Substrates Of Different Sizes Research Articles

Magnetic contrast layers with functional SiO2 coatings for soft-matter studies with polarized neutron reflectometry

This study introduces silicon substrates with a switchable magnetic contrast layer (MCL) for polarized neutron reflectometry (PNR) experiments at the solid–liquid interface to study soft-matter surface layers. During standard neutron reflectometry (NR) experiments on soft-matter samples, structural and compositional information is obtained by collecting experimental data with different isotopic contrasts on the same sample. This approach is normally referred to as contrast matching, and it can be achieved by using solvents with different isotopic contrast, e.g. different H2O/D2O ratios, and/or by selective deuteration of the molecules. However, some soft-matter systems might be perturbed by this approach, or it might be difficult to implement, particularly in the case of biological samples. In these scenarios, solid substrates with an MCL are an appealing alternative, as the magnetic contrast with the substrate can be used for partial recovery of information on the sample structure. More specifically, in this study, a magnetically soft Fe layer coated with SiO2 was produced by ion-beam sputter deposition on silicon substrates of different sizes. The structure was evaluated using X-ray reflectometry, atomic force microscopy, vibrating sample magnetometry and PNR. The collected data showed the high quality and repeatability of the MCL parameters, regardless of the substrate size or the thickness of the capping SiO2 layer. Previously proposed substrates with an iron MCL used an Au capping layer. The SiO2 capping layer proposed here allows reproduction of the typical surface of a standard silicon substrate used for NR experiments and is compatible with a large variety of soft-matter samples. This application is demonstrated with ready-to-use 50 × 50 × 10 mm substrates in PNR experiments for the characterization of a lipid bilayer in a single solvent contrast. Overall, the article highlights the potential of PNR with an MCL for the investigation of soft-matter samples.

Adhesion measurement of living cells based on electrical impedance.

Cells adherence provides specific information about physiology and pathology, the adhesion measurement between living cells and nanostructures can be measured by atomic force microscopy, but this detection technique is difficult to operate and costly. The adhesion height and effective contact area between cells and substrates are also the key factors affecting measurement value of the overall impedance. These factors change with structural parameters of the substrates, so the adhesion measurement between living cells and substrate can be indirectly reflected by the impedance value. To establish a mapping relationship between the impedance measurement and the adhesion measurement of living cells. The possibility of dynamic measurement of adhesion is realized by this method, and the experimental process is simplified. Laser interference technology was used to prepare nanoarray structures with different periods on the surface of silicon wafers for cells culture. Under the same experimental conditions, the impedance of living cells on the substrates of different cycle sizes were measured. The adhesion between cells and different substrates were analyzed by measuring impedance after the interaction between cells and substrate. The adhesion of living cells on the substrates of different sizes be analyzed, and the mapping relationship between the impedance and the adhesion measurement was established. The results showed that, the larger the impedance value between cells and substrate, the larger the effective contact area and the smaller the gap between them. The difference of adhesion height and effective adhesion area between living cells and substrates were obtained. This paper, a new method to measure the adhesion properties of living cells is presented, which provides theoretical basis for the related research.

Experimental and Numerical Analysis of the Influence of Microchannel Size and Structure on Boiling Heat Transfer

Computational fluid dynamics was used and a numerical simulation analysis of boiling heat transfer in microchannels with three depths and three cross-sectional profiles was conducted. The heat transfer coefficient and bubble generation process of three microchannel structures with a width of 80 μm and a depth of 40, 60, and 80 μm were compared during the boiling process, and the factors influencing bubble generation were studied. A visual test bench was built, and test substrates of different sizes were prepared using a micro-nano laser. During the test, the behavior characteristics of the bubbles on the boiling surface and the temperature change of the heated wall were collected with a high-speed camera and a temperature sensor. It was found that the microchannel with a depth of 80 μm had the largest heat transfer coefficient and shortest bubble growth period, the rectangular channel had a larger peak heat transfer coefficient and a lower frequency of bubble occurrence, while the V-shaped channel had the shortest growth period, i.e., the highest frequency of bubble occurrence, but its heat transfer coefficient was smaller than that of the rectangular channel.

