The effect of early dark matter halos on reionization

The annihilation of dark matter particles releases energy, ionizing some of the gas in the Universe. We investigate the effect of dark matter halos on reionization. We show that the effect depends on the assumed density profile, the particle mass, and the assumed minimum halo mass. For NFW halos and typical WIMPs, we find the effect to be quite small. However, light dark matter candidates in the MeV range can contribute significantly to reionization and can make an important contribution to the measured optical depth. This effect may be used to constrain light dark matter models. We also study the effect of varying the halo density profile on reionization.Comment: Minor changes from v2. Accepted for publication in Phys. Rev.

New Examples of Kochen-Specker Type Configurations on Three Qubits

A new example of a saturated Kochen-Specker (KS) type configuration of 64 rays in 8-dimensional space (the Hilbert space of a triple of qubits) is constructed. It is proven that this configuration has a tropical dimension 6 and that it contains a critical subconfiguration of 36 rays. A natural multicolored generalisation of the Kochen-Specker theory is given based on a concept of an entropy of a saturated configuration of rays.Comment: 24 page

AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes

Using a combination of computer methods for iterative database searches and multiple sequence alignment, we show that protein sequences related to the AAA family of ATPases are far more prevalent than reported previously. Among these are regulatory components of Lon and Clp proteases, proteins involved in DNA replication, recombination, and restriction (including subunits of the origin recognition complex, replication factor C proteins, MCM DNA-licensing factors and the bacterial DnaA, RuvB, and McrB proteins), prokaryotic NtrC-related transcription regulators, the Bacillus sporulation protein SpoVJ, Mg2+, and Co2+ chelatases, the Halobacterium GvpN gas vesicle synthesis protein, dynein motor proteins, TorsinA, and Rubisco activase. Alignment of these sequences, in light of the structures of the clamp loader delta' subunit of Escherichia coli DNA polymerase III and the hexamerization component of N-ethylmaleimide-sensitive fusion protein, provides structural and mechanistic insights into these proteins, collectively designated the AAA+ class. Whole-genome analysis indicates that this class is ancient and has undergone considerable functional divergence prior to the emergence of the major divisions of life. These proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes. The hexameric architecture often associated with this class can provide a hole through which DNA or RNA can be thread; this may be important for assembly or remodeling of DNA-protein complexes

Parity proofs of the Kochen-Specker theorem based on the 24 rays of Peres

A diagrammatic representation is given of the 24 rays of Peres that makes it easy to pick out all the 512 parity proofs of the Kochen-Specker theorem contained in them. The origin of this representation in the four-dimensional geometry of the rays is pointed out.Comment: 14 pages, 6 figures and 3 tables. Three references have been added. Minor typos have been correcte

Solution to the Mean King's problem with mutually unbiased bases for arbitrary levels

The Mean King's problem with mutually unbiased bases is reconsidered for arbitrary d-level systems. Hayashi, Horibe and Hashimoto [Phys. Rev. A 71, 052331 (2005)] related the problem to the existence of a maximal set of d-1 mutually orthogonal Latin squares, in their restricted setting that allows only measurements of projection-valued measures. However, we then cannot find a solution to the problem when e.g., d=6 or d=10. In contrast to their result, we show that the King's problem always has a solution for arbitrary levels if we also allow positive operator-valued measures. In constructing the solution, we use orthogonal arrays in combinatorial design theory.Comment: REVTeX4, 4 page

Mass Varying Neutrinos, Quintessence, and the Accelerating Expansion of the Universe

We analyze the Mass Varying Neutrino (MaVaN) scenario. We consider a minimal model of massless Dirac fermions coupled to a scalar field, mainly in the framework of finite temperature quantum field theory. We demonstrate that the mass equation we find has non-trivial solutions only for special classes of potentials, and only within certain temperature intervals. We give most of our results for the Ratra-Peebles Dark Energy (DE) potential. The thermal (temporal) evolution of the model is analyzed. Following the time arrow, the stable, metastable and unstable phases are predicted. The model predicts that the present Universe is below its critical temperature and accelerates. At the critical point the Universe undergoes a first-order phase transition from the (meta)stable oscillatory regime to the unstable rolling regime of the DE field. This conclusion agrees with the original idea of quintessence as a force making the Universe roll towards its true vacuum with zero \Lambda-term. The present MaVaN scenario is free from the coincidence problem, since both the DE density and the neutrino mass are determined by the scale M of the potential. Choosing M ~ 10^{-3} eV to match the present DE density, we can obtain the present neutrino mass in the range m ~ 10^{-2}-1 eV and consistent estimates for other parameters of the Universe.Comment: 29 pages, 7 figures. V. 3: Analysis of the dynamics of the Universe and some refs. added; extended version to be published in PR

Role of Predicted Metalloprotease Motif of Jab1/Csn5 in Cleavage of Nedd8 from Cul1

COP9 signalosome (CSN) cleaves the ubiquitin-like protein Nedd8 from the Cul1 subunit of SCF ubiquitin ligases. The Jab1/MPN domain metalloenzyme (JAMM) motif in the Jab1/Csn5 subunit was found to underlie CSN's Nedd8 isopeptidase activity. JAMM is found in proteins from archaea, bacteria, and eukaryotes, including the Rpn11 subunit of the 26S proteasome. Metal chelators and point mutations within JAMM abolished CSN-dependent cleavage of Nedd8 from Cul1, yet had little effect on CSN complex assembly. Optimal SCF activity in yeast and both viability and proper photoreceptor cell (R cell) development in Drosophila melanogaster required an intact Csn5 JAMM domain. We propose that JAMM isopeptidases play important roles in a variety of physiological pathways

Causality - Complexity - Consistency: Can Space-Time Be Based on Logic and Computation?

The difficulty of explaining non-local correlations in a fixed causal structure sheds new light on the old debate on whether space and time are to be seen as fundamental. Refraining from assuming space-time as given a priori has a number of consequences. First, the usual definitions of randomness depend on a causal structure and turn meaningless. So motivated, we propose an intrinsic, physically motivated measure for the randomness of a string of bits: its length minus its normalized work value, a quantity we closely relate to its Kolmogorov complexity (the length of the shortest program making a universal Turing machine output this string). We test this alternative concept of randomness for the example of non-local correlations, and we end up with a reasoning that leads to similar conclusions as in, but is conceptually more direct than, the probabilistic view since only the outcomes of measurements that can actually all be carried out together are put into relation to each other. In the same context-free spirit, we connect the logical reversibility of an evolution to the second law of thermodynamics and the arrow of time. Refining this, we end up with a speculation on the emergence of a space-time structure on bit strings in terms of data-compressibility relations. Finally, we show that logical consistency, by which we replace the abandoned causality, it strictly weaker a constraint than the latter in the multi-party case.Comment: 17 pages, 16 figures, small correction