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The mycosin protease (MycP) is widely conserved in type VII secretion (T7S) systems throughout Actinobacteria. Within the T7S systems of mycobacteria, also known as the ESX systems, MycP is essential for secretion, which is probably linked to its stabilizing effect on the ESX membrane complex. However, it is unknown how this is mediated, as MycP is not a stable component of this complex. In this study, we set out to create a chimeric fusion protein of EccB5 and MycP5, based on a chimeric gene of eccB and mycP in the T7S locus of Bifidobacterium dentium. We show that this fusion protein is functional and capable of complementing ESX-5 secretion in both an eccB5 and a mycP5 knockout in Mycobacterium marinum. To study the ESX complex containing this fusion protein in more detail, we replaced the original eccB5 and mycP5 of the Mycobacterium xenopi esx-5 locus, reconstituted in Mycobacterium smegmatis, with the chimeric gene. The EccB5-MycP5 fusion construct also restored ESX-5 secretion under these double knockout conditions. Subsequent protein pulldowns on the central complex component EccC5 showed that under these conditions, the EccB5-MycP5 fusion was specifically copurified and a stable component of the ESX-5 complex. Based on our results, we can conclude that MycP5 carries out its essential function in secretion in close proximity to EccB5, indicating that EccB5 is the direct interaction partner of MycP5.

This study investigates the delamination behavior of carbon-Dyneema hybrid composites with different hybridization schemes. It is found that hybridization improves both mode I and mode II fracture toughness of carbon-Dyneema interfaces. This is attributed to the large yarn size of Dyneema fibers, which results in an increase of the resin rich thickness at the interface between plies. The fracture surface with adjacent Dyneema fibers exhibits high surface roughness leading to higher fracture toughness. Additionally, the thicker resin-rich interface promotes a cohesive-type failure within the resin rich zone, while fracture in the thinner carbon-carbon interface is dominated by adhesive-type failure. The mode II delamination of the carbon-Dyneema interface shows an increasing resistance curve, which may be attributed to friction between the rough delamination surfaces. The results demonstrate that hybridization with Dyneema could potentially be an effective toughening technique for thermoset carbon fiber composites.

The present experimental study investigates shock wave mitigation capability of potentially new personal protective equipment (PPE) suspension pads made from polyurea and shear thickening fluid (STF). The shock tube test results show that when placed behind Twaron fabric systems with thickness ranging from 2 mm to 18 mm, the replacement of conventional flexible foam pad with STF and STF-infused foam pads with the same thickness of 20 mm greatly reduces the normalized peak pressure (by about 72% for each pad). However, this benefit is partially offset by a large increase in the normalized impulse (by about 78% for the STF pad and 131% for the STF-infused foam pad) which may cause the shock wave mitigation performance of these two pads to become less effective. Interestingly, the use of 4 mm thick polyurea pad can greatly reduce the normalized peak pressure and impulse as well (by about 74% and 49%, respectively). These results reveal that among the potentially new suspension pads tested, the polyurea pad displays the best shock wave mitigation performance. Therefore, polyurea has potential for use as a suspension pad in personal protective equipment requiring shock wave mitigation capability such as fabric ballistic vests, bomb suits and combat helmets.

Carbon fibers, especially those constructed from carbon nanotubes (CNTs), have attracted intensive interests from both scientific and engineering communities due to their outstanding physical properties. In this workHere we report, we find that the recently synthesized recently synthesized ultrathin diamond nanothread (DNT) not only possesses excellent torsional deformation capability, but also has excellent interfacial load transfer efficiency. Comparing with the (10,10) carbon nanotube bundles, (1) By considering a seven strand fiber, the flattening of nanotubes as observed in (10,10) CNT bundles is not observed in DNTdiamond nanothread bundle, which . This endows the DNT bundle withleads to a high torsional elastic limit that is almost three times higherfour times as obtained from the (10,10) CNT bundle. Pull-out tests reveal that (2) Pull-out tests reveal that tthe DNT diamond nanothread bundle has has an interface transfer load of more than twice that of the CNT carbon naontube bundle, corresponding to an order of magnitude higher in terms of . (3) Tthe interfacial shear strength of the DNT bundle is an order of magnitude higher than that of the CNT bundle. Such high interface load transfer efficiency is attributed to the zigzag morphology of DNT, which introduces a strong mechanical interlocking effect at the interface through the stick-slip motion (totally different from the load transfer mechanism in CNT bundle). The aforementioned three aspects are commonly used to gauge the performance of fibers. Obviously,These intriguing features enable DNT diamond nanothread as exhibits excellent potential candidate for constructing next generation carbon fibers., Comment: 6 figures, published, Nature Communications, 2017

Burkitt lymphoma (BL) is a malignant disease, which is frequently found in areas with holoendemic Plasmodium falciparum malaria. We have previously found that the VAR2CSA protein is present on malaria-infected erythrocytes and facilitates a highly specific binding to the placenta. ofCS is absent in other non-malignant tissues and thus VAR2CSA generally facilitates parasite sequestration and accumulation in pregnant women. In this study, we show that the specific receptor for VAR2CSA, the oncofetal chondroitin sulfate (ofCS), is likewise present in BL tissue and cell lines. We therefore explored whether ofCS in BL could act as anchor site for VAR2CSA-expressing infected erythrocytes. In contrast to the placenta, we found no evidence of in vivo sequestering of infected erythrocytes in the BL tissue. Furthermore, we found VAR2CSA-specific antibody titers in children with endemic BL to be lower than in control children from the same malaria endemic region. The abundant presence of ofCS in BL tissue and the absence of ofCS in non-malignant tissue encouraged us to examine whether recombinant VAR2CSA could be used to target BL. We confirmed the binding of VAR2CSA to BL-derived cells and showed that a VAR2CSA drug conjugate efficiently killed the BL-derived cell lines in vitro. These results identify ofCS as a novel therapeutic BL target and highlight how VAR2CSA could be used as a tool for the discovery of novel approaches for directing BL therapy.

