Revised Michaelis-Menten rate law with time-varying molecular concentrations

Despite over a century's use as a dominant paradigm in the description of biochemical rate processes, the Michaelis-Menten (MM) rate law stands on the restrictive assumption that the concentration of the complex of interacting molecules, at each moment, approaches an equilibrium much faster than the molecular concentration changes. The increasingly-appreciated, remedied form of the MM rate law is also based on this quasi-steady state assumption. Although this assumption may be valid for a range of biochemical systems, the exact extent of such systems is not clear. In this study, we relax the quasi-steady state requirement and propose the revised MM rate law for the interactions of molecules with active concentration changes over time. Our revised rate law, characterized by rigorously-derived time delay effects in molecular complex formation, improves the accuracy of models especially for protein-protein and protein-DNA interactions. Our simulation and empirical data analysis show that the improvement is not limited to the quantitatively better characterization of the dynamics, but also allows the prediction for qualitatively new patterns in the systems of interest. The latter include the oscillation condition and period patterns of the mammalian circadian clock and the spontaneous rhythmicity in the degradation rates of circadian proteins, both not properly captured by the previous approaches. Moreover, our revised rate law is capable of more accurate parameter estimation. This work offers an analytical framework for understanding rich dynamics of biomolecular systems, which goes beyond the quasi-steady state assumption.

An Object-Based Method for Tracking Convective Storms in Convection Allowing Models

The steady-state assumption commonly used in object-based tracking algorithms may be insufficient to determine the right track when a convective storm goes through a complicated evolution. Such an issue is exacerbated by the relatively coarse output frequency of current convection allowing model (CAM) forecasts (e.g., hourly), giving rise to many spatially well resolved but temporally not well resolved storms that steady-state assumption could not account for. To reliably track simulated storms in CAM outputs, this study proposed an object-based method with two new features. First, the method explicitly estimated the probability of each probable track based on either its immediate past and future motion or a reliable “first-guess motion” derived from storm climatology or near-storm environmental variables. Second, object size was incorporated into the method to help identify temporally not well resolved storms and minimize false tracks derived for them. Parameters of the new features were independently derived from a storm evolution analysis using 2-min Multi-Radar Multi-Sensor (MRMS) data and hourly CAM forecasts produced by the University of Oklahoma (OU) Multiscale data Assimilation and Predictability Laboratory (MAP) from May 2019. The performance of the new method was demonstrated with hourly MRMS and CAM forecast examples from May 2018. A systematic evaluation of four severe weather events indicated 99% accuracy achieved for over 600 hourly MRMS tracks derived with the proposed tracking method.

Toward transient subgrid-scale gravity wave representation in atmospheric models. Part I: Propagation model including non-dissipative direct wave-mean-flow interactions

Current gravity-wave (GW) parameterization (GWP) schemes are using the steady-state assumption, where an instantaneous balance between GWs and mean flow is postulated, thereby neglecting transient, non-dissipative direct interactions between the GW field and the resolved flow. These schemes rely exclusively on wave dissipation, by GW breaking or near critical layers, as a mechanism leading to forcing of the mean flow. In a transient GWP, without steady-state assumption, non-dissipative direct wave-mean-flow interactions are enabled as an additional mechanism. Idealized studies have shown that this is potentially important, so that the transient GWP Multi-Scale Gravity-Wave Model (MS-GWaM) has been implemented into a state-of-the-art weather and climate model. In this implementation, MS-GWaM leads to a zonal-mean circulation well in agreement with observations, and increases GW momentum-flux intermittency as compared to steady-state GWPs, bringing it into better agreement with super-pressure balloon observations. Transient effects taken into account by MS-GWaM are shown to make a difference even on monthly time-scales: in comparison with steady-state GWPs momentum fluxes in the lower stratosphere are increased and the amount of the missing drag at Southern Hemispheric high latitudes is decreased to a modest but non-negligible extent. An analysis of the contribution of different wavelengths to the GW signal in MS-GWaM suggests that small scale GWs play an important role down to horizontal and vertical wavelengths of 50km (or even smaller) and 200m respectively.

