Substrate Topology Research Articles

Molecular dynamics modeling of water nanodroplet spreading on topographically patterned silicon dioxide and silicon nitride substrates

This article reports the investigation of the spreading behavior of a nanodroplet in a droplet-based scalable nanomanufacturing process using Molecular Dynamics (MD) modeling and simulation. The objective of the study is to understand the effect of substrate topology on the wetting behavior of nanodroplets at the molecular level. A water nanodroplet spreading on silicon dioxide (SiO2) and silicon nitride (Si3N4) substrates with different topologies was studied. A migration of the SiO2–water system from a hydrophilic to hydrophobic interaction was observed with an increase in the aspect ratio of the patterns. In contrast, for the Si3N4–water system the fluid–structural interaction shifted from a hydrophobic to hydrophilic behavior for patterns with corresponding higher aspect ratios. The MD models were validated using molecular kinetic theory. This research provides a foundation for extending the functional range of substrate and solvent combinations by manipulating the substrate topology. The results of this work are expected to serve in the effective control of the hydrophobic/hydrophilic nature of the substrates and therefore aid in the prediction of nanofeature deposition in droplet-based micro/nanomanufacturing processes.

Novel radical tandem 1,6-enynes thioacylation/cyclization: Au–Pd nanoparticles catalysis versus thermal activation as a function of the substrate specificity

We studied the reactivity of 1,6-enynes with thioacetic acid (AcSH) under either thermal conditions or in the presence of catalytic amounts of supported Au or Au–Pd nanoparticles (NPs) under mild conditions. The 1,6-enynes undergo a tandem thioacylation/cyclization to original cyclic products featuring either a homoallylic thioester function or an enol thioester function depending on the substrate topology. Interestingly, the former process was found more efficient when performed in the presence of Au–Pd NPs while the latter process can be efficiently carried out under thermal conditions (100 °C). The reaction proceeds by a radical mechanism and the presence of precious metal NPs seems to stabilize the formation of free radical intermediates, as supported by experimental and theoretical results.

Adversarial topology discovery in network virtualization environments: a threat for ISPs?

Network virtualization is a new Internet paradigm which allows multiple virtual networks (VNets) to share the resources of a given physical infrastructure. The virtualization of entire networks is the natural next step after the virtualization of nodes and links. While the problem of how to embed a VNet (“guest network”) on a given resource network (“host network”) is algorithmically well-understood, much less is known about the security implications of this new technology. This paper introduces a new model to reason about one particular security threat: the leakage of information about the physical infrastructure—often a business secret. We initiate the study of this new problem and introduce the notion of request complexity which describes the number of VNet requests needed to fully disclose the substrate topology. We derive lower bounds and present algorithms achieving an asymptotically optimal request complexity for important graph classes such as trees, cactus graphs (complexity $$O(n)$$ ) as well as arbitrary graphs (complexity $$O(n^2)$$ ). Moreover, a general motif-based topology discovery framework is described which exploits the poset structure of the VNet embedding relation.

Virtual Optical Network Embedding (VONE) Over Elastic Optical Networks

Based on the concept of infrastructure as a service, optical network virtualization can facilitate the sharing of physical infrastructure among different users and applications. In this paper, we design algorithms for both transparent and opaque virtual optical network embedding (VONE) over flexible-grid elastic optical networks. For transparent VONE, we first formulate an integer linear programming (ILP) model that leverages the all-or-nothing multi-commodity flow in graphs. Then, to consider the continuity and consecutiveness of substrate fiber links' (SFLs') optical spectra, we propose a layered-auxiliary-graph (LAG) approach that decomposes the physical infrastructure into several layered graphs according to the bandwidth requirement of a virtual optical network request. With LAG, we design two heuristic algorithms: one applies LAG to achieve integrated routing and spectrum assignment in link mapping (i.e., local resource capacity (LRC)-layered shortest-path routing LaSP), while the other realizes coordinated node and link mapping using LAG (i.e., layered local resource capacity(LaLRC)-LaSP). The simulation results from three different substrate topologies demonstrate that LaLRC-LaSP achieves better blocking performance than LRC-LaSP and an existing benchmark algorithm. For the opaque VONE, an ILP model is also formulated. We then design a LRC metric that considers the spectrum consecutiveness of SFLs. With this metric, a novel heuristic for opaque VONE, consecutiveness-aware LRC-K shortest-path-first fit (CaLRC-KSP-FF), is proposed. Simulation results show that compared with the existing algorithms, CaLRC-KSP-FF can reduce the request blocking probability significantly.

