Topological Framework Research Articles

Fourfold-Interpenetrated MOF [Ni(pybz)2] as Coating Material in Gas Chromatographic Capillary Column for Separation.

A fourfold interpenetrated diamond-like topological metal-organic framework (MOF), Ni(pybz)2 [pybz = 4-(4-pyridyl)benzoate] was successfully synthesized and fully characterized. This MOF can serve as coating material in gas chromatographic capillary column for the separation of some low boiling point essential oils. The prepared columns have good recognition ability and excellent selectivity toward a series of organic compounds, including alcohols, aldehydes, ketones, carboxylic acid, ethers, ester, and amines. It is found that the strained metal sites, van der Waals interactions, C-H···π attraction, and weak nonclassical hydrogen bond contribute to the recognition and selectivity of prepared columns. The grand canonical Monte Carlo technique is used to simulate the interactions of the adsorbates with MOF. The calculated van der Waals energies agree with the results of gas chromatographic separation.

Links Between Network Topology and Socioeconomic Framework of Railway Transport: Evidence From Greece

Links Between Network Topology and Socioeconomic Framework of Railway Transport: Evidence From Greece

Numerical Short-Term Solar Activity Forecasting

AbstractIt is well known that the energy for solar eruptions comes from magnetic fields in solar active regions. Magnetic energy storage and dissipation are regarded as important physical processes in the solar corona. With incomplete theoretical modeling for eruptions in the solar atmosphere, activity forecasting is mainly supported with statistical models. Solar observations with high temporal and spatial resolution continuously from space well describe the evolution of activities in the solar atmosphere, and combined with three dimensional reconstruction of solar magnetic fields, makes numerical short-term (within hours to days) solar activity forecasting possible. In the current report, we propose the erupting frequency and main attack direction of solar eruptions as new forecasts and present the prospects for numerical short-term solar activity forecasting based on the magnetic topological framework in solar active regions.

Two new inorganic anions directed Zn(II)-tetrazole frameworks: Syntheses, structures and photoluminescent properties

Two new coordination polymers directed by different inorganic anions, namely [Zn2(mtz)(SO4)(OH)(H2O)]n (1) and [Zn6(mtz)9(NO3)2]n (2) (Hmtz = 5-methyl-1H-tetrazole) were synthesized under solvothermal conditions and characterized by single crystal X-ray diffraction analyses. Compound 1 features a three-dimensional (3D) framework based on one dimensional [Zn(OH)(mtz)]n chains, whereas compound 2 features a 3D (3, 4)-connected tpd topological framework based on one-dimensional 1D [Zn(mtz)]n nano-tubes. The different coordination modes of mtz− ligand may be induced by different inorganic anions. Moreover, the thermal stabilities and luminescent properties of compounds 1 and 2 were also investigated in detail.

Detection of Electromagnetic Inclusions Using Topological Sensitvity

In this article a topological sensitivity framework for far field detection of a diametrically small electromagnetic inclusion is established. The cases of single and multiple measurements of the electric far field scattering amplitude at a fixed frequency are taken into account. The performance of the algorithm is analyzed theoretically in terms of its resolution and sensitivity for locating an inclusion. The stability of the framework with respect to measurement and medium noises is discussed. Moreover, the quantitative results for signal-to-noise ratio are presented. A few numerical results are presented to illustrate the detection capabilities of the proposed framework with single and multiple measurements.

Syntheses, structures, photocatalysis properties and photoluminescent properties of four two-dimensional functional coordination polymers based on a semi-rigid tetracarboxylic acid

Four two-dimensional functional coordination polymers, namely [Co(H2L)(bibp)(H2O)]n (1), {[Ni(H2L)(bibp)(H2O)]·0.5H2O}n (2), [Co2(L)(bimb)]n (3) and [Zn2(L)(bimb)]n (4) (H4L=5,5′-(1,3-phenylenebis(methoxy))diisophthalic acid, bibp=4,4′-bis(imidazolyl)biphenyl, bimb=1,4-bis(imidazol)-butane) have been successfully hydrothermally synthesized. All of these four polymers were characterized by single-crystal X-ray diffraction, elemental analysis, IR spectra, powder X-ray diffraction (PXRD), and thermogravimetric (TG) analysis. All of the four CPs are shown the rare 2D+2D→2D network. Complexes 1 and 2 have the similar structures with the same new topological framework with the point symbol [44. 62] [4]2; complexes 3 and 4 are isomorphous and display [M2(COO)2(bimb)] (M=Co for 3, Zn for 4) binuclear SBUs based on sq1 framework with the point symbol [44. 62]. Moreover, the photocatalytic degradation of four Co(II) complexes 1–4 have been investigated.

