A Selective Advantage for Conservative Viruses

In this letter we study the full semi-conservative treatment of a model for the co-evolution of a virus and an adaptive immune system. Regions of viability are calculated for both conservatively and semi-conservatively replicating viruses interacting with a realistic semi-conservatively replicating immune system. The conservative virus is found to have a selective advantage in the form of an ability to survive in regions with a wider range of mutation rates than its semi-conservative counterpart. This may help explain the existence of a rich range of viruses with conservatively replicating genomes, a trait which is found nowhere else in nature.Comment: 4 pages, 2 figure

Involutivity of integrals for sine-Gordon, modified KdV and potential KdV maps

Closed form expressions in terms of multi-sums of products have been given in \cite{Tranclosedform, KRQ} of integrals of sine-Gordon, modified Korteweg-de Vries and potential Korteweg-de Vries maps obtained as so-called $(p,-1)$-traveling wave reductions of the corresponding partial difference equations. We prove the involutivity of these integrals with respect to recently found symplectic structures for those maps. The proof is based on explicit formulae for the Poisson brackets between multi-sums of products.Comment: 24 page

A Resolved Molecular Gas Disk around the Nearby A Star 49 Ceti

The A star 49 Ceti, at a distance of 61 pc, is unusual in retaining a substantial quantity of molecular gas while exhibiting dust properties similar to those of a debris disk. We present resolved observations of the disk around 49 Ceti from the Submillimeter Array in the J=2-1 rotational transition of CO with a resolution of 1.0x1.2 arcsec. The observed emission reveals an extended rotating structure viewed approximately edge-on and clear of detectable CO emission out to a distance of ~90 AU from the star. No 1.3 millimeter continuum emission is detected at a 3-sigma sensitivity of 2.1 mJy/beam. Models of disk structure and chemistry indicate that the inner disk is devoid of molecular gas, while the outer gas disk between 40 and 200 AU from the star is dominated by photochemistry from stellar and interstellar radiation. We determine parameters for a model that reproduces the basic features of the spatially resolved CO J=2-1 emission, the spectral energy distribution, and the unresolved CO J=3-2 spectrum. We investigate variations in disk chemistry and observable properties for a range of structural parameters. 49 Ceti appears to be a rare example of a system in a late stage of transition between a gas-rich protoplanetary disk and a tenuous, virtually gas-free debris disk.Comment: 11 pages, 6 figures, accepted for publication in Ap

Lithostratigraphy and depositional episodes of the Oligocene carbonate-rich Tikorangi Formation, Taranaki Basin, New Zealand

The subsurface Oligocene Tikorangi Formation is a unique and important oil producer in the onshore Waihapa-Ngaere Field, Taranaki Basin, being the only carbonate and fracture-producing reservoir within the basin. Core sample data from seven onshore wells (foredeep megafacies) and a single offshore well (basinal megafacies) are correlated with a suite of sonic and gamma-ray geophysical well log data to derive interpretative carbonate facies for the Tikorangi Formation. Four mixed siliciclastic-carbonate to carbonate facies have been defined: facies A-calcareous siliciclastite (75% carbonate). Single or interbedded combinations of these facies form the basis for identifying nine major lithostratigraphic units in the Tikorangi Formation that are correlatable between the eight wells in this study.The Tikorangi Formation accumulated across a shelf-slope-basin margin within a tectonically diversified basin setting, notably involving considerable off-shelf redeposition of sediment into a bounding foredeep. Analysis of gamma, sonic, and resistivity well logs identifies five major episodes of sedimentary evolution. Episode I comprises retrogradational siliciclastic-dominated redeposited units associated with foredeep subsidence. Episode II is a continuation of episode I retrogradation, but with increased mass-redeposited carbonate influx during accelerated foredeep subsidence and relative sea-level rise, the top marking the maximum flooding surface. Episode III involves a progradational sequence comprising relatively pure redeposited carbonate units associated with declining subsidence rates and minimal siliciclastic input, with movement of facies belts basinward. Episode IV consists of prograding aggradation involving essentially static facies belts dominated by often thick, periodically mass-emplaced, carbonate-rich units separated by thin background siliciclastic shale-like units. Episode V is a retrogradational sequence marking the reintroduction of siliciclastic material into the basin following uplift of Mesozoic basement associated with accelerated compressional tectonics along the Australia-Pacific plate boundary, initially diluting and ultimately extinguishing carbonate production factories and terminating deposition of the Tikorangi Formation

Petrogenesis of the Tikorangi Formation fracture reservoir, Waihapa-Ngaere Field, Taranaki Basin

