Effect of loading and geometry on the subsonic/intersonic transition of a bimaterial interface crack

An experimental investigation was conducted to study the nature of intersonic crack propagation along a bimaterial interface. A single edge notch/crack oriented along a polymer/metal interface was loaded predominantly in shear by impacting the specimen with a high velocity projectile fired from a gas gun. The stress field information around the propagating crack tip was recorded in real time by two different optical techniques--photoelasticity and coherent gradient sensing, in conjunction with high speed photography. Intersonic cracks on polymer/metal interfaces were found to propagate at speeds between the shear wave speed (c_s) and of the polymer. The nature of the crack tip fields during subsonic/intersonic transition and the conditions governing this transition were examined. Experimental observations showed the formation of a crack face contact zone as the interfacial crack speed exceeds the Rayleigh wave speed of the polymer. Subsequently, the contact zone was observed to expand in size, shrink and eventually collapse onto the intersonic crack tip. The recorded isochromatic fringe patterns showed multiple Mach wave formation associated with such a scenario. It is found that the nature of contact zone formation as well as its size and evolution differ substantially depending on the sign of the opening component of loading.     

Determinants of side chain conformational preferences in protein structures

A discriminatory function based on a statistical analysis of atomic contacts in protein structures is used for selecting side chain rotamers given a peptide main chain. The function allows us to rank different possible side chain conformations on the basis of contacts between side chain atoms and atoms in the environment. We compare the differences in constructing side chain conformations using contacts with only the local main chain, using the entire main chain, and by building pairs of side chains simultaneously with local main chain information. Using only the local main chain allows us to construct side chains with approximately 75% of the chi1 angles within 30 degrees of the experimental value, and an average side chain atom r.m.s.d. of 1.72 A in a set of 10 proteins. The results of constructing side chains for the 10 proteins are compared with the results of other side chain building methods previously published. The comparison shows similar accuracies. An advantage of the present method is that it can be used to select a small number of likely side chain conformations for each residue, thus permitting limited combinatorial searches for building multiple protein side chains simultaneously.      

A surface-anchored molecular four-level conductance switch based on single proton transfer

The development of a variety of nanoscale applications requires the fabrication and control of atomic or molecular switches that can be reversibly operated by light, a short-range force, electric current or other external stimuli. For such molecules to be used as electronic components, they should be directly coupled to a metallic support and the switching unit should be easily connected to other molecular species without suppressing switching performance. Here, we show that a free-base tetraphenyl-porphyrin molecule, which is anchored to a silver surface, can function as a molecular conductance switch. The saddle-shaped molecule has two hydrogen atoms in its inner cavity that can be flipped between two states with different local conductance levels using the electron current through the tip of a scanning tunnelling microscope. Moreover, by deliberately removing one of the hydrogens, a four-level conductance switch can be created. The resulting device, which could be controllably integrated into the surrounding nanoscale environment, relies on the transfer of a single proton and therefore contains the smallest possible atomistic switching unit.     

Tracing Hidden Herbivores: Time-Resolved Non-Invasive Analysis of Belowground Volatiles by Proton-Transfer-Reaction Mass Spectrometry (PTR-MS)

Root herbivores are notoriously difficult to study, as they feed hidden in the soil. However, root herbivores may be traced by analyzing specific volatile organic compounds (VOCs) that are produced by damaged roots. These VOCs not only support parasitoids in the localization of their host, but also may help scientists study belowground plant-herbivore interactions. Herbivore-induced VOCs are usually analyzed by gas-chromatography mass spectrometry (GC-MS), but with this off-line method, the gases of interest need to be preconcentrated, and destructive sampling is required to assess the level of damage to the roots. In contrast to this, proton-transfer-reaction mass spectrometry (PTR-MS) is a very sensitive on-line, non-invasive method. PTR-MS already has been successfully applied to analyze VOCs produced by aboveground (infested) plant parts. In this review, we provide a brief overview of PTR-MS and illustrate how this technology can be applied to detect specific root-herbivore induced VOCs from Brassica plants. We also specify the advantages and disadvantages of PTR-MS analyses and new technological developments to overcome their limitations.     

