Simplifying transformations for nonlinear systems: Part I, an optimisation-based variant of normal form analysis

This paper introduces the idea of a ‘simplifying transformation’ for nonlinear structural dynamic systems. The idea simply stated; is to bring under one heading, those transformations which ‘simplify’ structural dynamic systems or responses in some sense. The equations of motion may be cast in a simpler form or decoupled (and in this sense, nonlinear modal analysis is encompassed) or the responses may be modified in order to isolate and remove certain components. It is the latter sense of simplification which is considered in this paper. One can regard normal form analysis in a way as the removal of superharmonic content from nonlinear system response. In the current paper, this problem is cast in an optimisation form and the differential evolution algorithm is used

Relating tropical ocean clouds to moist processes using water vapor isotope measurements

We examine the co-variations of tropospheric water vapor, its isotopic composition and cloud types and relate these distributions to tropospheric mixing and distillation models using satellite observations from the Aura Tropospheric Emission Spectrometer (TES) over the summertime tropical ocean. Interpretation of these process distributions must take into account the sensitivity of the TES isotope and water vapor measurements to variations in cloud, water, and temperature amount. Consequently, comparisons are made between cloud-types based on the International Satellite Cloud Climatology Project (ISSCP) classification; these are clear sky, non-precipitating (e.g., cumulus), boundary layer (e.g., stratocumulus), and precipitating clouds (e.g. regions of deep convection). In general, we find that the free tropospheric vapor over tropical oceans does not strictly follow a Rayleigh model in which air parcels become dry and isotopically depleted through condensation. Instead, mixing processes related to convection as well as subsidence, and re-evaporation of rainfall associated with organized deep convection all play significant roles in controlling the water vapor distribution. The relative role of these moisture processes are examined for different tropical oceanic regions

How and why DNA barcodes underestimate the diversity of microbial eukaryotes

Background: Because many picoplanktonic eukaryotic species cannot currently be maintained in culture, direct sequencing of PCR-amplified 18S ribosomal gene DNA fragments from filtered sea-water has been successfully used to investigate the astounding diversity of these organisms. The recognition of many novel planktonic organisms is thus based solely on their 18S rDNA sequence. However, a species delimited by its 18S rDNA sequence might contain many cryptic species, which are highly differentiated in their protein coding sequences. Principal Findings: Here, we investigate the issue of species identification from one gene to the whole genome sequence. Using 52 whole genome DNA sequences, we estimated the global genetic divergence in protein coding genes between organisms from different lineages and compared this to their ribosomal gene sequence divergences. We show that this relationship between proteome divergence and 18S divergence is lineage dependant. Unicellular lineages have especially low 18S divergences relative to their protein sequence divergences, suggesting that 18S ribosomal genes are too conservative to assess planktonic eukaryotic diversity. We provide an explanation for this lineage dependency, which suggests that most species with large effective population sizes will show far less divergence in 18S than protein coding sequences. Conclusions: There is therefore a trade-off between using genes that are easy to amplify in all species, but which by their nature are highly conserved and underestimate the true number of species, and using genes that give a better description of the number of species, but which are more difficult to amplify. We have shown that this trade-off differs between unicellular and multicellular organisms as a likely consequence of differences in effective population sizes. We anticipate that biodiversity of microbial eukaryotic species is underestimated and that numerous ''cryptic species'' will become discernable with the future acquisition of genomic and metagenomic sequences

The vertical distribution of ozone instantaneous radiative forcing from satellite and chemistry climate models

We evaluate the instantaneous radiative forcing (IRF) of tropospheric ozone predicted by four state-of-the-art global chemistry climate models (AM2-Chem, CAM-Chem, ECHAM5-MOZ, and GISS-PUCCINI) against ozone distribution observed from the NASA Tropospheric Emission Spectrometer (TES) during August 2006. The IRF is computed through the application of an observationally constrained instantaneous radiative forcing kernels (IRFK) to the difference between TES and model-predicted ozone. The IRFK represent the sensitivity of outgoing longwave radiation to the vertical and spatial distribution of ozone under all-sky condition. Through this technique, we find total tropospheric IRF biases from -0.4 to + 0.7 W/m(2) over large regions within the tropics and midlatitudes, due to ozone differences over the region in the lower and middle troposphere, enhanced by persistent bias in the upper troposphere-lower stratospheric region. The zonal mean biases also range from -30 to + 50 mW/m(2) for the models. However, the ensemble mean total tropospheric IRF bias is less than 0.2 W/m(2) within the entire troposphere

Electrostatic Patch Effect in Cylindrical Geometry. I. Potential and Energy between Slightly Non-Coaxial Cylinders

We study the effect of any uneven voltage distribution on two close cylindrical conductors with parallel axes that are slightly shifted in the radial and by any length in the axial direction. The investigation is especially motivated by certain precision measurements, such as the Satellite Test of the Equivalence Principle (STEP). By energy conservation, the force can be found as the energy gradient in the vector of the shift, which requires determining potential distribution and energy in the gap. The boundary value problem for the potential is solved, and energy is thus found to the second order in the small transverse shift, and to lowest order in the gap to cylinder radius ratio. The energy consists of three parts: the usual capacitor part due to the uniform potential difference, the one coming from the interaction between the voltage patches and the uniform voltage difference, and the energy of patch interaction, entirely independent of the uniform voltage. Patch effect forces and torques in the cylindrical configuration are derived and analyzed in the next two parts of this work.Comment: 26 pages, 1 Figure. Submitted to Classical and Quantum Gravit