Diffusion of soluble organic substrates in aerobic granular sludge: Effect of molecular weight

Aerobic granular sludge (AGS) is an advanced biofilm-based technology for wastewater treatment. Diffusion of substrates into the granules is a key aspect of this technology. Domestic wastewater contains soluble organic substrates of different sizes that could potentially diffuse into the granules. In this study, the relation between the molecular weight of a substrate and its diffusion coefficient within the granule was studied with model substrates (polyethylene glycols (PEGs) with a molecular weight between 62 and 10 000 Da). The diffusion coefficients of the model substrates within granules from a full-scale installation were measured with the ‘transient uptake of a non-reactive solute’ method. The diffusion coefficients in the granules were not significantly different from the diffusion coefficients in water, at least up to 4000 Da molecular weight. This indicates that these PEGs were not obstructed by the granule matrix. The 10 kDa PEG behaved differently from the lighter PEGs, as it could not penetrate the entire granule. Furthermore, the granule structure was characterized with Environmental Scanning Electron Microscopy (ESEM). The granules displayed an open structure with large macropores and semi-solid regions, which contained microbial cells. The diffusion results suggest that most diffusing molecules were unobstructed in the macropores and barely obstructed in the semi-solid regions. Only the diffusion of the 10 kDa PEG seemed to be hindered by the semi-solid regions, but not by the macropores. Lastly, the apparent molecular weight distribution of domestic wastewater soluble COD was determined with ultrafiltration membranes of 100, 10, and 1 kDa molecular weight cut-off. The influent fractionation revealed that a large part (61–69%) of the influent soluble COD was lighter than 1 kDa. As molecules lighter than 1 kDa diffuse easily, the majority of the influent soluble COD can be considered as diffusible COD. These findings provide new insight into the availability of influent COD for granular sludge.

Crystal structure of human cysteamine dioxygenase provides a structural rationale for its function as an oxygen sensor

Cysteamine dioxygenase (ADO) plays a vital role in regulating thiol metabolism and preserving oxygen homeostasis in humans by oxidizing the sulfur of cysteamine and N-terminal cysteine-containing proteins to their corresponding sulfinic acids using O2 as a cosubstrate. However, as the only thiol dioxygenase that processes both small-molecule and protein substrates, how ADO handles diverse substrates of disparate sizes to achieve various reactions is not understood. The knowledge gap is mainly due to the three-dimensional structure not being solved, as ADO cannot be directly compared with other known thiol dioxygenases. Herein, we report the first crystal structure of human ADO at a resolution of 1.78 Å with a nickel-bound metal center. Crystallization was achieved through both metal substitution and C18S/C239S double mutations. The metal center resides in a tunnel close to an entry site flanked by loops. While ADO appears to use extensive flexibility to handle substrates of different sizes, it also employs proline and proline pairs to maintain the core protein structure and to retain the residues critical for catalysis in place. This feature distinguishes ADO from thiol dioxygenases that only oxidize small-molecule substrates, possibly explaining its divergent substrate specificity. Our findings also elucidate the structural basis for ADO functioning as an oxygen sensor by modifying N-degron substrates to transduce responses to hypoxia. Thus, this work fills a gap in structure–function relationships of the thiol dioxygenase family and provides a platform for further mechanistic investigation and therapeutic intervention targeting impaired oxygen sensing.

Autocitrullination of PAD4 does not alter its enzymatic activity: In vitro and in silico studies.

Protein arginine deiminase 4 (PAD4) is an enzyme capable of converting arginine (positively charged residue) into citrulline (neutral residue). PAD4 is a promiscuous enzyme since it citrullinates various substrates, including small peptides, large proteins and itself. The effect of autocitrullination on PAD4 activity remains controversial and inconclusive. We hypothesized that PAD4 autocitrullination may influence the activity of PAD4 by indirectly altering its binding to substrate. We employed mass spectrometry analysis to study the process of autocitrullination. The kinetics of citrullination of PAD4 and citrullinated PAD4 (citPAD4) towards substrates of different sizes (0.17-15.4 kDa), i.e. free arginine, a peptidyl substrate, and histone H3, were studied by colorimetric assay and Western blotting. Molecular dynamics (MD) simulations were performed to investigate structural dynamic and binding properties of PAD4/citPAD4 in the absence and presence of substrates. We observed that 23/27 arginine residues in PAD4 (85 %) can be citrullinated, including R372, R374 and R639 located near the substrate binding pocket. PAD4 and citPAD4 expressed comparable enzymatic activities towards different substrates. In agreement with experimental results, MD simulations indicated that autocitrullination does not change the shape of the substrate binding pocket and PAD4/citPAD4 exhibited comparable binding free energy with a H3-derived peptidyl substrate (6-TARKS-10). While the effect of autocitrullination on PAD4 activity thus far remained unclear and controversial, here we have demonstrated that autocitrullination does not affect the activity of PAD4. Thus, the regulation of PAD4 activity is probably not controlled by autocitrullination but likely by other mechanisms that need further investigation.

