Subexponential Algorithm for d-Cluster Edge Deletion: Exception or Rule?

The correlation clustering problem is a fundamental problem in both theory and practice, and it involves identifying clusters of objects in a data set based on their similarity. A traditional modeling of this question as a graph theoretic problem involves associating vertices with data points and indicating similarity by adjacency. Clusters then correspond to cliques in the graph. The resulting optimization problem, Cluster Editing (and several variants) are very well-studied algorithmically. In many situations, however, translating clusters to cliques can be somewhat restrictive. A more flexible notion would be that of a structure where the vertices are mutually ``not too far apart'', without necessarily being adjacent. One such generalization is realized by structures called s-clubs, which are graphs of diameter at most s. In this work, we study the question of finding a set of at most k edges whose removal leaves us with a graph whose components are s-clubs. Recently, it has been shown that unless Exponential Time Hypothesis fail (ETH) fails Cluster Editing (whose components are 1-clubs) does not admit sub-exponential time algorithm STACS, 2013]. That is, there is no algorithm solving the problem in time 2 degrees((k))n(O(1)). However, surprisingly they show that when the number of cliques in the output graph is restricted to d, then the problem can be solved in time O(2(O(root dk)) + m + n). We show that this sub-exponential time algorithm for the fixed number of cliques is rather an exception than a rule. Our first result shows that assuming the ETH, there is no algorithm solving the s-Club Cluster Edge Deletion problem in time 2 degrees((k))n(O(1)). We show, further, that even the problem of deleting edges to obtain a graph with d s-clubs cannot be solved in time 2 degrees((k))n(O)(1) for any fixed s, d >= 2. This is a radical contrast from the situation established for cliques, where sub-exponential algorithms are known.

Tetrathiomolybdate-Mediated Ring Opening of Isatoic Anhydrides: An Entry to S-Alkyl or S-Aryl 2-Aminobenzenecarbothioate Derivatives

Decarboxylative thioesterification of isatoic anhydrides mediated by benzyl(triethyl)ammonium tetrathiomolybdate gave the corresponding S-alkyl or S-aryl 2-aminobenzenecarbothioate derivatives at 60 degrees C. At ambient temperature, organic disulfides were reductive cleaved in the presence of tetrathiomolybdate to generate thiolate anions in situ; this was followed by attack on isatoic anhydrides to give the corresponding S-alkyl or S-aryl 2-aminobenzenecarbothioate derivatives. Additionally, it was shown that multistep reactions could be performed with tetrathiomolybdate, starting with an alkyl halide as a precursor of an alkyl disulfide, which, in turn, was used for ring opening of isatoic anhydrides.

Driving force of water entry into hydrophobic channels of carbon nanotubes: entropy or energy?

Spontaneous entry of water molecules inside single-wall carbon nanotubes (SWCNTs) has been confirmed by both simulations and experiments. Using molecular dynamics simulations, we have studied the thermodynamics of filling of a (6,6) carbon nanotube in a temperature range from 273 to 353K and with different strengths of the nanotube-water interaction. From explicit energy and entropy calculations using the two-phase thermodynamics method, we have presented a thermodynamic understanding of the filling behaviour of a nanotube. We show that both the energy and the entropy of transfer decrease with increasing temperature. On the other hand, scaling down the attractive part of the carbon-oxygen interaction results in increased energy of transfer while the entropy of transfer increases slowly with decreasing the interaction strength. Our results indicate that both energy and entropy favour water entry into (6,6) SWCNTs. Our results are compared with those of several recent studies of water entry into carbon nanotubes.

A stabilization approach for mesh-free simulations of systems developing shocks or extreme strain localizations

A new stabilization scheme, based on a stochastic representation of the discretized field variables, is proposed with a view to reduce or even eliminate unphysical oscillations in the mesh-free numerical simulations of systems developing shocks or exhibiting localized bands of extreme deformation in the response. The origin of the stabilization scheme may be traced to nonlinear stochastic filtering and, consistent with a class of such filters, gain-based additive correction terms are applied to the simulated solution of the system, herein achieved through the element-free Galerkin method, in order to impose a set of constraints that help arresting the spurious oscillations. The method is numerically illustrated through its Applications to inviscid Burgers' equations, wherein shocks may develop as a result of intersections of the characteristics, and to a gradient plasticity model whose response is often characterized by a developing shear band as the external load is gradually increased. The potential of the method in stabilized yet accurate numerical simulations of such systems involving extreme gradient variations in the response is thus brought forth. (C) 2014 Elsevier Ltd. All rights reserved.

