Partial alignment and measurement of residual dipolar couplings of proteins under high hydrostatic pressure

High-pressure NMR spectroscopy has emerged as a complementary approach for investigating various structural and thermodynamic properties of macromolecules. Noticeably absent from the array of experimental restraints that have been employed to characterize protein structures at high hydrostatic pressure is the residual dipolar coupling, which requires the partial alignment of the macromolecule of interest. Here we examine five alignment media that are commonly used at ambient pressure for this purpose. We find that the spontaneous alignment of Pf1 phage, d(GpG) and a C12E5/n-hexnanol mixture in a magnetic field is preserved under high hydrostatic pressure. However, DMPC/ DHPC bicelles and collagen gel are found to be unsuitable. Evidence is presented to demonstrate that pressure-induced structural changes can be identified using the residual dipolar coupling

Hard sphere packings within cylinders

The packing of hard spheres (HS) of diameter $\sigma$ in a cylinder has been used to model experimental systems, such as fullerenes in nanotubes and colloidal wire assembly. Finding the densest packings of HS under this type of confinement, however, grows increasingly complex with the cylinder diameter, $D$. Little is thus known about the densest achievable packings for $D>2.873\sigma$. In this work, we extend the identification of the packings up to $D=4.00\sigma$ by adapting Torquato-Jiao's adaptive-shrinking-cell formulation and sequential-linear-programming (SLP) technique. We identify 17 new structures, almost all of them chiral. Beyond $D\approx2.85\sigma$, most of the structures consist of an outer shell and an inner core that compete for being close packed. In some cases, the shell adopts its own maximum density configuration, and the stacking of core spheres within it is quasiperiodic. In other cases, an interplay between the two components is observed, which may result in simple periodic structures. In yet other cases, the very distinction between core and shell vanishes, resulting in more exotic packing geometries, including some that are three-dimensional extensions of structures obtained from packing hard disks in a circle.Comment: 11 pages, 11 figure

A novel downscaling technique for the linkage of global and regional air quality modeling

Recently, downscaling global atmospheric model outputs (GCTM) for the USEPA Community Multiscale Air Quality (CMAQ) Initial (IC) and Boundary Conditions (BC) have become practical because of the rapid growth of computational technologies that allow global simulations to be completed within a reasonable time. The traditional method of generating IC/BC by profile data has lost its advocates due to the weakness of the limited horizontal and vertical variations found on the gridded boundary layers. Theoretically, high quality GCTM IC/BC should yield a better result in CMAQ. Unfortunately, several researchers have found that the outputs from GCTM IC/BC are not necessarily better than profile IC/BC due to the excessive transport of O3 aloft in GCTM IC/BC. In this paper, we intend to investigate the effects of using profile IC/BC and global atmospheric model data. In addition, we are suggesting a novel approach to resolve the existing issue in downscaling. In the study, we utilized the GEOS-Chem model outputs to generate time-varied and layer-varied IC/BC for year 2002 with the implementation of tropopause determining algorithm in the downscaling process (i.e., based on chemical (O3) tropopause definition). The comparison between the implemented tropopause approach and the profile IC/BC approach is performed to demonstrate improvement of considering tropopause. It is observed that without using tropopause information in the downscaling process, unrealistic O3 concentrations are created at the upper layers of IC/BC. This phenomenon has caused over-prediction of surface O3 in CMAQ. In addition, the amount of over-prediction is greatly affected by temperature and latitudinal location of the study domain. With the implementation of the algorithm, we have successfully resolved the incompatibility issues in the vertical layer structure between global and regional chemistry models to yield better surface O3 predictions than profile IC/BC for both summer and winter conditions. At the same time, it improved the vertical O3 distribution of CMAQ outputs. It is strongly recommended that the tropopause information should be incorporated into any two-way coupled global and regional models, where the tropospheric regional model is used, to solve the vertical incompatibility that exists between global and regional models. doi:10.5194/acp-10-4013-2010 Publisher\u27s note: We have discovered that the previously published paper was not the latest version of the manuscript we intended to use. Some corrections made during the second ACPD reviewing process were not incorporated in the text. As a result, the figure numbers (i.e., figure number below the graph) were not referenced correctly in the manuscript. Therefore, we have decided to re-publish this paper as a corrigendum

A novel downscaling technique for the linkage of global and regional air quality modeling