A non-helical region in transmembrane helix 6 of hydrophobic amino acid transporter MhsT mediates substrate recognition.

MhsT of Bacillus halodurans is a transporter of hydrophobic amino acids and a homologue of the eukaryotic SLC6 family of Na+ -dependent symporters for amino acids, neurotransmitters, osmolytes, or creatine. The broad range of transported amino acids by MhsT prompted the investigation of the substrate recognition mechanism. Here, we report six new substrate-bound structures of MhsT, which, in conjunction with functional studies, reveal how the flexibility of a Gly-Met-Gly (GMG) motif in the unwound region of transmembrane segment 6 (TM6) is central for the recognition of substrates of different size by tailoring the binding site shape and volume. MhsT mutants, harboring substitutions within the unwound GMG loop and substrate binding pocket that mimick the binding sites of eukaryotic SLC6A18/B0AT3 and SLC6A19/B0AT1 transporters of neutral amino acids, exhibited impaired transport of aromatic amino acids that require a large binding site volume. Conservation of a general (G/A/C)ΦG motif among eukaryotic members of SLC6 family suggests a role for this loop in a common mechanism for substrate recognition and translocation by SLC6 transporters of broad substrate specificity.

Computational Design of Enantiocomplementary Epoxide Hydrolases for Asymmetric Synthesis of Aliphatic and Aromatic Diols.

The use of enzymes in preparative biocatalysis often requires tailoring enzyme selectivity by protein engineering. Herein we explore the use of computational library design and molecular dynamics simulations to create variants of limonene epoxide hydrolase that produce enantiomeric diols from meso‐epoxides. Three substrates of different sizes were targeted: cis‐2,3‐butene oxide, cyclopentene oxide, and cis‐stilbene oxide. Most of the 28 designs tested were active and showed the predicted enantioselectivity. Excellent enantioselectivities were obtained for the bulky substrate cis‐stilbene oxide, and enantiocomplementary mutants produced (S,S)‐ and (R,R)‐stilbene diol with >97 % enantiomeric excess. An (R,R)‐selective mutant was used to prepare (R,R)‐stilbene diol with high enantiopurity (98 % conversion into diol, >99 % ee). Some variants displayed higher catalytic rates (k cat) than the original enzyme, but in most cases K M values increased as well. The results demonstrate the feasibility of computational design and screening to engineer enantioselective epoxide hydrolase variants with very limited laboratory screening.

Arboreal Locomotion in Eurasian Harvest Mice Micromys Minutus (Rodentia: Muridae): The Gaits of Small Mammals.

Body size imposes significant constraints on arboreal locomotion. Despite the wealth of research in larger arboreal mammals, there is a lack of data on arboreal gaits of small mammals. In this context, the present study explores arboreal locomotion in one of the smallest rodents, the Eurasian harvest mice Micromys minutus (∼10 g). We examined gait metrics (i.e., diagonality, duty factor [DF], DF index, velocity, stride length, and stride frequency) of six adult male mice on simulated arboreal substrates of different sizes (2, 5, 10, and 25 mm) and inclinations (00 and 450 ). Micromys minutus employed slow, lateral sequence symmetrical gaits on the smaller substrates, which shifted to progressively faster symmetrical gaits of higher diagonality on larger substrates. Both ascents and descents were associated with a higher diagonality, and ascents with a higher DF index compared to horizontal locomotion, underscoring the role of the grasping hind feet. Velocity increase was brought about primarily by an increase in stride frequency, a pattern often encountered in other small mammals, with a secondary and significant contribution of stride length. These findings indicate that, except for velocity and the way it is regulated, there are no significant differences in gait metrics between larger and smaller arboreal mammals. Moreover, the locomotor adaptations of Eurasian harvest mice represent behavioral mechanisms that promote stable, safe, and continuous navigation along slender substrates and ultimately contribute to the successful exploitation of the arboreal milieu.

