Correlating AFM Probe Morphology to Image Resolution for Single-Wall Carbon Nanotube Tips

We report local-field-enhanced light emission from silicon nanocrystals close to a film of nanoporous gold. We resolve photoluminescence as the gold−Si nanocrystal separation distance is varied between 0 and 20 nm and observe a fourfold luminescence intensity enhancement concomitant with increases in the coupled silicon nanocrystal/nanoporous gold absorbance cross section and radiative decay rate. A detailed analysis of the luminescence data indicated a local-field-enhanced quantum efficiency of 58% for the Si nanocrystals coupled to the nanoporous gold layer

Modeling Collisionless Matter in General Relativity: A New Numerical Technique

We propose a new numerical technique for following the evolution of a self-gravitating collisionless system in general relativity. Matter is modeled as a scalar field obeying the coupled Klein-Gordon and Einstein equations. A phase space distribution function, constructed using covariant coherent states, obeys the relativistic Vlasov equation provided the de Broglie wavelength for the field is very much smaller than the scales of interest. We illustrate the method by solving for the evolution of a system of particles in a static, plane-symmetric, background spacetime.Comment: 6 pages, 3 postscript figures, submitted to Physical Review

Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation

Somatic hypermutation (SHM) plays a critical role in the maturation of antibodies, optimizing recognition initiated by recombination of V(D)J genes. Previous studies have shown that the propensity to mutate is modulated by the context of surrounding nucleotides and that SHM machinery generates biased substitutions. To investigate the intrinsic mutation frequency and substitution bias of SHMs at the amino acid level, we analyzed functional human antibody repertoires and developed mGSSP (method for gene-specific substitution profile), a method to construct amino acid substitution profiles from next-generation sequencing-determined B cell transcripts. We demonstrated that these gene-specific substitution profiles (GSSPs) are unique to each V gene and highly consistent between donors. We also showed that the GSSPs constructed from functional antibody repertoires are highly similar to those constructed from antibody sequences amplified from non-productively rearranged passenger alleles, which do not undergo functional selection. This suggests the types and frequencies, or mutational space, of a majority of amino acid changes sampled by the SHM machinery to be well captured by GSSPs. We further observed the rates of mutational exchange between some amino acids to be both asymmetric and context dependent and to correlate weakly with their biochemical properties. GSSPs provide an improved, position-dependent alternative to standard substitution matrices, and can be utilized to developing software for accurately modeling the SHM process. GSSPs can also be used for predicting the amino acid mutational space available for antigen-driven selection and for understanding factors modulating the maturation pathways of antibody lineages in a gene-specific context. The mGSSP method can be used to build, compare, and plot GSSPs1; we report the GSSPs constructed for 69 common human V genes (DOI: 10.6084/m9.figshare.3511083) and provide high-resolution logo plots for each (DOI: 10.6084/m9.figshare.3511085)

Selective functionalization of carbon nanotube tips allowing fabrication of new classes of nanoscale sensing and manipulation tools

Embodiments in accordance with the present invention relate to techniques for the growth and attachment of single wall carbon nanotubes (SWNT), facilitating their use as robust and well-characterized tools for AFM imaging and other applications. In accordance with one embodiment, SWNTs attached to an AFM tip can function as a structural scaffold for nanoscale device fabrication on a scanning probe. Such a probe can trigger, with nanometer precision, specific biochemical reactions or conformational changes in biological systems. The consequences of such triggering can be observed in real time by single-molecule fluorescence, electrical, and/or AFM sensing. Specific embodiments in accordance with the present invention utilize sensing and manipulation of individual molecules with carbon nanotubes, coupled with single-molecule fluorescence imaging, to allow observation of spectroscopic signals in response to mechanically induced molecular changes. Biological macromolecules such as proteins or DNA can be attached to nanotubes to create highly specific single-molecule probes for investigations of intermolecular dynamics, for assembling hybrid biological and nanoscale materials, or for developing molecular electronics. In one example, electrical wiring of single redox enzymes to carbon nanotube scanning probes allows observation and electrochemical control over single enzymatic reactions by monitoring fluorescence from a redox-active cofactor or the formation of fluorescent products. Enzymes ''nanowired'' to the tips of carbon nanotubes in accordance with embodiments of the present invention, may enable extremely sensitive probing of biological stimulus-response with high spatial resolution, including product-induced signal transduction

Band Calculations for Ce Compounds with AuCu3_{3}-type Crystal Structure on the basis of Dynamical Mean Field Theory I. CePd3_{3} and CeRh3_{3}

Band calculations for Ce compounds with the AuCu$_{3}$-type crystal structure were carried out on the basis of dynamical mean field theory (DMFT). The auxiliary impurity problem was solved by a method named NCA$f^{2}$vc (noncrossing approximation including the $f^{2}$ state as a vertex correction). The calculations take into account the crystal-field splitting, the spin-orbit interaction, and the correct exchange process of the $f^{1} \rightarrow f^{0},f^{2}$ virtual excitation. These are necessary features in the quantitative band theory for Ce compounds and in the calculation of their excitation spectra. The results of applying the calculation to CePd$_{3}$ and CeRh$_{3}$ are presented as the first in a series of papers. The experimental results of the photoemission spectrum (PES), the inverse PES, the angle-resolved PES, and the magnetic excitation spectra were reasonably reproduced by the first-principles DMFT band calculation. At low temperatures, the Fermi surface (FS) structure of CePd$_{3}$ is similar to that of the band obtained by the local density approximation. It gradually changes into a form that is similar to the FS of LaPd$_{3}$ as the temperature increases, since the $4f$ band shifts to the high-energy side and the lifetime broadening becomes large.}Comment: 12 pasges, 13 figure

Embodied cognitive ecosophy: the relationship of mind, body, meaning and ecology

The concept of embodied cognition has had a major impact in a number of disciplines. The extent of its consequences on general knowledge and epistemology are still being explored. Embodied cognition in human geography has its own traditions and discourses but these have become somewhat isolated in the discipline itself. This paper argues that findings in other disciplines are of value in reconceptualising embodied cognition in human geography and this is explored by reconsidering the concept of ecosophy. Criticisms of ecosophy as a theory are considered and recent work in embodied cognition is applied to consider how such criticisms might be addressed. An updated conceptualisation is proposed, the embodied cognitive ecosophy, and three characteristics arising from this criticism and synthesis are presented with a view to inform future discussions of ecosophy and emotional geography

Influence of Elastic Deformation on Single-Wall Carbon Nanotube Atomic Force Microscopy Probe Resolution

We have previously reported that 4−6 nm diameter single-wall carbon nanotube (SWNT) probes used for tapping-mode atomic force microscopy (AFM) can exhibit lateral resolution that is significantly better than the probe diameter when prone nanotubes are imaged on a flat SiO_2 surface. To further investigate this phenomenon, accurate models for use in atomistic molecular dynamics simulations were constructed on the basis of transmission electron microscopy (TEM) and AFM data. Probe−sample interaction potentials were generated by utilization of force fields derived from ab initio quantum mechanics calculations and material bulk and surface properties, and the resulting force curves were integrated numerically with the AFM cantilever equation of motion. The simulations demonstrate that, under the AFM imaging conditions employed, elastic deformations of both the probe and sample nanotubes result in a decrease of the apparent width of the sample. This behavior provides an explanation for the unexpected resolution improvement and illustrates some of the subtleties involved when imaging is performed with SWNT probes in place of conventional silicon probes. However, the generality of this phenomenon for other AFM imaging applications employing SWNT probes remains to be explored