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

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)

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