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Search Results: 1 - 10 of 221717 matches for " Richard P Oliver "
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On the dynamics of planetesimals embedded in turbulent protoplanetary discs
Richard P. Nelson,Oliver Gressel
Physics , 2010, DOI: 10.1111/j.1365-2966.2010.17327.x
Abstract: (abridged) Angular momentum transport and accretion in protoplanetary discs are generally believed to be driven by MHD turbulence via the magneto-rotational instability (MRI). The dynamics of solid bodies embedded in such discs (dust grains, boulders, planetesimals and planets) may be strongly affected by the turbulence, such that the formation pathways for planetary systems are determined in part by the strength and spatial distribution of the turbulent flow. We examine the dynamics of planetesimals, with radii between 1m \^a 10 km, embedded in turbulent protoplanetary discs, using three dimensional MHD simulations. The planetesimals experience gas drag and stochastic gravitational forces due to the turbulent disc. We use, and compare the results from, local shearing box simulations and global models in this study. The main aims of this work are to examine: the growth, and possible saturation, of the velocity dispersion of embedded planetesimals as a function of their size and disc parameters; the rate of radial migration and diffusion of planetesimals; the conditions under which the results from shearing box and global simulations agree. We find good agreement between local and global simulations when shearing boxes of dimension 4H x 16H x 2H are used (H being the local scale height). The magnitude of the density fluctuations obtained is sensitive to the box size, due to the excitation and propagation of spiral density waves. This affects the stochastic forcing experienced by planetesimals. [...] Our models show that fully developed MHD turbulence in protoplanetary discs would have a destructive effect on embedded planetesimals. Relatively low levels of turbulence are required for traditional models of planetesimal accretion to operate, this being consistent with the existence of a dead zone in protoplanetary discs.
RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences
James K Hane, Richard P Oliver
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-478
Abstract: We present RIPCAL http://www.sourceforge.net/projects/ripcal webcite, a software tool for the automated analysis of RIP in fungal genomic DNA repeats, which performs both RIP index and alignment-based analyses. We demonstrate the ability of RIPCAL to detect RIP within known RIP-affected sequences of Neurospora crassa and other fungi. We also predict and delineate the presence of RIP in the genome of Stagonospora nodorum – a Dothideomycete pathogen of wheat. We show that RIP has affected different members of the S. nodorum rDNA tandem repeat to different extents depending on their genomic contexts.The RIPCAL alignment-based method has considerable advantages over RIP indices for the analysis of whole genomes. We demonstrate its application to the recently published genome assembly of S. nodorum.Over 100 fungal genome sequences have been obtained or are in the pipeline [1] and next-generation sequencing technologies will further accelerate the accumulation of data over the next decade. This rapidly growing array of sequence information presents many new challenges for analysis. There is an urgent need to develop and implement efficient tools to describe features of new genomes. Repeat-induced point mutation (RIP) is one such area of fungal biology requiring efficient analytical tools. RIP is an irreversible genome defence mechanism first detected in Neurospora crassa [2,3] and subsequently in Magnaporthe grisea [4,5], Podospora anserina [6] and Leptosphaeria maculans [7]. RIP is believed to be a defence against transposons, rendering them inactive and protecting sexual progeny from the expression of transposon genes.Direct experimental observation of RIP requires both that the fungal species can be crossed under laboratory conditions and that the strain can be transformed with multiple copies of a transgene. Very few fungal species are amenable to such analysis and these procedures are slow in all cases. RIP-like processes can also be detected by in-silico analysis of
In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes
James K Hane, Richard P Oliver
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-655