European boundaries in question?

This introduction provides a descriptive typology and normative analysis of the ways boundaries are being questioned in Europe. We distinguish between boundary-making (defining or redefining the territorial borders of a polity), boundary-crossing (determining the rules of access to territorial borders) and boundary-unbundling (allowing boundary-making and boundary-crossing to vary between policies and polities), noting each of these categories possesses internal and external dimensions. Cosmopolitans and statists offer contrasting normative evaluations of these processes, favouring weakening and maintaining or strengthening state boundaries respectively. We endorse a demoicratic approach lying between these two as better reflecting how individuals relate to each other and to the EU, a view shared by some but not all contributors to this volume. We conclude by situating the contributions within our topological framework, highlighting how they illustrate the contemporary questioning of European boundaries.

Making sense of a messy object : how to use social topology as an analytic tool for ethnography of objects

This theoretical-methodological essay seeks to answer the question, “How can one make sense of a messy object?” The denomination “messy” refers to a situation in which the object of ethnographic research is interpretatively complex to such a degree that the ethnographer may become trapped in the attempt to capture all of the various facets of the object at once (Law & Singleton, 2005). We focus on blood as a messy object and study it in the context of a Belgian Blood Establishment, the organization charged with the provision of safe and sufficient amounts of blood for a region. Existing research has dealt with the messiness of blood through epistemological response, casting it in four “blood stories” – the gift relationship, the blood economy, biological citizenship, and blood safety. While these stories have enhanced our understanding of blood, we argue that they are examples of perspectivalism (Mol, 2002). Although they do frame blood from various angles, they fail to grasp the entanglement of technological, biomedical, political, and socio-technical aspects of this “bio-object” (Vermeulen et al., 2012). This essay takes a different turn and attempts to mediate the difficulties by formulating an ontological response through careful consideration of the social topology framework (Law & Mol, 2001; Mol & Law, 1994). For every space (Euclidian, network, fluid, and fire), we provide a comprehensive summary of the theory, after which we delineate specific elements from this theory to induce conceptual sensitivity and propose research questions that follow from these elements. In this endeavor, we attempt to highlight the unique value of this framework for the ethnography of objects, as compared to the frameworks that initially gave rise to the theory.

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment.

CTCF is an architectural protein with a critical role in connecting higher-order chromatin folding in pluripotent stem cells. Recent reports have suggested that CTCF binding is more dynamic during development than previously appreciated. Here, we set out to understand the extent to which shifts in genome-wide CTCF occupancy contribute to the 3D reconfiguration of fine-scale chromatin folding during early neural lineage commitment. Unexpectedly, we observe a sharp decrease in CTCF occupancy during the transition from naïve/primed pluripotency to multipotent primary neural progenitor cells (NPCs). Many pluripotency gene-enhancer interactions are anchored by CTCF, and its occupancy is lost in parallel with loop decommissioning during differentiation. Conversely, CTCF binding sites in NPCs are largely preexisting in pluripotent stem cells. Only a small number of CTCF sites arise de novo in NPCs. We identify another zinc finger protein, Yin Yang 1 (YY1), at the base of looping interactions between NPC-specific genes and enhancers. Putative NPC-specific enhancers exhibit strong YY1 signal when engaged in 3D contacts and negligible YY1 signal when not in loops. Moreover, siRNA knockdown of Yy1 specifically disrupts interactions between key NPC enhancers and their target genes. YY1-mediated interactions between NPC regulatory elements are often nested within constitutive loops anchored by CTCF. Together, our results support a model in which YY1 acts as an architectural protein to connect developmentally regulated looping interactions; the location of YY1-mediated interactions may be demarcated in development by a preexisting topological framework created by constitutive CTCF-mediated interactions.

Novel metal-organic and supramolecular 3D frameworks constructed from flexible biphenyl-2,5,3′-tricarboxylate blocks: Synthesis, structural features and properties

