State Dependent Statistical Timing Model for Voltage Scaled Circuits

This paper presents a novel statistical state-dependent timing model for voltage over scaled (VoS) logic circuits that accurately and rapidly finds the timing distribution of output bits. Using this model erroneous VoS circuits can be represented as error-free circuits combined with an error-injector. A case study of a two point DFT unit employing the proposed model is presented and compared to HSPICE circuit simulation. Results show an accurate match, with significant speedup gains

A Mechanistic Study of Carbonic Anhydrase Enhanced Calcite Dissolution

Carbonic anhydrase (CA) has been shown to promote calcite dissolution (Liu, 2001, https://doi.org/10.1111/j.1755-6724.2001.tb00531.x; Subhas et al., 2017, https://doi.org/10.1073/pnas.1703604114), and understanding the catalytic mechanism will facilitate our understanding of the oceanic alkalinity cycle. We use atomic force microscopy (AFM) to directly observe calcite dissolution in CA‐bearing solution. CA is found to etch the calcite surface only when in extreme proximity (~1 nm) to the mineral. Subsequently, the CA‐induced etch pits create step edges that serve as active dissolution sites. The possible catalytic mechanism is through the adsorption of CA on the calcite surface, followed by proton transfer from the CA catalytic center to the calcite surface during CO2 hydration. This study shows that the accessibility of CA to particulate inorganic carbon (PIC) in the ocean is critical in properly estimating oceanic CaCO3 and alkalinity cycles

A Mechanistic Study of Carbonic Anhydrase Enhanced Calcite Dissolution

Carbonic anhydrase (CA) has been shown to promote calcite dissolution (Liu, 2001, https://doi.org/10.1111/j.1755-6724.2001.tb00531.x; Subhas et al., 2017, https://doi.org/10.1073/pnas.1703604114), and understanding the catalytic mechanism will facilitate our understanding of the oceanic alkalinity cycle. We use atomic force microscopy (AFM) to directly observe calcite dissolution in CA‐bearing solution. CA is found to etch the calcite surface only when in extreme proximity (~1 nm) to the mineral. Subsequently, the CA‐induced etch pits create step edges that serve as active dissolution sites. The possible catalytic mechanism is through the adsorption of CA on the calcite surface, followed by proton transfer from the CA catalytic center to the calcite surface during CO2 hydration. This study shows that the accessibility of CA to particulate inorganic carbon (PIC) in the ocean is critical in properly estimating oceanic CaCO3 and alkalinity cycles

An Atomic Force Microscopy Study of Calcite Dissolution in Seawater

We present the first examination of calcite dissolution in seawater using Atomic Force Microscopy (AFM). We quantify step retreat velocity and etch pit density to compare dissolution in seawater to low ionic strength water, and also to compare calcite dissolution under AFM conditions to those conducted in bulk solution experiments (e.g. Subhas et al., 2015, Dong et al., 2018). Bulk dissolution rates and step retreat velocities are slower at high and mid-saturation state (Ω) values and become comparable to low ionic strength water rates at low Ω. The onset of defect-assisted etch pit formation in seawater is at Ω ∼ 0.85 (defined as Ω_(critical)), higher than in low ionic strength water (Ω ∼ 0.54). There is an abrupt increase in etch pit density (from ∼10⁶ cm⁻² to ∼10⁸ cm⁻²) occurring when Ω falls below 0.7 in seawater, compared to Ω ∼ 0.1 in low ionic strength water, suggesting a transition from defect-assisted dissolution to homogeneous dissolution much closer to equilibrium in seawater. The step retreat velocity (v) does not scale linearly with undersaturation (1-Ω) across an Ω range of 0.4 to 0.9 in seawater, potentially indicating a high order correlation between kink rate and Ω for non-Kossel crystals such as calcite, or surface complexation processes during calcite dissolution in seawater

An Atomic Force Microscopy Study of Calcite Dissolution in Seawater

We present the first examination of calcite dissolution in seawater using Atomic Force Microscopy (AFM). We quantify step retreat velocity and etch pit density to compare dissolution in seawater to low ionic strength water, and also to compare calcite dissolution under AFM conditions to those conducted in bulk solution experiments (e.g. Subhas et al., 2015, Dong et al., 2018). Bulk dissolution rates and step retreat velocities are slower at high and mid-saturation state (Ω) values and become comparable to low ionic strength water rates at low Ω. The onset of defect-assisted etch pit formation in seawater is at Ω ∼ 0.85 (defined as Ω_(critical)), higher than in low ionic strength water (Ω ∼ 0.54). There is an abrupt increase in etch pit density (from ∼10⁶ cm⁻² to ∼10⁸ cm⁻²) occurring when Ω falls below 0.7 in seawater, compared to Ω ∼ 0.1 in low ionic strength water, suggesting a transition from defect-assisted dissolution to homogeneous dissolution much closer to equilibrium in seawater. The step retreat velocity (v) does not scale linearly with undersaturation (1-Ω) across an Ω range of 0.4 to 0.9 in seawater, potentially indicating a high order correlation between kink rate and Ω for non-Kossel crystals such as calcite, or surface complexation processes during calcite dissolution in seawater