Atomic Layer Deposited Protective Layers

This paper reviews the use of Atomic Layer Deposition (ALD) in protective coatings. Because of the growth principle ALD allows the deposition of dense conformal films on substrates of different size and shape. Recently, ALD has received increasingly interest in deposition of protective coatings. In protective coatings oxides are the most common materials and especially Al, Ti, and Ta oxides have been applied. The use of nanolaminates enables improving the protection properties. Since ALD films are pinhole-free and often thin they are used to protect against moisture, radiation, out-gassing but not often against corrosion of metals. Very good moisture barriers are obtained with thin ALD oxide layers on polymers and cardboard. This property is also very attractive in encapsulation of OLEDs. In studies of energy technology materials protection of electrodes in Li-ion batteries, fuel cells and supercapacitors by ALD has been reported and significant improvement in the stability has been achieved. Yet another area is protection of silver jewelry from tarnishing by a thin oxide layer. In traditional corrosion protection of metals ALD films have proven to be useful in tailoring of interfaces and sealing of defects in coatings made by other techniques.

Relationship between Enzyme/Substrate Properties and Enzyme Efficiency in Hydrolases

Hydrolase enzymes are involved in breaking different chemical bonds in diverse substrates of different sizes and complexity such as proteins, carbohydrates, lipids, and nucleic acids. This work presents a systematic analysis of the kinetic, structural, and biological information on hydrolases, taking into account the presence of different cofactors, the number of chains (i.e., oligomerization state), the number of amino acid residues, and the physicochemical properties of the substrates. Specific trends related to the catalytic activity of this large and rather diverse class of enzymes, including activation free energies, binding free energies, and enzyme efficiencies are revealed and rationalized. The results show that despite the diversity of hydrolases, their substrates, and reactions, hydrolases have quite characteristic activation free energies, substrate binding free energies, and enzyme efficiencies. Different subclasses of hydrolases employ different strategies to achieve these values, including t...

Lens Forming by Stack Dispensing for LED Wafer Level Packaging

In this paper, a moldless stack dispensing method to form an light-emitting diode (LED) lens at the wafer level is presented. This method uses a dispensing process to form a lens with high $H/L$ ratio, where $H$ and $L$ stand for the height and the base length of the lens. Silicon wafer is used as the substrate. V-groove trenches are made on the surface of the wafer to define the size of the substrates. In the dispensing process, a droplet of encapsulant is dispensed on the substrate to form a base heap. After the base heap is cured, a second droplet of encapsulant is dispensed on top of the base heap and cured. The stacked encapsulant forms a lens with high $H/L$ ratio. Dispensing on substrates sized from $3{~\rm mm} \times 3$ mm to $5{~\rm mm} \times 5$ mm is investigated. For each size of substrate, experiments are performed to obtain the maximum volume of the encapsulant without overflowing (the critical volume) for both the base heap and the stacked layer. The results show that despite size differences, substrates of different sizes have a similar critical volume for both the base heap and the stacked layer. The ratio of critical volume of base heap to stacked layer remains at around 1:1. Consequently, the highest $H/L$ values of substrates with different sizes stay at around 0.33. Both critical $k$ and $H/L$ show no obvious correlation to the size of substrate. The method is implemented on a functional LED package. Investigations on the geometry of the lens and optical characteristics of the encapsulated LED packages are shown. The results show that the stacked encapsulation modifies the light distribution and improves the radiant power of an LED package.