Unexpected mitochondrial genome diversity revealed by targeted single-cell genomics of heterotrophic flagellated protists

This is the author accepted manuscript. The final version is available from Nature Research via the DOI in this recordData availability: Complete mtDNA sequences assembled from this study are available at GenBank under the accession numbers MK188935 to MK188947, MN082144 and MN082145. Sequencing data are available under NCBI BioProject PRJNA379597. Reads have been deposited at NCBI Sequence Read Archive with accession number SRP102236. Partial mtDNA contigs and other important contigs mentioned in the text are available from Figshare at https://doi.org/10.6084/m9.figshare.7314728. Nuclear SAG assemblies are available from Figshare at https://doi.org/10.6084/m9.figshare.7352966. A protocol is available from protocols.io at: https://doi.org/10.17504/protocols.io.ywpfxdn.Code availability: The bioinformatic workflow is available at https://doi.org/10.5281/zenodo.192677; additional statistical analysis code is available at https://doi.org/10.6084/m9.figshare.9884309.Most eukaryotic microbial diversity is uncultivated, under-studied and lacks nuclear genome data. Mitochondrial genome sampling is more comprehensive, but many phylogenetically important groups remain unsampled. Here, using a single-cell sorting approach combining tubulin-specific labelling with photopigment exclusion, we sorted flagellated heterotrophic unicellular eukaryotes from Pacific Ocean samples. We recovered 206 single amplified genomes, predominantly from underrepresented branches on the tree of life. Seventy single amplified genomes contained unique mitochondrial contigs, including 21 complete or near-complete mitochondrial genomes from formerly under-sampled phylogenetic branches, including telonemids, katablepharids, cercozoans and marine stramenopiles, effectively doubling the number of available samples of heterotrophic flagellate mitochondrial genomes. Collectively, these data identify a dynamic history of mitochondrial genome evolution including intron gain and loss, extensive patterns of genetic code variation and complex patterns of gene loss. Surprisingly, we found that stramenopile mitochondrial content is highly plastic, resembling patterns of variation previously observed only in plants.Gordon and Betty Moore FoundationLeverhulme TrustDavid and Lucile Packard FoundationRoyal SocietyEuropean Molecular Biology OrganizationCONICYT FONDECYTGenome Canad

Nanohertz Frequency Determination for the Gravity Probe B HF SQUID Signal

In this paper, we present a method to measure the frequency and the frequency change rate of a digital signal. This method consists of three consecutive algorithms: frequency interpolation, phase differencing, and a third algorithm specifically designed and tested by the authors. The succession of these three algorithms allowed a 5 parts in 10^10 resolution in frequency determination. The algorithm developed by the authors can be applied to a sampled scalar signal such that a model linking the harmonics of its main frequency to the underlying physical phenomenon is available. This method was developed in the framework of the Gravity Probe B (GP-B) mission. It was applied to the High Frequency (HF) component of GP-B's Superconducting QUantum Interference Device (SQUID) signal, whose main frequency fz is close to the spin frequency of the gyroscopes used in the experiment. A 30 nHz resolution in signal frequency and a 0.1 pHz/sec resolution in its decay rate were achieved out of a succession of 1.86 second-long stretches of signal sampled at 2200 Hz. This paper describes the underlying theory of the frequency measurement method as well as its application to GP-B's HF science signal.Comment: The following article has been submitted to Review of Scientific Instruments. After it is published, it will be found at (http://rsi.aip.org/

Evaluation of ACCMIP Outgoing Longwave Radiation from Tropospheric Ozone Using TES Satellite Observations.

We use simultaneous observations of tropospheric ozone and outgoing longwave radiation (OLR) sensitivity to tropospheric ozone from the Tropospheric Emission Spectrometer (TES) to evaluate model tropospheric ozone and its effect on OLR simulated by a suite of chemistry-climate models that participated in the Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP). The ensemble mean of ACCMIP models show a persistent but modest tropospheric ozone low bias (5-20 ppb) in the Southern Hemisphere (SH) and modest high bias (5-10 ppb) in the Northern Hemisphere (NH) relative to TES ozone for 2005-2010. These ozone biases have a significant impact on the OLR. Using TES instantaneous radiative kernels (IRK), we show that the ACCMIP ensemble mean tropospheric ozone low bias leads up to 120mW/ sq. m OLR high bias locally but zonally compensating errors reduce the global OLR high bias to 39+/- 41mW/ sq. m relative to TES data. We show that there is a correlation (Sq. R = 0.59) between the magnitude of the ACCMIP OLR bias and the deviation of the ACCMIP preindustrial to present day (1750-2010) ozone radiative forcing (RF) from the ensemble ozone RF mean. However, this correlation is driven primarily by models whose absolute OLR bias from tropospheric ozone exceeds 100mW/ sq. m. Removing these models leads to a mean ozone radiative forcing of 394+/- 42mW/ sq. m. The mean is about the same and the standard deviation is about 30% lower than an ensemble ozone RF of 384 +/- 60mW/ sq. m derived from 14 of the 16 ACCMIP models reported in a companion ACCMIP study. These results point towards a profitable direction of combining satellite observations and chemistry-climate model simulations to reduce uncertainty in ozone radiative forcing