Direct observation of yield in films by flat punch indentation

In regular indentation many strain states are simultaneously present in the indented region, so measured parameters such as hardness and modulus are average values over a wide range of strains. Testing of structures such as pillars, levers or film bulges enables determination of yield point and modulus with uniform strains in the sample, but requires specialised sample preparation and can be significantly affected by surface condition. Here we show how in-situ indentation with a flat punch allows direct observation of a discrete yield point in soft films on more rigid substrates. The yield point is clearly observable from the load displacement behaviour and from post indent AFM imaging. The film is in uniform uniaxial strain. Finite element simulations show that effective self-confinement by surrounding film material leads to uniformity throughout the film material down to surprisingly low aspect ratios around 4:1. This occurs for a significant range of stresses above the yield point. Eventually at even higher stresses the film material is extruded laterally. The characteristics of the yield event will be described as a function of temperature and film thickness for thin to ultrathin films. At higher aspect ratio and with sufficient stiffness of punch and substrate, quantitative, in-situ measurement of intrinsic stress vs. strain to well beyond the elastic limit becomes possible for thin films. The extent to which full constitutive relations for polymer films can be determied will be discussed, along with limitations of the technique

Phylometrics: a pipeline for inferring phylogenetic trees from a sequence relationship network perspective

<p>Abstract</p> <p>Background</p> <p>Comparative sequence analysis of the 16S rRNA gene is frequently used to characterize the microbial diversity of environmental samples. However, sequence similarities do not always imply functional or evolutionary relatedness due to many factors, including unequal rates of change and convergence. Thus, relying on top BLASTN hits for phylogenetic studies may misrepresent the diversity of these constituents. Furthermore, attempts to circumvent this issue by including a large number of BLASTN hits per sequence in one tree to explore their relatedness presents other problems. For instance, the multiple sequence alignment will be poor and computationally costly if not relying on manual alignment, and it may be difficult to derive meaningful relationships from the resulting tree. Analyzing sequence relationship networks within collective BLASTN results, however, reveal sequences that are closely related despite low rank.</p> <p>Results</p> <p>We have developed a web application, Phylometrics, that relies on networks of collective BLASTN results (rather than single BLASTN hits) to facilitate the process of building phylogenetic trees in an automated, high-throughput fashion while offering novel tools to find sequences that are of significant phylogenetic interest with minimal human involvement. The application, which can be installed locally in a laboratory or hosted remotely, utilizes a simple wizard-style format to guide the user through the pipeline without necessitating a background in programming. Furthermore, Phylometrics implements an independent job queuing system that enables users to continue to use the system while jobs are run with little or no degradation in performance. </p> <p>Conclusions</p> <p>Phylometrics provides a novel data mining method to screen supplied DNA sequences and to identify sequences that are of significant phylogenetic interest using powerful analytical tools. Sequences that are identified as being similar to a number of supplied sequences may provide key insights into their functional or evolutionary relatedness. Users require the same basic computer skills as for navigating most internet applications.</p

Quantum point contact on graphite surface

The conductance through a quantum point contact created by a sharp and hard metal tip on the graphite surface has features which to our knowledge have not been encountered so far in metal contacts or in nanowires. In this paper we first investigate these features which emerge from the strongly directional bonding and electronic structure of graphite, and provide a theoretical understanding for the electronic conduction through quantum point contacts. Our study involves the molecular-dynamics simulations to reveal the variation of interlayer distances and atomic structure at the proximity of the contact that evolves by the tip pressing toward the surface. The effects of the elastic deformation on the electronic structure, state density at the Fermi level, and crystal potential are analyzed by performing self-consistent-field pseudopotential calculations within the local-density approximation. It is found that the metallicity of graphite increases under the uniaxial compressive strain perpendicular to the basal plane. The quantum point contact is modeled by a constriction with a realistic potential. The conductance is calculated by representing the current transporting states in Laue representation, and the variation of conductance with the evolution of contact is explained by taking the characteristic features of graphite into account. It is shown that the sequential puncturing of the layers characterizes the conductance.Comment: LaTeX, 11 pages, 9 figures (included), to be published in Phys. Rev. B, tentatively scheduled for 15 September 1998 (Volume 58, Number 12

Application of isothermal titration calorimetry in evaluation of protein–nanoparticle interactions

Nanoparticles (NPs) offer a number of advantages over small organic molecules for controlling protein behaviour inside the cell. Protein binding to the surface of NPs depends on their surface characteristics, composition and method of preparation (Mandal et al. in J Hazard Mater 248–249:238–245, 2013). It is important to understand the binding affinities, stoichiometries and thermodynamical parameters of NP–protein interactions in order to see which interaction will have toxic and hazardous consequences and thus to prevent it. On the other side, because proteins are on the brink of stability, they may experience interactions with some types of NPs that are strong enough to cause denaturation or significantly change their conformations with concomitant loss of their biological function. Structural changes in the protein may cause exposure of new antigenic sites, “cryptic” peptide epitopes, potentially triggering an immune response which can promote autoimmune disease (Treuel et al. in ACS Nano 8(1):503–513, 2014). Mechanistic details of protein structural changes at NP surface have still remained elusive. Understanding the formation and persistence of the protein corona is critical issue; however, there are no many analytical methods which could provide detailed information about the NP–protein interaction characteristics and about protein structural changes caused by interactions with nanoparticles. The article reviews recent studies in NP–protein interactions research and application of isothermal titration calorimetry (ITC) in this research. The study of protein structural changes upon adsorption on nanoparticle surface and application of ITC in these studies is emphasized. The data illustrate that ITC is a versatile tool for evaluation of interactions between NPs and proteins. When coupled with other analytical methods, it is important analytical tool for monitoring conformational changes in proteins

Advances in atomic force microscopy

This article reviews the progress of atomic force microscopy (AFM) in ultra-high vacuum, starting with its invention and covering most of the recent developments. Today, dynamic force microscopy allows to image surfaces of conductors \emph{and} insulators in vacuum with atomic resolution. The mostly used technique for atomic resolution AFM in vacuum is frequency modulation AFM (FM-AFM). This technique, as well as other dynamic AFM methods, are explained in detail in this article. In the last few years many groups have expanded the empirical knowledge and deepened the theoretical understanding of FM-AFM. Consequently, the spatial resolution and ease of use have been increased dramatically. Vacuum AFM opens up new classes of experiments, ranging from imaging of insulators with true atomic resolution to the measurement of forces between individual atoms.Comment: In press (Reviews of Modern Physics, scheduled for July 2003), 86 pages, 44 figure

Expression and Characterization of Drosophila Signal Peptide Peptidase-Like (sppL), a Gene That Encodes an Intramembrane Protease

Intramembrane proteases of the Signal Peptide Peptidase (SPP) family play important roles in developmental, metabolic and signaling pathways. Although vertebrates have one SPP and four SPP-like (SPPL) genes, we found that insect genomes encode one Spp and one SppL. Characterization of the Drosophila sppL gene revealed that the predicted SppL protein is a highly conserved structural homolog of the vertebrate SPPL3 proteases, with a predicted nine-transmembrane topology, an active site containing aspartyl residues within a transmembrane region, and a carboxy-terminal PAL domain. SppL protein localized to both the Golgi and ER. Whereas spp is an essential gene that is required during early larval stages and whereas spp loss-of-function reduced the unfolded protein response (UPR), sppL loss of function had no apparent phenotype. This was unexpected given that genetic knockdown phenotypes in other organisms suggested significant roles for Spp-related proteases