Helicoidal laminates mimicking the laminar structure of the exoskeleton of crustaceans have been reported to resist higher out-of-plane loads than the common cross-ply and quasi-isotropic fiber-reinforced laminates. Some have reported that smaller inter-ply angle improves strength of helicoidal laminates but others have reported the opposite. A few important material parameters that dictate the failure mechanism of helicoidal laminates have recently been proposed based on proof-of-concept carbon fiber-reinforced laminates, which is not the best material system to benefit from a helicoidal configuration. This study investigates the out-of-plane loading performance of helicoidal laminates with various inter-ply angles, ply thicknesses, and materials. Result shows that the failure mechanism is dictated by the competition between spiraling matrix split and delamination followed by fiber breakage regardless of the laminate material system. Spiraling matrix split resistance decreases as pitch (ratio of inter-ply angle to ply thickness) and matrix toughness decreases. This study provides guidelines for the optimization of helicoidal laminates. Coexistence of spiraling matrix split and fiber damage is often seen on the failed laminate with the highest peak load. The optimal inter-ply angle provides the optimal spiraling matrix split resistance; so, neither spiraling matrix split nor fiber/delamination damage becomes dominant. Since resistance to spiraling matrix split decreases as pitch or matrix toughness decreases, the optimal inter-ply angle will increase for laminates with weaker matrix or thicker plies and vice versa.

Mycobacteria, including the infamous pathogen Mycobacterium tuberculosis , are high-GC Gram-positive bacteria with a distinctive cell envelope. Although there is a typical inner membrane, the mycobacterial cell envelope is unusual in having its peptidoglycan layer connected to a polymer of arabinogalactan, which in turn is covalently attached to long-chain mycolic acids that help form a highly impermeable mycobacterial outer membrane. This complex double-membrane, or diderm, cell envelope imparts mycobacteria with unique requirements for protein export into and across the cell envelope for secretion into the extracellular environment. In this article, we review the four protein export pathways known to exist in mycobacteria: two conserved systems that exist in all types of bacteria (the Sec and Tat pathways) and two specialized systems that exist in mycobacteria, corynebacteria, and a subset of low-GC Gram-positive bacteria (the SecA2 and type VII secretion pathways). We describe the progress made over the past 15 years in understanding each of these mycobacterial export pathways, and we highlight the need for research to understand the specific steps of protein export across the mycobacterial outer membrane.

Mycobacteria use type VII secretion systems to secrete proteins across their highly hydrophobic diderm cell envelope. Pathogenic mycobacteria, such as Mycobacterium tuberculosis and Mycobacterium marinum, have up to five of these systems, named ESX-1 to ESX-5. Most of these systems contain a set of five conserved membrane components, of which the four Ecc proteins form the core membrane-embedded secretion complex. The fifth conserved membrane protein, mycosin protease (MycP), is not part of the core complex but is essential for secretion, as it stabilizes this membrane complex. Here we investigated which MycP domains are required for this stabilization by producing hybrid constructs between MycP 1 and MycP 5 in M. marinum and analyzed their effect on ESX-1 and ESX-5 secretion. We found that both the protease and transmembrane domain are required for the ESX system-specific function of mycosins. In addition, we observed that the transmembrane domain strongly affects MycP protein levels. We also show that the extended loops 1 and 2 in the protease domain are probably primarily involved in MycP stability, whereas loop 3 and the MycP 5 -specific loop 5 are dispensable. The atypical propeptide, or N-terminal extension, is required only for MycP stability. Finally, we show that the protease domain of MycP P1 , encoded by the esx-P1 locus on the pRAW plasmid, is functionally redundant to the protease domain of MycP 5 . These results provide the first insight into the regions of mycosins involved in interaction with and stabilization of their respective ESX complexes.

It is commonly claimed that ultra-high molecular weight polyethylene (UHMWPE) laminates offer high energy absorption during projectile impact with a cross-ply configuration. In this study, we explored alternative configurations with the aim of achieving better ballistic resistance than that of the cross-ply architecture. The UHMWPE laminates were fabricated from Endumax® cross-ply SHIELD XF23 using a hot press machine and material properties were obtain from Endumax® unidirectional (UD) tape TA23 coupon specimens. A solid steel sphere was used as the projectile. It was found that thinner laminates have higher the specific ballistic limit suggesting that it is more effective to deploy multiple stacks of thin laminated panels spaced apart than to bond all the laminas to form a single thick laminate. Experiments confirmed that while the multiple laminate systems always outperformed a single laminate comprising the same number of laminas, it was also best not to space the laminates apart. When simply stacked without spacing, the multi-laminate arrangement significantly enhanced the ballistic performance (about 10% increase in ballistic limit over the single panel). Adjacent laminates in the multi-laminate system were then rotated 45o relative to each other and then bonded together to form a single laminate with multiple blocks of similarly oriented laminas. This ply block configuration also had higher ballistic limit than the single cross-ply laminate for thin laminates but showed no advantage for thick laminates.

In this work, we report on the effective implementation of the direct and scalable floating catalyst method to synthesize self-supporting carbon nanotube (CNT) aerogels at high deposition rates. Through the adaptable process conditions, the highly porous and ultralight CNT aerogels with densities ranging from 0.55 to 32 mg/cm3 are synthesized. The aerogels exhibit high porosity (>98%) and surface areas of up to 170 m2/g with tortuous pores easy accessible to molecules of interest. Their superior electrical conductivity (up to 106 S/m), in comparison with CNT aerogels produced through other methods, indicates high potential for energy applications. The thermal conductivity has been observed to be within the range of 0.127–0.137 W/m·K as a consequence of the ultralight structure. Polymer infiltration and subsequent curing do not disturb the three-dimensional percolating CNT network and constitute an accessible method for the production of various lightweight polymeric composites. The polydimethylsiloxane-based composites (4.5% wt) with electrical conductivity enhanced by ∼16 orders of magnitude and thermal conductivity double that of pure matrix are particularly promising for use in bio-integrated devices and flexible composites.

