Substrate Topology Research Articles

Antibacterial potency of type VI amidase effector toxins is dependent on substrate topology and cellular context.

Members of the bacterial T6SS amidase effector (Tae) superfamily of toxins are delivered between competing bacteria to degrade cell wall peptidoglycan. Although Taes share a common substrate, they exhibit distinct antimicrobial potency across different competitor species. To investigate the molecular basis governing these differences, we quantitatively defined the functional determinants of Tae1 from Pseudomonas aeruginosa PAO1 using a combination of nuclear magnetic resonance and a high-throughput in vivo genetic approach called deep mutational scanning (DMS). As expected, combined analyses confirmed the role of critical residues near the Tae1 catalytic center. Unexpectedly, DMS revealed substantial contributions to enzymatic activity from a much larger, ring-like functional hot spot extending around the entire circumference of the enzyme. Comparative DMS across distinct growth conditions highlighted how functional contribution of different surfaces is highly context-dependent, varying alongside composition of targeted cell walls. These observations suggest that Tae1 engages with the intact cell wall network through a more distributed three-dimensional interaction interface than previously appreciated, providing an explanation for observed differences in antimicrobial potency across divergent Gram-negative competitors. Further binding studies of several Tae1 variants with their cognate immunity protein demonstrate that requirements to maintain protection from Tae activity may be a significant constraint on the mutational landscape of tae1 toxicity in the wild. In total, our work reveals that Tae diversification has likely been shaped by multiple independent pressures to maintain interactions with binding partners that vary across bacterial species and conditions.

Electronic and topological properties of Bi(110) ultrathin films grown on a Cu(111) substrate

The electronic and topological properties of Bi(110) ultrathin films epitaxially grown on a Cu(111) substrate are investigated using scanning tunneling microscopy/spectroscopy, combined with density functional theory calculations. Bilayer-by-bilayer growth of the ultrathin Bi(110) films is observed, which manifests a structure of black-phosphorus-like Bi bilayers (BLs), with thickness up to 4 BLs. The surface atomic buckling heights in the 1-BL and 2-BL films are clearly identified to depend on the stacking modes with respect to the well-ordered Bi atoms in the adlayer covered on the Cu(111) surface. Our results demonstrate that while the electronic and topological properties of 1-BL films greatly depend on the stacking modes between the Bi(110) bilayer and the adlayer, the 2-BL films show well-decoupled electronic properties from the Cu substrate and nontrivial topologies robust against surface atomic buckling height benefitting from the interbilayer coupling. Our calculations further show that besides the parameter of buckling heights, the topological nontrivial-to-trivial transition can also be induced by changing the interbilayer distance and the vertical intralayer bond length.

Sensing Alzheimer’s Disease Utilizing Au Electrode by Controlling Nanorestructuring

This paper reports the development of Alzheimer’s disease (AD) sensor through early detection of amyloid-beta (Aβ) (1–42) using simple nanorestructuring of Au sheet plate by oxidation-reduction cycle (ORC) via the electrochemical system. The topology of Au substrates was enhanced through the roughening and Au grains grown by a simple ORC technique in aqueous solutions containing 0.1 mol/L KCl electrolytes. The roughened substrate was then functionalized with the highly specific antibody β-amyloid Aβ (1–28) through HS-PEG-NHS modification, which enabled effective and direct detection of Aβ (1–42) peptide. The efficacy of the ORC method had been exhibited in the polished Au surface by approximately 15% larger electro-active sites compared to the polished Au without ORC. The ORC polished structure demonstrated a rapid, accurate, precise, reproducible, and highly sensitive detection of Aβ (1–42) peptide with a low detection limit of 10.4 fg/mL and a wide linear range of 10−2 to 106 pg/mL. The proposed structure had been proven to have potential as an early-stage Alzheimer’s disease (AD) detection platform with low-cost fabrication and ease of operation.

Improving Mechanical Ice Protection Systems with Substrate Parametric and Topology Optimization

Improving Mechanical Ice Protection Systems with Substrate Parametric and Topology Optimization

WASP integrates substrate topology and cell polarity to guide neutrophil migration.