Negative hyperconjugation and red-, blue- or zero-shift in X-Z center dot center dot center dot Y complexes

A generalized explanation is provided for the existence of the red-and blue-shifting nature of X-Z bonds (Z = H, halogens, chalcogens, pnicogens, etc.) in X-Z center dot center dot center dot Y complexes based on computational studies on a selected set of weakly bonded complexes and analysis of existing literature data. The additional electrons and orbitals available on Z in comparison to H make for dramatic differences between the H-bond and the rest of the Z-bonds. The nature of the X-group and its influence on the X-Z bond length in the parent X-Z molecule largely controls the change in the X-Z bond length on X-Z center dot center dot center dot Y bond formation; the Y-group usually influences only the magnitude of the effects controlled by X. The major factors which control the X-Z bond length change are: (a) negative hyperconjugative donation of electron density from X-group to X-Z sigma* antibonding molecular orbital (ABMO) in the parent X-Z, (b) induced negative hyperconjugation from the lone pair of electrons on Z to the antibonding orbitals of the X-group, and (c) charge transfer (CT) from the Y-group to the X-Z sigma* orbital. The exchange repulsion from the Y-group that shifts partial electron density at the X-Z sigma* ABMO back to X leads to blue-shifting and the CT from the Y-group to the sigma* ABMO of X-Z leads to red-shifting. The balance between these two opposing forces decides red-, zero- or blue-shifting. A continuum of behaviour of X-Z bond length variation is inevitable in X-Z center dot center dot center dot Y complexes.

Peculiar morphological transitions induced by nanoparticles in polymeric blends: retarded relaxation or altered interfacial tension?

Nanoparticles of different shapes can induce peculiar morphologies in binary polymer blends depending on their position. It is envisaged that the increased yield stress of the filled phase slows down the relaxation resulting in arresting the peculiar morphologies which otherwise is thermodynamically unfavourable due to the increased interfacial area. This essentially means that the highly irregular structures can be preserved even without altering the interfacial tension between the phases! On the other hand, in the case of interfacially adsorbed particles, the resulting solid-like interface can also preserve the irregular structures. These phenomenal transitions in filled blends are very different from the classical copolymer compatibilized polymer blends. Moreover, these irregular structures can further pave way in designing conducting polymer blends involving conducting nanoparticles and revisiting our understanding of the concept of double percolation!

Bioengineering of AAV2 Capsid at Specific Serine, Threonine, or Lysine Residues Improves Its Transduction Efficiency in Vitro and in Vivo

We hypothesized that the AAV2 vector is targeted for destruction in the cytoplasm by the host cellular kinase/ubiquitination/proteasomal machinery and that modification of their targets on AAV2 capsid may improve its transduction efficiency. In vitro analysis with pharmacological inhibitors of cellular serine/threonine kinases (protein kinase A, protein kinase C, casein kinase II) showed an increase (20-90%) on AAV2-mediated gene expression. The three-dimensional structure of AAV2 capsid was then analyzed to predict the sites of ubiquitination and phosphorylation. Three phosphodegrons, which are the phosphorylation sites recognized as degradation signals by ubiquitin ligases, were identified. Mutation targets comprising eight serine (S) or seven threonine (T) or nine lysine (K) residues were selected in and around phosphodegrons on the basis of their solvent accessibility, overlap with the receptor binding regions, overlap with interaction interfaces of capsid proteins, and their evolutionary conservation across AAV serotypes. AAV2-EGFP vectors with the wild-type (WT) capsid or mutant capsids (15 S/T -> alanine A] or 9 K -> arginine R] single mutant or 2 double K -> R mutants) were then evaluated in vitro. The transduction efficiencies of 11 S/T -> A and 7 K -> R vectors were significantly higher (similar to 63-90%) than the AAV2-WT vectors (similar to 30-40%). Further, hepatic gene transfer of these mutant vectors in vivo resulted in higher vector copy numbers (up to 4.9-fold) and transgene expression (up to 14-fold) than observed from the AAV2-WT vector. One of the mutant vectors, S489A, generated similar to 8-fold fewer antibodies that could be cross-neutralized by AAV2-WT. This study thus demonstrates the feasibility of the use of these novel AAV2 capsid mutant vectors in hepatic gene therapy.