This work explores the application of a new one-dimensional carbon nanomaterial, the diamond nanothread (DNT), as a reinforcement for nanocomposites. Owing to the existence of Stone-Wales transformation defects, the DNT intrinsically possesses irregular surfaces, which is expected to enhance the non-covalent interfacial load transfer. Through a series of in silico pull-out studies of the DNT in polyethylene (PE) matrix, we found that the load transfer between DNT and PE matrix is dominated by the non-covalent interactions, in particular the van der Waals interactions. Although the hydrogenated surface of the DNT reduces the strength of the van der Waals interactions at the interface, the irregular surface of the DNT can compensate for the weak bonds. These factors lead to an interfacial shear strength of the DNT/PE interface comparable with that of the carbon nanotube (CNT)/PE interface. Our results show that the DNT/PE interfacial shear strength remains high even as the number of Stone-Wales transformation defects decreases. It can be enhanced further by increasing the PE density or introduction of functional groups to the DNT, both of which greatly increase the non-covalent interactions., in press, early view online in Advanced Functional Materials, 2016

Finding fundamental and general mechanisms for electrochemical reactions, such as the oxygen evolution reaction (OER) from water and reduction of CO2, plays vital roles in developing the desired electrocatalysts for facilitating solar fuel production. Recently, density functional theory (DFT) calculations have shown that there is a universal scaling relation of adsorption energy between key intermediate species, HO(ad) and HOO(ad), on the surface of metal oxides as OER electrocatalysts. In this paper, a kinetic and thermodynamic model for the four-electron electrochemical reaction based on previous OER mechanisms proposed by DFT calculations is developed to further investigate the electrocatalytic properties over a wide range of metal oxides and photosystem II. The OER activity of metal oxides (i.e. electrocatalytic current) calculated from the DFT-calculated equilibrium potentials with kinetic properties, such as the rate constants for interfacial electron transfer and catalytic turnover, can lead to a volcano-shaped trend that agrees with the results observed in experiments. In addition, the kinetic aspects of the impact on the electrocatalysts are evaluated. Finally, comparing the results of metal oxides and photosystem II, and fitting experimental voltammograms give further insights into kinetic and thermodynamic roles. Here, the general guidelines for designing OER electrocatalysts with unified kinetic and thermodynamic properties are presented.

It is challenging to recover the strength of fiber-reinforced laminates after they have suffered severe damage that normally results in fiber rupture. Most non-invasive repairs can only effectively mend delamination and matrix cracks. Instead of attempting to heal the damaged fiber, this study presents a bioinspired laminate design that diverts fiber damage into matrix split to facilitate recovery even in the event of a catastrophic failure. In this study, hybrid carbon fiber reinforced laminated systems fabricated from alternating layers of thermoplastic and epoxy based prepregs are investigated. Other than being able to sustain higher out-of-plane loads than the common cross-ply laminates, it is also observed that significantly less fiber damage occurs for helicoidal laminates as compared to cross-ply laminates. Helicoidal laminates with small inter-ply angles are able to recover up to 91% of their out-of-plane loading strength whereas only 56% of the strength is restored for cross-ply laminates.

An experimental study was conducted to find out the effects of compaction of sand on the ballistic resistance of the sandbag. The implementation of various sandbag fabrics, namely, polyethylene, polypropylene, polyvinylchloride and Twaron, was also investigated. The sandbags were tested under various configurations - uncompacted, manually compacted, vacuum compacted and pneumatically compacted by inserting an inflatable airbag into the sandbag. Depending on their fabric strength, the sandbags were pneumatically compacted or pressurized up to different inflation pressures. Burlap, polyethylene and polypropylene sandbags were tested at 0.5 bar and polyvinyl sandbags at 0.5 and 1.0 bars while Twaron sandbags were tested at 0.5, 1.0 and 2.0 bars. All sandbag specimens were subjected to ballistic impact by a spherical steel projectile. The increase in inflation pressure led to the rise in shear resistance of the sand through compaction and the rise in fabric pretension as well, resulting in better ballistic resistances (higher ballistic limit and energy absorbed) of the sandbag specimens. With the aid of inflatable airbags, it is possible for sandbags of less expensive and lower strength fabrics to exceed the ballistic resistances of uncompacted and manually compacted high performance Twaron sandbags.

The cell envelope of mycobacteria is a highly unique and complex structure that is functionally equivalent to that of Gram-negative bacteria to protect the bacterial cell. Defects in the integrity or assembly of this cell envelope must be sensed to allow the induction of stress response systems. The promoter that is specifically and most strongly induced upon exposure to ethambutol and isoniazid, first line drugs that affect cell envelope biogenesis, is the iniBAC promoter. In this study, we set out to identify the regulator of the iniBAC operon in Mycobacterium marinum using an unbiased transposon mutagenesis screen in a constitutively iniBAC-expressing mutant background. We obtained multiple mutants in the mce1 locus as well as mutants in an uncharacterized putative transcriptional regulator (MMAR_0612). This latter gene was shown to function as the iniBAC regulator, as overexpression resulted in constitutive iniBAC induction, whereas a knockout mutant was unable to respond to the presence of ethambutol and isoniazid. Experiments with the M. tuberculosis homologue (Rv0339c) showed identical results. RNAseq experiments showed that this regulatory gene was exclusively involved in the regulation of the iniBAC operon. We therefore propose to name this dedicated regulator iniBAC Regulator (IniR). IniR belongs to the family of signal transduction ATPases with numerous domains, including a putative sugar-binding domain. Upon testing different sugars, we identified trehalose as an activator and metabolic cue for iniBAC activation, which could also explain the effect of the mce1 mutations. In conclusion, cell envelope stress in mycobacteria is regulated by IniR in a cascade that includes trehalose., Author summary The mycobacterial cell wall is a complex and unique structure that protects extremely well against harmful compounds. Understanding the biogenesis and functioning of this cell envelope is essential to be able to effectively target mycobacteria. One way to uncover cell envelope functionality is to study stress mechanisms that are induced when the cell envelope is damaged. Here, we describe the identification of a major cell envelope stress regulator and the inducing signal. As stress inducers we have used antimycobacterial drugs that target the biogenesis of the mycobacterial cell envelope, as these have previously been shown to specifically induce the major cell wall stress operon iniBAC. We have identified a multi-domain regulator that is essential for the induction of this operon to transduce cell envelope stress and named this IniR. Importantly, we were also able to show that cell envelope stress signaling was induced by free trehalose. Trehalose is a central unit in many mycobacterial lipids and mycobacteria have a dedicated trehalose salvage pathway that is used when lipids are degraded and recycled. We hypothesize that lipid turnover and concomitant release of free trehalose in the cell envelope is a signal for cell envelope stress in mycobacteria.