Carbapenemase NDM-1, Structural Analysis of the Catalytic Mechanism

The New Delhi Metallo β-lactamase (NDM-1), first identified in Klebsiella pneumoniae has been shown to hydrolyze nearly all clinical β-lactam antibiotics including carbapenems, considered "last resort" antibiotics. Its gene resides on mobile plasmids that move between different strains of bacteria posing a serious global threat to human health. There have also been reports of several variants, up to NDM-9, some with increased carbapenemase activity. As part of the NIGMS PSI:Biology effort, the Midwest Center for Structural Genomics (MCSG) together with the Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors partnership, made significant progress in investigating the enzyme atomic structure and catalytic mechanism. A large number of protein constructs as well as mutants were made and a number of high-resolution structures of NDM-1 (no Zn, one Zn, two Zn, two Mn or Cd, and complexed with antibiotics) and NDM-1 variants, NDM-2, NDM-3, NDM-4, NDM-5 and NDM-6 have been determined. We have determined the two structures of Michaelis complex: NDM-1 with two cadmium ions and a mixture of hydrolyzed and unhydrolyzed ampicillin (1.50 Å) and one with two cadmium ions and partly hydrolyzed faropenem (2.00 Å). The crystal structures revealed a ligand-binding pocket consisting of several flexible loops capable of accommodating many β-lactam substrates of different sizes and shapes. The structures with various metals suggest that the distance between the two metal atoms is closely correlated with substrate binding efficiency and hydrolysis and the pH-dependency of catalytic activity. For better understanding of catalytic mechanism of NDM-1, particularly the dynamics of substrate binding and the energy surfaces along the suggested reaction pathways, molecular dynamics calculations and hybrid classical/quantum (QM/MM) calculations were performed. This work was supported by NIH Grant GM094585 and by the U.S. DOE, OBER contract DE-AC02-06CH11357

Platinum embedded within carbon nanospheres for shape selective liquid phase hydrogenation

Reactant shape selective catalysis occurs when substrates of different sizes and shapes are consumed at different rates over catalysts that combine molecular sieving transport processes with reaction. By contrast the same substrates react at nearly equivalent rates over catalysts that have large, open pores that do not induce any form of molecular sieving. Here we describe the design and synthesis of reactant shape selective catalysts for liquid phase hydrogenation reactions. Using an emulsion polymerization of furfuryl alcohol, we have made catalysts that consist of microporous carbon nanospheres within which are embedded platinum nanoparticles. The porosity of the carbon spheres was found to be a key parameter affecting catalyst activity and selectivity; porosity was varied by adding pore forming agents, such as polyethylene glycol with different molecular weights, during synthesis, or by mild oxidation of the as-synthesized catalyst using carbon dioxide. In addition to increasing porosity to reduce mass transfer limitations, a synthesis of smaller carbon spheres (<200nm) was devised to reduce the micropore diffusion length. Decreasing the particle size of the catalyst by adjusting the surfactant composition during polymerization, improved the effectiveness factor by approximately one order of magnitude making it as active as a comparable standard metal catalyst.

The twin-arginine translocation (Tat) protein export pathway

The twin-arginine translocation (Tat) protein export system is present in the cytoplasmic membranes of most bacteria and archaea and has the highly unusual property of transporting fully folded proteins. The system must therefore provide a transmembrane pathway that is large enough to allow the passage of structured macromolecular substrates of different sizes but that maintains the impermeability of the membrane to ions. In the Gram-negative bacterium Escherichia coli, this complex task can be achieved by using only three small membrane proteins: TatA, TatB and TatC. In this Review, we summarize recent advances in our understanding of how this remarkable machine operates.

Deformation of Multilayer Flexible Electronics Subjected to Torque

Flexibility is one of remarkable characteristics of flexible electronics. Therefore, the analysis of flexible electronics deformation caused by external torques will help its design. In this work, analytical derivation is conducted for flexible electronics treated as multilayer structures. In experiments, an electric motor under computer control exerts a torque to generate torsion, whose twist angles are obtained by using both optical encoder measurement and theoretical calculation. Comparisons are made between experimental and theoretical results for bare PEN (polyethylene naphthalate) substrates of different sizes, multilayer PET (polyethylene terephthalate) substrates, and ITO (indium tin oxide)-coated PET substrates. Finally, a laser displacement sensor is used to measure the out-of-plane deformation for validating the proposed theoretical model.