Abstract: DeRIP is a new software tool developed to predict the original sequence of a RIP-mutated region prior to the occurrence of RIP. In this study, we apply deRIP to the genome of the wheat pathogen Stagonospora nodorum SN15 and predict the origin of several previously uncharacterised classes of repetitive DNA.Five new classes of transposon repeats and four classes of endogenous gene repeats were identified after deRIP. The deRIP process is a new tool for fungal genomics that facilitates the identification and understanding of the role and origin of fungal repetitive DNA. DeRIP is open-source and is available as part of the RIPCAL suite at http://www.sourceforge.net/projects/ripcal webcite.Repeat-induced point mutation (RIP) is a genome defence mechanism found within filamentous ascomycete fungi that is purported to combat transposon invasion. RIP mutates duplicated DNA sequences during sexual reproduction, thereby inactivating genes encoded in both copies. First discovered in Neurospora crassa [1,2], RIP was later demonstrated in the Ascomycetes Magnaporthe oryzae [3,4], Podospora anserina [5], Leptosphaeria maculans [6] and Fusarium graminearum [7]. Putative RIP events have also been detected bioinformatically in Aspergillus fumigatus [8], Fusarium oxysporum [9-11], Aspergillus nidulans [12], Neurospora tetrasperma [13], Microbotryum violaceum [14], Aspergillus oryzae [15], Magnaporthe oryzae [16], Colletotrichum cereal [17], Aspergillus niger [18], Penicillium chysogenum [18] and most recently in Stagonospora nodorum [19,20]. Given this broad distribution, it is reasonable to assume that RIP is widespread across, but so far restricted to, filamentous ascomycota and basidiomycota.The mechanism by which RIP operates is yet to be fully understood, but the following observations have been made. RIP involves transition mutations from C:G to T:A nucleotide base pairs in duplicated DNA; this affects both copies of the repeat and occurs prior to meiosis [1,2]. In the majority
Breathing Life Into Dead-Zones
Umurhan Orkan M.,Nelson Richard P.,Gressel Oliver
EPJ Web of Conferences , 2013, DOI: 10.1051/epjconf/20134603003
Abstract: The terrestrial planet formation regions of protoplanetary disks are generally sufficiently cold to be con- sidered non-magnetized and, consequently, dynamically inactive. However, recent investigations of these so-called “Dead-Zones” indicate the possibility that disks with strong mean radial temperature gradients can support instabilities associated with disk-normal gradients of the basic Keplerian shear profile. This process, known as the Goldreich-Schubert-Fricke (GSF) instability, is the instability of short radial wavelength inertial modes and depends wholly on the presence of vertical gradients of the mean Keplerian (zonal) flow. We report here high resolution fully nonlinear axisymmetric numerical studies of this instability and find a number of features including how, in the nonlinear saturated state, unstable discs become globally distorted, with strong vertical oscillations occurring at all radii due to local instability. We find that nonaxisymmetric numerical experiments are accompanied by significant amounts angular momentum transport (α ~ 0001). This instability should be operating in the Dead-Zones of protoplanetary disks at radii greater than 10-15 AU in minimum mass solar nebula models.
Global hydromagnetic simulations of a planet embedded in a dead zone: gap opening, gas accretion and formation of a protoplanetary jet
Oliver Gressel,Richard P. Nelson,Neal J. Turner,Udo Ziegler
Physics , 2013, DOI: 10.1088/0004-637X/779/1/59
Abstract: We present global hydrodynamic and magnetohydrodynamic (MHD) simulations with mesh refinement of accreting planets embedded in protoplanetary disks (PPDs). The magnetized disk includes Ohmic resistivity that depends on the overlying mass column, leading to turbulent surface layers and a dead zone near the midplane. The main results are: (i) The accretion flow in the Hill sphere is intrinsically 3D for hydrodynamic and MHD models. Net inflow toward the planet is dominated by high latitude flows. A circumplanetary disk (CPD) forms. Its midplane flows outward in a pattern whose details differ between models. (ii) Gap opening magnetically couples and ignites the dead zone near the planet, leading to stochastic accretion, a quasi-turbulent flow in the Hill sphere and a CPD whose structure displays high levels of variability. (iii) Advection of magnetized gas onto the rotating CPD generates helical fields that launch magnetocentrifugally driven outflows. During one specific epoch a highly collimated, one-sided jet is observed. (iv) The CPD's surface density $\sim30{\rm\,g\,cm^{-2}}$, small enough for significant ionization and turbulence to develop. (v) The accretion rate onto the planet in the MHD simulation reaches a steady value $8 \times 10^{-3} {\rm M_\oplus yr^{-1}}$, and is similar in the viscous hydrodynamic runs. Our results suggest that gas accretion onto a forming giant planet within a magnetized PPD with dead zone allows rapid growth from Saturnian to Jovian masses. As well as being relevant for giant planet formation, these results have important implications for the formation of regular satellites around gas giant planets.