Biphenyl-2,5,3′-tricarboxylic acid (H3L) was selected as an unexplored tricarboxylate building block and applied for the hydrothermal synthesis of three novel coordination compounds, namely a 0D tetramer [Co4(HL)2(μ3-HL)2(phen)6(H2O)2]·3H2O (1) and two 3D metal-organic frameworks (MOFs) [Cd3(μ5-L)(μ6-L)(py)(μ-H2O)2(H2O)]n·H2O (2) and [Zn3(μ4-L)2(2,2′-bpy)(μ-4,4′-bpy)]n·2H2O (3). These products were easily generated in aqueous medium from the corresponding metal(II) chlorides, H3L, and various N-donor ancillary ligands, selected from 1,10-phenanthroline (phen), pyridine (py), 2,2′-bipyridine (2,2′-bpy), and 4,4′-bipyridine (4,4′-bpy). Compounds 1–3 were isolated as stable crystalline solids and were fully characterized by IR and UV–vis spectroscopy, elemental, thermogravimetric (TGA), powder (PXRD) and single-crystal X-ray diffraction analyses. Compound 1 possesses a discrete tetracobalt(II) structure, which is extended into a 3D H-bonded network with the pcu topology. In contrast, MOF 2 discloses a very complex trinodal 4,5,12-connected net with an undocumented topology, while MOF 3 features the nce/I topological framework. The magnetic (for 1) and luminescence (for 2 and 3) properties were also studied and discussed. The present study thus widens a still very limited family of metal-organic and supramolecular frameworks driven by flexible biphenyl-2,5,3′-tricarboxylate building blocks.

A topological framework for signed permutations

In this paper, we present a topological framework for studying signed permutations and their reversal distance. This framework is based on a presentation of orientable and non-orientable fatgraphs via sectors. As an application, we give an alternative approach and interpretation of the Hannenhalli–Pevzner formula for the reversal distance of sorting signed permutations. This is obtained by constructing a bijection between signed permutations and certain equivalence classes of fatgraphs, called π-maps. We study the action of reversals and show that they either splice, glue or half-flip external vertices, which implies that any reversal changes the topological genus by at most one. We show that the lower bound of the reversal distance of a signed permutation equals the topological genus of its π-maps. We then discuss how the new topological model connects to other sorting problems.

Structural diversity of four coordination polymers based on 5-nitro-1,2,3-benzenetricarboxylic acid (H3nbta): Solvothermal syntheses, structural characterizations and properties

Four 3D coordination compounds, named [Cd3(nbta)2(bix)2(H2O)2]·H2O (1), Zn3(nbta)2(biim)3 (2), Zn6(nbta)4(btd)5 (3) and [Co3(nbta)2(bid)(H2O)8]·4H2O (4) (bix=1,4-bis(imidazole-1-ylmethyl)benzene, biim=1,1′-(1,4-butanediyl)bis(imidazole), btd=1,10-bis(1,2,4-triazol-1-yl)decane, bid=1,10-bis(imidazole-1-yl)decane), and H3nbta=5-nitro-1,2,3-benzenetricarboxylic acid), have been synthesized by solvothermal methods and structurally characterized by X-ray diffraction studies. In compound 1, every nbta3- anion connects four CdII ions to give a 2D layer, and the layers are pillared by bix ligands to generate a 3D framework with a Schläfli symbol of (3·4·63·7)(4·64·8)(43·63)(34·42·66·76·88·92). For compound 2, every nbta3- anion connects three ZnII ions to give a 2D layer structure, the 2D layers are further connected into a facinating 3D framework by biim ligands with (3,4)-connected (3·6·7)(3·5·62·7·8)(3·52·6·8·9)(5·6·8·10·112) topology. In compound 3, the nbta3- anions are connected by ZnII ions to generate a 2D layer, and the layers are bridged by btd ligands to build a fascinating 3D framework with (4·6·7·8·92)(4·6·8·92·10)(4·93·102)(4·6·8·9·102)(4·6·7·8·9·10)(4·6·7·8·102)(42·6·7·8·9) topology. In compound 4, the nbta3- aions are connected by CoII ions into a 2D layer, the 2D layers are linked by bid ligands to generate a 3D 103 topological framework. Furthermore, the IR spectra, TGA, PXRD, elemental analyses, the solid-state luminescence of compounds 1–3 have been studied.

Stable Zr(IV)-Based Metal–Organic Frameworks with Predesigned Functionalized Ligands for Highly Selective Detection of Fe(III) Ions in Water

