Treatise on Invertebrate Paleontology, Part W, conodonts, conoidal shells, worms, trace fossils: comments and additions

18 p., 21 fig.http://paleo.ku.edu/contributions.htm

Is keV ion induced pattern formation on Si(001) caused by metal impurities?

We present ion beam erosion experiments performed in ultra high vacuum using a differentially pumped ion source and taking care that the ion beam hits the Si(001) sample only. Under these conditions no ion beam patterns form on Si for angles below 45 degrees with respect to the global surface normal using 2 keV Kr ions and fluences of 2 x 10^22 ions/m^2. In fact, the ion beam induces a smoothening of preformed patterns. Simultaneous sputter deposition of stainless steel in this angular range creates a variety of patterns, similar to those previously ascribed to clean ion beam induced destabilization of the surface profile. Only for grazing incidence with incident angles between 60 degrees and 83 degrees pronounced ion beam patterns form. It appears that the angular dependent stability of Si(001) against pattern formation under clean ion beam erosion conditions is related to the angular dependence of the sputtering yield, and not primarily to a curvature dependent yield as invoked frequently in continuum theory models.Comment: 15 pages, 7 figures. This is an author-created, un-copyedited version of an article published in Nanotechnology. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from i

Stress-driven instability in growing multilayer films

We investigate the stress-driven morphological instability of epitaxially growing multilayer films, which are coherent and dislocation-free. We construct a direct elastic analysis, from which we determine the elastic state of the system recursively in terms of that of the old states of the buried layers. In turn, we use the result for the elastic state to derive the morphological evolution equation of surface profile to first order of perturbations, with the solution explicitly expressed by the growth conditions and material parameters of all the deposited layers. We apply these results to two kinds of multilayer structures. One is the alternating tensile/compressive multilayer structure, for which we determine the effective stability properties, including the effect of varying surface mobility in different layers, its interplay with the global misfit of the multilayer film, and the influence of asymmetric structure of compressive and tensile layers on the system stability. The nature of the asymmetry properties found in stability diagrams is in agreement with experimental observations. The other multilayer structure that we study is one composed of stacked strained/spacer layers. We also calculate the kinetic critical thickness for the onset of morphological instability and obtain its reduction and saturation as number of deposited layers increases, which is consistent with recent experimental results. Compared to the single-layer film growth, the behavior of kinetic critical thickness shows deviations for upper strained layers.Comment: 27 pages, 11 figures; Phys. Rev. B, in pres

Ab initio study of step formation and self-diffusion on Ag(100)

Using the plane wave pseudopotential method we performed density functional theory calculations on the stability of steps and self-diffusion processes on Ag(100). Our calculated step formation energies show that the {111}-faceted step is more stable than the {110}-faceted step. In accordance with experimental observations we find that the equilibrium island shape should be octagonal very close to a square with predominately {111}-faceted steps. For the (100) surface of fcc metals atomic migration proceeds by a hopping or an exchange process. For Ag(100) we find that adatoms diffuse across flat surfaces preferentially by hopping. Adatoms approaching the close-packed {111}-faceted step edges descend from the upper terrace to the lower level by an atomic exchange with an energy barrier almost identical to the diffusion barrier on flat surface regions. Thus, within our numerical accuracy (approx +- 0.05 eV) there is no additional step-edge barrier to descent. This provides a natural explanation for the experimental observations of the smooth two-dimensional growth in homoepitaxy of Ag(100). Inspection of experimental results of other fcc crystal surfaces indicates that our result holds quite generally.Comment: 10 pages, 9 figures. Submitted to Phys. Rev B (October 31, 1996

Structural and magnetic properties of Mn-implanted Si

Structural and ferromagnetic properties in Mn implanted, p-type Si were investigated. High resolution structural analysis techniques like synchrotron X-ray diffraction revealed the formation of MnSi1.7 nanoparticles already in the as implanted samples. Depending on the Mn-fluence, the size increases from 5 nm to 20 nm upon rapid thermal annealing. No significant evidence is found for Mn substituting Si sites either in the as-implanted or annealed samples. The observed ferromagnetism yields a saturation moment of 0.21 mu_B per implanted Mn at 10 K, which could be assigned to MnSi1.7 nanoparticles as revealed by a temperature dependent magnetization measurement.Comment: 21 pages, 6 figures, accepted for publicaiton at Phys. Rev.