Dead zones as safe-havens for planetesimals: influence of disc mass and external magnetic field
Oliver Gressel,Richard P. Nelson,Neal J. Turner
Physics , 2012, DOI: 10.1111/j.1365-2966.2012.20701.x
Abstract: (Abridged) Planetesimals embedded in a protoplanetary disc are stirred by gravitational torques exerted by density fluctuations in the surrounding turbulence. In particular, planetesimals in a disc supporting fully developed magneto-rotational turbulence are readily excited to velocity dispersions above the threshold for catastrophic disruption, halting planet formation. We aim to examine the stirring of planetesimals lying instead in a magnetically-decoupled midplane dead zone, stirred only by spiral density waves propagating out of the disc's magnetically-coupled turbulent surface layers. We extend previous studies to include a wider range of disc models, and explore the effects of varying the disc column density and external magnetic field strength. [...] The strength of the stirring is found to be independent of the gas surface density, which is contrary to the increase with disc mass expected from a simple linear wave picture. The discrepancy arises from the shearing out of density waves as they propagate into the dead zone, resulting in density structures near the midplane that exert weaker stochastic torques on average. We provide a simple analytic fit to our numerically obtained torque amplitudes that accounts for this effect. The stirring on the other hand depends sensitively on the net vertical magnetic flux, up to a saturation level above which magnetic forces dominate in the turbulent layers. For the majority of our models, the equilibrium planetesimal velocity dispersions lie between the thresholds for disrupting strong and weak aggregates, suggesting that collision outcomes will depend on material properties. However, discs with relatively weak magnetic fields yield reduced stirring, and their dead zones provide safe-havens even for the weakest planetesimals against collisional destruction.
Linear and nonlinear evolution of the vertical shear instability in accretion discs
Richard P. Nelson,Oliver Gressel,Orkan M. Umurhan
Physics , 2012, DOI: 10.1093/mnras/stt1475
Abstract: (Abridged) We analyse the stability and evolution of power-law accretion disc models. These have midplane densities that follow radial power-laws, and have either temperature or entropy distributions that are power-law functions of cylindrical radius. We employ two different hydrodynamic codes to perform 2D-axisymmetric and 3D simulations that examine the long-term evolution of the disc models as a function of the power-law indices of the temperature or entropy, the thermal relaxation time of the fluid, and the viscosity. We present a stability analysis of the problem that we use to interpret the simulation results. We find that disc models whose temperature or entropy profiles cause the equilibrium angular velocity to vary with height are unstable to the growth of modes with wavenumber ratios |k_R/k_Z| >> 1 when the thermodynamic response of the fluid is isothermal, or the thermal evolution time is comparable to or shorter than the local dynamical time scale. These discs are subject to the Goldreich-Schubert-Fricke (GSF) or `vertical shear' linear instability. Development of the instability involves excitation of vertical breathing and corrugation modes in the disc, with the corrugation modes in particular being a feature of the nonlinear saturated state. Instability operates when the dimensionless disc kinematic viscosity nu < 10^{-6} (Reynolds numbers Re>H c_s/nu > 2500). In 3D the instability generates a quasi-turbulent flow, and the Reynolds stress produces a fluctuating effective viscosity coefficient whose mean value reaches alpha ~ 6 x 10^{-4} by the end of the simulation. The vertical shear instability in disc models which include realistic thermal physics has yet to be examined. Should it occur, however, our results suggest that it will have significant consequences for their internal dynamics, transport properties, and observational appearance.
On the dynamics of planetesimals embedded in turbulent protoplanetary discs with dead zones
Oliver Gressel,Richard P. Nelson,Neal J. Turner
Physics , 2011, DOI: 10.1111/j.1365-2966.2011.18944.x
Abstract: (abridged) Accretion in protoplanetary discs is thought to be driven by [...] turbulence via the magnetorotational instability (MRI). Recent work has shown that a planetesimal swarm embedded in a fully turbulent disc is subject to strong excitation of the velocity dispersion, leading to collisional destruction of bodies with radii R_p < 100 km. Significant diffusion of planetesimal semimajor axes also arises, leading to large-scale spreading of the planetesimal population throughout the inner regions of the protoplanetary disc, in apparent contradiction of constraints provided by the distribution of asteroids within the asteroid belt. In this paper, we examine the dynamics of planetesimals embedded in vertically stratified turbulent discs, with and without dead zones. Our main aims are to examine the turbulent excitation of the velocity dispersion, and the radial diffusion, of planetesimals in these discs. We employ three dimensional MHD simulations [...], along with an equilibrium chemistry model [...] We find that planetesimals in fully turbulent discs develop large random velocities that will lead to collisional destruction/erosion for bodies with sizes below 100 km, and undergo radial diffusion on a scale \sim 2.5 au over a 5 Myr disc life time. But planetesimals in a dead zone experience a much reduced excitation of their random velocities, and equilibrium velocity dispersions lie between the disruption thresholds for weak and strong aggregates for sizes R_p < 100 km. We also find that radial diffusion occurs over a much reduced length scale \sim 0.25 au over the disc life time, this being consistent with solar system constraints. We conclude that planetesimal growth via mutual collisions between smaller bodies cannot occur in a fully turbulent disc. By contrast, a dead zone may provide a safe haven in which km-sized planetesimals can avoid mutual destruction through collisions.