A closer look at the relationship between slab (un)bending and double seismic zone seismicity

<p>The origin of double seismic zones (DSZs), parallel planes of intraslab seismicity observed in many subduction zones around the globe, is still highly debated. While most researchers assume that fluid release from prograde metamorphic reactions in the slab is an important control on DSZ occurrence, the role of slab unbending is currently unclear.<br>Slab bending at the outer rise is instrumental in hydrating the downgoing oceanic plate through bend faulting, and is evident from earthquake focal mechanisms (prevalence of shallow normal faulting events). Observations from NE Japan show that focal mechanisms of DSZ earthquakes are downdip compressive in the upper and downdip extensive in the lower plane of the DSZ, which strongly hints at slab unbending. This coincidence of slab unbending and DSZ seismicity in NE Japan has given rise to several models in which unbending forces are a prerequisite for DSZ occurrence.</p><p>To globally test a potential correlation of slab unbending with DSZ seismicity, we derived downdip slab surface curvatures on trench-perpendicular profiles every 50 km along all major oceanic slabs using the slab2 grids of slab surface depth. We here make a steady-state assumption, i.e. we assume that the slab geometry is relatively constant with time, so that the downdip gradient of slab curvature corresponds to slab (un)bending. We compiled the loci and depth extent of all DSZ observations avalable in literature, and compare these to the slab bending or unbending estimates.</p><p>Preliminary results indicate that while there is a clear correspondence between the depth of slab unbending to DSZ seismicity in the Japan-Kurile slab, most other slabs do not show this correlation. Moreover, some DSZs deviate from the above-mentioned focal mechanism pattern and exhibit downdip extension in both planes (e.g. Northern Chile, New Zealand). It appears that the global variability of slab geometries in the depth range 50-200 km is larger than anticipated, and DSZ seismicity is not limited to slabs where unbending is prevalent at these depths. The Northern Chile case is especially interesting because focal mechanisms there not only do not fit the pattern observed in NE Japan, but also can not be explained with the current slab geometry alone. This could indicate a direct influence of ongoing metamorphic reactions on focal mechanisms (e.g. via volume reduction and densification), or it may be a hint that our steady-state assumption is invalid for the Nazca slab here (i.e. that it is in the process of changing its geometry).</p>

Intermittency of gravity waves modelled by a transient gravity-wave parametrization coupled with convective sources

<p class="Normal tm5"><span class="tm6">The intermittency of gravity waves (GWs) is investigated using Multi-Scale Gravity Wave Model (MS-GWaM) implemented in the upper-atmosphere extension of ICON model. The intermittency of GWs is originated from that of wave sources but altered during propagation of the waves. Conventional GW parametrization (GWP), which diagnoses vertical profiles of GW properties under the steady-state assumption, can take into account the source intermittency if the GWP employs flow-dependent sources, while it cannot present the change of intermittency by transient evolutions of GWs. MS-GWaM is a prognostic model that explicitly solves the evolution of positions of waves (as well as their wavenumbers and amplitudes) in time and thus capable of describing the intermittency change. In order to include the source intermittency and variability, we couple the convective source, as diagnosed by subgrid-scale cumulus parametrization in ICON, to MS-GWaM, based on an analytic formulation of GW response to this source. In addition to this, a spatio-temporally uniform, persistent source is prescribed in the extratropics to take into account other non-orographic sources. Orographic sources are currently not used. The GW intermittency is measured by the Gini index, and is found to be quite high in the tropics, compared to that in the extratropics. In both regions, the index has similar values to those obtained from superpressure balloon observations reported in previous studies. A control experiment is performed using GWP based on the steady-state assumption, but coupled to the same wave sources, to assess the effects of transient modelling using MS-GWaM on the simulated intermittency. From comparison to the control experiment, the intermittency is found to increase largely for GWs from the uniform source but to decrease for convective GWs by the transient modelling.</span></p>