Dose, exposure time, and resolution in Serial X-ray Crystallography

The resolution of X-ray diffraction microscopy is limited by the maximum dose that can be delivered prior to sample damage. In the proposed Serial Crystallography method, the damage problem is addressed by distributing the total dose over many identical hydrated macromolecules running continuously in a single-file train across a continuous X-ray beam, and resolution is then limited only by the available molecular and X-ray fluxes and molecular alignment. Orientation of the diffracting molecules is achieved by laser alignment. We evaluate the incident X-ray fluence (energy/area) required to obtain a given resolution from (1) an analytical model, giving the count rate at the maximum scattering angle for a model protein, (2) explicit simulation of diffraction patterns for a GroEL-GroES protein complex, and (3) the frequency cut off of the transfer function following iterative solution of the phase problem, and reconstruction of an electron density map in the projection approximation. These calculations include counting shot noise and multiple starts of the phasing algorithm. The results indicate counting time and the number of proteins needed within the beam at any instant for a given resolution and X-ray flux. We confirm an inverse fourth power dependence of exposure time on resolution, with important implications for all coherent X-ray imaging. We find that multiple single-file protein beams will be needed for sub-nanometer resolution on current third generation synchrotrons, but not on fourth generation designs, where reconstruction of secondary protein structure at a resolution of 0.7 nm should be possible with short exposures.Comment: 19 pages, 7 figures, 1 tabl

Stokes–Brinkman formulation for prediction of void formation in dual-scale fibrous reinforcements: a BEM/DR-BEM simulation

A numerical study of voids formation in dual-scale fibrous reinforcements is presented. Flow fields in channels (Stokes) and tows (Brinkman) are solved via direct Boundary Element Method and Dual Reciprocity Boundary Element Method, respectively. The present approach uses only boundary discretization and Dual Reciprocity domain interpolation, which is advantageous in this type of moving boundary problems and leads to an accurate representation of the moving interfaces. A problem admitting analytical solution, previously solved by domain-meshing techniques, is used to assess the accuracy of the present approach, obtaining satisfactory results. Fillings of Representative Unitary Cells at constant pressure are considered to analyze the influence of capillary ratio, jump stress coefficient and two formulations (Stokes-Brinkman and Stokes-Darcy) on the filling process, void formation and void characterization. Filling times, fluid front shapes, void size and shape, time and space evolution of the saturation, are influenced by these parameters, but voids location is not

Partially and Fully Frustrated Coupled Oscillators With Random Pinning Fields

We have studied two specific models of frustrated and disordered coupled Kuramoto oscillators, all driven with the same natural frequency, in the presence of random external pinning fields. Our models are structurally similar, but differ in their degree of bond frustration and in their finite size ground state properties (one has random ferro- and anti-ferromagnetic interactions; the other has random chiral interactions). We have calculated the equilibrium properties of both models in the thermodynamic limit using the replica method, with emphasis on the role played by symmetries of the pinning field distribution, leading to explicit predictions for observables, transitions, and phase diagrams. For absent pinning fields our two models are found to behave identically, but pinning fields (provided with appropriate statistical properties) break this symmetry. Simulation data lend satisfactory support to our theoretical predictions.Comment: 37 pages, 7 postscript figure

El Nin˜o Impact on Mollusk Biomineralization: Implications for Trace Element Proxy Reconstructions and the Paleo-Archeological Record

Marine macroinvertebrates are ideal sentinel organisms to monitor rapid environmental changes associated with climatic phenomena. These organisms build up protective exoskeletons incrementally by biologically-controlled mineralization, which is deeply rooted in long-term evolutionary processes. Recent studies relating potential rapid environmental fluctuations to climate change, such as ocean acidification, suggest modifications on carbonate biominerals of marine invertebrates. However, the influence of known, and recurrent, climatic events on these biological processes during active mineralization is still insufficiently understood. Analysis of Peruvian cockles from the 1982–83 large magnitude El Nin˜o event shows significant alterations of the chemico-structure of carbonate biominerals. Here, we show that bivalves modify the main biomineralization mechanism during the event to continue shell secretion. As a result, magnesium content increases to stabilize amorphous calcium carbonate (ACC), inducing a rise in Mg/Ca unrelated to the associated increase in sea-surface temperature. Analysis of variations in Sr/Ca also suggests that this proxy should not be used in these bivalves to detect the temperature anomaly, while Ba/Ca peaks are recorded in shells in response to an increase in productivity, or dissolved barium in seawater, after the event. Presented data contribute to a better understanding of the effects of abrupt climate change on shell biomineralization, while also offering an alternative view of bivalve elemental proxy reconstructions.Furthermore, biomineralization changes in mollusk shells can be used as a novel potential proxy to provide a more nuanced historical record of El Nin˜o and similar rapid environmental change events

