Approximation of Bayesian inverse problems for PDEs

Inverse problems are often ill posed, with solutions that depend sensitively on data. In any numerical approach to the solution of such problems, regularization of some form is needed to counteract the resulting instability. This paper is based on an approach to regularization, employing a Bayesian formulation of the problem, which leads to a notion of well posedness for inverse problems, at the level of probability measures. The stability which results from this well posedness may be used as the basis for quantifying the approximation, in finite dimensional spaces, of inverse problems for functions. This paper contains a theory which utilizes this stability property to estimate the distance between the true and approximate posterior distributions, in the Hellinger metric, in terms of error estimates for approximation of the underlying forward problem. This is potentially useful as it allows for the transfer of estimates from the numerical analysis of forward problems into estimates for the solution of the related inverse problem. It is noteworthy that, when the prior is a Gaussian random field model, controlling differences in the Hellinger metric leads to control on the differences between expected values of polynomially bounded functions and operators, including the mean and covariance operator. The ideas are applied to some non-Gaussian inverse problems where the goal is determination of the initial condition for the Stokes or Navier–Stokes equation from Lagrangian and Eulerian observations, respectively

Variational data assimilation using targetted random walks

The variational approach to data assimilation is a widely used methodology for both online prediction and for reanalysis (offline hindcasting). In either of these scenarios it can be important to assess uncertainties in the assimilated state. Ideally it would be desirable to have complete information concerning the Bayesian posterior distribution for unknown state, given data. The purpose of this paper is to show that complete computational probing of this posterior distribution is now within reach in the offline situation. In this paper we will introduce an MCMC method which enables us to directly sample from the Bayesian\ud posterior distribution on the unknown functions of interest, given observations. Since we are aware that these\ud methods are currently too computationally expensive to consider using in an online filtering scenario, we frame this in the context of offline reanalysis. Using a simple random walk-type MCMC method, we are able to characterize the posterior distribution using only evaluations of the forward model of the problem, and of the model and data mismatch. No adjoint model is required for the method we use; however more sophisticated MCMC methods are available\ud which do exploit derivative information. For simplicity of exposition we consider the problem of assimilating data, either Eulerian or Lagrangian, into a low Reynolds number (Stokes flow) scenario in a two dimensional periodic geometry. We will show that in many cases it is possible to recover the initial condition and model error (which we describe as unknown forcing to the model) from data, and that with increasing amounts of informative data, the uncertainty in our estimations reduces

MCMC methods for functions modifying old algorithms to make\ud them faster

Many problems arising in applications result in the need\ud to probe a probability distribution for functions. Examples include Bayesian nonparametric statistics and conditioned diffusion processes. Standard MCMC algorithms typically become arbitrarily slow under the mesh refinement dictated by nonparametric description of the unknown function. We describe an approach to modifying a whole range of MCMC methods which ensures that their speed of convergence is robust under mesh refinement. In the applications of interest the data is often sparse and the prior specification is an essential part of the overall modeling strategy. The algorithmic approach that we describe is applicable whenever the desired probability measure has density with respect to a Gaussian process or Gaussian random field prior, and to some useful non-Gaussian priors constructed through random truncation. Applications are shown in density estimation, data assimilation in fluid mechanics, subsurface geophysics and image registration. The key design principle is to formulate the MCMC method for functions. This leads to algorithms which can be implemented via minor modification of existing algorithms, yet which show enormous speed-up on a wide range of applied problems

Efficient transduction of primary vascular cells by the rare adenovirus serotype 49 vector

