Assimilation of GOSAT Methane in the Hemispheric CMAQ; Part I: Design of the Assimilation System

We present a parametric Kalman filter data assimilation system using GOSAT methane observations within the hemispheric CMAQ model. The assimilation system produces forecasts and analyses of concentrations and explicitly computes its evolving error variance while remaining computationally competitive with other data assimilation schemes such as 4-dimensional variational (4D-Var) and ensemble Kalman filter (EnKF). The error variance in this system is advected using the native advection scheme of the CMAQ model and updated at each analysis while the error correlations are kept fixed. We discuss extensions to the CMAQ model to include methane transport and emissions (both anthropogenic and natural) and perform a bias correction for the GOSAT observations. The results using synthetic observations show that the analysis error and analysis increments follow the advective flow while conserving the information content (i.e., total variance). We also demonstrate that the vertical error correlation contributes to the inference of variables down to the surface. In a companion paper, we use this assimilation system to obtain optimal assimilation of GOSAT observations.

Kinesin and Myosin Motors Compete to Drive Rich Multi-Phase Dynamics in Programmable Cytoskeletal Composites

The cytoskeleton of biological cells relies on a diverse population of motors, filaments, and binding proteins acting in concert to enable non-equilibrium processes ranging from mitosis to chemotaxis. The cytoskeleton’s versatile reconfigurability, programmed by interactions between its constituents, make it a foundational active matter platform. However, current active matter endeavors are limited largely to single force-generating components acting on a single substrate – far from the composite cytoskeleton in live cells. Here, we engineer actin-microtubule composites, driven by kinesin and myosin motors and tuned by crosslinkers, that restructure into diverse morphologies from interpenetrating filamentous networks to de-mixed amorphous clusters. Our Fourier analyses reveal that kinesin and myosin compete to delay kinesin-driven restructuring and suppress de-mixing and flow, while crosslinking accelerates reorganization and promotes actin-microtubule correlations. The phase space of non-equilibrium dynamics falls into three broad classes– slow reconfiguration, fast advective flow, and multi-mode ballistic dynamics – with structure-dynamics relations described by the relative contributions of elastic and dissipative responses to motor-generated forces.

Viscoelastic RNA entanglement and advective flow underlie nucleolar form and function

The nucleolus facilitates transcription, processing, and assembly of ribosomal RNA (rRNA), the most abundant RNA in cells. Nucleolar function is facilitated by its multiphase liquid properties, but nucleolar fluidity and its connection to ribosome biogenesis remain unclear. Here, we used quantitative imaging, mathematical modeling, and pulse-chase nucleotide labelling to map nucleolar rRNA dynamics. Inconsistent with a purely diffusive process, rRNA steadily expands away from the transcriptional sites, moving in a slow (~1 Å/s), radially-directed fashion. This motion reflects the viscoelastic properties of a highly concentrated gel of entangled rRNA, whose constant polymerization drives steady outward flow. We propose a new viscoelastic rRNA release model, where nucleolar rRNA cleavage and processing reduce entanglement, fluidizing the nucleolar periphery to facilitate release of mature pre-ribosomal particles.

Numerical studies of the advective flow of heptadecane in a horizontal layer with a longitudinal temperature gradient at the lower boundary

Numerical studies of the convective flow of heptadecane in a horizontal layer with a suddenly applied longitudinal temperature gradient at the lower high-thermal conductivity boundary have been carried out by the finite element method. A system of nonstationary dimensionless equations of free convection containing stream function, velocity vortex, and temperature as variables was solved. The calculations were carried out with a free upper boundary with and without taking into account the influence of the thermocapillary effect.

The challenge in measuring low-permeability materials: a comparison of different approaches

The German repository site selection procedure calls for a radioactive waste containment zone with a low-permeability host rock (kf<10-10 m s−1, StandAG §23, 5) and long-term sealing by barrier materials (EndlSiAnfV, 2020; ESK, 2019). The potential host rocks, clay and rock salt, as well as the considered barrier materials, bentonite and compacted crushed salt, show permeability in the range of kf∼10-16 m s−1 (K∼10-21 m2). These low values suggest that advective flow is as slow as diffusive mass flux. Measuring such low permeability with adequate accuracy challenges measurement setups and respective error evaluation. Methodologies. Several low-permeability measurements are carried out by transient tests, e.g. by monitoring controlled fluid pressure changes in: (1) pressure decay and (2) oscillating pulse tests. The first method (1) deviates permeability from the time needed to compensate pressure differences through the sample. The latter (2) monitors phase shift and amplitude attenuation of controlled pressure pulses passing through the sample. Any permeability measurement needs to be post-processed, e.g. for: (1) material-intrinsic controls (saturation state, storativity, the fluids' compressibility, etc.), (2) environmental controls (temperature, confining pressures, etc.) and (3) theoretical considerations (Klinkenberg correction, multi-phase wetting angles, etc.). Salts. A porosity-permeability relation was found down to K=10-19 m2 (e.g., Popp et al., 2007). Testing fluids were NaCl brine, oils, He and N2 as a fluid. As a matter of current research, a critical, low-permeability value might be associated with the so-called “percolation threshold” that defines the minimal requirements for an interconnected pore system (e.g., DAEF, 2016). Clays. A major challenge is the long duration of sample saturation (up to several months) and pressure equilibration (often days), as well as precise, temperature-compensated measuring and the determination of the samples' storativity (e.g., Winhausen et al., 2021). Testing fluids are commonly designed mixtures mimicking the rocks' pore waters. Geotechnical barrier materials. The permeability testing performed is similar to that of salt and clays mentioned above. However, both barrier materials, crushed salt and bentonite, have significant permeability early after emplacement. This is beneficial, as it allows the outflow of unwanted canister corrosion gases. Eventually, the permeability drops by orders of magnitude and the barriers become tight seals in the long-term. Here, identifying the gas entry/breakthrough pressure has been valuable (e.g., Rothfuchs et al., 2007). Figure 1 shows a preliminary sensitivity analysis as an example of pressure decay measurements. It suggests that the pressure equilibration term (c), and hence the test duration, is most sensitive to the calculation of low permeability. However, the large variation of (representative) material and environmental controls make permeability measurements complex. This workshop aims to encourage discussions on uncertainty and sensitivity of the influencing controls, such that it may lead to a “best-practice” guide for permeability measurements.