The high strength to weight ratio, good corrosion resistance, and excellent fatigue property make carbon fiber-reinforced plastics a competitive material solution to replace steel in deepwater riser application. In this work, scaled-down composite riser joints were fabricated using a filament-winding machine. The prototypes comprise several carbon fiber-reinforced plastic layers wound over an aluminum liner. They consist of a middle tubular section and two metal-composite interface end fittings for the transfer of load between joints. A series of mechanical tests, including tension and combined tension-bending loading tests were performed to characterize their structural capacity and evaluate the improvement in performance over a purely metallic mandrel. In addition, finite element analyses incorporating elastic–plastic properties of the metallic liner, interfacial failure, and complex carbon fiber-reinforced plastics failure modes were carried out. The numerical predictions are in good agreement with the experimental measurements. The experimentally verified FE framework was then extended to design and analyze a full-scale composite riser model for performance prediction to accelerate the application of composite risers by shortening product development cycle and reducing prototyping costs.

This study reports on the shock wave protective performance of woven Twaron fabric impregnated with shear thickening fluid (STF). The STF was prepared from a combination of mechanical and ultrasonic mixing of fumed silica nanoparticles dispersed in liquid polyethylene glycol (PEG) polymer. The shear thickening characteristics were determined from rheological tests. Two shock wave parameters governing blast related injuries are used to evaluate the performance of the STF treated fabrics – peak pressure and rate of pressure rise. The results of our shock tube tests demonstrate that the STF treated fabric composites offer superior shock wave protection as compared to untreated (neat) fabric and fabric impregnated with PEG only. After STF treatment, the normalised average peak pressure amplification is significantly reduced from 2.46 to 1.49 while the attenuation in normalised maximum rate of pressure rise is even more pronounced – from 2.3 to 0.76. Apparent material density is found to correlate with the average peak pressure and maximum rate of pressure rise. This implies that the density increases enough to increase the equilibrium sound speed in the fabric, and therefore preclude the formation of shock wave in the fabric. Ballistic tests using steel projectiles were also conducted to check that the STF treated fabrics continued to enhance ballistic protection as reported by other researchers. Overall, the results show that the STF treated fabrics have potential applications not only for ballistic protection but also for shock wave mitigation.

The cure conversion is a key determinant of the characteristics of many thermosetting polymers. Their curing process can be monitored using experimental tools such as FTIR and DSC; however, these techniques can only provide a qualitative measure of the extent of curing reaction rather than a quantitative determination of cure conversion. In fact, the actual cure conversion in epoxy systems is not known. Many molecular simulation works assume that the cure conversion limit approaches 100% although it is unrealistic. In this work, a parametric study based on model size and a radial distribution function (RDF) of relevant functional groups reveals that a topological cure conversion limit may exist and is estimated to be about 70% for a typical epoxide-amine system based on the chosen force field and simulation conditions. Beyond this, atoms within the model may form isolated clusters and the molecular model fails to converge to an equilibrated topology with structural homogeneity. It is found that the predicted dependencies of thermal and mechanical properties on cure conversion are in concurrence with accepted norms and only show deviation when the cure conversion exceeds the limit.

A multiscale approach based on Pseudo Amorphous Cell (PAC) is employed to study nanoscale sliding of a silicon ball against a polyethylene (PE) substrate. In this multiscale approach, the domain is firstly constructed as a tessellation of identical Amorphous Cells (ACs). For small deformation regions, the number of degrees of freedoms (DOF) is then reduced by computing the displacements of only vertices of the ACs instead of the atoms within. The reduction is achieved by determining an accurate mapping relationship between the atomistic displacements and the displacements of the vertices of the PACs. During sliding, the polymer chains generally line up in the sliding direction. The coefficient of friction is comparable to some experiment values. Under constant load control, it is found that the penetration depth increases and then decreases to a steady value during the sliding.

A hierarchical multiscale model for nylon 6/clay nanocomposites is adopted to study its damage and post-damage behavior. The 3D representative volume element (RVE) of the nanocomposites at the macroscale comprises a nylon 6 matrix with embedded silicate layers. Taking into consideration the interactions between nylon 6 and the clay particulates, a gallery inter-layer was inserted between the intercalated silicate layers and an interphase layer was added around the silicate. Both gallery and interphase layers were treated as interfaces in this study. Molecular dynamics (MD) simulations were performed to obtain the material behavior of the interfaces. Results from the MD simulations were used to parameterize a traction–separation law which was incorporated into the RVE to model interfacial degradation. The damage of bulk nylon 6, on the other hand, was governed by the Gurson–Tvergaard–Needleman (GTN) model. The finite element method (FEM) was used to simulate the RVE model under quasi-static uniaxial stress loading. The constitutive relationship and fracture patterns of the nylon 6/clay model with 2.5% weight fraction of clay were studied. The apparent yield stress is found to increase while the ductility decreases when the clay particle size increases or the number of silicate layers decreases. The effect of interfacial strength on the properties of the nanocomposites is also presented. When the interfacial strength was relatively low, debonding of the interphase layer is the cause for damage initiation; a higher cohesive strength of the interfaces will lead to damage initiation from the polymer matrix around the interphase layer. This is due to inherent weak adhesion strength of the polymer chains, which was also observed through experimental results.

A cost effective and scalable recipe for fabricating biodegradable cellulose aerogels from paper waste has been realized. The green aerogel is macroporous and has extremely low density and thermal conductivity: 0.04 g cm −3 and 0.029–0.032 Wm −1 K −1 , respectively. It is highly absorbent, absorbing 18–20 times its weight in liquid. Up to 99.8% of the liquid is recovered simply by squeezing the aerogel. The fabrication can be optimized for absorbing polar (water) or non-polar liquids (oil). Coating the aerogel with methyltrimethoxysilane improves its hydrophobicity without affecting its absorbency. Mechanically, the aerogel is flexible yet strong making a wide range of applications possible.

Polyprolylene is commonly used for crude oil spill cleaning, but it has low absorption capacity and is nonbiodegradable. In our work, a green, ultralight, and highly porous material was successfully prepared from paper waste cellulose fibers. The material was functionalized with methyltrimethoxysilane (MTMS) to enhance its hydrophobicity and oleophilicity. Water contact angles of 143 and 145° were obtained for the MTMS-coated recycled cellulose aerogel. The aerogel achieved high absorption capacities of 18.4, 18.5, and 20.5 g/g for three different crude oils at 25 °C, respectively. In the investigated temperature range of 10, 25, 40, and 60 °C for the absorption of the tested crude oil on the aerogel, a highest absorption capacity of 24.4 g/g was obtained. It was found that the viscosity of the crude oils is the main factor affecting their absorption onto the aerogel. The strong affinity of the MTMS-coated recycled cellulose aerogel to the oils makes the aerogel a good absorbent for crude oil spill cleaning.