Neointima formation and vascular remodelling through vascular smooth muscle cell migration and proliferation can limit the long term success of coronary interventions, for example in coronary artery bypass grafting (CABG). Ex vivo gene therapy has the potential to reduce unnecessary cell proliferation and limit neointima formation in vascular pathologies. To date the species C adenovirus serotype 5 (Ad5) has been commonly used for pre-clinical gene therapy, however its suitability is potentially limited by relatively poor tropism for vascular cells and high levels of pre-existing immunity in the population. To avoid these limitations, novel species of adenovirus are being tested; here we investigate the potential of adenovirus 49 (Ad49) for use in gene therapy. Transduction of primary human vascular cells by a range of adenovirus serotypes was assessed; Ad49 demonstrated highest transduction of both vascular smooth muscle and endothelial cells. Gene transfer with Ad49 in vascular smooth muscle and endothelial cells was possible following short exposure times (*lt;1hr) and with low MOI which is clinically relevant. Ex vivo delivery to surplus CABG tissue showed efficient gene transfer with Ad49, consistent with the in vitro findings. Luminal infusion of Ad49GFP into intact CABG samples ex vivo resulted in efficient vessel transduction. In addition, no seroprevelance rates to Ad49 were observed in a Scottish cohort of patients from cardiovascular clinics, thus circumventing issues with pre-existing immunity. Our results show Ad49 has tropism for vascular cells in vitro and ex vivo and demonstrate Ad49 may be an improved vector for local vascular gene therapy compared to current alternatives

Electrochemical detection of TNT at cobalt phthalocyanine mediated screen-printed electrodes and application to detection of airborne vapours

We describe the use of cobalt phthalocyanine as a mediator to improve the sensitivity for the electrochemical detection of TNT. Commercial screen-printed electrodes containing cobalt phthalocyanine were employed for determination of TNT. Improved sensitivities compared to screen-printed carbon electrodes without phthalocyanine were observed, current response for cyclic voltammetric measurements at modified electrodes being at least double that of unmodified electrodes. A synergistic effect between oxygen and TNT reduction was also observed. Correlation between TNT concentrations and sensor output was observed between 0–200 µM TNT. Initial proof-of-concept experiments combining electrochemical determinations, with the use of an air-sampling cyclone, are also reported

Binary Black-Hole Mergers in Magnetized Disks: Simulations in Full General Relativity

We present results from the first fully general relativistic, magnetohydrodynamic (GRMHD) simulations of an equal-mass black hole binary (BHBH) in a magnetized, circumbinary accretion disk. We simulate both the pre and post-decoupling phases of a BHBH-disk system and both "cooling" and "no-cooling" gas flows. Prior to decoupling, the competition between the binary tidal torques and the effective viscous torques due to MHD turbulence depletes the disk interior to the binary orbit. However, it also induces a two-stream accretion flow and mildly relativistic polar outflows from the BHs. Following decoupling, but before gas fills the low-density "hollow" surrounding the remnant, the accretion rate is reduced, while there is a prompt electromagnetic (EM) luminosity enhancement following merger due to shock heating and accretion onto the spinning BH remnant. This investigation, though preliminary, previews more detailed GRMHD simulations we plan to perform in anticipation of future, simultaneous detections of gravitational and EM radiation from a merging BHBH-disk system.Comment: 5 pages, 5 figure

Density-and trait-mediated effects of a parasite and a predator in a tri-trophic food web

1. Despite growing interest in ecological consequences of parasitism in food webs, relatively little is known about effects of parasites on long-term population dynamics of non-host species or about whether such effects are density- or trait- mediated. 2. We studied a tri-trophic food chain comprised of: (i) a bacterial basal resource (Serratia fonticola), (ii) an intermediate consumer (Paramecium caudatum), (iii) a top predator (Didinium nasutum), and (iv) a parasite of the intermediate consumer (Holospora undulata). A fully-factorial experimental manipulation of predator and parasite presence/absence was combined with analyses of population dynamics, modelling, and analyses of host (Paramecium) morphology and behavior. 3. Predation and parasitism each reduced the abundance of the intermediate consumer (Paramecium), and parasitism indirectly reduced the abundance of the basal resource (Serratia). However, in combination, predation and parasitism had non-additive effects on the abundance of the intermediate consumer, as well as on that of the basal resource. In both cases, the negative effect of parasitism seemed to be effaced by predation. 4. Infection of the intermediate consumer reduced predator abundance. Modelling and additional experimentation revealed that this was most likely due to parasite reduction of intermediate host abundance (a density-mediated effect), as opposed to changes in predator functional or numerical response. 5. Parasitism altered morphological and behavioural traits, by reducing host cell length and increasing the swimming speed of cells with moderate parasite loads. Additional tests showed no significant difference in Didinium feeding rate on infected and uninfected hosts, suggesting that the combination of these modifications does not affect host vulnerability to predation. However, estimated rates of encounter with Serratia based on these modifications were higher for infected Paramecium than for uninfected Paramecium. 6. A mixture of density-mediated and trait-mediated indirect effects of parasitism on non- host species creates rich and complex possibilities for effects of parasites in food webs that should be included in assessments of possible impacts of parasite eradication or introduction

