Unique Network Topology Research Articles

Systems-level reconstruction of kinase phosphosignaling networks regulating endothelial barrier integrity using temporal data.

Phosphosignaling networks control cellular processes. We built kinase-mediated regulatory networks elicited by thrombin stimulation of brain endothelial cells using two computational strategies: Temporal Pathway Synthesizer (TPS), which uses phosphoproteomics data as input, and Temporally REsolved KInase Network Generation (TREKING), which uses kinase inhibitor screens. TPS and TREKING predicted overlapping barrier-regulatory kinases connected with unique network topology. Each strategy effectively describes regulatory signaling networks and is broadly applicable across biological systems.

Systems-level reconstruction of kinase phosphosignaling networks regulating endothelial barrier integrity using temporal data.

Phosphosignaling networks control cellular processes. We built kinase-mediated regulatory networks elicited by thrombin stimulation of brain endothelial cells using two computational strategies: Temporal Pathway Synthesizer (TPS), which uses phosphoproetiomics data as input, and Temporally REsolved KInase Network Generation (TREKING), which uses kinase inhibitor screens. TPS and TREKING predicted overlapping barrier-regulatory kinases connected with unique network topology. Each strategy effectively describes regulatory signaling networks and is broadly applicable across biological systems.

Endohedrally Functionalized Metal–Organic Cage-Cross-Linked Polymer Gels as Modular Heterogeneous Catalysts

The immobilization of homogeneous catalysts onto supports to improve recyclability while maintaining catalytic efficiency is often a trial-and-error process limited by poor control of the local catalyst environment and few strategies to append catalysts to support materials. Here, we introduce a modular heterogenous catalysis platform that addresses these challenges. Our approach leverages the well-defined interiors of self-assembled Pd12L24 metal-organic cages/polyhedra (MOCs): simple mixing of a catalyst-ligand of choice with a polymeric ligand, spacer ligands, and a Pd salt induces self-assembly of Pd12L24-cross-linked polymer gels featuring endohedrally catalyst-functionalized junctions. Semi-empirical calculations show that catalyst incorporation into the MOC junctions of these materials has minimal affect on the MOC geometry, giving rise to well-defined nanoconfined catalyst domains as confirmed experimentally using several techniques. Given the unique network topology of these freestanding gels, they are mechanically robust regardless of their endohedral catalyst composition, allowing them to be physically manipulated and transferred from one reaction to another to achieve multiple rounds of catalysis. Moreover, by decoupling the catalyst environment (interior of MOC junctions) from the physical properties of the support (the polymer matrix), this strategy enables catalysis in environments where homogeneous catalyst analogues are not viable, as demonstrated for the Au(I)-catalyzed cyclization of 4-pentynoic acid in aqueous media.

Front Cover: Mn2+ substitution within the {V14As8} polyoxovanadate archetype results in {Mn2V12As8} shells with trans‐positioned heterometal positions (Z. Anorg. Allg. Chem. 22/2021)

The cover picture shows the core fragments of the {Mn2V12As8O40} cluster, which forms as [MnII4VIV12AsIII8O40(dien)4(H2O)]⋅3.5H2O under solvothermal conditions. Starting with the well-known α-{V14As8O42} cluster, two trans-postioned square-pyramidal VO5 groups are exchanged by two unusual MnNO5 moieties. In the crystal lattice, the {Mn2V12As8} shell is further covalently expanded into a {Mn6V12As8} group by one MnN4O(H2O), two MnNO5 and by one MnN5O unit. The {Mn6V12As8} moieties are interlinked into layers by Mn-Ot-V and V-Ot-Mn-dien-Mn-Ot-V bridges, producing a unique network topology. More information can be found in the Article by W. Bensch et al. (DOI: 10.1002/zaac.202100201).

Chemically Robust and Bifunctional Co(II)-Framework for Trace Detection of Assorted Organo-toxins and Highly Cooperative Deacetalization-Knoevenagel Condensation with Pore-Fitting-Induced Size-Selectivity.

Acute detection of assorted classes of organo-toxins in a practical environment is an important sustainable agenda, whereas cooperative and recyclable catalysis can mitigate hazards by minimizing energy requirements and reducing waste generation. We constructed an acid-/base-stable Co(II)-framework with a unique network topology, wherein unidirectional porous channels are decorated by anionic [Co2(μ2-OH)(COO)4(H2O)3] secondary building units and neutral [CoN2(COO)2] nodes. An intense luminescent signature of the hydrolytically robust framework is harnessed for the selective, fast-responsive, and regenerable detection of two detrimental organo-aromatics, 4-aminophenol (4-AP) and 2,4,6-trinitrophenol (TNP). Alongside remarkable quenching, their nanomolar detection limits (4-AP: 99.5 nM; TNP: 67.2 nM) rank among the lowest reported values in water and corroborate their ultra-sensitivity. Density functional theory (DFT) calculations verify the electron-transfer route of sensing through portraying redistribution of energy levels of molecular orbitals in a three-dimensional network by each analyte and further envisages non-covalent host-guest interactions. Benefiting from the concurrent existence of an open-metal site and a triphenylamine-moiety-functionalized ligand, the activated framework acts as an outstandingly cooperative heterogeneous catalyst in deacetalization-Knoevenagel condensation under mild conditions. The acid-base dual catalysis is detailed for the first time from combined inputs of control experiments and DFT validations. To the best of tandem reaction, larger-sized substrate exhibits insignificant conversion, and certifies rarest pore-fitting induced size-selectivity.

802.11p Profile Adaptive MAC Protocol for Non-Safety Messages on Vehicular Ad Hoc Networks

<p>Vehicular Ad hoc Networks (VANET) play a vital Vehicle to Infrastructure (V2I) correspondence frameworks where vehicle are convey by communicating and conveying data transmitted among each other. Because of both high versatility and high unique network topology, congestion control should be executed distributedly. Optimizing the congestion control in term of delay rate, packet delivery ratio (PDR) and throughput could limit the activity of data packet transmissions. These have not been examined altogether so far – but rather this characteristic will be fundamental for VANET system execution and network system performance. This paper exhibits a novel strategy for congestion control and data transmission through Service Control Channel (SCH) in VANET. The Taguchi strategy has been connected in getting the optimize value of parameter for congstion control in highway environment. This idea lessens the pointless activity of data transmission and decreases the likelihood of congested in traffic in view of execution for measuring the delay rate, packet delivery ratio (PDR) and throughput. The proposed execution performance is estimated with the typical VANET environment in V2I topology in highway driving conditions and the simulation results demonstrate and enhance network execution performance with effective data transmission capacity.</p>

Anomalous thermodynamic properties of ice XVI and metastable hydrates

A new ice polymorph, called ice XVI, has recently been discovered experimentally by extracting the guest molecules from Ne hydrate. The ice and its filled form (clathrate hydrate) have a unique network topology which results in several interesting properties. Here we provide a theoretical method to calculate thermodynamic properties of a semiopen system in equilibrium with guest gas and thus occupancy of the guest can be varied with temperature and pressure. Experimental observations such as the disappearance of negative thermal expansivity and contraction of the host lattice upon encaging guest molecules are well reproduced, and those behaviors are elucidated in terms of the free energy of cage occupation and its temperature and pressure dependence. We propose an application of the method for preparing ice XVI to create metastable clathrate hydrates having intriguing properties with much lower occupancy of guest molecules than that at equilibrium, which otherwise cannot form.

Three-Dimensional Heterometallic Coordination Networks: Syntheses, Crystal Structures, Topologies, and Heterogeneous Catalysis

This work presents the synthesis of {Co3+-Zn2+} and {Co3+-Cd2+} heterometallic coordination networks. These networks are originated from two unique Co3+-based metalloligands containing appended arylcarboxylic acid groups at the strategically placed positions. Such appended arylcarboxylate groups coordinate the secondary metal ions, Zn2+ and Cd2+, to afford distinct three-dimensional networks. All four networks display orderly arrangement of secondary metal ions and unique network topologies including an unprecedented one. These networks have been shown to act as the heterogeneous and reusable catalysts for the Knoevenagel condensation reactions and cyanation reactions of assorted aldehydes. Cyanation reactions nicely demonstrate the substrate size-exclusion catalysis.

Perceiving who and when to leverage data delivery for maritime networks: An optimal stopping view

The advances in the integration of wireless communication and sensor technologies have stimulated an innovative paradigm named Crowd Sensing Networks, which caters to the exponential growth of service demands on the sea and drives the development of potential maritime wideband networks. This paper investigates the issue of sensed traffic data scheduling between vessels, combining Time Division Long Term Evolution (TD-LTE) and delay-tolerant networks (DTNs) on the sea. Specially, we propose a unique network topology which combines maritime crowd sensing network and delay tolerant networks, i.e., a store-carry-and-forward routing topology is explored to address the intermittent network connectivity in maritime context. Notably, the alternative eco-friendly green energy in maritime environment will make the scheduling issue more challenging. To the best of our knowledge, this is the first work to do such investigation with the goal of minimizing the costs associated with end-to-end delay of data delivery and energy consumption of DTN throw box. On this basis, we design the scheme of data cooperation transmission between vessels that the hosting vessel decides which DTN throw box to store the data, and when a vessel arrives, the DTN throw box determines whether to stop, i.e., let the arriving vessel carry the data, or skip it and continue to wait for other vessels. A Two-step Time and Energy Oriented Optimal-stopping (TTEOO) algorithm leveraging backward induction method is proposed, based on the optimal stopping rules. Simulation results are presented to show the effectiveness of the proposed method, in terms of consumption cost and data delivery ratio.

An Analytical Comparison of Social Network Measures

Network science spans many different fields of study, ranging from psychology to biology to the social sciences. A number of descriptive network measures have been identified for use within these fields; however, little research examines the relationships of these measures for possible statistical dependence. The research presented in this paper uses Spearman's rank correlation coefficient to examine the statistical dependence between pairs of 24 widely accepted social network measures. Confidence intervals are compared to determine whether computation times between measures in the same correlation group are significantly different. We use a three-factor, four-level, full-factorial experimental design to construct a test set of 64 unique network topologies. The three factors of interest are the network structural properties of size, cluster ability, and the scale-free parameter. A set of 320 networks are generated from a power law degree distribution using a random graph generation algorithm. Results indicate that there exists high correlation among 14 of the 24 tested network measures, many of which also exhibit statistically significant differences with respect to computation time. These findings are of interest to analysts seeking to identify measures that provide similar ranked outcomes and where computational efficiency is an important consideration.

Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks

Bacteria contain multiple sigma factors, each targeting diverse, but often overlapping sets of promoters, thereby forming a complex network. The layout and deployment of such a sigma factor network directly impacts global transcriptional regulation and ultimately dictates the phenotype. Here we integrate multi-omic data sets to determine the topology, the operational, and functional states of the sigma factor network in Geobacter sulfurreducens, revealing a unique network topology of interacting sigma factors. Analysis of the operational state of the sigma factor network shows a highly modular structure with σ(N) being the major regulator of energy metabolism. Surprisingly, the functional state of the network during the two most divergent growth conditions is nearly static, with sigma factor binding profiles almost invariant to environmental stimuli. This first comprehensive elucidation of the interplay between different levels of the sigma factor network organization is fundamental to characterize transcriptional regulatory mechanisms in bacteria.

New Zn2+ Metal Organic Frameworks with Unique Network Topologies from the Combination of Trimesic Acid and Amino-Alcohols