Interfacial lubrication plays an important role in the functional performance of nanoelectrome-chanical (NEMS) systems. Here, we used molecular dynamics simulation to analyze the lubricating effect of a perfluoropolyether (PFPE) film to reveal the mechanism behind our experimental observations and understand the performance of the film. There was good agreement in the trends of the coefficients of friction between our simulation results and experimental characterizations. By studying the atomic motion, interfacial mechanics and polymer chain deformation, we found that PFPE films provide good lubrication because their linear flowability promotes surface reconstruction. Our simulations suggest that a high performance lubricant film needs to have low resistance to shear deformation, possess high linear flowability, promote surface reconstruction and adhere effectively to the substrates.

Ultra high interface/volume ratio is an important feature of polymer-clay nanocomposites resulting from the nanometer scale dimensions of the clay particle. An understanding of the behavior of these interfaces on the molecular level is essential as they are largely responsible for the material propertiesof nanocomposites. In polymer-clay nanocomposites the concept of a binding energy is too simplified to be able to account for the presence of multi-phase interfaces. The gallery interface within intercalated clay particles and the interphase region with the polymer matrix are investigated. They are subjected to Mode I splitting deformation through molecular dynamics simulations and characterized by their traction–separation relationships. Several key parameters including peak strength, fracture energy and final splitting separation distances are qualified from the traction–separation curves which can be integrated into continuum models. The simulations reveal that the alkyl chain length of surfactants plays an essential role in the mechanical performance of these interfaces.

As a potential building block for the next generation of devices or multifunctional materials that are spreading almost every technology sector, one-dimensional (1D) carbon nanomaterial has received intensive research interests. Recently, a new ultra-thin diamond nanothread (DNT) has joined this palette, which is a 1D structure with poly-benzene sections connected by Stone-Wales (SW) transformation defects. Using large-scale molecular dynamics simulations, we found that this sp3 bonded DNT can transit from a brittle to a ductile characteristic by varying the length of the poly-benzene sections, suggesting that DNT possesses entirely different mechanical responses than other 1D carbon allotropies. Analogously, the SW defects behave like a grain boundary that interrupts the consistency of the poly-benzene sections. For a DNT with a fixed length, the yield strength fluctuates in the vicinity of a certain value and is independent of the "grain size". On the other hand, both yield strength and yield strain show a clear dependence on the total length of DNT, which is due to the fact that the failure of the DNT is dominated by the SW defects. Its highly tunable ductility together with its ultra-light density and high Young's modulus makes diamond nanothread ideal for creation of extremely strong three-dimensional nano-architectures., Comment: published, Nanoscale, 2016

Binding details of roscovitine, ATP and HHASPRK peptide in complex with both unphosphorylated and phosphorylated cyclin-dependent kinase 5 (CDK5) from molecular dynamics simulations using a crystal structure of CDK2/cyclinA/ATP/HHASPRK and three CDK5/p25/roscovitine systems as references are presented. The influence of phosphorylation on well-conserved amino acids (Thr14 and Tyr15) on the conformation of the inhibition loop (G-loop) is investigated. The simulations suggest that the long ATP phosphate group affects the conformation of the loop differently in different complexes. Binding patterns of ATP in CDK5 are then studied and compared with those in CDK2. The residues on the G-loop affect the conformation of the ATP phosphate group and thus influence the hydrogen bonding network around the ligand. In addition, bindings of the peptide in CDK5 are investigated and compared with that in the crystal structure. Also, the possible conformation of the terminal lysine side chain of the peptide is analysed and ...

This article presents progressive failure analysis of double-notched carbon/epoxy composite laminates with different scales. A numerical analysis strategy based on material property degradation method (MPDM) and cohesive elements (CE) is developed to model progressive failure of scaled double-notched composite laminates, where the material property degradation method is used to model the intralaminar failure and the cohesive elements are employed to account for the delamination at the interfaces. Different failure theories are considered in the material property degradation method–cohesive element approach and a comparative study of these failure theories is presented. The mesh dependency of the material property degradation method–cohesive element approach is investigated with different notch and element types for the double-notched composite laminates. Size scaling effects are also studied by traditional fracture models and the material property degradation method–cohesive element approach, significantly revealing a trend in strength reduction of notched composites with increasing specimen size. The predictions are compared with the experimental results and reasonably good agreement is observed.

Mechanisms governing the tribological behavior of polymer-on-polymer sliding were investigated by molecular dynamics simulations. Three main mechanisms governing frictional behavior were identified. Interfacial "brushing" of molecular chain ends over one another was observed as the key contribution to frictional forces. With an increase of the sliding speed, fluctuations in frictional forces reduced in both magnitude and periodicity, leading to dynamic frictional behavior. While "brushing" remained prevalent, two additional irreversible mechanisms, "combing" and "chain scission", of molecular chains were observed when the interfaces were significantly diffused.

Adenylylsulfate reductase (adenosine 5′-phosphosulfate reductase, APS reductase or APSR, E.C.1.8.99.2) catalyzes the conversion of APS to sulfite in dissimilatory sulfate reduction. APSR was isolated and purified directly from massive anaerobically grown Desulfovibrio gigas, a strict anaerobe, for structure and function investigation. Oligomerization of APSR to form dimers–α_2β_2, tetramers–α_4β_4, hexamers–α_6β_6, and larger oligomers was observed during purification of the protein. Dynamic light scattering and ultracentrifugation revealed that the addition of adenosine monophosphate (AMP) or adenosine 5′-phosphosulfate (APS) disrupts the oligomerization, indicating that AMP or APS binding to the APSR dissociates the inactive hexamers into functional dimers. Treatment of APSR with β-mercaptoethanol decreased the enzyme size from a hexamer to a dimer, probably by disrupting the disulfide Cys156—Cys162 toward the C-terminus of the β-subunit. Alignment of the APSR sequences from D. gigas and A. fulgidus revealed the largest differences in this region of the β-subunit, with the D. gigas APSR containing 16 additional amino acids with the Cys156—Cys162 disulfide. Studies in a pH gradient showed that the diameter of the APSR decreased progressively with acidic pH. To crystallize the APSR for structure determination, we optimized conditions to generate a homogeneous and stable form of APSR by combining dynamic light scattering, ultracentrifugation, and electron paramagnetic resonance methods to analyze the various oligomeric states of the enzyme in varied environments.