Recently, downscaling global atmospheric model outputs (GCTM) for the USEPA Community Multiscale Air Quality (CMAQ) Initial (IC) and Boundary Conditions (BC) have become practical because of the rapid growth of computational technologies that allow global simulations to be completed within a reasonable time. The traditional method of generating IC/BC by profile data has lost its advocates due to the weakness of the limited horizontal and vertical variations found on the gridded boundary layers. Theoretically, high quality GCTM IC/BC should yield a better result in CMAQ. Unfortunately, several researchers have found that the outputs from GCTM IC/BC are not necessarily better than profile IC/BC due to the excessive transport of O3 aloft in GCTM IC/BC. In this paper, we intend to investigate the effects of using profile IC/BC and global atmospheric model data. In addition, we are suggesting a novel approach to resolve the existing issue in downscaling. In the study, we utilized the GEOS-Chem model outputs to generate time-varied and layer-varied IC/BC for year 2002 with the implementation of tropopause determining algorithm in the downscaling process (i.e., based on chemical (O3) tropopause definition). The comparison between the implemented tropopause approach and the profile IC/BC approach is performed to demonstrate improvement of considering tropopause. It is observed that without using tropopause information in the downscaling process, unrealistic O3 concentrations are created at the upper layers of IC/BC. This phenomenon has caused over-prediction of surface O3 in CMAQ. In addition, the amount of over-prediction is greatly affected by temperature and latitudinal location of the study domain. With the implementation of the algorithm, we have successfully resolved the incompatibility issues in the vertical layer structure between global and regional chemistry models to yield better surface O3 predictions than profile IC/BC for both summer and winter conditions. At the same time, it improved the vertical O3 distribution of CMAQ outputs. It is strongly recommended that the tropopause information should be incorporated into any two-way coupled global and regional models, where the tropospheric regional model is used, to solve the vertical incompatibility that exists between global and regional models

Phase Transformations in Binary Colloidal Monolayers

Phase transformations can be difficult to characterize at the microscopic level due to the inability to directly observe individual atomic motions. Model colloidal systems, by contrast, permit the direct observation of individual particle dynamics and of collective rearrangements, which allows for real-space characterization of phase transitions. Here, we study a quasi-two-dimensional, binary colloidal alloy that exhibits liquid-solid and solid-solid phase transitions, focusing on the kinetics of a diffusionless transformation between two crystal phases. Experiments are conducted on a monolayer of magnetic and nonmagnetic spheres suspended in a thin layer of ferrofluid and exposed to a tunable magnetic field. A theoretical model of hard spheres with point dipoles at their centers is used to guide the choice of experimental parameters and characterize the underlying materials physics. When the applied field is normal to the fluid layer, a checkerboard crystal forms; when the angle between the field and the normal is sufficiently large, a striped crystal assembles. As the field is slowly tilted away from the normal, we find that the transformation pathway between the two phases depends strongly on crystal orientation, field strength, and degree of confinement of the monolayer. In some cases, the pathway occurs by smooth magnetostrictive shear, while in others it involves the sudden formation of martensitic plates.Comment: 13 pages, 7 figures. Soft Matter Latex template was used. Published online in Soft Matter, 201

Ammonia emission abatement does not fully control reduced forms of nitrogen deposition

Human activities and population growth have increased the natural burden of reactive nitrogen (N) in the environment. Excessive N deposition on Earth’s surface leads to adverse feedbacks on ecosystems and humans. Similar to that of air pollution, emission control is recognized as an efficient means to control acid deposition. Control of nitrogen oxides (NO_x = NO + NO₂) emissions has led to reduction in deposition of oxidized nitrogen (NO_y, the sum of all oxidized nitrogen species, except nitrous oxide [N₂O]). Reduced forms of nitrogen (NH_x = ammonia [NH₃] + ammonium [NH₄⁺]) deposition have, otherwise, increased, offsetting the benefit of reduction in NO_y deposition. Stringent control of NH₃ emissions is being considered. In this study, we assess the response of N deposition to N emission control on continental regions. We show that significant reduction of NHx deposition is unlikely to be achieved at the early stages of implementing NH₃ emission abatement. Per-unit NH₃ emission abatement is shown to result in only 60–80% reduction in NH_x deposition, which is significantly lower than the demonstrated 80–120% benefit of controlling NO_x emissions on NO_y deposition. This 60–80% effectiveness of NH_x deposition reduction per unit NH₃ emission abatement reflects, in part, the effects of simultaneous reductions in NO_x and SO₂ emissions