Exploring the Use of Virtual Worlds as a Scientific Research Platform: The Meta-Institute for Computational Astrophysics (MICA)

We describe the Meta-Institute for Computational Astrophysics (MICA), the first professional scientific organization based exclusively in virtual worlds (VWs). The goals of MICA are to explore the utility of the emerging VR and VWs technologies for scientific and scholarly work in general, and to facilitate and accelerate their adoption by the scientific research community. MICA itself is an experiment in academic and scientific practices enabled by the immersive VR technologies. We describe the current and planned activities and research directions of MICA, and offer some thoughts as to what the future developments in this arena may be.Comment: 15 pages, to appear in the refereed proceedings of "Facets of Virtual Environments" (FaVE 2009), eds. F. Lehmann-Grube, J. Sablating, et al., ICST Lecture Notes Ser., Berlin: Springer Verlag (2009); version with full resolution color figures is available at http://www.mica-vw.org/wiki/index.php/Publication

Efficient O-demethylation of lignin monoaromatics using the peroxygenase activity of cytochrome P450 enzymes

A crucial reaction in harnessing renewable carbon from lignin is O-demethylation. We demonstrate the selective O-demethylation of syringol and guaiacol using different cytochrome P450 enzymes. These can efficiently use hydrogen peroxide which, when compared to nicotinamide cofactor-dependent monooxygenases and synthetic methods, allows for cheap and clean O-demethylation of lignin-derived aromatics.Alix C. Harlington, Keith E. Shearwin, Stephen G. Bell and Fiona Whela

Selective biocatalytic hydroxylation of unactivated methylene C-H bonds in cyclic alkyl substrates

The cytochrome P450 monooxygenase CYP101B1 from Novosphingobium aromaticivorans selectively hydroxylated methylene C-H bonds in cycloalkyl rings. Cycloketones and cycloalkyl esters containing C6, C8, C10 and C12 rings were oxidised with high selectively on the opposite side of the ring to the carbonyl substituent. Cyclodecanone was oxidised to oxabicycloundecanol derivatives in equilibrium with the hydroxycyclodecanones.Md Raihan Sarkar, Samrat Dasgupta, Simon M. Pyke and Stephen G. Bel

Gravitational Mesoscopic Constraints in Cosmological Dark Matter Halos

We present an analysis of the behaviour of the `coarse-grained' (`mesoscopic') rank partitioning of the mean energy of collections of particles composing virialized dark matter halos in a Lambda-CDM cosmological simulation. We find evidence that rank preservation depends on halo mass, in the sense that more massive halos show more rank preservation than less massive ones. We find that the most massive halos obey Arnold's theorem (on the ordering of the characteristic frequencies of the system) more frequently than less massive halos. This method may be useful to evaluate the coarse-graining level (minimum number of particles per energy cell) necessary to reasonably measure signatures of `mesoscopic' rank orderings in a gravitational system.Comment: LaTeX, 15 pages, 3 figures. Accepted for publication in Celestial Mechanics and Dynamical Astronomy Journa

Efficient hydroxylation of cycloalkanes by co-addition of decoy molecules to variants of the cytochrome P450 CYP102A1

The wild-type cytochrome P450 (CYP) monooxygenase enzyme CYP102A1 (P450Bm3) has low activity for cycloalkane oxidation. The oxidation of these substrates by variants of this enzyme in combination with perfluorinated decoy molecules (PFCs) was investigated to improve productivity. The use of rate accelerating variants, which have mutations located outside of the substrate binding pocket as well as an active site variant of CYP102A1 (A74G/F87V/L188Q) all enhanced cycloalkane oxidation (C5 to C10). The addition of the decoy molecules to the wild-type and the rate accelerating mutants of CYP102A1 boosted the substrate oxidation rates even further. However, the levels of cycloalkanol product decreased with the larger alkanes when the decoy molecules were used with the variant A74G/F87V/L188Q, which contained mutations within the substrate binding pocket. For the majority of the enzymes and PFC decoy molecule combinations the highest levels of oxidation were obtained with cyclooctane. When larger second generation decoy molecules, based on modified amino acids were utilised there was a significant improvement in the oxidation of the smaller cycloalkanes by the wild-type enzyme and one other variant. This resulted in significant improvements in biocatalytic oxidation of cyclopentane and cyclohexane. However, the use of these optimised decoy molecules did not significantly improve cycloalkane oxidation over the fluorinated fatty acid derivatives when combined with the best rate accelerating variant, R47L/Y51F/I401P. Overall our approach enabled the cycloalkanes to be oxidised 300- to 8000-fold more efficiently than the wild-type enzyme at product formation rates in excess of 500 and up to 1700 nmol·nmol-CYP−1·min−1.Shaghayegh Dezvarei, Hiroki Onoda, Osami Shoji, Yoshihito Watanabe, Stephen G. Bel