The crystal structures of two active forms of dissimilatory sulphite reductase (Dsr) from Desulfovibrio gigas, Dsr-I and Dsr-II, are compared at 1.76 and 2.05 A resolution respectively. The dimeric α_2β_2γ_2 structure of Dsr-I contains eight [4Fe–4S] clusters, two saddle-shaped sirohaems and two flat sirohydrochlorins. In Dsr-II, the [4Fe–4S] cluster associated with the sirohaem in Dsr-I is replaced by a [3Fe–4S] cluster. Electron paramagnetic resonance (EPR) of the active Dsr-I and Dsr-II confirm the co-factor structures, whereas EPR of a third but inactive form, Dsr-III, suggests that the sirohaem has been demetallated in addition to its associated [4Fe–4S] cluster replaced by a [3Fe–4S] centre. In Dsr-I and Dsr-II, the sirohydrochlorin is located in a putative substrate channel connected to the sirohaem. The γ-subunit C-terminus is inserted into a positively charged channel formed between the α- and β-subunits, with its conserved terminal Cysγ104 side-chain covalently linked to the CHA atom of the sirohaem in Dsr-I. In Dsr-II, the thioether bond is broken, and the Cysγ104 side-chain moves closer to the bound sulphite at the sirohaem pocket. These different forms of Dsr offer structural insights into a mechanism of sulphite reduction that can lead to S_3O_6^(2−), S_2O_3^(2−) and S^(2−).

The increasing demand for portable electronics has led to the shrinking in size of electronic components and solder joint dimensions. The industry also made a transition towards the adoption of lead-free solder alloys, commonly based around the Sn–Ag–Cu alloys. As knowledge of the processes and operational reliability of these lead-free solder joints (used especially in advanced packages) is limited, it has become a major concern to characterise the mechanical performance of these interconnects amid the greater push for greener electronics by the European Union. In this study, bulk solder tensile tests were performed to characterise the mechanical properties of SAC 105 (Sn–1%wt Ag–0.5%wt Cu) and SAC 405 (Sn–4%wt Ag–0.5%wt Cu) at strain rates ranging from 0.0088 s −1 to 57.0 s −1 . Solder joint array shear and tensile tests were also conducted on wafer-level chip scale package (WLCSP) specimens of different solder alloy materials under two test rates of 0.5 mm/s (2.27 s −1 ) and 5 mm/s (22.73 s −1 ). These WLCSP packages have an array of 12 × 12 solder bumps (300 μm in diameter); and double redistribution layers with a Ti/Cu/Ni/Au under-bump metallurgy (UBM) as their silicon-based interface structure. The bulk solder tensile tests show that Sn–Ag–Cu alloys exhibit higher mechanical strength (yield stress and ultimate tensile strength) with increasing strain rate. A rate-dependent model of yield stress and ultimate tensile strength (UTS) was developed based on the test results. Good mechanical performance of package pull-tests at high strain rates is often correlated to a higher percentage of bulk solder failures than interface failures in solder joints. The solder joint array tests show that for higher test rates and Ag content, there are less bulk solder failures and more interface failures. Correspondingly, the average solder joint strength, peak load and ductility also decrease under higher test rate and Ag content. The solder joint results relate closely to the higher rate sensitivity of SAC 405 in gaining material strength which might prove detrimental to solder joint interfaces that are less rate sensitive. In addition, specimens under shear yielded more bulk solder failures, higher average solder joint strength and ductility than specimens under tension.

Vanadium oxide nanobelts have been synthesized on Si or SiN substrates by simply heating vanadium foils on a hotplate. As-grown nanobelts were characterized as V 2 O 5 · n H 2 O (0.3 n 2 O 5 phase and a polycrystalline structure was observed. The Young’s modulus of the annealed nanobelts showed more consistent values at an average of 28.9 GPa, lower than the calculated modulus of bulk α-V 2 O 5 at 68 GPa.

The objective of this research is to develop a smart hip protector by incorporating shear thickening fluid (STF) into conventional foam hip protectors. The shear thickening properties of fumed silica particles dispersed in liquid polyethylene glycol (PEG) were determined from rheological tests. Dynamic drop tests, using a 4 kg drop platen at 0.5 m drop height, were conducted to study how STF improves energy absorption as compared to unfilled foam and PEG filled foam. The results show that PEG filled foam reduces the mean peak force transmitted by a further 55% and mean peak displacement by 32.5% as compared to the unfilled foam; the STF filled foam further reduces mean peak force and displacement by 15% and 41% respectively when compared to the PEG filled foam. At a displacement of 22 mm, the STF filled foam absorbs 7.4 times more energy than the PEG filled foam. The results of varying the drop mass and drop height show that the energy absorbed per unit displacement for STF filled foam is always higher than that of PEG filled foam. Finally, the effectiveness of a prototype of hip protector made from 15 mm thick STF filled foam in preventing hip fractures was studied under two different loading conditions: distributed load (plate drop test) and concentrated load (ball drop test). The results of the plate and ball drop tests show that among all hip protectors tested in this study, only the prototype can reduce the mean peak impact force to be lower than the force required to fracture a hip bone (3.1 kN) regardless of the type of loading. Moreover, the peak force of the prototype is about half of this value, suggesting thinner prototype could have been used instead. These findings show that STF is effective in improving the performance of hip protectors.

In the current work, CDK5/p25 complexes were pulled apart by applying external forces with steered molecular dynamics (SMD) simulations. The crucial interactions between the kinase and the activation protein were investigated and the SMD simulations showed that several activation-relevant motifs of CDK5 leave p25 in sequence during the pulling and lead to an apo-CDK2 like CDK5 structure after separation. Based on systematic examination of hydrogen bond breaking and classical MD/molecular mechanics-generalized Born/surface area) (MM-GBSA) calculations, a CDK5 activation mechanism by p25 is suggested. This is the first step towards the systemic development of CDK inhibitors and the mechanism proposed could lead to a better understanding of the protein-protein recognition characteristics between the kinase and its activator.

