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

Production of Gravitational Waves in the nMSSM

During a strongly first-order phase transition gravitational waves are produced by bubble collisions and turbulent plasma motion. We analyze the relevant characteristics of the electroweak phase transition in the nMSSM to determine the generated gravitational wave signal. Additionally, we comment on correlations between the production of gravitational waves and baryogenesis. We conclude that the gravitational wave relic density in this model is generically too small to be detected in the near future by the LISA experiment. We also consider the case of a "Standard Model" with dimension-six Higgs potential, which leads to a slightly stronger signal of gravitational waves.Comment: 29 pages, 7 figures; published version, some comments adde

Supergauge interactions and electroweak baryogenesis

We present a complete treatment of the diffusion processes for supersymmetric electroweak baryogenesis that characterizes transport dynamics ahead of the phase transition bubble wall within the symmetric phase. In particular, we generalize existing approaches to distinguish between chemical potentials of particles and their superpartners. This allows us to test the assumption of superequilibrium (equal chemical potentials for particles and sparticles) that has usually been made in earlier studies. We show that in the Minimal Supersymmetric Standard Model, superequilibrium is generically maintained -- even in the absence of fast supergauge interactions -- due to the presence of Yukawa interactions. We provide both analytic arguments as well as illustrative numerical examples. We also extend the latter to regions where analytical approximations are not available since down-type Yukawa couplings or supergauge interactions only incompletely equilibrate. We further comment on cases of broken superequilibrium wherein a heavy superpartner decouples from the electroweak plasma, causing a kinematic bottleneck in the chain of equilibrating reactions. Such situations may be relevant for baryogenesis within extensions of the MSSM. We also provide a compendium of inputs required to characterize the symmetric phase transport dynamics.Comment: 49 pages, 9 figure

Monitoring carbon dioxide concentration for early detection of spoilage in stored grain

Field experiments were conducted in storage silos to evaluate carbon dioxide sensors to monitor spoilage in grain prior to spoilage detection by traditional methods such as visual inspections and temperature cables. Carbon dioxide concentrations in the storage silo were monitored up to eight months and correlated to the presence of stored-product insects, molds and mycotoxin levels in the stored grain. The data showed that safe grain storage was observed at CO2 concentrations of 400 to 500 ppm. Higher concentrations of CO2 clearly showed mold spoilage or insect activity inside the grain storage silo. Carbon dioxide concentrations of 500 to 1200 ppm indicated onset of mold infection where as CO2 concentrations of 1500 to 4000 ppm and beyond clearly indicated severe mold infection or stored-product insects infestation. The percent kernel infection was in the range of 30% for CO2 concentrations of 500 to 1000 ppm to 90% for CO2 concentrations of 9000 ppm. Fungal concentrations were in the range of 2.0 ×102 colony forming units per gram (cfu/g) at 500 ppm CO2 concentration to 6.5 ×107 cfu/g at 9000 ppm CO2 concentration. Fungi of genera Aspergillus spp., Penicillium spp., and Fusarium spp. were isolated from spoiled grain. High concentration of fungi and presence of mycotoxins (aflatoxin: 2 ppb and Deoxynivalenol (DON): 1 ppm) were correlated with high CO2 concentration in the silos. The findings from this research will be helpful in providing more timely information regarding safe storage limits, aeration requirements and costs of spoilage mitigation measures such as turning, aerating and fumigating grain. Additionally, it will provide information on preventive stored grain quality management practices that should reduce residue levels of mycotoxins, pesticides and other foreign material in our food supply. The CO2 monitoring technology will increase the quality and quantity of stored grain, while saving the U.S. and global grain production, handling and processing industry millions of dollars annually. Keywords: Carbon dioxide, Grain storage, Stored-product insects, Mold and mycotoxi

Inclusion of quasi-vertex views in a brain-dedicated multi-pinhole SPECT system for improved imaging performance