To control their movement, cells need to coordinate actin assembly with the geometric features of their substrate. Here, we uncover a role for the actin regulator WASP in the 3D migration of neutrophils. We show that WASP responds to substrate topology by enriching to sites of inward, substrate-induced membrane deformation. Superresolution imaging reveals that WASP preferentially enriches to the necks of these substrate-induced invaginations, a distribution that could support substrate pinching. WASP facilitates recruitment of the Arp2/3 complex to these sites, stimulating local actin assembly that couples substrate features with the cytoskeleton. Surprisingly, WASP only enriches to membrane deformations in the front half of the cell, within a permissive zone set by WASP's front-biased regulator Cdc42. While WASP KO cells exhibit relatively normal migration on flat substrates, they are defective at topology-directed migration. Our data suggest that WASP integrates substrate topology with cell polarity by selectively polymerizing actin around substrate-induced membrane deformations in the front half of the cell.

Atomistic modeling of physical vapor deposition on complex topology substrates

Molecular Dynamics simulations of Cu physical vapor deposition are employed to investigate the effects of substrate topology and line of sight on the synthesis of thin films on Cu substrates. The deposition and surface relaxation processes of sputtering Cu ions are simulated considering various angles of incidence (0–60°) and sputtering energies (1, 10, 25, and 50 eV). Cu substrates are constructed with three different surface geometries: i) a flat Cu (111) surface; ii) a sinusoidal shaped substrate with a period of 127.6 Å and amplitude 20 Å; and iii) a combined substrate composed of a flat Cu (111) surface and a cylinder of radius 63.8 Å, floating 50 Å above the flat surface. Results from simulations with low impact energy (1 eV) show a strong effect of the angle of incidence on the roughness of the thin film produced on the flat surface. For non-flat substrates, areas with no line of sight have diminished film coverage, which is offset by increasing the deposition energy. Higher energy atoms have greater adatom mobility enabling the coverage of regions with no line of sight and the reduction of surface roughness. The results show a lower sticking probability for highly energetic deposition at high angles of deposition, effectively promoting film coverage in areas with no line of sight through physical redeposition processes, which is augmented by particle-induced sputtering. These atomistic insights are relevant for the understanding of physical vapor deposition processes on convoluted topology substrates, such as magnetron sputtering on metamaterial lattices.

Granular Media Friction Pad for Robot Shoes—Hexagon Patterning Enhances Friction on Wet Surfaces

For maximizing friction forces of robotic legs on an unknown/unpredictable substrate, we introduced the granular media friction pad, consisting of a thin elastic membrane encasing loosely filled granular material. On coming into contact with a substrate, the fluid-like granular material flows around the substrate asperities and achieves large contact areas with the substrate. Upon applying load, the granular material undergoes the jamming transition, rigidifies and becomes solid-like. High friction forces are generated by mechanical interlocking on rough substrates, internal friction of the granular media and by the enhanced contact area caused by the deformation of the membrane. This system can adapt to a large variety of dry substrate topologies. To further increase its performance on moist or wet substrates, we adapted the granular media friction pad by structuring the outside of the membrane with a 3D hexagonal pattern. This results in a significant increase in friction under lubricated conditions, thus greatly increasing the universal applicability of the granular media friction pad for a multitude of environments.

Effects of forces on chromatin.

Chromatin is a unique structure of DNA and histone proteins in the cell nucleus and the site of dynamic regulation of gene expression. Soluble factors are known to affect the chromatin structure and function via activating or inhibiting specific transcription factors. Forces on chromatin come from exogenous stresses on the cell surface and/or endogenous stresses, which are regulated by substrate mechanics, geometry, and topology. Forces on chromatin involve direct (via adhesion molecules, cytoskeleton, and the linker of nucleoskeleton and cytoskeleton complexes) and indirect (via diffusion and/or translocation processes) signaling pathways to modulate levels of chromatin folding and deformation to regulate transcription, which is controlled by histone modifications and depends on magnitude, direction, rate/frequency, duration, and modes of stresses. The rapid force transmission pathway activates multiple genes simultaneously, and the force may act like a “supertranscription factor.” The indirect mechanotransduction pathways and the rapid force transmission pathway together exert sustained impacts on the chromatin, the nucleus, and cell functions.