A series of functionalized isoindigos structurally related to meisoindigo (1-methylisoindigo), a therapeutic agent used for the treatment of a form of leukemia, were synthesized and evaluated for antiproliferative activities on a panel of human cancer cells. Two promising compounds (1-phenpropylisoindigo and 1-(p-methoxy-phenethyl)-isoindigo) that were more potent than meisoindigo and comparable to 6-bromoindirubin-3'-oxime on leukemic K562 and liver HuH7 cells were identified. Structure-activity relationships showed the importance of keeping one of the lactam NH in an unsubstituted state. Substitution of the other lactam NH with aryl or arylalkyl side chains retained or improved activity in most instances. An intact exocyclic double bond was also essential, possibly to maintain planarity and rigidity of the isoindigo scaffold. None of the compounds were found to inhibit CDK2 in an in vitro assay, in spite of reports linking the antiproliferative activities of meisoindigo and other isoindigos to CDK2 inhibition. Hence, these functionalized isoindigos disrupted cell growth and proliferation by other mechanistic pathways that did not involve CDK2 inhibition.

A cyclin-dependent kinase (CDK) 5 inhibitory peptide (CIP) from p25 was recently reported to inhibit CDK5/p25 activity in vitro but had no effect on endogenous cdc2 kinase activity. This may lead to a specific CDK5 inhibition strategy in the treatment of neurodegeneration. However, the mechanism of the inhibition remains unclear. In this work, molecular dynamics simulations and energy decomposition calculation models were set up to investigate the deregulation mechanisms of CIP on CDK5 activity. The results show that truncation of the N, and C terminals of p25 introduces important conformational changes into a hydrophobic pocket that is crucial for accommodating Ile153 on the activation loop of CDK5. In addition, such truncations lead to distortion and displacement of the activation loop and consequently affect binding of the substrate peptide. New inhibition sites for selectively inhibiting the activity of CDK5 are also suggested.

The current-voltage (I-V) characteristics of small-diameter hydrogenated and pristine silicon nanowires (SiNWs) are calculated by nonequilibrium Green's function combined with density functional theory. We show that the I-V characteristics depend strongly on length, growth orientation, and surface modification of the SiNWs. In particular, a length of 3 nm is suggested for the nanowires to retrieve its intrinsic conducting properties from the influences of both the electrodes and metal/semiconductor mismatched surface contact; surface reconstruction would enhance the conductance in hydrogenated SiNW, which is explained by the extra conducting eigenchannel found in the transmission spectrum, suggesting possible surface conducting channel. Discussions with available experimental data are given.

Earlier work from our laboratory has indicated that a hemerythrin-like protein was over-produced together with the particulate methane monooxygenase (pMMO) when Methylococcus capsulatus (Bath) was grown under high copper concentrations. A homologue of hemerythrin had not previously been found in any prokaryote. To confirm its identity as a hemerythrin, we have isolated and purified this protein by ion-exchange, gel-filtration and hydrophobic interaction chromatography, and characterized it by mass spectrometry, UV-visible, CD, EPR and resonance Raman spectroscopy. On the basis of biophysical and multiple sequence alignment analysis, the protein isolated from M. capsulatus (Bath) is in accord with hemerythrins previously reported from higher organisms. Determination of the Fe content in conjunction with molecular-weight estimation and mass analysis indicates that the native hemerythrin in M. capsulatus (Bath) is a monomer with molecular mass 14.8 kDa, in contrast to hemerythrins from other eukaryotic organisms, where they typically exist as a tetramer or higher oligomers.

We present a theoretical study on a series of novel organometallic sandwich molecular wires (SMWs), which are constructed with alternating iron atoms and cyclopentadienyl (Cp) rings, using DFT and nonequilibrium Green's function techniques. It is found that that the SMWs are stable, flexible structures having half-metallic (HM) properties with 100% negative spin polarization near the Fermi level in the ground state. Some SMWs of finite size show a nearly perfect spin filter effect (SFE) when coupled between ferromagnetic electrodes. Moreover, their I-V curves exhibit negative differential resistance (NDR), which is essential for certain electronic applications. The SMWs are the first linear molecules with HM, high SFE, and NDR and can be easily synthesized. In addition, we also analyze the underlying mechanisms via the transmission spectra and spin-dependent calculations. These findings strongly suggest that the SMWs are promising materials for application in molecular electronics.

We present an approach to multiscale modeling of polymers whereby atomistic scale domains coexist with continuum-like domains. The atomistic domains faithfully predict severe deformation of polymer chains while the continuum domains allow the computation to scale up the size of the model without incurring excessive computational costs associated with fully atomistic models and without the introduction of spurious forces across the boundary of atomistic and continuum-like domains. The polymer domain is firstly constructed as a tessellation of Amorphous Cells (AC). For regions of small deformation, the number of degrees of freedom is then reduced by computing the displacements of only the vertices of the ACs instead of the atoms within. This is achieved by determining, a priori, the atomistic displacements within such Pseudo Amorphous Cells associated with orthogonal deformation modes of the cell. Simulations of nanoindentation of a polymer substrate using full molecular mechanics computation and our multiscale approach give almost identical prediction of indentation force and the strain contours of the polymer. We further demonstrate the capability of performing adaptive simulations during which domains that were discretized into cells revert to full atomistic domains when their strain attain a predetermined threshold.