DNA Origami Based Visualization System for Studying Site-Specific Recombination Events

Site-specific recombination involves reciprocal exchange between defined DNA sites. The reaction initiates from the formation of a recombinase-DNA synaptic complex, in which two recombination sites arrange in an appropriate configuration. However, there is incomplete information about how the topological state of the substrate influences the synapsis and outcome of the reaction. Here, we show that Cre-mediated recombination can be regulated by controlling the orientation and topology of the loxP substrate in a DNA frame nanoscaffold. High-speed atomic force microscopy analyses revealed that the loxP-containing substrate strands in the antiparallel orientation can be recombined only through formation of synaptic complexes. By tethering Holliday junction (HJ) intermediates to DNA frames in different connection patterns and using them as a starting substrate, we found that the topological state of the HJ intermediates dictates the outcome of the resolution. Our approach should provide a new platform for structural-functional studies of various DNA targeting enzymes, especially which require formation of synaptic complexes.

Thin Polymer Brush Decouples Biomaterial’s Micro-/Nanotopology and Stem Cell Adhesion

Surface morphology and chemistry of polymers used as biomaterials, such as tissue engineering scaffolds, have a strong influence on the adhesion and behavior of human mesenchymal stem cells. Here we studied semicrystalline poly(ε-caprolactone) (PCL) substrate scaffolds, which exhibited a variation of surface morphologies and roughness originating from different spherulitic superstructures. Substrates were obtained by varying the parameters of the thermal processing, that is, crystallization conditions. The cells attached to these polymer substrates adopted different morphologies responding to variations in spherulite density and size. In order to decouple substrate topology effects on the cells, sub-100 nm bioadhesive polymer brush coatings of oligo(ethylene glycol) methacrylates were grafted from PCL and functionalized with fibronectin. On surfaces featuring different surface textures, dense and sub-100 nm thick brush coatings determined the response of cells, irrespective to the underlying topology. Thus, polymer brushes decouple substrate micro-/nanoscale surface topology and the adhesion of stem cells.

Influence of Osmotic Pressure on Adhesion of Lipid Vesicles to Solid Supports

The adhesion of lipid vesicles to solid supports represents an important step in the molecular self-assembly of model membrane platforms. A wide range of experimental parameters are involved in controlling this process, including substrate material and topology, lipid composition, vesicle size, solution pH, ionic strength, and osmotic pressure. At present, it is not well understood how the magnitude and direction of the osmotic pressure exerted on a vesicle influence the corresponding adsorption kinetics. In this work, using quartz crystal microbalance with dissipation (QCM-D) monitoring, we have experimentally studied the role of osmotic pressure in the adsorption of zwitterionic vesicles onto silicon oxide. The osmotic pressure was induced by changing the ionic strength of the solvent across an appreciably wider range (from 25 to 1000 mM NaCl outside of the vesicle, and 125 mM NaCl inside of the vesicle, unless otherwise noted) compared to that used in earlier works. Our key finding is demonstration that, by changing osmotic pressure, all three generic types of the kinetics of vesicle adsorption and rupture can be observed in one system, including (i) adsorption of intact vesicles, (ii) adsorption and rupture after reaching a critical vesicle coverage, and (iii) rupture just after adsorption. Furthermore, theoretical analysis of pressure-induced deformation of adsorbed vesicles and a DLVO-type analysis of the vesicle-substrate interaction qualitatively support our observations. Taken together, the findings in this work demonstrate that osmotic pressure can either promote or impede the rupture of adsorbed vesicles on silicon oxide, and offer experimental evidence to support adhesion energy-based models that describe the adsorption and spontaneous rupture of vesicles on solid supports.

