Experimental Challenges for Quantum Gravity

The existence of a new fundamental scale may lead to modified dispersion relations for particles at high energies. Such modifications seem to be realized with the Planck scale in certain descriptions of quantum gravity. We apply effective field theory to this problem and identify dimension 5 operators that would lead to cubic modifications of dispersion relations for Standard Model particles. We also discuss other issues related to this approach including various experimental bounds on the strength of these interactions. Further we sketch a scenario where mixing of these operators with dimensions 3 and 4 due to quantum effects is minimal.Comment: QTS3 proceedings; review of hep-ph/0301124 plus extended discussio

Can Chandra resolve the remaining cosmic X-ray background?

The deepest extragalactic X-ray observation, the 2 Ms Chandra Deep Field North (CDF-N), resolves ~80% of the total extragalactic cosmic X-ray background (CXB) in the 1-2 keV band. Recent work has shown that 70% of the remaining CXB flux is associated with sources detected by the Hubble Space Telescope (HST). This paper uses the existing CDF-N data to constrain the X-ray flux distribution of these X-ray undetected HST sources, by comparing the number of 0.5-2 keV X-ray counts at the HST positions to those expected for model flux distributions. In the simple case where all the undetected HST X-ray sources have the same 0.5-2 keV flux, the data are best fit by 1.5-3 counts per source in 2 Ms, compared to a detection limit (at 10% completeness) of 9 counts. Assuming a more realistic power-law logN-logS distribution [N(>S) S^-alpha], the data favor a relatively steep flux distribution, with alpha=1.1^+0.5_-0.3 (limits are 99% confidence). This slope is very similar to that previously found for faint normal and starburst galaxies in the CDF-N. These results suggest deeper Chandra observations will detect a new population of faint X-ray sources, but extremely deep exposures are needed to resolve the remainder of the soft CXB. In the most optimistic scenario, when the HST sources have the flattest allowed flux distribution and all the sources without HST counterparts are detected, observations 5 times more sensitive than the existing ones would resolve at most ~60% of the remaining soft CXB.Comment: 9 emulateapj pages, 8 figures, v3: matches version to appear in ApJ (note correction to approximation of Poisson errors

Polarization and structure of relativistic parsec-scale AGN jets

(Abridged) We consider the polarization properties of optically thin synchrotron radiation emitted by relativistically moving electron--positron jets carrying large-scale helical magnetic fields. In our model, the jet is cylindrical, and the emitting plasma moves parallel to the jet axis with a characteristic Lorentz factor $\Gamma$. We draw attention to the strong influence that the bulk relativistic motion of the emitting relativistic particles has on the observed polarization. We conclude that large-scale magnetic fields can explain the salient polarization properties of parsec-scale AGN jets. Since the typical degrees of polarization are $\leq 15$, the emitting parts of the jets must have comparable rest-frame toroidal and poloidal fields. In this case, most relativistic jets are strongly dominated by the toroidal magnetic field component in the observer's frame, $B_\phi/B_z \sim \Gamma$. We also discuss the possibility that relativistic AGN jets may be electromagnetically (Poynting flux) dominated. In this case, dissipation of the toroidal magnetic field (and not fluid shocks) may be responsible for particle acceleration.Comment: submitted to MNRAS; 45 pages, 16 figure

Ultraviolet modifications of dispersion relations in effective field theory

The existence of a fundamental ultraviolet scale, such as the Planck scale, may lead to modifications of the dispersion relations for particles at high energies, in some scenarios of quantum gravity. We apply effective field theory to this problem and identify dimension 5 operators that do not mix with dimensions 3 and 4 and lead to cubic modifications of dispersion relations for scalars, fermions, and vector particles. Further we show that, for electrons, photons and light quarks, clock comparison experiments bound these operators at 10^{-5}/Mpl.Comment: Version to appear in Phys.Rev.Let

Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach.

Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, in which a ligand in a wrong pose achieves a better docking score than that of native pose, arise as additional protein conformations are added. In the current study, we developed a new ligand-biased ensemble receptor docking method and composite scoring function which combine the use of ligand-based atomic property field (APF) method with receptor structure-based docking. This method helps us to correctly dock 30 out of 36 ligands presented by the D3R docking challenge. For the six mis-docked ligands, the cognate receptor structures prove to be too different from the 40 available experimental Pocketome conformations used for docking and could be identified only by receptor sampling beyond experimentally explored conformational subspace

Hybridizing Non-dominated Sorting Algorithms: Divide-and-Conquer Meets Best Order Sort

Many production-grade algorithms benefit from combining an asymptotically efficient algorithm for solving big problem instances, by splitting them into smaller ones, and an asymptotically inefficient algorithm with a very small implementation constant for solving small subproblems. A well-known example is stable sorting, where mergesort is often combined with insertion sort to achieve a constant but noticeable speed-up. We apply this idea to non-dominated sorting. Namely, we combine the divide-and-conquer algorithm, which has the currently best known asymptotic runtime of $O(N (\log N)^{M - 1})$, with the Best Order Sort algorithm, which has the runtime of $O(N^2 M)$ but demonstrates the best practical performance out of quadratic algorithms. Empirical evaluation shows that the hybrid's running time is typically not worse than of both original algorithms, while for large numbers of points it outperforms them by at least 20%. For smaller numbers of objectives, the speedup can be as large as four times.Comment: A two-page abstract of this paper will appear in the proceedings companion of the 2017 Genetic and Evolutionary Computation Conference (GECCO 2017

Rubisco evolution in C4 eudicots: an analysis of Amaranthaceae sensu lato

BACKGROUND Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyses the key reaction in the photosynthetic assimilation of CO₂. In C₄ plants CO₂ is supplied to Rubisco by an auxiliary CO₂-concentrating pathway that helps to maximize the carboxylase activity of the enzyme while suppressing its oxygenase activity. As a consequence, C₄ Rubisco exhibits a higher maximum velocity but lower substrate specificity compared with the C₃ enzyme. Specific amino-acids in Rubisco are associated with C₄ photosynthesis in monocots, but it is not known whether selection has acted on Rubisco in a similar way in eudicots. METHODOLOGY/PRINCIPAL FINDINGS We investigated Rubisco evolution in Amaranthaceae sensu lato (including Chenopodiaceae), the third-largest family of C₄ plants, using phylogeny-based maximum likelihood and Bayesian methods to detect Darwinian selection on the chloroplast rbcL gene in a sample of 179 species. Two Rubisco residues, 281 and 309, were found to be under positive selection in C₄ Amaranthaceae with multiple parallel replacements of alanine by serine at position 281 and methionine by isoleucine at position 309. Remarkably, both amino-acids have been detected in other C₄ plant groups, such as C₄ monocots, illustrating a striking parallelism in molecular evolution. CONCLUSIONS/SIGNIFICANCE Our findings illustrate how simple genetic changes can contribute to the evolution of photosynthesis and strengthen the hypothesis that parallel amino-acid replacements are associated with adaptive changes in Rubisco.This research was funded by NERC (http://www.nerc.ac.uk/; grant number NE/H007741/1)

Environmental Dependence of Masses and Coupling Constants

We construct a class of scalar field models coupled to matter that lead to the dependence of masses and coupling constants on the ambient matter density. Such models predict a deviation of couplings measured on the Earth from values determined in low-density astrophysical environments, but do not necessarily require the evolution of coupling constants with the redshift in the recent cosmological past. Additional laboratory and astrophysical tests of \Delta \alpha and \Delta(m_p/m_e) as functions of the ambient matter density are warranted.Comment: 20 pages, no figures, references added, minor editorial change