The crystal structure of the particulate methane monooxygenase (pMMO) from Methylococcus capsulatus (Bath) has been reported recently [Lieberman, R. L., and Rosenzweig, A. C. (2005) Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane, Nature 434, 177-182]. Subsequent work has shown that the preparation on which the X-ray analysis is based might be missing many of the important metal cofactors, including the putative trinuclear copper cluster at the active site as well as ca. 10 copper ions (E-clusters) that have been proposed to serve as a buffer of reducing equivalents to re-reduce the copper atoms at the active site following the catalytic chemistry [Chan, S. I., Wang, V. C.-C., Lai, J. C.-H., Yu, S. S.-F., Chen, P. P.-Y., Chen, K. H.-C., Chen, C.-L., and Chan, M. K. (2007) Redox potentiometry studies of particulate methane monooxygenase: Support for a trinuclear copper cluster active site, Angew. Chem., Int. Ed. 46, 1992-1994]. Since the aqueous-exposed domains of the 45 kDa subunit (PmoB) have been suggested to be the putative binding domains for the E-cluster copper ions, we have cloned and overexpressed in Escherichia coli the two aqueous-exposed subdomains toward the N- and C-termini of the subunit: the N-terminal subdomain (residues 54-178) and the C-terminal subdomain (residues 257-394 and 282-414). The recombinant C-terminal water-exposed subdomain is shown to behave like a Cu(I) sponge, taking up to ca. 10 Cu(I) ions cooperatively when cupric ions are added to the protein fragment in the presence of dithiothreitol or ascorbate. In addition, circular dichroism measurements reveal that the C-terminal subdomain folds into a beta-sheet structure in the presence of Cu(I). The propensity for the C-terminal subdomain to bind Cu(I) is consistent with the high redox potential(s) determined for the E-cluster copper ions in the pMMO. These properties of the E-clusters are in accordance with the function proposed for these copper ions in the turnover cycle of the enzyme.

A simple thermal vapor deposition technique to synthesize crystalline tungsten oxide nanorods in ambient condition is presented. Using a commercial thermal hot plate, a pure 99.9% tungsten foil is heated at 485 ± 5 °C under ambient conditions with a piece of 150 μm thick glass cover slide pressing on the tungsten foil. Single crystalline WO3-x nanorods, with a preferential growth axis in the [001] direction, are found to deposit on the cover slide facing the heated tungsten foil. The structure, morphology, and composition of the WO3-x nanorods were characterized using the scanning electron microscopy, transmission electron microscopy, energy dispersive spectrometry, Raman spectroscopy, and X-ray diffraction. In addition, mechanical properties of the as-synthesized nanorods were investigated by employing the three-point bend test using an atomic force microscope. The elastic modulus of the nanorods was found to be in the 10−110 GPa range, and it increases with decreasing diameter of the nanorods. The tungs...

Large scale ab initio molecular dynamics simulations were performed to investigate how Cu/ultra low-k systems are improved when N is incorporated into the pore-sealing layers. It was found that the high affinity of N to Ta and H gives rise to new phases that prevent H atoms from penetrating the Ta diffusion barrier layer. Consequently, the Ta layer forms organized structures with good barrier performance and electrical conductivity. Furthermore, a continuous ductile film is formed to seal the highly porous polymer dielectrics. Interfacial adhesion between the pore-sealing layer and the dielectrics is also enhanced by inter-diffusion.

We report an efficient method to synthesize vertically aligned Co3O4 nanostructures on the surface of cobalt foils. This synthesis is accomplished by simply heating the cobalt foils in the presence of oxygen gas. The resultant morphologies of the nanostructures can be tailored to be either one-dimensional nanowires or two-dimensional nanowalls by controlling the reactivity and the diffusion rate of the oxygen species during the growth process. A possible growth mechanism governing the formation of such nanostructures is discussed. The field-emission properties of the as-synthesized nanostructures are investigated in detail. The turn-on field was determined to be 6.4 and 7.7 V μm–1 for nanowires and nanowalls, respectively. The nanowire samples show superior field-emission characteristics with a lower turn-on field and higher current density because of their sharp tip geometry and high aspect ratio.

Ab initio molecular dynamics simulations were carried out to study low-k/ultra low-k dielectric systems comprising Cu/Ta/SiLK-like polymer. A study of the motion of single metal atoms of Cu and Ta in the SiLK-like polymer showed that Cu atom motions are effected by jumps between cavities inside the polymer and that Ta is more sluggish than Cu not only because of its larger mass but also because of stronger affinity to the polymer. It was also found that crosslinking of the polymer did not affect the motion of the metal atoms. Simulations of deposition showed that a thin Ta diffusion barrier does not have good structural integrity to prevent Cu-diffusion when directly deposited onto the SiLK; the barrier performance was greatly improved after introducing a Si-based film between the Ta and SiLK.

Molecular dynamics simulations were performed to elucidate the interactions of CDK2 and CDK5 complexes with three inhibitors: R-roscovitine, S-roscovitine, and indirubin-3'-oxime. The preference of the two complexes for R-roscovitine over the S enantiomer, as reported by the experiment, was also found by the simulations. More importantly, the simulations showed that the cause of the stronger affinity for the R enantiomer is the presence of an important hydrogen bond between R-roscovitine and the kinases not found with S-roscovitine. The simulations also showed two amino acid mutations in the active site of CDK5/R-roscovitine that favor binding-enhanced electrostatic contributions, making the inhibitor more effective for CDK5 than for CDK2. This suggests that the effectiveness of roscovitine-like inhibitors can be improved by enhancing their electrostatic interaction with the kinases. Finally, molecular mechanics-Possion-Boltzmann/surface area calculations of the CDK5/indirubin-3'-oxime system in both water-excluded and water-included environments gave significantly different electrostatic contributions to the binding. The simulations detected the displacement of a water molecule in the active site of the water-included CDK/indirubin-3'-oxime system. This resulted in a more conserved binding pattern than the water-excluded structure. Hence, in the design of new indirubin-like inhibitors, it is important to include the water molecule in the analysis.

The interface of fiber and matrix strongly influences the performance and strength of fiber-reinforced composite materials. Due to the limitations of continuum mechanics at the nanometer length scale, atomistic level computer simulation has started to play an important role in the understanding of such interfacial systems. Our study focuses on a typical crosslinked interfacial system of glass-epoxy composite with the presence of silanes. To explore the mechanical properties of the interfacial network system, Coarse-grained Molecular Dynamics is used. Currently it is not possible to study mechanical properties of interfacial systems purely through ab initio molecular dynamics simulations because of the huge computational resources required. Although pure atomistic classical molecular dynamics simulations have been used to study systems comprising billions of atoms, classical MD simulation do not take into account the effects of crosslinking of molecular chains. A new force field, which combines the Lennard-Jones potential and a finiteextensible nonlinear elastic attractive potential, is proposed and incorporated in a bead-spring model to simulate glass/epoxy interfacial system with the crosslinked structure of silanes. The finite-extensible nonlinear elastic attractive potential is included to control the motion and breakage of polymer chains. Interfacial adhesion and mechanical properties were studied through the simulation of mechanically separating the interfacial system.