Micropatterning of polymer substrates for cell culture

The cell microenvironment such as substrate topology plays an important role in biological processes. In this study, microgrooves were successfully produced on surfaces of both thermoplastic and thermoset polymers using cost-effective techniques for mass production. The micropatterning of thermoplastic polystyrene (PS) petri dish was accomplished efficiently using an in-house developed low-cost hot embossing system. The high replication fidelity of the microgroove with depth and width of 2μm and spacing of 2μm was achieved by using silicone rubber as a soft counter mold. This patterned petri dish subsequently served as the cast to replicate the micropattern onto thermoset polydimethylsiloxane (PDMS). It was found that the micropattern increased the hydrophobicity of both PS and PDMS surfaces. The effect of the substrate micropattern on cellular behaviors was preliminarily investigated with untreated and treated PS petri dish as well as PDMS. The results show that the micropattern significantly improved cell adhesion and proliferation for cells cultured on untreated PS petri dish and PDMS substrates. Moreover, the micropattern induced obvious cell alignment along the microgrooves for culturing on all substrates which were studied.

Characterization of Nematic Liquid Crystals at Microwave Frequencies

The use of nematic liquid crystal (LC) mixtures for microwave frequency applications presents a fundamental drawback: many of these mixtures have not been properly characterized at these frequencies, and researchers do not have an a priori clear idea of which behavior they can expect. This work is focused on developing a new procedure for the extraction of the main parameters of a nematic liquid crystal: dielectric permittivity and loss tangent at 11 GHz under different polarization voltages; splay elastic constant K11, which allows calculation of the threshold voltage (Vth); and rotational viscosity γ11, which allows calculating the response time of any arbitrary device. These properties will be calculated by using a resonator-based method, which is implemented with a new topology of substrate integrated transmission line. The LC molecules should be rotated (polarized) by applying an electric field in order to extract the characteristic parameters; thus, the transmission line needs to have two conductors and low electric losses in order to preserve the integrity of the measurements. This method was applied to a well-known liquid crystal mixture (GT3-23002 from MERCK) obtaining the permittivity and loss tangent versus bias voltage curves, the splay elastic constant, and the rotational viscosity of the mixture. The results validate the viability of the proposed method.

Effects of Surface Chemistry and Topology on the Kinesin-Driven Motility of Microtubule Shuttles.

Nanoscale transport using the kinesin-microtubule system has been successfully used in applications ranging from self-assembly, to biosensing, to biocomputation. Realization of such applications necessitates robust microtubule motility particularly in the presence of complex sample matrices that can affect the interactions of the motors with the surface and the transport function. In the present work, we explored how the chemical nature and nanoscale topology of various surfaces affected kinesin-microtubule transport. Specifically, we characterized microtubule motility on three distinct interfaces: (i) surfaces modified with self-assembled monolayers (SAMs) displaying three different terminal groups, (ii) SAM-modified surfaces with adsorbed fetal bovine serum (FBS) proteins, and (iii) surfaces where the FBS layer was silicified to preserve an underlying surface topology. The composition and topology of each surface was confirmed with a number of techniques including X-ray photoelectron spectroscopy (XPS), water contact angle, atomic force microscopy (AFM), and scanning electron microscopy (SEM). The majority of surfaces, with the exception of those with the hydrophobic SAM, supported gliding motility consistent with the glass control. Differences in the displacement, velocity, and trajectory of the leading tip of the microtubule were observed in relation to the specific surface chemistry and, to a lesser extent, the nanoscale topology of the different substrates. Overall, this work broadens our understanding of how surface functionality and topology affect kinesin-based transport and provides valuable insights regarding future development of biosensing and probing applications that rely on biomolecular transport.

Mechanism of Type IA Topoisomerases.