Global simulations of protoplanetary disks with ohmic resistivity and ambipolar diffusion
Oliver Gressel,Neal J. Turner,Richard P. Nelson,Colin P. McNally
Physics , 2015, DOI: 10.1088/0004-637X/801/2/84
Abstract: Protoplanetary disks are believed to accrete onto their central T Tauri star because of magnetic stresses. Recently published shearing box simulations indicate that Ohmic resistivity, ambipolar diffusion and the Hall effect all play important roles in disk evolution. In the presence of a vertical magnetic field, the disk remains laminar between 1-5au, and a magnetocentrifugal disk wind forms that provides an important mechanism for removing angular momentum. Questions remain, however, about the establishment of a true physical wind solution in the shearing box simulations because of the symmetries inherent in the local approximation. We present global MHD simulations of protoplanetary disks that include Ohmic resistivity and ambipolar diffusion, where the time-dependent gas-phase electron and ion fractions are computed under FUV and X-ray ionization with a simplified recombination chemistry. Our results show that the disk remains laminar, and that a physical wind solution arises naturally in global disk models. The wind is sufficiently efficient to explain the observed accretion rates. Furthermore, the ionization fraction at intermediate disk heights is large enough for magneto-rotational channel modes to grow and subsequently develop into belts of horizontal field. Depending on the ionization fraction, these can remain quasi-global, or break-up into discrete islands of coherent field polarity. The disk models we present here show a dramatic departure from our earlier models including Ohmic resistivity only. It will be important to examine how the Hall effect modifies the evolution, and to explore the influence this has on the observational appearance of such systems, and on planet formation and migration.
Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum
Scott Bringans, James K Hane, Tammy Casey, Kar-Chun Tan, Richard Lipscombe, Peter S Solomon, Richard P Oliver
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-301
Abstract: In this study, we subjected soluble mycelial proteins to proteolysis followed by 2D LC MALDI-MS/MS. Comparison of the detected peptides with the gene models validated 2134 genes. 62% of these genes (1324) were not supported by prior EST evidence. Of the 2134 validated genes, all but 188 were version 2 annotations. Statistical analysis of the validated gene models revealed a preponderance of cytoplasmic and nuclear localised proteins, and proteins with intracellular-associated GO terms. These statistical associations are consistent with the source of the peptides used in the study. Comparison with a 6-frame translation of the S. nodorum genome assembly confirmed 905 existing gene annotations (including 119 not previously confirmed) and provided evidence supporting 144 genes with coding exon frameshift modifications, 604 genes with extensions of coding exons into annotated introns or untranslated regions (UTRs), 3 new gene annotations which were supported by tblastn to NR, and 44 potential new genes residing within un-assembled regions of the genome.We conclude that 2D LC MALDI-MS/MS is a powerful, rapid and economical tool to aid in the annotation of fungal genomic assemblies.The primary goal of most, if not all, genome sequence projects is to elucidate the gene, and hence protein, content of the organism. The gene set is the key tool to elucidate the interesting biological aspects of the organism. The prediction of genes from assembled genomic data has traditionally relied on two types of data; sequenced transcripts and homology to gene sequences in related organisms. Based on these data, various in silico methods to predict gene models can be applied. Experience in intensively studied model organisms suggests that such methods still struggle to provide a reliable gene set. As more and more genome sequences of distantly related non-model species become available, the need for efficient, rapid and accurate methods of gene prediction becomes more and more pronounced.J
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