The subsurface mid-Tertiary Tikorangi Formation is the sole limestone and the only fracture-producing hydrocarbon reservoir within Taranaki Basin. This study, based on core material from seven wells in the onshore Waihapa/Ngaere Field, uses a range of petrographic (standard, CL, UV, SEM) and geochemical techniques (stable isotope, trace element data, XRD) to unravel a complex diagenetic history for the Tikorangi Formation. A series of eight major geological-diagenetic events for the host rock and fracture systems have been established, ranging from burial cementation through to hydrocarbon emplacement within mineralized fractures. For each diagenetic event a probable temperature field has been identified which, combined with a geohistory plot, has enabled the timing of events to be determined. This study has shown that the Tikorangi Formation comprises a complex mixed siliciclastic-carbonate-rich sequence of rocks that exhibit generally tight, pressure-dissolved, and well cemented fabrics with negligible porosity and permeability other than in fractures. Burial cementation of the host rocks occurred at temperatures of 27-37°C from about 0.5-1.0 km burial depths. Partial replacement dolomitisation occurred during late burial diagenesis at temperatures of 36-50°C and at burial depths of about 1.0 km, without any secondary porosity development. Fracturing occurred after dolomitisation and was associated with compression and thrusting on the Taranaki Fault. The location of more carbonate/dolomite-rich units may have implications for the location of better-developed fracture network systems and for hydrocarbon prospectivity and production. Hydrocarbon productivity has been ultimately determined by original depositional facies, diagenesis, and deformation. Within the fracture systems, a complex suite of vein calcite, dolomite, quartzine, and celestite minerals has been precipitated prior to hydrocarbon emplacement, which have substantially healed and reduced fracture porosities and permeabilities. The occurrence of multiple vein mineral phases, collectively forming a calcite/dolomite-celestite-quartzine mineral assemblage, points to fluid compositions varying both spatially and temporally. The fluids responsible for vein mineralisation in the Tikorangi Formation probably involved waters of diverse origins and compositions. Vein mineralisation records a history of changing pore fluid chemistry and heating during burial, punctuated by changes in the relative input and mixing of downward circulating meteoric and upwelling basinal fluids. A sequence of mineralisation events and their probable burial depth/temperature fields have been defined, ranging from temperatures of 50-80°C and burial depths of 1.0-2.3 km. Hydrocarbon emplacement has occurred over the last 6 m.y. following the vein mineralization events. The Tikorangi Formation must continue to be viewed as a potential fracture reservoir play within Taranaki Basin

Lithostratigraphy and depositional episodes of the Oligocene carbonate-rich Tikorangi Formation, Taranaki Basin, New Zealand

The subsurface Oligocene Tikorangi Formation is a unique and important oil producer in the onshore Waihapa-Ngaere Field, Taranaki Basin, being the only carbonate and fracture-producing reservoir within the basin. Core sample data from seven onshore wells (foredeep megafacies) and a single offshore well (basinal megafacies) are correlated with a suite of sonic and gamma-ray geophysical well log data to derive interpretative carbonate facies for the Tikorangi Formation. Four mixed siliciclastic-carbonate to carbonate facies have been defined: facies A-calcareous siliciclastite (75% carbonate). Single or interbedded combinations of these facies form the basis for identifying nine major lithostratigraphic units in the Tikorangi Formation that are correlatable between the eight wells in this study.The Tikorangi Formation accumulated across a shelf-slope-basin margin within a tectonically diversified basin setting, notably involving considerable off-shelf redeposition of sediment into a bounding foredeep. Analysis of gamma, sonic, and resistivity well logs identifies five major episodes of sedimentary evolution. Episode I comprises retrogradational siliciclastic-dominated redeposited units associated with foredeep subsidence. Episode II is a continuation of episode I retrogradation, but with increased mass-redeposited carbonate influx during accelerated foredeep subsidence and relative sea-level rise, the top marking the maximum flooding surface. Episode III involves a progradational sequence comprising relatively pure redeposited carbonate units associated with declining subsidence rates and minimal siliciclastic input, with movement of facies belts basinward. Episode IV consists of prograding aggradation involving essentially static facies belts dominated by often thick, periodically mass-emplaced, carbonate-rich units separated by thin background siliciclastic shale-like units. Episode V is a retrogradational sequence marking the reintroduction of siliciclastic material into the basin following uplift of Mesozoic basement associated with accelerated compressional tectonics along the Australia-Pacific plate boundary, initially diluting and ultimately extinguishing carbonate production factories and terminating deposition of the Tikorangi Formation

The staircase method: integrals for periodic reductions of integrable lattice equations

We show, in full generality, that the staircase method provides integrals for mappings, and correspondences, obtained as traveling wave reductions of (systems of) integrable partial difference equations. We apply the staircase method to a variety of equations, including the Korteweg-De Vries equation, the five-point Bruschi-Calogero-Droghei equation, the QD-algorithm, and the Boussinesq system. We show that, in all these cases, if the staircase method provides r integrals for an n-dimensional mapping, with 2r<n, then one can introduce q<= 2r variables, which reduce the dimension of the mapping from n to q. These dimension-reducing variables are obtained as joint invariants of k-symmetries of the mappings. Our results support the idea that often the staircase method provides sufficiently many integrals for the periodic reductions of integrable lattice equations to be completely integrable. We also study reductions on other quad-graphs than the regular 2D lattice, and we prove linear growth of the multi-valuedness of iterates of high-dimensional correspondences obtained as reductions of the QD-algorithm.Comment: 40 pages, 23 Figure

Tuning quantum fluctuations with an external magnetic field: Casimir-Polder interaction between an atom and a graphene sheet

We investigate the dispersive Casimir-Polder interaction between a Rubidium atom and a suspended graphene sheet subjected to an external magnetic field B. We demonstrate that this concrete physical system allows for an unprecedented control of dispersive interactions at micro and nanoscales. Indeed, we show that the application of an external magnetic field can induce a 80% reduction of the Casimir-Polder energy relative to its value without the field. We also show that sharp discontinuities emerge in the Casimir-Polder interaction energy for certain values of the applied magnetic field at low temperatures. Moreover, for sufficiently large distances these discontinuities show up as a plateau-like pattern with a quantized Casimir-Polder interaction energy, in a phenomenon that can be explained in terms of the quantum Hall effect. In addition, we point out the importance of thermal effects in the Casimir-Polder interaction, which we show that must be taken into account even for considerably short distances. In this case, the discontinuities in the atom-graphene dispersive interaction do not occur, which by no means prevents the tuning of the interaction in ~50% by the application of the external magnetic field.Comment: The first two authors listed contributed equally to this work and are joint first authors. 5 pages, 4 figure