Explicit solution for a Gaussian wave packet impinging on a square barrier

The collision of a quantum Gaussian wave packet with a square barrier is solved explicitly in terms of known functions. The obtained formula is suitable for performing fast calculations or asymptotic analysis. It also provides physical insight since the description of different regimes and collision phenomena typically requires only some of the terms.Comment: To be published in J. Phys.

Chemically active substitutional nitrogen impurity in carbon nanotubes

We investigate the nitrogen substitutional impurity in semiconducting zigzag and metallic armchair single-wall carbon nanotubes using ab initio density functional theory. At low concentrations (less than 1 atomic %), the defect state in a semiconducting tube becomes spatially localized and develops a flat energy level in the band gap. Such a localized state makes the impurity site chemically and electronically active. We find that if two neighboring tubes have their impurities facing one another, an intertube covalent bond forms. This finding opens an intriguing possibility for tunnel junctions, as well as the functionalization of suitably doped carbon nanotubes by selectively forming chemical bonds with ligands at the impurity site. If the intertube bond density is high enough, a highly packed bundle of interlinked single-wall nanotubes can form.Comment: 4 pages, 4 figures; major changes to the tex

Pollination: A key event controlling the expression of genes related to phytohormone biosynthesis during grapevine berry formation

Berry formation is the process of ovary conversion into a functional fruit, and is characterized by abrupt changes in the content of several phytohormones, associated with pollination and fertilization. Much effort has been made in order to improve our understanding of berry development, particularly from veraison to post-harvest time. However, the period of berry formation has been poorly investigated, despite its importance. Phytohormones are involved in the control of fruit formation; hence it is important to understand the regulation of their content at this stage. Grapevine is an excellent fleshy-fruit plant model since its fruits have particularities that differentiate them from those of commonly studied organisms. For instance, berries are prepared to cope with stress by producing several antioxidants and they are non-climacteric fruits. Also its genome is fully sequenced, which allows to identify genes involved in developmental processes. In grapevine, no link has been established between pollination and phytohormone biosynthesis, until recently. Here we highlight relevant findings regarding pollination effect on gene expression related to phytohormone biosynthesis, and present results showing how quickly this effect is achieved

The Problem of Non-Renewable Energy Resources in the Production of Physical Capital

This paper studies the possibilities of technical progress to deal with the growth limit problem imposed by the usage of non-renewable energy resources, when physical capital production is relatively more energy-intensive than consumption. In particular, this work presents the conditions under which energy-saving technologies can sustain long-run growth, although energy is produced by means of non-renewable energy resources. The mechanism behind that is energy efficiency

Thermal Background Corrections to the Neutrino Electromagnetic Vertex in Models with Charged Scalar Bosons

We calculate the correction to the neutrino electromagnetic vertex due to background of electrons in a large class of models, as the supersymmetric model with explicit breaking of R-parity, where charged scalar bosons couple to leptons and which are able to provide an astrophysically interesting value for the neutrino magnetic (electric) moment, $\mu_\nu\sim 10^{-12}\:\mu_B$. We show that the medium contribution to the chirality flipping magnetic (electric) dipole moment is not significant, however a new chirality flipping, but helicity conserving, term arises. It signals the presence of ${\cal CP}$ and ${\cal CPT}$ asymmetries in the medium and is associated to the longitudinal photon and therefore disappears in the vacuum. We estimate the contribution of this new term to the rate of the plasmon decay process $\gamma_{pl}\rightarrow \nu\nu$ in the core of degenerate stars, showing that it can be comparable with the contribution coming from the vacuum magnetic (dipole) moment. We also calculate the correction to the effective potential of a propagating neutrino in presence of a magnetic field due to a chirality preserving contribution to the diagonal magnetic moment from the medium. This contribution is identical for particles and antiparticles and so need not to vanish for Majorana neutrinos.Comment: DFPD 93/TH/75, SISSA 93/183/A preprint, 25 pages + 4 figures available by e-mail reques