The effects of water velocity and sediment size on Acroneuria abnormis (Plecoptera: Perlidae) entrainment

We investigated the roles that velocity and substrate size play in the drift of stonefly larvae (Acroneuria abnormis). Acroneuria were introduced into an experimental flume containing homogeneous substrates of different size (small gravel, large gravel, or cobble), or a mixture of various substrate sizes. For each substrate Acroneuria were subjected to three different velocities (0.3, 0.6 and 0.9 ms−1) corresponding to base flow conditions in real streams, and the number of individuals entrained into the water column was measured. Entrainment was nearly two times higher from the smallest substrates than larger substrates and the heterogeneous mixture of substrate sizes. Higher entrainment from the small particles appeared to result from lower availability of refugia among particles and movement of particles under the higher water velocities. Entrainment generally increased with increasing discharge on small and large, but not intermediate-sized, particles. Our results suggest there may be dynamic Acroneuria entrainment under low flow conditions in streams.

Mechanics and Ecological Role of Swimming Behavior in the Caddisfly Larvae Triaenodes tardus

Caddisfly larvae are typically restricted to benthic microhabitats due to the presence of mobile tubular cases constructed out of mineral or organic material. Members of one family (Leptoceridae) use setae on extended metathoracic legs to swim. We describe the swimming behavior of a North American caddisfly, Triaenodes tardus, and experimentally evaluate two hypotheses proposed to explain this behavior. Triaenodes swam 1.47 cm/s, while carrying almost twice their mass in the case material. The larvae employ a stereotypic sequence of motions that likely reduce resistance during the upstroke and increases forward momentum during the downstroke. When placed on substrates of different sizes, larvae swam more on fine sediments but did not elevate off the sediment. After larvae were provided with living or artificial vegetation, the number of swimming bouts decreased compared to a pre-treatment observation period. These results indicate swimming likely does not function to facilitate movement off fine sediments, but rather, helps larvae locate and move between aquatic macrophytes which are the primary habitat of this, and other, swimming species.

Distance-Dependent Fluorescence Quenching of Conjugated Polymers on Au/Ag Striped Nanorods

To understand the effect of metal surface−polymer separation on fluorescent signal intensity, we describe here our initial investigation on the fluorescent behavior of conjugated polymers near metal nanorods by attenuating the thickness of SiO2 coatings as the spacer. Our preliminary results show that the amount of fluorescence of conjugated polymers quenched by Au/Ag striped nanorods exponentially decays away from the surface in the range of 0−20 nm. This distance-dependent fluorescence quenching phenomenon is consistent with that of small organic dye molecules with a similar fluorescent profile near a metal surface. Furthermore, the results confirm that it is a valid assumption that the previously proposed superquenching model for conjugated polymers in solution is applicable to the polymers attached to a solid surface. The absolute size of polymers is irrelevant in quenching studies. Similar distance-dependent quenching trends are observed for conjugated polymers placed near metal surfaces of different length scales. However, theoretical fitting of the experimental data illustrates subtle differences in the quenching efficiency offered by the metal substrates of different sizes to the polymer. The finding from this study allows us to obtain fluorescence measurements in a reproducible fashion, which is critical in using conjugated polymers as the signaling probes in quantitatively reporting the amount of target analytes bound to metal particles.

Structures of an Isopenicillin N Converting Ntn-Hydrolase Reveal Different Catalytic Roles for the Active Site Residues of Precursor and Mature Enzyme

Penicillium chrysogenum Acyl coenzyme A:isopenicillin N acyltransferase (AT) performs the last step in the biosynthesis of hydrophobic penicillins, exchanging the hydrophilic side chain of a precursor for various hydrophobic side chains. Like other N-terminal nucleophile hydrolases AT is produced as an inactive precursor that matures upon posttranslational cleavage. The structure of a Cys103Ala precursor mutant shows that maturation is autoproteolytic, initiated by Cys103 cleaving its preceding peptide bond. The crystal structure of the mature enzyme shows that after autoproteolysis residues 92-102 fold outwards, exposing a buried pocket. This pocket is structurally and chemically flexible and can accommodate substrates of different size and polarity. Modeling of a substrate-bound state indicates the residues important for catalysis. Comparison of the proposed autoproteolytic and substrate hydrolysis mechanisms shows that in both events the same catalytic residues are used, but that they perform different roles in catalysis.