With brain-dedicated multi-detector systems employing pinhole apertures the usage of detectors facing the top of the patient\u27s head (i.e., quasi-vertex views) can provide the advantage of additional viewing from close to the brain for improved detector coverage. In this paper, we report the results of simulation and reconstruction studies to investigate the impact of the quasi-vertex views on the imaging performance of AdaptiSPECT-C, a brain-dedicated stationary SPECT system under development. In this design, both primary and scatter photons from regions located inferior to the brain can contribute to SPECT projections acquired by the quasi-vertex views, and thus degrade AdaptiSPECT-C imaging performance. In this work, we determined the proportion, origin, and nature (i.e., primary, scatter, and multiple-scatter) of counts emitted from structures within the head and throughout the body contributing to projections from the different AdaptiSPECT-C detector rings, as well as from a true vertex view detector. We simulated phantoms used to assess different aspects of image quality (i.e., uniform sphere and Derenzo), as well as anthropomorphic phantoms with multiple count levels emulating clinical(123)I activity distributions (i.e., DaTscan and perfusion). We determined that attenuation and scatter in the patient\u27s body greatly diminish the probability of the photons emitted outside the volume of interest reaching to detectors and being recorded within the 15% photopeak energy window. In addition, we demonstrated that the inclusion of the residual of such counts in the system acquisition does not degrade visual interpretation or quantitative analysis. The addition of the quasi-vertex detectors increases volumetric sensitivity, angular sampling, and spatial resolution leading to significant enhancement in image quality, especially in the striato-thalamic and superior regions of the brain. Besides, the use of quasi-vertex detectors improves the recovery of clinically relevant metrics such as the striatal binding ratio and mean activity in selected cerebral structures

Functional microdomains in G-protein-coupled receptors: the conserved arginine-cage motif in the gonadotropin-releasing hormone receptor

An Arg present in the third transmembrane domain of all rhodopsin-like G-protein-coupled receptors is required for efficient signal transduction. Mutation of this Arg in the gonadotropin-releasing hormone receptor to Gln, His, or Lys abolished or severely impaired agonist-stimulated inositol phosphate generation, consistent with Arg having a role in receptor activation. To investigate the contribution of the surrounding structural domain in the actions of the conserved Arg, an integrated microdomain modeling and mutagenesis approach has been utilized. Two conserved residues that constrain the Arg side chain to a limited number of conformations have been identified. In the inactive wild-type receptor, the Arg side chain is proposed to form an ionic interaction with Asp3.49(138). Experimental results for the Asp3. 49(138) --> Asn mutant receptor show a modestly enhanced receptor efficiency, consistent with the hypothesis that weakening the Asp3. 49(138)-Arg3.50(139) interaction by protonation of the Asp or by the mutation to Asn favors activation. With activation, the Asp3. 49(138)-Arg3.50(139) ionic bond would break, and the unrestrained Arg would be prevented from orienting itself toward the water phase by a steric clash with Ile3.54(143). The mutation Ile3.54(143) --> Ala, which eliminates this clash in simulations, causes a marked reduction in measured receptor signaling efficiency, implying that solvation of Arg3.50(139) prevents it from functioning in the activation of the receptor. These data are consistent with residues Asp3.49(138) and Ile3.54(143) forming a structural motif, which helps position Arg in its appropriate inactive and active receptor conformations

The Baryon asymmetry in the Standard Model with a low cut-off

We study the generation of the baryon asymmetry in a variant of the standard model, where the Higgs field is stabilized by a dimension-six interaction. Analyzing the one-loop potential, we find a strong first order electroweak phase transition for Higgs masses up to at least 170 GeV. Dimension-six operators induce also new sources of CP violation. We compute the baryon asymmetry in the WKB approximation. Novel source terms in the transport equations enhance the generated baryon asymmetry. For a wide range of parameters the model predicts a baryon asymmetry close to the observed value.Comment: 22 pages, latex, 6 figure

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach