Thon rings from amorphous ice and implications of beam-induced Brownian motion in single particle electron cryo-microscopy

We have recorded dose-fractionated electron cryo-microscope images of thin films of pure flash-frozen amorphous ice and pre-irradiated amorphous carbon on a Falcon~II direct electron detector using 300 keV electrons. We observe Thon rings \cite{Thon1966} in both the power spectrum of the summed frames and the sum of power spectra from the individual frames. The Thon rings from amorphous carbon images are always more visible in the power spectrum of the summed frames whereas those of amorphous ice are more visible in the sum of power spectra from the individual frames. This difference indicates that while pre-irradiated carbon behaves like a solid during the exposure, amorphous ice behaves like a fluid with the individual water molecules undergoing beam-induced motion. Using the measured variation in the power spectra amplitude with number of electrons per image we deduce that water molecules are randomly displaced by mean squared distance of $\sim$ 1.1 \AA$^{2}$ for every incident 300 keV e$^{-}$/\AA$^2$. The induced motion leads to an optimal exposure with 300 keV electrons of 4.0 e$^{-}$/\AA$^2$ per image with which to see Thon rings centred around the strong 3.7{\AA} scattering peak from amorphous ice. The beam-induced movement of the water molecules generates pseudo-Brownian motion of embedded macromolecules. The resulting blurring of single particle images contributes an additional term, on top of that from radiation damage, to the minimum achievable B-factor for macromolecular structure determination.Comment: 11 pages, 6 figures, Supplementary information 6 pages with 5 figure

Comparison of optimal performance at 300keV of three direct electron detectors for use in low dose electron microscopy

Low dose electron imaging applications such as electron cryo-microscopy are now benefitting from the improved performance and flexibility of recently introduced electron imaging detectors in which electrons are directly incident on backthinned CMOS sensors. There are currently three commercially available detectors of this type: the Direct Electron DE-20, the FEI Falcon II and the Gatan K2 Summit. These have different characteristics and so it is important to compare their imaging properties carefully with a view to optimise how each is used. Results at 300 keV for both the modulation transfer function (MTF) and the detective quantum efficiency (DQE) are presented. Of these, the DQE is the most important in the study of radiation sensitive samples where detector performance is crucial. We find that all three detectors have a better DQE than film. The K2 Summit has the best DQE at low spatial frequencies but with increasing spatial frequency its DQE falls below that of the Falcon II

Collinearity, convergence and cancelling infrared divergences

The Lee-Nauenberg theorem is a fundamental quantum mechanical result which provides the standard theoretical response to the problem of collinear and infrared divergences. Its argument, that the divergences due to massless charged particles can be removed by summing over degenerate states, has been successfully applied to systems with final state degeneracies such as LEP processes. If there are massless particles in both the initial and final states, as will be the case at the LHC, the theorem requires the incorporation of disconnected diagrams which produce connected interference effects at the level of the cross-section. However, this aspect of the theory has never been fully tested in the calculation of a cross-section. We show through explicit examples that in such cases the theorem introduces a divergent series of diagrams and hence fails to cancel the infrared divergences. It is also demonstrated that the widespread practice of treating soft infrared divergences by the Bloch-Nordsieck method and handling collinear divergences by the Lee-Nauenberg method is not consistent in such cases.Comment: 29 pages, 17 figure

Chronic nitrogen fertilization and carbon sequestration in grassland soils: evidence of a microbial enzyme link

Chronic nitrogen (N) fertilization can greatly affect soil carbon (C) sequestration by altering biochemical interactions between plant detritus and soil microbes. In lignin-rich forest soils, chronic N additions tend to increase soil C content partly by decreasing the activity of lignin-degrading enzymes. In cellulose-rich grassland soils it is not clear whether cellulose-degrading enzymes are also inhibited by N additions and what consequences this might have on changes in soil C content. Here we address whether chronic N fertilization has affected (1) the C content of light versus heavier soil fractions, and (2) the activity of four extracellular enzymes including the C-acquiring enzyme β-1,4-glucosidase (BG; necessary for cellulose hydrolysis). We found that 19 years of chronic N-only addition to permanent grassland have significantly increased soil C sequestration in heavy but not in light soil density fractions, and this C accrual was associated with a significant increase (and not decrease) of BG activity. Chronic N fertilization may increase BG activity because greater N availability reduces root C:N ratios thus increasing microbial demand for C, which is met by C inputs from enhanced root C pools in N-only fertilized soils. However, BG activity and total root mass strongly decreased in high pH soils under the application of lime (i.e. CaCO3), which reduced the ability of these organo-mineral soils to gain more C per units of N added. Our study is the first to show a potential ‘enzyme link’ between (1) long-term additions of inorganic N to grassland soils, and (2) the greater C content of organo-mineral soil fractions. Our new hypothesis is that the ‘enzyme link’ occurs because (a) BG activity is stimulated by increased microbial C demand relative to N under chronic fertilization, and (b) increased BG activity causes more C from roots and from microbial metabolites to accumulate and stabilize into organo-mineral C fractions. We suggest that any combination of management practices that can influence the BG ‘enzyme link’ will have far reaching implications for long-term C sequestration in grassland soils

Infra-Red Finite Charge Propagation

The Coulomb gauge has a long history and many uses. It is especially useful in bound state applications. An important feature of this gauge is that the matter fields have an infra-red finite propagator in an on-shell renormalisation scheme. This is, however, only the case if the renormalisation point is chosen to be the static point on the mass shell, p = (m, 0, 0, 0). In this letter we show how to extend this key property of the Coulomb gauge to an arbitrary relativistic renormalisation point. This is achieved through the introduction of a new class of gauges of which the Coulomb gauge is a limiting case. A physical explanation for this result is given.Comment: 8 pages, plain TeX, to appear in Modern Physics Letters

Intense isolectin-B4 binding in rat dorsal root ganglion neurons distinguishes c-fiber nociceptors with broad action potentials and high nav1.9 expression

Binding to isolectin-B4 (IB4) and expression of tyrosine kinase A (trkA) (the high-affinity NGF receptor) have been used to define two different subgroups of nociceptive small dorsal root ganglion (DRG) neurons. We previously showed that only nociceptors have high trkA levels. However, information about sensory and electrophysiological properties in vivo of single identified IB4-binding neurons, and about their trkA expression levels, is lacking. IB4-positive (IB4+) and small dark neurons had similar size distributions. We examined IB4-binding levels in >120 dye-injected DRG neurons with sensory and electrophysiological properties recorded in vivo. Relative immunointensities for trkA and two TTX-resistant sodium channels (Nav1.8 and Nav1.9) were also measured in these neurons. IB4+ neurons were classified as strongly or weakly IB4+. All strongly IB4+ neurons were C-nociceptor type (C-fiber nociceptive or unresponsive). Of 32 C-nociceptor-type neurons examined, ~50% were strongly IB4+, ~20% were weakly IB4+ and ~30% were IB4–. A{delta} low-threshold mechanoreceptive (LTM) neurons were weakly IB4+ or IB4–. All 33 A-fiber nociceptors and all 44 A{alpha}/beta-LTM neurons examined were IB4–. IB4+ compared with IB4– C-nociceptor-type neurons had longer somatic action potential durations and rise times, slower conduction velocities, more negative membrane potentials, and greater immunointensities for Nav1.9 but not Nav1.8. Immunointensities of IB4 binding in C-neurons were positively correlated with those of Nav1.9 but not Nav1.8. Of 23 C-neurons tested for both trkA and IB4, ~35% were trkA+/IB4+ but with negatively correlated immunointensities; 26% were IB4+/trkA–, and 35% were IB4–/trkA+. We conclude that strongly IB4+ DRG neurons are exclusively C-nociceptor type and that high Nav1.9 expression may contribute to their distinct membrane properties

The factorisation of glue and mass terms in SU(N) gauge theories

In this paper we investigate the structure of the glue in Zwanziger's gauge invariant expansion for the A^2-type mass term in Yang-Mills theory. We show how to derive this expansion, in terms of the inverse covariant Laplacian, and extend it to higher orders. In particular, we give an explicit expression, for the first time, for the next to next to leading order term. We further show that the expansion is not unique and give examples of the resulting ambiguity.Comment: 22 page

The Fermi surface and f-valence electron count of UPt3

Combining old and new de Haas-van Alphen (dHvA) and magnetoresistance data, we arrive at a detailed picture of the Fermi surface of the heavy fermion superconductor UPt3. Our work was partially motivated by a new proposal that two 5f valence electrons per formula unit in UPt3 are localized by correlation effects -- agreement with previous dHvA measurements of the Fermi surface was invoked in its support. Comprehensive comparison with our new observations shows that this 'partially localized' model fails to predict the existence of a major sheet of the Fermi surface, and is therefore less compatible with experiment than the originally proposed 'fully itinerant' model of the electronic structure of UPt3. In support of this conclusion, we offer a more complete analysis of the fully itinerant band structure calculation, where we find a number of previously unrecognized extremal orbits on the Fermi surface.Comment: 23 pages, 12 figures, latex, iopart clas

One-Loop Amplitudes in Euclidean Quantum Gravity

This paper studies the linearized gravitational field in the presence of boundaries. For this purpose, $\zeta$-function regularization is used to perform the mode-by-mode evaluation of BRST-invariant Faddeev-Popov amplitudes in the case of flat Euclidean four-space bounded by a three-sphere. On choosing the de Donder gauge-averaging term, the resulting $\zeta(0)$ value is found to agree with the space-time covariant calculation of the same amplitudes, which relies on the recently corrected geometric formulas for the asymptotic heat kernel in the case of mixed boundary conditions. Two sets of mixed boundary conditions for Euclidean quantum gravity are then compared in detail. The analysis proves that one cannot restrict the path-integral measure to transverse-traceless perturbations. By contrast, gauge-invariant amplitudes are only obtained on considering from the beginning all perturbative modes of the gravitational field, jointly with ghost modes.Comment: 26 pages, plain TeX, no figure

Serving the People of the Tennessee Valley: Perspectives on Learning, Growth and Management Internships

The purpose of this project was to examine three students’ different paths and perspectives of internships at the Tennessee Valley Authority (TVA) in the Learning, Growth and Management Department (LG&M). The need for this project was highlighted by a lack of internship practicum-based information presented in past research conferences. This poster first examines the different teams and functions of those teams that the interns were apart of during their internships at TVA. Then the project identifies types of jobs that I-O Psychology Masters candidates can expect to be qualified and/or recruited for within the constraints of TVA and the LG&M department. Next, key projects, and SIOP competencies strengthened through these projects, will be discussed. Finally, recommendations for students seeking internships and companies seeking to recruit top quality I-O students are given. In sum, while this project only examines three students’ paths at one company and in one department, we believe this information will help I-O psychology students identify internships that can develop important competencies that SIOP has designated as necessary to be a successful I-O psychology practitioner and offer helpful recommendations for students and companies alike