Topoisomerases in the type IA subfamily can catalyze change in topology for both DNA and RNA substrates. A type IA topoisomerase may have been present in a last universal common ancestor (LUCA) with an RNA genome. Type IA topoisomerases have since evolved to catalyze the resolution of topological barriers encountered by genomes that require the passing of nucleic acid strand(s) through a break on a single DNA or RNA strand. Here, based on available structural and biochemical data, we discuss how a type IA topoisomerase may recognize and bind single-stranded DNA or RNA to initiate its required catalytic function. Active site residues assist in the nucleophilic attack of a phosphodiester bond between two nucleotides to form a covalent intermediate with a 5′-phosphotyrosine linkage to the cleaved nucleic acid. A divalent ion interaction helps to position the 3′-hydroxyl group at the precise location required for the cleaved phosphodiester bond to be rejoined following the passage of another nucleic acid strand through the break. In addition to type IA topoisomerase structures observed by X-ray crystallography, we now have evidence from biophysical studies for the dynamic conformations that are required for type IA topoisomerases to catalyze the change in the topology of the nucleic acid substrates.

Integrated optimization design of smart morphing wing for accurate shape control

Smart morphing wing, which is equipped with smart materials and able to change structural geometry adaptively, can further improve aerodynamic efficiency of aircraft. This paper presents a new integrated layout and topology optimization design for morphing wing driven by shape memory alloys (SMAs). By simultaneously optimizing the layout of smart actuators and topology of wing substrate, the ultimately determined configuration can achieve smooth, continuous and accurate geometric shape changes. In addition, aerodynamic analysis is carried out to compare smart morphing wing with traditional hinged airfoil. Finally, the optimized smart wing structure is constructed and tested to demonstrate and verify the morphing functionality. Application setbacks are also pointed out for further investigation.

A Service Function Chain Deployment Method Based on Network Flow Theory for Load Balance in Operator Networks

Network function virtualization technology makes the deployment and management of network service more flexible and elastic by decoupling network function from dedicated hardware. The service requests of network function virtualization are usually deployed in the form of a service function chain. In order to solve the problems of load imbalance, unreasonable utilization of substrate resources, and the high delay of the service function chain deployment in operator networks, a service function chain deployment method based on the network flow theory is proposed in this paper. First, on the basis of perceiving the substrate network resources and topology with a software-defined network controller in real time, a candidate node set is determined according to the resource constraints and the locations of ingress/egress switch nodes that service flow flows in/out. Second, the candidate node set, the ingress/egress switch nodes and the connection between them are used to form a directed network, and the service function chain deployment problem is transformed into an optimal path selection problem. Then, a node disassembling method is used to transform the directed network into a capacity-flow-cost network. Finally, a minimum-cost maximum-flow algorithm is used to find the optimal deployment path and complete the service function chain deployment. Experiments show that the method proposed in this paper can guarantee the load balance of operator networks, reduce the average transmission delay of service flow, and make the utilization of substrate resources more reasonable.

Oblique angled plasma etching for 3D silicon structures with wiggling geometries

Three dimensional (3D) silicon micro- and nanostructures have attracted special research interest, particularly in photonic and electrochemical devices, due to the extra degrees of freedom for manipulation of device performance and properties. However, it is still considered to be difficult to fabricate 3D silicon structures with an arbitrary geometric form in a scalable volume, especially with standard fabrication techniques, which are intrinsically directional and anisotropic. In this work we proposed a unique method of oblique-angled plasma etching from various angles, thus multilayered silicon structures with wiggling geometries can be fabricated in a controllable manner both in micro- and nanoscale. The mechanism is explained as induced modifications of substrate topology and surface charging when a glass pad is attached on the sample surface, thus the incoming ion fluxes can be directed to the substrate surface with an off-normal angle. The process is convenient to perform without additional modifications on the plasma etching systems. At the same time, it provides more possibilities in the toolkit for fabricating 3D silicon structures with conventional fabrication technologies.