Constructing side chains on near-native main chains for ab initio protein structure prediction

Is there value in constructing side chains while searching proteinconformational space during an ab initio simulation? If so,what is the most computationally efficient method for constructingthese side chains? To answer these questions, four publishedapproaches were used to construct side chain conformations ona range of near-native main chains generated by ab initio proteinstructure prediction methods. The accuracy of these approacheswas compared with a naive approach that selects the most frequentlyobserved rotamer for a given amino acid to construct side chains.An all-atom conditional probability discriminatory functionis useful at selecting conformations with overall low all-atomroot mean square deviation (r.m.s.d.) and the discriminationimproves on sets that are closer to the native conformation.In addition, the naive approach performs as well as more sophisticatedmethods in terms of the percentage of     

Structure Prediction of Partial-Length Protein Sequences

Protein structure information is essential to understand protein function. Computational methods to accurately predict protein structure from the sequence have primarily been evaluated on protein sequences representing full-length native proteins. Here, we demonstrate that top-performing structure prediction methods can accurately predict the partial structures of proteins encoded by sequences that contain approximately 50% or more of the full-length protein sequence. We hypothesize that structure prediction may be useful for predicting functions of proteins whose corresponding genes are mapped expressed sequence tags (ESTs) that encode partial-length amino acid sequences. Additionally, we identify a confidence score representing the quality of a predicted structure as a useful means of predicting the likelihood that an arbitrary polypeptide sequence represents a portion of a foldable protein sequence (“foldability”). This work has ramifications for the prediction of protein structure with limited or noisy sequence information, as well as genome annotation.     

A knowledge-based scoring function based on residue triplets for protein structure prediction

One of the general paradigms for ab initio protein structure prediction involves sampling the conformational space such that a large set of decoy (candidate) structures are generated and then selecting native-like conformations from those decoys using various scoring functions. In this study, based on a physical/geometric approach first suggested by Banavar and colleagues, we formulate a knowledge-based scoring function, which uses the radii of curvature formed among triplets of residues in a protein conformation. By analyzing its performance on various decoy sets, we determine a good set of parameters--the distance cutoff and the number of distance bins--to use for configuring such a function. Furthermore, we investigate the effect of using various approaches for compiling the prior distribution on the performance of the knowledge-based function. Possible extensions to the current form of the residue triplet scoring function are discussed.     

A 600-MHz superscalar floating-point processor

The floating-point unit of a 600-MHz, out-of order, superscalar RISC Alpha microprocessor is described. The unit achieves 59 SpecFP95 and can transfer register data at up to 9.6 GB/s. It has two independent pipelines for multiply and add/subtract operations, with iterative divide and square-root circuits, and is fabricated in a 2.2-V, 0.35-μm CMOS process     

A Fermi‐Level‐Pinning‐Free 1D Electrical Contact at the Intrinsic 2D MoS2–Metal Junction

Currently 2D crystals are being studied intensively for use in future nanoelectronics, as conventional semiconductor devices face challenges in high power consumption and short channel effects when scaled to the quantum limit. Toward this end, achieving barrier‐free contact to 2D semiconductors has emerged as a major roadblock. In conventional contacts to bulk metals, the 2D semiconductor Fermi levels become pinned inside the bandgap, deviating from the ideal Schottky–Mott rule and resulting in significant suppression of carrier transport in the device. Here, MoS₂ polarity control is realized without extrinsic doping by employing a 1D elemental metal contact scheme. The use of high‐work‐function palladium (Pd) or gold (Au) enables a high‐quality p‐type dominant contact to intrinsic MoS₂, realizing Fermi level depinning. Field‐effect transistors (FETs) with Pd edge contact and Au edge contact show high performance with the highest hole mobility reaching 330 and 432 cm² V^?1 s^?1 at 300 K, respectively. The ideal Fermi level alignment allows creation of p‐ and n‐type FETs on the same intrinsic MoS₂ flake using Pd and low‐work‐function molybdenum (Mo) contacts, respectively. This device acts as an efficient inverter, a basic building block for semiconductor integrated circuits, with gain reaching 15 at V_D = 5 V.