Comment: 9 pages, 1 figure, to appear in IJMP

Structural Changes of Yellow Cameleon Domains Observed by Quantitative FRET Analysis and Polarized Fluorescence Correlation Spectroscopy

Förster resonance energy transfer (FRET) is a widely used method for monitoring interactions between or within biological macromolecules conjugated with suitable donor-acceptor pairs. Donor fluorescence lifetimes in absence and presence of acceptor molecules are often measured for the observation of FRET. However, these lifetimes may originate from interacting and noninteracting molecules, which hampers quantitative interpretation of FRET data. We describe a methodology for the detection of FRET that monitors the rise time of acceptor fluorescence on donor excitation thereby detecting only those molecules undergoing FRET. The large advantage of this method, as compared to donor fluorescence quenching method used more commonly, is that the transfer rate of FRET can be determined accurately even in cases where the FRET efficiencies approach 100% yielding highly quenched donor fluorescence. Subsequently, the relative orientation between donor and acceptor chromophores is obtained from time-dependent fluorescence anisotropy measurements carried out under identical conditions of donor excitation and acceptor detection. The FRET based calcium sensor Yellow Cameleon 3.60 (YC3.60) was used because it changes its conformation on calcium binding, thereby increasing the FRET efficiency. After mapping distances and orientation angles between the FRET moieties in YC3.60, cartoon models of this FRET sensor with and without calcium could be created. Independent support for these representations came from experiments where the hydrodynamic properties of YC3.60 under ensemble and single-molecule conditions on selective excitation of the acceptor were determined. From rotational diffusion times as found by fluorescence correlation spectroscopy and consistently by fluorescence anisotropy decay analysis it could be concluded that the open structure (without calcium) is flexible as opposed to the rather rigid closed conformation. The combination of two independent methods gives consistent results and presents a rapid and specific methodology to analyze structural and dynamical changes in a protein on ligand bindin

Hybridization between wild and cultivated potato species in the Peruvian Andes and biosafety implications for deployment of GM potatoes

The nature and extent of past and current hybridization between cultivated potato and wild relatives in nature is of interest to crop evolutionists, taxonomists, breeders and recently to molecular biologists because of the possibilities of inverse gene flow in the deployment of genetically-modified (GM) crops. This research proves that natural hybridization occurs in areas of potato diversity in the Andes, the possibilities for survival of these new hybrids, and shows a possible way forward in case of GM potatoes should prove advantageous in such areas