Black Hole-Neutron Star Binaries in General Relativity: Quasiequilibrium Formulation

We present a new numerical method for the construction of quasiequilibrium models of black hole-neutron star binaries. We solve the constraint equations of general relativity, decomposed in the conformal thin-sandwich formalism, together with the Euler equation for the neutron star matter. We take the system to be stationary in a corotating frame and thereby assume the presence of a helical Killing vector. We solve these coupled equations in the background metric of a Kerr-Schild black hole, which accounts for the neutron star's black hole companion. In this paper we adopt a polytropic equation of state for the neutron star matter and assume large black hole--to--neutron star mass ratios. These simplifications allow us to focus on the construction of quasiequilibrium neutron star models in the presence of strong-field, black hole companions. We summarize the results of several code tests, compare with Newtonian models, and locate the onset of tidal disruption in a fully relativistic framework.Comment: 17 pages, 7 figures; added discussion, tables; PRD in pres

Collapse of Uniformly Rotating Stars to Black Holes and the Formation of Disks

Simulations in general relativity show that the outcome of collapse of a marginally unstable, uniformly rotating star spinning at the mass-shedding limit depends critically on the equation of state. For a very stiff equation of state, which is likely to characterize a neutron star, essentially all of the mass and angular momentum of the progenitor are swallowed by the Kerr black hole formed during the collapse, leaving nearly no residual gas to form a disk. For a soft equation of state with an adiabatic index \Gamma - 4/3 << 1, which characterizes a very massive or supermassive star supported predominantly by thermal radiation pressure, as much as 10% of the mass of the progenitor avoids capture and goes into a disk about the central hole. We present a semi-analytic calculation that corroborates these numerical findings and shows how the final outcome of such a collapse may be determined from simple physical considerations. In particular, we employ a simple energy variational principle with an approximate, post-Newtonian energy functional to determine the structure of a uniformly rotating, polytropic star at the onset of collapse as a function of polytropic index n, where \Gamma = 1+1/n. We then use this data to calculate the mass and spin of the final black hole and ambient disk. We show that the fraction of the total mass that remains in the disk falls off sharply as 3-n (equivalently, \Gamma - 4/3) increases.Comment: 11 pages, 2 figures, 2 tables, AASTeX; accepted to appear in The Astrophysical Journa

Head-on collisions of binary white dwarf--neutron stars: Simulations in full general relativity

We simulate head-on collisions from rest at large separation of binary white dwarf -- neutron stars (WDNSs) in full general relativity. Our study serves as a prelude to our analysis of the circular binary WDNS problem. We focus on compact binaries whose total mass exceeds the maximum mass that a cold degenerate star can support, and our goal is to determine the fate of such systems. A fully general relativistic hydrodynamic computation of a realistic WDNS head-on collision is prohibitive due to the large range of dynamical time scales and length scales involved. For this reason, we construct an equation of state (EOS) which captures the main physical features of NSs while, at the same time, scales down the size of WDs. We call these scaled-down WD models "pseudo-WDs (pWDs)". Using pWDs, we can study these systems via a sequence of simulations where the size of the pWD gradually increases toward the realistic case. We perform two sets of simulations; One set studies the effects of the NS mass on the final outcome, when the pWD is kept fixed. The other set studies the effect of the pWD compaction on the final outcome, when the pWD mass and the NS are kept fixed. All simulations show that 14%-18% of the initial total rest mass escapes to infinity. All remnant masses still exceed the maximum rest mass that our cold EOS can support (1.92 solar masses), but no case leads to prompt collapse to a black hole. This outcome arises because the final configurations are hot. All cases settle into spherical, quasiequilibrium configurations consisting of a cold NS core surrounded by a hot mantle, resembling Thorne-Zytkow objects. Extrapolating our results to realistic WD compactions, we predict that the likely outcome of a head-on collision of a realistic, massive WDNS system will be the formation of a quasiequilibrium Thorne-Zytkow-like object.Comment: 24 pages, 14 figures, matches PRD published version, tests of HRSC schemes with piecewise polytropes adde