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

©2008 Pandit and Skolnick; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article is available from: http://www.biomedcentral.com/1471-2105/9/531doi:10.1186/1471-2105-9-531Background: Protein tertiary structure comparisons are employed in various fields of contemporary structural biology. Most structure comparison methods involve generation of an initial seed alignment, which is extended and/or refined to provide the best structural superposition between a pair of protein structures as assessed by a structure comparison metric. One such metric, the TM-score, was recently introduced to provide a combined structure quality measure of the coordinate root mean square deviation between a pair of structures and coverage. Using the TM-score, the TM-align structure alignment algorithm was developed that was often found to have better accuracy and coverage than the most commonly used structural alignment programs; however, there were a number of situations when this was not true. Results: To further improve structure alignment quality, the Fr-TM-align algorithm has been developed where aligned fragment pairs are used to generate the initial seed alignments that are then refined using dynamic programming to maximize the TM-score. For the assessment of the structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TMalign, we examined various alignment quality assessment scores such as PSI and TM-score. The assessment showed that the structural alignment quality from Fr-TM-align is better in comparison to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have a higher TM-score (~9%) and coverage (~7%) in comparison to those generated by TM-align. Fr- TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is computationally more expensive than TM-align. Conclusion: Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The source code and executables of Fr- TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/

Identification of plasma lipid biomarkers for prostate cancer by lipidomics and bioinformatics

Background: Lipids have critical functions in cellular energy storage, structure and signaling. Many individual lipid molecules have been associated with the evolution of prostate cancer; however, none of them has been approved to be used as a biomarker. The aim of this study is to identify lipid molecules from hundreds plasma apparent lipid species as biomarkers for diagnosis of prostate cancer. Methodology/Principal Findings: Using lipidomics, lipid profiling of 390 individual apparent lipid species was performed on 141 plasma samples from 105 patients with prostate cancer and 36 male controls. High throughput data generated from lipidomics were analyzed using bioinformatic and statistical methods. From 390 apparent lipid species, 35 species were demonstrated to have potential in differentiation of prostate cancer. Within the 35 species, 12 were identified as individual plasma lipid biomarkers for diagnosis of prostate cancer with a sensitivity above 80%, specificity above 50% and accuracy above 80%. Using top 15 of 35 potential biomarkers together increased predictive power dramatically in diagnosis of prostate cancer with a sensitivity of 93.6%, specificity of 90.1% and accuracy of 97.3%. Principal component analysis (PCA) and hierarchical clustering analysis (HCA) demonstrated that patient and control populations were visually separated by identified lipid biomarkers. RandomForest and 10-fold cross validation analyses demonstrated that the identified lipid biomarkers were able to predict unknown populations accurately, and this was not influenced by patient's age and race. Three out of 13 lipid classes, phosphatidylethanolamine (PE), ether-linked phosphatidylethanolamine (ePE) and ether-linked phosphatidylcholine (ePC) could be considered as biomarkers in diagnosis of prostate cancer. Conclusions/Significance: Using lipidomics and bioinformatic and statistical methods, we have identified a few out of hundreds plasma apparent lipid molecular species as biomarkers for diagnosis of prostate cancer with a high sensitivity, specificity and accuracy

Heteroepitaxial growth of ferromagnetic MnSb(0001) films on Ge/Si(111) virtual substrates

Molecular beam epitaxial growth of ferromagnetic MnSb(0001) has been achieved on high quality, fully relaxed Ge(111)/Si(111) virtual substrates grown by reduced pressure chemical vapor deposition. The epilayers were characterized using reflection high energy electron diffraction, synchrotron hard X-ray diffraction, X-ray photoemission spectroscopy, and magnetometry. The surface reconstructions, magnetic properties, crystalline quality, and strain relaxation behavior of the MnSb films are similar to those of MnSb grown on GaAs(111). In contrast to GaAs substrates, segregation of substrate atoms through the MnSb film does not occur, and alternative polymorphs of MnSb are absent

Spin Structure of the Proton from Polarized Inclusive Deep-Inelastic Muon-Proton Scattering

We have measured the spin-dependent structure function $g_1^p$ in inclusive deep-inelastic scattering of polarized muons off polarized protons, in the kinematic range $0.003 < x < 0.7$ and $1 GeV^2 < Q^2 < 60 GeV^2$. A next-to-leading order QCD analysis is used to evolve the measured $g_1^p(x,Q^2)$ to a fixed $Q^2_0$. The first moment of $g_1^p$ at $Q^2_0 = 10 GeV^2$ is $\Gamma^p = 0.136\pm 0.013(stat.) \pm 0.009(syst.)\pm 0.005(evol.)$. This result is below the prediction of the Ellis-Jaffe sum rule by more than two standard deviations. The singlet axial charge $a_0$ is found to be $0.28 \pm 0.16$. In the Adler-Bardeen factorization scheme, $\Delta g \simeq 2$ is required to bring $\Delta \Sigma$ in agreement with the Quark-Parton Model. A combined analysis of all available proton and deuteron data confirms the Bjorken sum rule.Comment: 33 pages, 22 figures, uses ReVTex and smc.sty. submitted to Physical Review