DROI: Energy-efficient virtual network embedding algorithm based on dynamic regions of interest

Network virtualization is an important technology for the next generation of the internet. Moreover, energy-efficient virtual network embedding has gradually become a research hotspot due to the increase in energy awareness. Given the lack of consideration of substrate and virtual network topology information in energy-efficient virtual network embedding, this work applies spectral clustering based on field theory to extract substrate network features. Dynamic regions of interest are also established to find embedding areas with energy-saving potential for virtual networks. The largest matching area of a virtual network on a substrate network is identified by considering virtual network topology information. Experimental results show that the proposed approach greatly improves energy-saving relative to existing algorithms.

Synthesis of oligophosphonate aromatic systems using the Michaelis-Arbuzov reaction and microwave radiation

The microwave-assisted Michaelis-Arbuzov reaction of 2-aryloxy-1,3,2-dioxaphosphinanes was investigated. The dioxaphosphinane groups immobilized on dinaphthylmethane or resorcinarene core react with alkyl/arylalkyl halides/bromoethyl acetate with opening of the phosphinane ring to give linear unsymmetrical phosphonates. The number and spatial orientation of the resulting phosphonate groups depend on the structure and topology of the aromatic substrate and the nature of the alkylating reagent.

A projection‐based method for topology optimization of structures with graded surfaces

SummaryGraded surfaces widely exist in natural structures and inspire engineers to apply functionally graded (FG) materials to cover structural surfaces for performance improvement, protection, or other special functionalities. However, how to design such structures with FG surfaces by topology optimization is a quite challenging problem due to the difficulty for determining material properties of structural surfaces with prescribed variation rule. This paper presents a novel projection‐based method for topology optimization of this class of FG structures. Firstly, a projection process is proposed for ensuring the material properties of the surfaces vary with a prescribed function. A criterion of determining the values of parameters in projection process is given by a strict theoretical derivation, and then, a new interpolation function is established, which is capable of simultaneously obtaining clear substrate topologies and realizable FG surfaces. Though such structures are actually multimaterial gradient structures, only the design variables of single‐material topology optimization problem are needed. In the current research, the classical compliance minimization problem with a mass constraint is considered and the robust formulation is used to control the length scale of substrates. Several 2D and 3D numerical examples illustrate the validity and applicability of the proposed method.

Polarization effect in tip-enhanced infrared nanospectroscopy studies of the selective Y5 receptor antagonist Lu AA33810

A novel approach of combining conventional infrared spectroscopy (IR) and atomic force microscopy (AFM) is presented to better understand the behavior of a drug adsorbed on a metal substrate at the nanoscale level. Tip-enhanced infrared nanospectroscopy (TEIRA) was used for the first time to investigate Lu AA33810, a selective brain-penetrating Y5 receptor antagonist, after immobilization on gold nanoparticles (GNPs). Here, a gold coated AFM tip and gold substrate were used to obtain the near-field electromagnetic field trapping effect. Because of the huge signal enhancement, it was possible to obtain the spectral information regarding the self-assembled monolayer of the investigated molecule. The effect of two orthogonal polarizations (p- and s-polarization modulations) of the excitation laser beam on the spectral patterns is also discussed. The results show that there is a strong relationship between the state of polarization of the incident radiation and the relative infrared band intensities. Another factor affecting the observed spectral differences is the topology of the metal substrate, which may result in the induction of a cross-polarization effect. The performed analysis indicates that the C–C bond from the cyclohexyl group is oriented almost parallel to the metal surface. Conversely, the p- and s-polarized spectral variations suggest that the O=S=O angle is high enough to enable the simultaneous interaction of both oxygen atoms with the GNPs.

EFFECT OF SYNTHESIZING PARAMETERS ON MORPHOLOGY AND DIAMETER OF CARBON NANOTUBES GROWN BY THERMAL CVD METHOD

Carbon nanotubes were synthesized by thermal chemical vapor deposition method. There were parameters of the synthesizing process which influence the morphology and quality of nanotubes such as substrate material, the topology of substrates, the reduction process, and growing temperature. The topology of substrate affected the uniform of nanotubes. The reduction process using NH3 reductant helped reducing diameter of carbon nanotubes. Growing temperature complexly modified the quality of carbon nanotubes.