Metal-organic frameworks are a class of attractive materials for fluorescent sensing. Improvement of hydrolytic stability, sensitivity, and selectivity of function is the key to advance application of fluorescent MOFs in aqueous media. In this work, two stable MOFs, [Zr6O4(OH)8(H2O)4(L1)2] (BUT-14) and [Zr6O4(OH)8(H2O)4(L2)2] (BUT-15), were designed and synthesized for the detection of metal ions in water. Two new ligands utilized for construction of the MOFs, namely, 5',5‴-bis(4-carboxyphenyl)-[1,1':3',1″:4″,1‴:3‴,1''''-quinquephenyl]-4,4''''-dicarboxylate (L1) and 4,4',4″,4‴-(4,4'-(1,4-phenylene)bis(pyridine-6,4,2-triyl))tetrabenzoate (L2), are structurally similar with the only difference being that the latter is functionalized by pyridine N atoms. The two MOFs are isostructural with a sqc-a topological framework structure, and highly porous with the Brunauer-Emmett-Teller (BET) surface areas of 3595 and 3590 m2 g-1, respectively. Interestingly, they show intense fluorescence in water, which can be solely quenched by trace amounts of Fe3+ ions. The detection limits toward the Fe3+ ions were calculated to be 212 and 16 ppb, respectively. The efficient fluorescent quenching effect is attributed to the photoinduced electron transfer between Fe3+ ions and the ligands in these MOFs. Moreover, the introduced pyridine N donors in the ligand of BUT-15 additionally donate their lone-pair electrons to the Fe3+ ions, leading to significantly enhanced detection ability. It is also demonstrated that BUT-15 exhibits an uncompromised performance for the detection of Fe3+ ions in a simulated biological system.

Robust detection and segmentation of cell nuclei in biomedical images based on a computational topology framework.

The segmentation of cell nuclei is an important step towards the automated analysis of histological images. The presence of a large number of nuclei in whole-slide images necessitates methods that are computationally tractable in addition to being effective. In this work, a method is developed for the robust segmentation of cell nuclei in histological images based on the principles of persistent homology. More specifically, an abstract simplicial homology approach for image segmentation is established. Essentially, the approach deals with the persistence of disconnected sets in the image, thus identifying salient regions that express patterns of persistence. By introducing an image representation based on topological features, the task of segmentation is less dependent on variations of color or texture. This results in a novel approach that generalizes well and provides stable performance. The method conceptualizes regions of interest (cell nuclei) pertinent to their topological features in a successful manner. The time cost of the proposed approach is lower-bounded by an almost linear behavior and upper-bounded by O(n2) in a worst-case scenario. Time complexity matches a quasilinear behavior which is O(n1+ɛ) for ε < 1. Images acquired from histological sections of liver tissue are used as a case study to demonstrate the effectiveness of the approach. The histological landscape consists of hepatocytes and non-parenchymal cells. The accuracy of the proposed methodology is verified against an automated workflow created by the output of a conventional filter bank (validated by experts) and the supervised training of a random forest classifier. The results are obtained on a per-object basis. The proposed workflow successfully detected both hepatocyte and non-parenchymal cell nuclei with an accuracy of 84.6%, and hepatocyte cell nuclei only with an accuracy of 86.2%. A public histological dataset with supplied ground-truth data is also used for evaluating the performance of the proposed approach (accuracy: 94.5%). Further validations are carried out with a publicly available dataset and ground-truth data from the Gland Segmentation in Colon Histology Images Challenge (GlaS) contest. The proposed method is useful for obtaining unsupervised robust initial segmentations that can be further integrated in image/data processing and management pipelines. The development of a fully automated system supporting a human expert provides tangible benefits in the context of clinical decision-making.

PEG-Induced Synthesis of Coordination-Polymer Isomers with Tunable Architectures and Iodine Capture.

Controllable synthesis of coordination polymer (CP) isomers and revealing their structure-property relationships remain enormous challenges. Three new supramolecular isomers have been synthesized by tuning the poly(ethylene glycol) (PEG) content in the feed. These supramolecular isomers have the same framework formula of [Cu2 I2 (tppe)] and different architectures from the classical 2D stacking framework to a 3D entangled system with the coexistence of interpenetration and polycatenation, and a 3D topological framework. Interestingly, these CPs could be utilized for capturing iodine molecules. According to multiple complementary experiments and crystallographic analyses, iodine capture is mainly based on halogen-bond interactions in the inorganic {Cu2 I2 } building blocks of the framework. The present study describes a structure-property relationship in supramolecular isomerism with distinct topological structures.

Syntheses, structures and selective dye adsorption of five formic-based coordination polymers prepared by in-situ hydrolysis of N, N′-dimethylformamide