Nitrogen isotopic constraints on nutrient transport to the upper ocean

Ocean circulation supplies the surface ocean with the nutrients that fuel global ocean productivity. However, the mechanisms and rates of water and nutrient transport from the deep ocean to the upper ocean are poorly known. Here, we use the nitrogen isotopic composition of nitrate to place observational constraints on nutrient transport from the Southern Ocean surface into the global pycnocline (roughly the upper 1.2 km), as opposed to directly from the deep ocean. We estimate that 62 ± 5% of the pycnocline nitrate and phosphate originate from the Southern Ocean. Mixing, as opposed to advection, accounts for most of the gross nutrient input to the pycnocline. However, in net, mixing carries nutrients away from the pycnocline. Despite the quantitative dominance of mixing in the gross nutrient transport, the nutrient richness of the pycnocline relies on the large-scale advective flow, through which nutrient-rich water is converted to nutrient-poor surface water that eventually flows to the North Atlantic.

Advection Drives Nitrate Past the Microphytobenthos in Intertidal Sands, Fueling Deeper Denitrification

Nitrification rates are low in permeable intertidal sand flats such that the water column is the primary source of nitrate to the sediment. During tidal inundation, nitrate is supplied to the pore space by advection rather than diffusion, relieving the microorganisms that reside in the sand from nitrate limitation and supporting higher denitrification rates than those observed under diffusive transport. Sand flats are also home to an abundant community of benthic photosynthetic microorganisms, the microphytobenthos (MPB). Diatoms are an important component of the MPB that can take up and store high concentrations of nitrate within their cells, giving them the potential to alter nitrate availability in the surrounding porewater. We tested whether nitrate uptake by the MPB near the sediment surface decreases its availability to denitrifiers along deeper porewater flow paths. In laboratory experiments, we used NOx (nitrate + nitrite) microbiosensors to confirm that, in the spring, net NOx consumption in the zone of MPB photosynthetic activity was stimulated by light. The maximum potential denitrification rate, measured at high spatial resolution using microsensors with acetylene and nitrate added, occurred below 1.4 cm, much deeper than light-induced NOx uptake (0.13 cm). Therefore, the shallower MPB had the potential to decrease NOx supply to the deeper sediments and limit denitrification. However, when applying a realistic downward advective flow to sediment from our study site, NOx always reached the depths of maximum denitrification potential, regardless of light availability or season. We conclude that during tidal inundation porewater advection overwhelms any influence of shallow NOx uptake by the MPB and drives water column NOx to the depths of maximum denitrification potential.

Beach sand oil spills select for generalist microbial populations

The specialization-disturbance hypothesis predicts that, in the event of a disturbance, generalists are favored, while specialists are selected against. This hypothesis has not been rigorously tested in microbial systems and it remains unclear to what extent it could explain microbial community succession patterns following perturbations. Previous field observations of Pensacola Beach sands that were impacted by the Deepwater Horizon (DWH) oil spill provided evidence in support of the specialization-disturbance hypothesis. However, ecological drift as well as uncounted environmental fluctuations (e.g., storms) could not be ruled out as confounding factors driving these field results. In this study, the specialization-disturbance hypothesis was tested on beach sands, disturbed by DWH crude oil, ex situ in closed laboratory advective-flow chambers that mimic in situ conditions in saturated beach sediments. The chambers were inoculated with weathered DWH oil and unamended chambers served as controls. The time series of shotgun metagenomic and 16S rRNA gene amplicon sequence data from a two-month long incubation showed that functional diversity significantly increased while taxonomic diversity significantly declined, indicating a decrease in specialist taxa. Thus, results from this laboratory study corroborate field observations, providing verification that the specialization-disturbance hypothesis can explain microbial succession patterns in crude oil impacted beach sands.