A series of new Zn2+-trimesate (btc3-) metal organic frameworks (MOFs) has been isolated in the presence of various amino-alcohols under solvothermal conditions. Thus, the reaction of ZnCl2 with trimesic acid (H3btc) and the amino-alcohols triethanolamine (teoa), 2-(hydroxymethyl)piperidine (hmpip), N-tert-butyldiethanolamine (tbdeoa), 1,4-bis(2-hydroxyethyl)piperazine (bhep), N-methyldiethanolamine (mdeoa), or 4-(2-hydroxyethyl)morpholine (hem) in a 1.6:1:5.6 molar ratio in DMF afforded compounds (teoaH)2[Zn(btc)1.33] (MOAAF-1) (MOAAF = metal organic amino-alcohol framework), (NH2Me2)2(hmpipH)[Zn3(btc)3] (MOAAF-2), (NH2Me2)(tbdmaH)2[Zn3(btc)3] (MOAAF-3) (tbdma = N-tert-butyl-dimethylamine), (NH2Me2)(bhepH2)[Zn3(btc)3] (MOAAF-4), (NH2Me2)[Zn4(btc)3(mdeoa)2] (MOAAF-5), and (NH2Me2)[Zn4(btc)3(hem)2] (MOAAF-6), respectively. The compounds display 3D structures with relatively large cavities (4–10 Å) and high potential solvent-accessible areas (38–68% of the unit cell volumes). A number of novel structural features are revealed in the reported MOFs, such as unprecedented dinuclear [Zn2(COO)5]−1 secondary building units (SBUs) and unique network topologies (e.g., in compounds MOAAF-2, MOAAF-3, MOAAF-5, and MOAAF-6). The amino-alcohols employed played a key role for the appearance of such novel structural features in MOAAF 1–6 since they were found to act as bases responsible for the deprotonation of H3btc, templates, and chelating ligands. Specifically, most of the compounds synthesized were shown to be templated by protonated amino-alcohols that are involved in hydrogen bonding interactions with the frameworks, whereas in two cases (compounds MOAAF-5 and MOAAF-6) the amino-alcohols acted as chelating ligands affecting significantly the underline topology of the MOFs. The thermal stability and photoluminescence properties of the MOFs are also discussed. This work represents the initial systematic investigation on the use of combination of amino-alcohols and polycarboxylate ligands for the synthesis of new MOFs, demonstrating it as a powerful synthetic strategy for the isolation of novel MOFs.

Ethernet Topology Discovery for Networks With Incomplete Information

In this paper, we investigate the problem of finding the layer-2 network topology of large, heterogeneous multisubnet Ethernet networks that may include uncooperative network nodes. We prove that finding a layer-2 network topology for a given incomplete input is an NP-hard problem, even for single subnet networks, and that deciding whether a given input defines a unique network topology is a co-NP-hard problem. We design several heuristic algorithms to find network topology, evaluate their complexity, and provide criteria for instances in which the input guarantees a unique network topology. We have implemented one of our algorithms and conducted extensive experiments on the Kent State University Computer Science network. Our experiments demonstrate that our approach is quite practical and discovers the accurate network topology of multisubnet networks whose input may not necessarily be complete.

Chemical structure, network topology, and porosity effects on the mechanical properties of Zeolitic Imidazolate Frameworks

The mechanical properties of seven zeolitic imidazolate frameworks (ZIFs) based on five unique network topologies have been systematically characterized by single-crystal nanoindentation studies. We demonstrate that the elastic properties of ZIF crystal structures are strongly correlated to the framework density and the underlying porosity. For the systems considered here, the elastic modulus was found to range from 3 to 10 GPa, whereas the hardness property lies between 300 MPa and 1.1 GPa. Notably, these properties are superior to those of other metal-organic frameworks (MOFs), such as MOF-5. In substituted imidazolate frameworks, our results show that their mechanical properties are mainly governed by the rigidity and bulkiness of the substituted organic linkages. The framework topology and the intricate pore morphology can also influence the degree of mechanical anisotropy. Our findings present the previously undescribed structure-mechanical property relationships pertaining to hybrid open frameworks that are important for the design and application of new MOF materials.

Cover Picture: Utilization of Self‐Sorting Processes To Generate Dynamic Combinatorial Libraries with New Network Topologies (Chem. Eur. J. 4/2006)

Dynamic combinatorial libraries can be regarded as adaptive chemical networks, in which the library members are connected by exchange reactions. In the Full Paper by K. Severin et al. on page 1058 ff., a library of metallamacrocyclic ruthenium and iridium complexes with a unique network topology is described.