The structural complexity of the Gammaproteobacteria flagellar motor is related to the type of its torque-generating stators

The bacterial flagellar motor is a cell-envelope-embedded macromolecular machine that functions as a propeller to move the cell. Rather than being an invariant machine, the flagellar motor exhibits significant variability between species, allowing bacteria to adapt to, and thrive in, a wide range of environments. For instance, different torque- generating stator modules allow motors to operate in conditions with different pH and sodium concentrations and some motors are adapted to drive motility in high-viscosity environments. How such diversity evolved is unknown. Here we use electron cryo-tomography to determine the in situ macromolecular structures of the flagellar motors of three Gammaproteobacteria species: Legionella pneumophila, Pseudomonas aeruginosa, and Shewanella oneidensis MR-1, providing the first views of intact motors with dual stator systems. Complementing our imaging with bioinformatics analysis, we find a correlation between the stator system of the motor and its structural complexity. Motors with a single H+-driven stator system have only the core P- and L-rings in their periplasm; those with dual H+-driven stator systems have an extra component elaborating their P-ring; and motors with Na+- (or dual Na+-H+)- driven stator systems have additional rings surrounding both their P- and L-rings. Our results suggest an evolution of structural complexity that may have enabled pathogenic bacteria like L. pneumophila and P. aeruginosa to colonize higher-viscosity environments in animal hosts

Ultrastructure of Shewanella oneidensis MR-1 nanowires revealed by electron cryotomography

Bacterial nanowires have garnered recent interest as a proposed extracellular electron transfer (EET) pathway that links the bacterial electron transport chain to solid-phase electron acceptors away from the cell. Recent studies showed that Shewanella oneidensis MR-1 produces outer membrane (OM) and periplasmic extensions that contain EET components and hinted at their possible role as bacterial nanowires. However, their fine structure and distribution of cytochrome electron carriers under native conditions remained unclear, making it difficult to evaluate the potential electron transport (ET) mechanism along OM extensions. Here, we report high-resolution images of S. oneidensis OM extensions, using electron cryotomography (ECT). We developed a robust method for fluorescence light microscopy imaging of OM extension growth on electron microscopy grids and used correlative light and electron microscopy to identify and image the same structures by ECT. Our results reveal that S. oneidensis OM extensions are dynamic chains of interconnected outer membrane vesicles (OMVs) with variable dimensions, curvature, and extent of tubulation. Junction densities that potentially stabilize OMV chains are seen between neighboring vesicles in cryotomograms. By comparing wild type and a cytochrome gene deletion mutant, our ECT results provide the likely positions and packing of periplasmic and outer membrane proteins consistent with cytochromes. Based on the observed cytochrome packing density, we propose a plausible ET path along the OM extensions involving a combination of direct hopping and cytochrome diffusion. A mean-field calculation, informed by the observed ECT cytochrome density, supports this proposal by revealing ET rates on par with a fully packed cytochrome network

Redox linked flavin sites in extracellular decaheme proteins involved in microbe-mineral electron transfer

Extracellular microbe-mineral electron transfer is a major driving force for the oxidation of organic carbon in many subsurface environments. Extracellular multi-heme cytochromes of the Shewenella genus play a major role in this process but the mechanism of electron exchange at the interface between cytochrome and acceptor is widely debated. The 1.8 Å x-ray crystal structure of the decaheme MtrC revealed a highly conserved CX8C disulfide that, when substituted for AX8A, severely compromised the ability of S. oneidensis to grow under aerobic conditions. Reductive cleavage of the disulfide in the presence of flavin mononucleotide (FMN) resulted in the reversible formation of a stable flavocytochrome. Similar results were also observed with other decaheme cytochromes, OmcA, MtrF and UndA. The data suggest that these decaheme cytochromes can transition between highly reactive flavocytochromes or less reactive cytochromes, and that this transition is controlled by a redox active disulfide that responds to the presence of oxygen

Stable sub-complexes observed in situ suggest a modular assembly pathway of the bacterial flagellar motor

The self-assembly of cellular macromolecular machines such as the bacterial flagellar motor requires the spatio- temporal synchronization of gene expression, protein localization and association of a dozen or more unique components. In Salmonella and Escherichia coli, a sequential, outward assembly mechanism has been proposed for the flagellar motor starting from the inner membrane, with each subsequent component stabilizing the last. Here, using electron cryo-tomography of intact Legionella pneumophila, Pseudomonas aeruginosa and Shewanella oneidensis cells, we observe stable outer-membrane-embedded sub-complexes of the flagellar motor. These sub- complexes consist of the periplasmic embellished P- and L-rings, in the absence of other flagellar components, and bend the membrane inward dramatically. Additionally, we also observe independent inner-membrane sub- complexes consisting of the C- and MS-rings and export apparatus. These results suggest an alternate model for flagellar motor assembly in which outer- and inner-membrane-associated sub-complexes form independently and subsequently join, enabling later steps of flagellar production to proceed