Dynamics of Co-translational Membrane Protein Integration and Translocation via the Sec Translocon

An important aspect of cellular function is the correct targeting and delivery of newly synthesized proteins. Central to this task is the machinery of the Sec translocon, a transmembrane channel that is involved in both the translocation of nascent proteins across cell membranes and the integration of proteins into the membrane. Considerable experimental and computational effort has focused on the Sec translocon and its role in nascent protein biosynthesis, including the correct folding and expression of integral membrane proteins. However, the use of molecular simulation methods to explore Sec-facilitated protein biosynthesis is hindered by the large system sizes and long (i.e., minute) timescales involved. In this work, we describe the development and application of a coarse-grained simulation approach that addresses these challenges and allows for direct comparison with both in vivo and in vitro experiments. The method reproduces a wide range of experimental observations, providing new insights into the underlying molecular mechanisms, predictions for new experiments, and a strategy for the rational enhancement of membrane protein expression levels

Method and apparatus for spur-reduced digital sinusoid synthesis

A technique for reducing the spurious signal content in digital sinusoid synthesis is presented. Spur reduction is accomplished through dithering both amplitude and phase values prior to word-length reduction. The analytical approach developed for analog quantization is used to produce new bounds on spur performance in these dithered systems. Amplitude dithering allows output word-length reduction without introducing additional spurs. Effects of periodic dither similar to that produced by a pseudo-noise (PN) generator are analyzed. This phase dithering method provides a spur reduction of 6(M + 1) dB per phase bit when the dither consists of M uniform variates. While the spur reduction is at the expense of an increase in system noise, the noise power can be made white, making the power spectral density small. This technique permits the use of a smaller number of phase bits addressing sinusoid look-up tables, resulting in an exponential decrease in system complexity. Amplitude dithering allows the use of less complicated multipliers and narrower data paths in purely digital applications, as well as the use of coarse-resolution, highly-linear digital-to-analog converters (DAC's) to obtain spur performance limited by the DAC linearity rather than its resolution

Doubly-Shadowed Regions in Lunar Polar Craters: Hydrogen Accumulation in the Presence of Recursive Plasma Wakes

Permanently shadowed regions (PSRs) of the Moon have been identified as unique environments of extreme cold and comprise a natural cold trap for sequestering volatiles [Paige et al. 2010]. The diverse chemical composition of the LCROSS impact plume provided evidence for a volatile-rich and chemically-complex PSR environment [Cola prete et al. 2010, Schultz et al. 2010]. Additionally, the polar electrostatic environment is highly complex, with the possibility of strong, localized electric fields that divert solar wind ions directly into polar cold traps [Farrell et al. 2010, Zimmerman et al. 2011]. Thus, regional plasma physics processes couple directly with volatile sequestration. In the present work, kinetic simulations show that recursive plasma wake structure arises in the presence of step-like topographic features (Le. doubly-shadowed craters). Combining the plasma code with a numerical sputtering model demonstrates that solar wind protons can be either a hydrogen source via implantation or a volatile loss mechanism via sputtering, depending on properties of the regolith and solar wind. The present model provides a novel theoretical pathway toward understanding the lunar surface/solar wind physical and chemical interactions for complex topography near the poles

Light Availability and Phytoplankton Growth Beneath Arctic Sea Ice: Integrating Observations and Modeling

Observations of the seasonal light field in the upper Arctic Ocean are critical to understanding the impacts of changing Arctic ice conditions on phytoplankton growth in the water column. Here we discuss data from a new sensor system, deployed in seasonal ice cover north‐east of Utqiaġvik, Alaska in March 2014. The system was designed to provide observations of light and phytoplankton biomass in the water column during the formation of surface melt ponds and the transition from ice to open water. Hourly observations of downwelling irradiance beneath the ice (at 2.9, 6.9, and 17.9 m depths) and phytoplankton biomass (at 2.9 m depth) were transmitted via Iridium satellite from 9 March to 10 November 2014. Evidence of an under‐ice phytoplankton bloom (Chl a ∼8 mg m−3) was seen in June and July. Increases in light intensity observed by the buoy likely resulted from the loss of snow cover and development of surface melt ponds. A bio‐optical model of phytoplankton production supported this probable trigger for the rapid onset of under‐ice phytoplankton growth. Once under‐ice light was no longer a limiting factor for photosynthesis, open water exposure almost marginally increased daily phytoplankton production compared to populations that remained under the adjacent ice. As strong effects of climate change continue to be documented in the Arctic, the insight derived from autonomous buoys will play an increasing role in understanding the dynamics of primary productivity where ice and cloud cover limit the utility of ocean color satellite observations

Lunar Crater Mini-Wakes: Structure, Variability, and Volatiles

Within a permanently shadowed lunar crater the horizontal flow of solar wind is obstructed by upstream topography, forming a regional plasma mini-wake. In the present work kinetic simulations are utilized to investigate how the most prominent structural aspects of a crater mini-wake are modulated during passage of a solar storm. In addition, the simulated particle fluxes are coupled into an equivalent-circuit model of a roving astronaut,. including triboelectric charging due to frictional contact with the lunar regolith, to characterize charging of the astronaut suit during the various stages of the storm. In some cases, triboelectric charging of the astronaut suit becomes effectively perpetual, representing a critical engineering concern for roving within shadowed lunar regions. Finally, the present results suggest that wake structure plays a critical role in modulating the spatial distribution of volatiles at the lunar poles