Five functional coordination polymers (formic-based CPs) namely: {[Cu2(CHOO)3(bibp)2]·CHOO}n (1), {[Co2(CHOO)3(bibp)2]·NO3·H2O}n (2), {[Ni2(CHOO)3(bibp)2]·NO3·H2O}n (3) [Co(CHOO)2(bbibp)]n (4) and [Zn(CHOO)2(bbibp)]n (5) (bibp=4,4′-bis(imidazolyl)biphenyl, bbibp=4,4′-bis(benzoimidazo-1-yl)biphenyl) have been successfully hydrothermally synthesized using the in-situ hydrolysis of N, N′-dimethylformamide (DMF) as the source of formate. All of these five polymers were characterized by single-crystal X-ray diffraction, elemental analysis, IR spectra, powder X-ray diffraction (PXRD), and thermogravimetric (TG) analysis. Complexes 1–3 have the similar three-dimensional 3D kag topological framework built from the bibp ligand as the support member between the neighboring formic planes. Both complexes 4 and 5 have the similar one-dimensional 1D linear chain which is further assembled into 3D supermolecular structure by C–H…O hydrogen bonds. The dyes adsorption experiments have also been investigated systematically. The results show that complexes 2 and 3 exhibit high selective adsorption ability towards anionic dyes in their aqueous solution. Moreover, complex 2 displays good reversibility in the process of the dyes adsorption-release. Meanwhile, the unusual blocking phenomenon was firstly observed when complex 2 was in MO/OIV aqueous solutions with different concentration.

Auxilary Ligand Directed Zinc(II) Metal‐Organic Frameworks with Different Topological Networks

By altering auxiliary N‐donor ligands, two ZnII compounds, [Zn3(HL)2(4,4′‐bipy)3]n (1) and [Zn4(L)2(bpp)]n (2) (H4L = 3‐(2′,4′‐dicarboxylphenoxy)phthalic acid, 4,4′‐bipy = 4,4′‐bipyridine, and bpp = 1,3‐bis(4‐pyridyl)propane), were obtained under hydrothermal conditions. Structural analyses revealed that compound 1 features a trinodal (3,4,4)‐connected 3D topological framework, and compound 2 displays a (3,8)‐connected 3D pillar‐layered framework with a tfz‐d topology. Furthermore, the thermal stabilities and the luminescent properties of compounds 1 and 2 were investigated.

Dynamic wireless network shaping via moving cells: The nomadic nodes case

AbstractWithin the Fifth Generation framework of dynamic network topology and moving cells, the nomadic node (NN) concept is seen as a promising paradigm to provide coverage extension and capacity improvement on demand as well as to attain reduced capital expenditure and operational expenditure when compared with fixed‐node deployment, such as microcells. This paper proposes an enabling architecture for the NN operation in the framework of a wireless network, and then analyzes the physical layer aspects of the problem and investigates the performance of NN operation in the context of a realistic multi‐cellular wireless network, with the help of site‐specific propagation modeling and real geographical databases.The produced results provide useful insights into the performance of the NN operation; the results show that the NN operation is beneficial both in line‐of‐sight and non‐line‐of‐sight scenarios and demonstrate that the NN selection strategy, which is based on the backhaul signal‐to‐interference‐plus‐noise ratio with a 10 dB power window, offers almost identical performance with the optimum end‐to‐end throughput algorithm.

Tuning the iron redox state inside a microporous porphyrinic metal organic framework.

Two new 3D porphyrin-based metal organic frameworks were obtained by solvothermally reacting iron(iii) chloride, a free base (5,10,15,20-tetrakis[4-(2,3,4,5-tetrazolyl)phenyl]porphyrin) (H2TTPP) and either pyrazine or 1,4-diazabicyclo[2.2.2]octane (DABCO). Both MOFs displayed a 3-D open framework of the fry topology, where the inorganic building unit is a chain of corner-sharing FeN4O2 octahedra and the porphyrinic linker is metallated with iron during the reaction course, with the N-donor base bridging the iron of the porphyrinic cores. Through thorough structural and spectroscopic analyses of the pyrazine containing material the chemical formula [FeIIpzTTP(FeDMF1-xFeOHx)]n was inferred (x ≥ 0.25). Whereas the already reported carboxylate analogue is built up from a pure iron(iii) inorganic chain, here spectroscopic and structural studies evidenced a mixed valence iron(ii/iii) state, evidencing that, in agreement with the HSAB theory, the substitution of a carboxylate function by a tetrazolate one allows redox tuning. Finally, both materials feature one-dimensional channels of ca. 8 × 12 Å within the structures with permanent microporosity.

A Bayesian Topological Framework for the Identification and Reconstruction of Subcellular Motion

Microscopy imaging allows detailed observations of intracellular movements and the acquisition of large datasets that can be fully analyzed only by automated algorithms. Here, we develop a computational method for the automatic identification and reconstruction of trajectories followed by subcellular particles captured in microscopy image data. The method operates on stacks of raw image data and computes the complete set of contained trajectories. The method utilizes topological data analysis and standard image processing techniques and makes no assumptions about the underlying dynamics besides continuity. We test the developed method successfully against artificial and experimental datasets. Application of the method on the experimental data reveals good agreement with manual tracking and benchmarking yields performance scores competitive to the existing state-of-the-art tracking methods.