Implementation of higher-order absorbing boundary conditions for the Einstein equations

We present an implementation of absorbing boundary conditions for the Einstein equations based on the recent work of Buchman and Sarbach. In this paper, we assume that spacetime may be linearized about Minkowski space close to the outer boundary, which is taken to be a coordinate sphere. We reformulate the boundary conditions as conditions on the gauge-invariant Regge-Wheeler-Zerilli scalars. Higher-order radial derivatives are eliminated by rewriting the boundary conditions as a system of ODEs for a set of auxiliary variables intrinsic to the boundary. From these we construct boundary data for a set of well-posed constraint-preserving boundary conditions for the Einstein equations in a first-order generalized harmonic formulation. This construction has direct applications to outer boundary conditions in simulations of isolated systems (e.g., binary black holes) as well as to the problem of Cauchy-perturbative matching. As a test problem for our numerical implementation, we consider linearized multipolar gravitational waves in TT gauge, with angular momentum numbers l=2 (Teukolsky waves), 3 and 4. We demonstrate that the perfectly absorbing boundary condition B_L of order L=l yields no spurious reflections to linear order in perturbation theory. This is in contrast to the lower-order absorbing boundary conditions B_L with L<l, which include the widely used freezing-Psi_0 boundary condition that imposes the vanishing of the Newman-Penrose scalar Psi_0.Comment: 25 pages, 9 figures. Minor clarifications. Final version to appear in Class. Quantum Grav

Explicit solution of the linearized Einstein equations in TT gauge for all multipoles

We write out the explicit form of the metric for a linearized gravitational wave in the transverse-traceless gauge for any multipole, thus generalizing the well-known quadrupole solution of Teukolsky. The solution is derived using the generalized Regge-Wheeler-Zerilli formalism developed by Sarbach and Tiglio.Comment: 9 pages. Minor corrections, updated references. Final version to appear in Class. Quantum Gra

Simple, stable, and affordable : Towards long-term ecosystem scale flux measurements of VOCs

Non peer reviewe

Lag time determination in DEC measurements with PTR-MS

The disjunct eddy covariance (DEC) method has emerged as a popular technique for micrometeorological flux measurements of volatile organic compounds (VOCs). It has usually been combined with proton transfer reaction mass spectrometry (PTR-MS), an online technique for VOC concentration measurements. However, the determination of the lag time between wind and concentration measurements has remained an important challenge. To address this issue, we studied the effect of different lag time methods on DEC fluxes. The analysis was based on both actual DEC measurements with PTR-MS and simulated DEC data derived from high frequency H&lt;sub&gt;2&lt;/sub&gt;O measurements with an infrared gas analyzer. Conventional eddy covariance fluxes of H&lt;sub&gt;2&lt;/sub&gt;O served as a reference in the DEC simulation. The individual flux measurements with PTR-MS were rather sensitive to the lag time methods, but typically this effect averaged out when the median fluxes were considered. The DEC simulation revealed that the maximum covariance method was prone to overestimation of the absolute values of fluxes. The constant lag time methods, one based on a value calculated from the sampling flow and the sampling line dimensions and the other on a typical daytime value, had a tendency to underestimate. The visual assessment method and our new averaging approach utilizing running averaged covariance functions did not yield statistically significant errors and thus fared better than the habitual choice, the maximum covariance method. Given this feature and the potential for automatic flux calculation, we recommend using the averaging approach in DEC measurements with PTR-MS. It also seems well suited to conventional eddy covariance applications when measuring fluxes near the detection limit

Testing outer boundary treatments for the Einstein equations

Various methods of treating outer boundaries in numerical relativity are compared using a simple test problem: a Schwarzschild black hole with an outgoing gravitational wave perturbation. Numerical solutions computed using different boundary treatments are compared to a `reference' numerical solution obtained by placing the outer boundary at a very large radius. For each boundary treatment, the full solutions including constraint violations and extracted gravitational waves are compared to those of the reference solution, thereby assessing the reflections caused by the artificial boundary. These tests use a first-order generalized harmonic formulation of the Einstein equations. Constraint-preserving boundary conditions for this system are reviewed, and an improved boundary condition on the gauge degrees of freedom is presented. Alternate boundary conditions evaluated here include freezing the incoming characteristic fields, Sommerfeld boundary conditions, and the constraint-preserving boundary conditions of Kreiss and Winicour. Rather different approaches to boundary treatments, such as sponge layers and spatial compactification, are also tested. Overall the best treatment found here combines boundary conditions that preserve the constraints, freeze the Newman-Penrose scalar Psi_0, and control gauge reflections.Comment: Modified to agree with version accepted for publication in Class. Quantum Gra

Grass silage for biorefinery – Separation efficiency and aerobic stability of silage and solid fraction

201

Structure alignment based on coding of local geometric measures

BACKGROUND: A structure alignment method based on a local geometric property is presented and its performance is tested in pairwise and multiple structure alignments. In this approach, the writhing number, a quantity originating from integral formulas of Vassiliev knot invariants, is used as a local geometric measure. This measure is used in a sliding window to calculate the local writhe down the length of the protein chain. By encoding the distribution of writhing numbers across all the structures in the protein databank (PDB), protein geometries are represented in a 20-letter alphabet. This encoding transforms the structure alignment problem into a sequence alignment problem and allows the well-established algorithms of sequence alignment to be employed. Such geometric alignments offer distinct advantages over structural alignments in Cartesian coordinates as it better handles structural subtleties associated with slight twists and bends that distort one structure relative to another. RESULTS: The performance of programs for pairwise local alignment (TLOCAL) and multiple alignment (TCLUSTALW) are readily adapted from existing code for Smith-Waterman pairwise alignment and for multiple sequence alignment using CLUSTALW. The alignment algorithms employed a blocked scoring matrix (TBLOSUM) generated using the frequency of changes in the geometric alphabet of a block of protein structures. TLOCAL was tested on a set of 10 difficult proteins and found to give high quality alignments that compare favorably to those generated by existing pairwise alignment programs. A set of protein comparison involving hinged structures was also analyzed and TLOCAL was seen to compare favorably to other alignment methods. TCLUSTALW was tested on a family of protein kinases and reveal conserved regions similar to those previously identified by a hand alignment. CONCLUSION: These results show that the encoding of the writhing number as a geometric measure allow high quality structure alignments to be generated using standard algorithms of sequence alignment. This approach provides computationally efficient algorithms that allow fast database searching and multiple structure alignment. Because the geometric measure can employ different window sizes, the method allows the exploration of alignments on different, well-defined length scales

Axisymmetric evolution of Einstein equations and mass conservation

For axisymmetric evolution of isolated systems, we prove that there exists a gauge such that the total mass can be written as a positive definite integral on the spacelike hypersurfaces of the foliation and the integral is constant along the evolution. The conserved mass integral controls the square of the extrinsic curvature and the square of first derivatives of the intrinsic metric. We also discuss applications of this result for the global existence problem in axial symmetry.Comment: A mistake in the proof of Lemma 5.1 is corrected. This version includes the Corrigendum that appears in Class. Quantum Grav. 26 (2009) 12980