New evidence for strong nonthermal effects in Tycho's supernova remnant

For the case of Tycho's supernova remnant (SNR) we present the relation between the blast wave and contact discontinuity radii calculated within the nonlinear kinetic theory of cosmic ray (CR) acceleration in SNRs. It is demonstrated that these radii are confirmed by recently published Chandra measurements which show that the observed contact discontinuity radius is so close to the shock radius that it can only be explained by efficient CR acceleration which in turn makes the medium more compressible. Together with the recently determined new value $E_{sn}=1.2\times 10^{51}$ erg of the SN explosion energy this also confirms our previous conclusion that a TeV gamma-ray flux of $(2-5)\times 10^{-13}$ erg/(cm$^2$s) is to be expected from Tycho's SNR. Chandra measurements and the HEGRA upper limit of the TeV gamma-ray flux together limit the source distance $d$ to $3.3\leq d\leq 4$ kpc.Comment: 5 pages, 4 figures. Accepted for publication in Astrophysics and Space Science, Proc. of "The Multi-Messenger Approach to High-Energy Gamma-ray Sources (Third Workshop on the Nature of Unidentified High-Energy Sources)", Barcelona, July 4-7, 200

3D-HST+CANDELS : the evolution of the galaxy size-mass distribution since z=3

Spectroscopic+photometric redshifts, stellar mass estimates, and rest-frame colors from the 3D-HST survey are combined with structural parameter measurements from CANDELS imaging to determine the galaxy size-mass distribution over the redshift range 0 < z < 3. Separating early- and late-type galaxies on the basis of star-formation activity, we confirm that early-type galaxies are on average smaller than late-type galaxies at all redshifts, and we find a significantly different rate of average size evolution at fixed galaxy mass, with fast evolution for the early-type population, R eff∝(1 + z)–1.48, and moderate evolution for the late-type population, R eff∝(1 + z)-0.75Peer reviewedFinal Accepted Versio

Rearrangement-free hydroxylation of methylcubanes by a cytochrome P450: the case for dynamical coupling of C-H abstraction and rebound

The highly strained cubylmethyl radical undergoes one of the fastest radical rearrangements known (reported k = 2.9 × 1010 s-1 at 25 °C) through scission of two bonds of the cube. The rearrangement has previously been used as a mechanistic probe to detect radical-based pathways in enzyme-catalyzed C-H oxidations. This paper reports the discovery of highly selective cytochrome P450-catalyzed methylcubane oxidations which notionally proceed via cubylmethyl radical intermediates yet are remarkably free of rearrangement. The bacterial cytochrome P450 CYP101B1 from Novosphingobium aromaticivorans DSM 12444 is found to hydroxylate the methyl group of a range of methylcubane substrates containing a regio-directing carbonyl functionality at C-4. Unlike other reported P450-catalyzed methylcubane oxidations, the designed methylcubanes are hydroxylated with high efficiency and selectivity, giving cubylmethanols in yields of up to 93%. The lack of cubane core ring-opening implies that the cubylmethyl radicals formed during these CYP101B1-catalyzed hydroxylations must have very short lifetimes, of just a few picoseconds, which are too short for them to manifest the side reactivity characteristic of a fully equilibrated P450 intermediate. We propose that the apparent ultrafast radical rebound can be explained by a mechanism in which C-H abstraction and C-O bond formation are merged into a dynamically coupled process, effectively bypassing a discrete radical intermediate. Related dynamical phenomena can be proposed to predict how P450s may achieve various other modes of reactivity by controlling the formation and fate of radical intermediates. In principle, dynamical ideas and two-state reactivity are each individually able to explain apparent ultrashort radical lifetimes in P450 catalysis, but they are best considered together.Md. Raihan Sarkar, Sevan D. Houston, G. Paul Savage, Craig M. Williams, Elizabeth H. Krenske, Stephen G. Bell and James J. De Vos

A 15.7-minAM CVn binary discovered in K2

We present the discovery of SDSS J135154.46−064309.0, a short-period variable observed using 30-mincadence photometry in K2 Campaign 6. Follow-up spectroscopy and high-speed photometry support a classification as a new member of the rare class of ultracompact accreting binaries known as AM CVn stars. The spectroscopic orbital period of 15.65 ± 0.12 min makes this system the fourth-shortest-period AM CVn known, and the second system of this type to be discovered by the Kepler spacecraft. The K2 data show photometric periods at 15.7306 ± 0.0003 min, 16.1121 ± 0.0004 min, and 664.82 ± 0.06 min, which we identify as the orbital period, superhump period, and disc precession period, respectively. From the superhump and orbital periods we estimate the binary mass ratio q = M2/M1= 0.111 ± 0.005, though this method of mass ratio determination may not be well calibrated for helium-dominated binaries. This system is likely to be a bright foreground source of gravitational waves in the frequency range detectable by Laser Interferometer Space Antenna, and may be of use as a calibration source if future studies are able to constrain the masses of its stellar components

Cosmology, Particle Physics and Superfluid 3He

Many direct parallels connect superfluid 3He with the field theories describing the physical vacuum, gauge fields and elementary fermions. Superfluid $^3$He exhibits a variety of topological defects which can be detected with single-defect sensitivity. Modern scenarios of defect-mediated baryogenesis can be simulated by the interaction of the 3He vortices and domain walls with fermionic quasiparticles. Formation of defects in a symmetry-breaking phase transition in the early Universe, which could be responsible for large-scale structure formation and for microwave-background anisotropy, also may be modelled in the laboratory. This is supported by the recent observation of vortex formation in neutron-irradiated 3He-B where the "primordial fireball" is formed in an exothermic nuclear reaction.Comment: Invited talk at LT-21 Conference, 20 pages, 3 figures available at request, compressed ps file of the camera-ready format with 3 figures is at ftp://boojum.hut.fi/pub/publications/lowtemp/LTL-96006.ps.g