1,753 research outputs found
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
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
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)
Band Calculations for Ce Compounds with AuCu-type Crystal Structure on the basis of Dynamical Mean Field Theory I. CePd and CeRh
Band calculations for Ce compounds with the AuCu-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 NCAvc
(noncrossing approximation including the 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 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 and
CeRh 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 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 as the temperature increases, since the
band shifts to the high-energy side and the lifetime broadening becomes
large.}Comment: 12 pasges, 13 figure
Prospects of observing a quasar HII region during the Epoch of Reionization with redshifted 21cm
We present a study of the impact of a bright quasar on the redshifted 21cm
signal during the Epoch of Reionization (EoR). Using three different
cosmological radiative transfer simulations, we investigate if quasars are
capable of substantially changing the size and morphology of the H II regions
they are born in. We choose stellar and quasar luminosities in a way that is
favourable to seeing such an effect. We find that even the most luminous of our
quasar models is not able to increase the size of its native H II region
substantially beyond those of large H II regions produced by clustered stellar
sources alone. However, the quasar H II region is found to be more spherical.
We next investigate the prospects of detecting such H II regions in the
redshifted 21cm data from the Low Frequency Array (LOFAR) by means of a matched
filter technique. We find that H II regions with radii ~ 25 comoving Mpc or
larger should have a sufficiently high detection probability for 1200 hours of
integration time. Although the matched filter can in principle distinguish
between more and less spherical regions, we find that when including realistic
system noise this distinction can no longer be made. The strong foregrounds are
found not to pose a problem for the matched filter technique. We also
demonstrate that when the quasar position is known, the redshifted 21cm data
can still be used to set upper limits on the ionizing photon rate of the
quasar. If both the quasar position and its luminosity are known, the
redshifted 21 cm data can set new constrains on quasar lifetimes.Comment: 17 pages, 12 figures, 3 tables, accepted for publication in MNRAS;
changes in introduction and 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
On the Gauge/Gravity Correspondence and the Open/Closed String Duality
In this article we review the conditions for the validity of the
gauge/gravity correspondence in both supersymmetric and non-supersymmetric
string models. We start by reminding what happens in type IIB theory on the
orbifolds C^2/Z_2 and C^3/(Z_2 x Z_2), where this correspondence beautifully
works. In these cases, by performing a complete stringy calculation of the
interaction among D3 branes, it has been shown that the fact that this
correspondence works is a consequence of the open/closed duality and of the
absence of threshold corrections. Then we review the construction of type 0
theories with their orbifolds and orientifolds having spectra free from both
open and closed string tachyons and for such models we study the validity of
the gauge/gravity correspondence, concluding that this is not a peculiarity of
supersymmetric theories, but it may work also for non-supersymmetric models.
Also in these cases, when it works, it is again a consequence of the
open/closed string duality and of vanishing threshold corrections.Comment: Invited review article for Int. J. Mod. Phys. A, 95 pages, 2 figures,
3 tables, LaTeX. References and acknowledgements adde
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
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