A Review of Haptic Feedback Teleoperation Systems for Micromanipulation and Microassembly

This paper presents a review of the major haptic feedback teleoperation systems for micromanipulation. During the last decade, the handling of micrometer-sized objects has become a critical issue. Fields of application from material science to electronics demonstrate an urgent need for intuitive and flexible manipulation systems able to deal with small-scale industrial projects and assembly tasks. Two main approaches have been considered: fully automated tasks and manual operation. The first one require fully pre determined tasks, while the later necessitates highly trained operators. To overcome these issues the use of haptic feedback teleoperation where the user manipulates the tool through a joystick whilst feeling a force feedback, appears to be a promising solution as it allows high intuitiveness and flexibility. Major advances have been achieved during this last decade, starting with systems that enable the operator to feel the substrate topology, to the current state-of-the-art where 3D haptic feedback is provided to aid manipulation tasks. This paper details the major achievements and the solutions that have been developed to propose 3D haptic feedback for tools that often lack 3D force measurements. The use of virtual reality to enhance the immersion is also addressed. The strategies developed provide haptic feedback teleoperation systems with a high degree of assistance and for a wide range of micromanipulation tools. Based on this expertise on haptic for micromanipulation and virtual reality assistance it is now possible to propose microassembly systems for objects as small as 1 to 10 micrometers. This is a mature field and will benefit small-scale industrial projects where precision and flexibility in microassembly are required.

Topology-aware virtual network embedding based on closeness centrality

Network virtualization aims to provide a way to overcome ossification of the Internet. However, making efficient use of substrate resources requires effective techniques for embedding virtual networks: mapping virtual nodes and virtual edges onto substrate networks. Previous research has presented several heuristic algorithms, which fail to consider that the attributes of the substrate topology and virtual networks affect the embedding process. In this paper, for the first time, we introduce complex network centrality analysis into the virtual network embedding, and propose virtual network embedding algorithms based on closeness centrality. Due to considering of the attributes of nodes and edges in the topology, our studies are more reasonable than existing work. In addition, with the guidance of topology quantitative evaluation, the proposed network embedding approach largely improves the network utilization efficiency and decreases the embedding complexity. We also investigate our algorithms on real network topologies (e.g., AT&T, DFN) and random network topologies. Experimental results demonstrate the usability and capability of the proposed approach.

Concealing Surface Topography by Attachment of Nanometer-Thick Film

Concealing of surface topology of substrates by decal-like attachment of nanomembrane is demonstrated. The nanomembrane attachment provides a flat surface on various substrates, including porous substrates, and the surface property such as wettability was changed to that of the nanomembrane. The monitoring of drying process revealed that a nanomembrane with certain thickness tolerates their flexural deflection during the procedure. Moreover, the supporting position of nanomembranes as well as the physical properties of nanomembranes strongly affected the degree of deflection. The decal-like attachment of nanomembranes shown here is potentially a powerful method for creating a new functional surface that is independent of the topological and chemical properties of the original substrate.

19-Fluorine nuclear magnetic resonance chemical shift variability in trifluoroacetyl species

19-Fluorine nuclear magnetic resonance chemical shift variability in trifluoroacetyl species Joseph C SloopSchool of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA, USAAbstract: This review examines the variability of chemical shifts observed in 19-fluorine (19F) nuclear magnetic resonance spectra for the trifluoroacetyl (TFA) functional group. The range of 19F chemical shifts reported spectra for the TFA group varies generally from −85 to −67 ppm relative to CFCl3. The literature revealed several factors that impact chemical shifts of the TFA moiety - substrate topology, electronic environment, solvent polarity, and concentration effects. Often these effects conspire to cause deshielding of the TFA group by up to 15 ppm. These factors will be examined for a series of TFA-functionalized acyclic, cyclic, aromatic, and heterocyclic molecules.Keywords: 19F NMR, chemical shift, shielding, trifluoroacetyl group, fluorinated diketones, triketones

Collagen remodeling by phagocytosis is determined by collagen substrate topology and calcium-dependent interactions of gelsolin with nonmuscle myosin IIA in cell adhesions

We examine how collagen substrate topography, free intracellular calcium ion concentration ([Ca(2+)]i, and the association of gelsolin with nonmuscle myosin IIA (NMMIIA) at collagen adhesions are regulated to enable collagen phagocytosis. Fibroblasts plated on planar, collagen-coated substrates show minimal increase of [Ca(2+)]i, minimal colocalization of gelsolin and NMMIIA in focal adhesions, and minimal intracellular collagen degradation. In fibroblasts plated on collagen-coated latex beads there are large increases of [Ca(2+)]i, time- and Ca(2+)-dependent enrichment of NMMIIA and gelsolin at collagen adhesions, and abundant intracellular collagen degradation. NMMIIA knockdown retards gelsolin recruitment to adhesions and blocks collagen phagocytosis. Gelsolin exhibits tight, Ca(2+)-dependent binding to full-length NMMIIA. Gelsolin domains G4-G6 selectively require Ca(2+) to interact with NMMIIA, which is restricted to residues 1339-1899 of NMMIIA. We conclude that cell adhesion to collagen presented on beads activates Ca(2+) entry and promotes the formation of phagosomes enriched with NMMIIA and gelsolin. The Ca(2+) -dependent interaction of gelsolin and NMMIIA in turn enables actin remodeling and enhances collagen degradation by phagocytosis.

Impact of reducing agent, temperature, and substrate topology on diastereoselectivity of the intermolecular coupling reactions, or how “free” are cobalt-complexed propargyl radicals?

Applicability of the term "free radical" to organometallic radicals was studied by using the stereoselectivity of radical C-C bond formation as a diagnostic tool. Based on diastereoselectivity data, it was concluded that the reduction of π-bonded, Co2(CO)6-complexed propargyl cations with heterogeneous reducing agents (Zn, Mg) generates "free radicals", while homogeneous reductants (Cp2Co, Na-Ph2CO) produce "sequestered radicals", presumably associated with reductant-derived oxidized species. The latter are comparable in molecular volume to the requisite radical species, thus restricting the motion and conformational freedoms of converging, transition metal-complexed propargyl radicals. Diastereoselectivity of intermolecular reactions is determined to be much less sensitive toward temperature variation (Δde = 6-22%) than in intramolecular radical cyclizations (Δde = 106%).

Structures and Function of Remora Adhesion

ABSTRACTRemoras (echeneid fish) reversibly attach and detach to marine hosts, almost instantaneously, to “hitchhike” and feed. The adhesion mechanisms that they use are remarkably insensitive to substrate topology and quite different from the latching and suction cup-based systems associated with other species at similar length scales. Remora adhesion is also anisotropic; drag forces induced by the swimming host increase adhesive strength, while rapid detachment occurs when the remora reverses this shear load. In this work, an investigation of the adhesive system’s functional morphology and tissue properties was carried out initially through dissection and x-ray microtomographic analyses. Resulting finite element models of these components have provided new insights into the adaptive, hierarchical nature of the mechanisms and a path toward a wide range of engineering applications.

Achieving effective resilience for QoS-aware application mapping

Overlay mapping provides a flexible and effective means of application deployment by selecting a subset of nodes and links from the substrate-hosting network to meet, or even enhance, the requirements of the application. In order to take full advantage of the potential of overlay mapping given the features of the substrate network, such as topology and performance characteristics, it is critical to carefully choose the subset of hosting nodes. This is to balance the effectiveness of the overlay mapping with substrate network constraints and resource usage. In this paper, we investigate how to provide effective resilience for a QoS-aware overlay mapping so as to make the mapped applications resilient against substrate network failure(s) whilst providing enhanced QoS. We first formulate the problem as an Integer Linear Program (ILP). Using simulations with small networks, existing methods are shown to be capable of achieving enhanced QoS but lack effective resilience when compared against the optimal ILP solution. To address this issue, a novel heuristic is proposed which incorporates substrate topology information. Through simulations with synthetic and real networks, the effectiveness of the new heuristic is confirmed.

Altered Angiogenesis in Caveolin-1 Gene–Deficient Mice Is Restored by Ablation of Endothelial Nitric Oxide Synthase

Caveolin-1 is an essential structural protein of caveolae, specialized plasma membrane organelles highly abundant in endothelial cells, where they regulate multiple functions including angiogenesis. Caveolin-1 exerts a tonic inhibition of endothelial nitric oxide synthase (eNOS) activity. Accordingly, caveolin-1 gene-disrupted mice have enhanced eNOS activity as well as increased systemic nitric oxide (NO) levels. We hypothesized that excess eNOS activity, secondary to caveolin deficiency, would mediate the decreased angiogenesis observed in caveolin-1 gene-disrupted mice. We tested tumor angiogenesis in mice lacking either one or both proteins, using in vitro, ex vivo, and in vivo assays. We show that endothelial cell migration, tube formation, cell sprouting from aortic rings, tumor growth, and angiogenesis are all significantly impaired in both caveolin-1-null and eNOS-null mice. We further show that these parameters were either partially or fully restored in double knockout mice that lack both caveolin-1 and eNOS. Furthermore, the effects of genetic ablation of eNOS are mimicked by the administration of the NOS inhibitor N-nitro-L-arginine methyl ester hydrochloride (L-NAME), including the reversal of the caveolin-1-null mouse angiogenic phenotype. This study is the first to demonstrate the detrimental effects of unregulated eNOS activity on angiogenesis, and shows that impaired tumor angiogenesis in caveolin-1-null mice is, at least in part, the result of enhanced eNOS activity.

Importance of substrate network topology information for achieving effective enhanced resilience in overlay mapping

The impact of substrate network topology availability and its accuracy in achieving enhanced resilience in overlay mapping is analysed. Overlay mapping aims to find a mapping solution for a given overlay request whereby substrate network resources are assigned in such a fashion that diversified backup paths can be secured and so provide enhanced resilience whilst meeting a specific quality of service requirement(s). Based on evaluations exploiting a real-network dataset as well as synthetic topologies, the significance of possessing substrate topology information is demonstrated. Moreover, as this information is typically not readily available or is incomplete, mechanisms are compared that can obtain more accurate inferred substrate information in order to improve further the performance of overlay mapping solutions in providing effective resilience.

Xwalk: computing and visualizing distances in cross-linking experiments

Motivation: Chemical cross-linking of proteins or protein complexes and the mass spectrometry-based localization of the cross-linked amino acids in peptide sequences is a powerful method for generating distance restraints on the substrate's topology.Results: Here, we introduce the algorithm Xwalk for predicting and validating these cross-links on existing protein structures. Xwalk calculates and displays non-linear distances between chemically cross-linked amino acids on protein surfaces, while mimicking the flexibility and non-linearity of cross-linker molecules. It returns a ‘solvent accessible surface distance’, which corresponds to the length of the shortest path between two amino acids, where the path leads through solvent occupied space without penetrating the protein surface.Availability: Xwalk is freely available as a web server or stand-alone JAVA application at http://www.xwalk.org.Contact: abdullah@imsb.biol.ethz.ch; aebersold@imsb.biol.ethz.chSupplementary information: Supplementary data are available at Bioinformatics online.

Developing thin‐film‐composite forward osmosis membranes on the PES/SPSf substrate through interfacial polymerization

AbstractA new scheme has been developed to fabricate high‐performance forward osmosis (FO) membranes through the interfacial polymerization reaction on porous polymeric supports. p‐Phenylenediamine and 1,3,5‐trimesoylchloride were adopted as the monomers for the in‐situ polycondensation reaction to form a thin aromatic polyamide selective layer of 150 nm in thickness on the substrate surface, a lab‐made polyethersulfone (PES)/sulfonated polysulfone (SPSf)‐alloyed porous membrane with enhanced hydrophilicity. Under FO tests, the FO membrane achieved a higher water flux of 69.8 LMH when against deionized water and 25.2 LMH when against a model 3.5 wt % NaCl solution under 5.0 M NaCl as the draw solution in the pressure‐retarded osmosis mode. The PES/SPSf thin‐film‐composite (TFC)‐FO membrane has a smaller structural parameter S of 238 μm than those reported data. The morphology and topology of substrates and TFC‐FO membranes have been studied by means of atomic force microscopy and scanning electronic microscopy. © 2011 American Institute of Chemical Engineers AIChE J, 2012

Effect of LaAlO3 twin-domain topology on local dc and microwave properties of cuprate films

Different imaging modes of low temperature laser scanning microscopy (LTLSM) have been applied to probe local optical and superconducting properties, as well as the spatial variations in thermoelectric and electronic (both dc and rf) transport, in a YBa2Cu3O6.95/LaAlO3 (YBCO/LAO) superconducting microstrip resonator with micron-range resolution. Additionally, the local sources of microwave nonlinearity (NL) were mapped in two-dimensions simultaneously by using the LTLSM in two-tone rf intermodulation distortion contrast mode as a function of (x,y) position of the laser beam perturbation on the sample. The influence of the direction of individual twin-domain YBCO blocks on its NL properties was analyzed in detail. The result shows the direct spatial correlation between NL microwave and dc electronic transport properties of the YBCO film that are imposed by the underlying twin-domain topology of the LAO substrate. In these circumstances, the scale of local NL current densities JIM(x,y) in different areas of the YBCO microstrip quantitatively coincide with the scale of local critical current densities Jc(x,y) measured at the same positions.