Mycobacterium tuberculosis RecG Protein but Not RuvAB or RecA Protein Is Efficient at Remodeling the Stalled Replication Forks IMPLICATIONS FOR MULTIPLE MECHANISMS OF REPLICATION RESTART IN MYCOBACTERIA

Aberrant DNA replication, defects in the protection, and restart of stalled replication forks are major causes of genome instability in all organisms. Replication fork reversal is emerging as an evolutionarily conserved physiological response for restart of stalled forks. Escherichia coli RecG, RuvAB, and RecA proteins have been shown to reverse the model replication fork structures in vitro. However, the pathways and the mechanisms by which Mycobacterium tuberculosis, a slow growing human pathogen, responds to different types of replication stress and DNA damage are unclear. Here, we show that M. tuberculosis RecG rescues E. coli Delta recG cells from replicative stress. The purified M. tuberculosis RecG (MtRecG) and RuvAB(MtRuvAB) proteins catalyze fork reversal of model replication fork structures with and without a leading strand single-stranded DNA gap. Interestingly, single-stranded DNA-binding protein suppresses the MtRecG- and MtRuvAB-mediated fork reversal with substrates that contain lagging strand gap. Notably, our comparative studies with fork structures containing template damage and template switching mechanism of lesion bypass reveal that MtRecG but not MtRuvAB or MtRecA is proficient in driving the fork reversal. Finally, unlike MtRuvAB, we find that MtRecG drives efficient reversal of forks when fork structures are tightly bound by protein. These results provide direct evidence and valuable insights into the underlying mechanism of MtRecG-catalyzed replication fork remodeling and restart pathways in vivo.

Synthesis of Hollow Nanotubes of Zn2SiO4 or SiO2: Mechanistic Understanding and Uranium Adsorption Behavior

We report a facile synthesis of Zn2SiO4 nanotubes using a two-step process consisting of a wet-chemical synthesis of core-shell ZnO@SiO2 nanorods followed by thermal annealing. While annealing in air leads to the formation of hollow Zn2SiO4, annealing under reducing atmosphere leads to the formation of SiO2 nanotubes. We rationalize the formation of the silicate phase at temperatures much lower than the temperatures reported in the literature based on the porous nature of the silica shell on the ZnO nanorods. We present results from in situ transmission electron microscopy experiments to clearly show void nucleation at the interface between ZnO and the silica shell and the growth of the silicate phase by the Kirkendall effect. The porous nature of the silica shell is also responsible for the etching of the ZnO leading to the formation of silica nanotubes under reducing conditions. Both the hollow silica and silicate nanotubes exhibit good uranium sorption at different ranges of pH making them possible candidates for nuclear waste management.

Pd-Catalyzed Hydroborylation of Alkynes: A Ligand Controlled Regioselectivity Switch for the Synthesis of alpha- or beta-Vinylboronates

A ligand controlled selective hydroborylation of alkynes to alpha- or beta-vinylboronates has been developed using a Pd catalyst. The high alpha-selectivity displayed by this reaction can be switched to furnish beta-vinylboronates by altering the ligand from a trialkylphosphine to N-heterocyclic carbene. A variety of terminal alkynes are shown to furnish the corresponding alpha- or beta-vinylboronates in good to excellent selectivity and yield. The mechanistic studies suggest that the solvent is the proton source and bromobenzene functions as an important additive in driving this reaction forward.

In-plane modulated smectic (A)over-tilde vs smectic `A' lamellar structures in poly(ethyl or propyl ether imine) dendrimers

A pair of first and second generation poly(alkyl ether imine) dendrimers is prepared, having covalently attached cholesteryl moieties at their peripheries. The pairs in each generation differ in the alkyl-linker which constitute the dendritic core moieties, even when the number of cholesteryl moieties remains uniform in each pair. The dendrimer pairs are two first and second generation poly(ethyl ether imine) and poly(propyl ether imine) dendrimers, modified with 4 and 8 cholesteryl esters at the peripheries in each pair, respectively. The dendrimer pairs exhibit differing thermotropic mesophase properties. Microscopic, thermal and X-ray diffraction studies reveal a lamellar mesophase for the first generation ethyl-, first and second generation propyl-linker dendrimers. Whereas, the second generation ethyl-linker dendrimer exhibits a layered structure with a superimposed in-plane modulation, the length of which corresponds to a rectangular column width. The role of the dendrimer core moieties with differing linkers in modifying the mesophase properties is studied. (C) 2016 Elsevier Ltd. All rights reserved.

Pd-Catalyzed Hydroborylation of Alkynes: A Ligand Controlled Regioselectivity Switch for the Synthesis of alpha- or beta-Vinylboronates

A ligand controlled selective hydroborylation of alkynes to alpha- or beta-vinylboronates has been developed using a Pd catalyst. The high alpha-selectivity displayed by this reaction can be switched to furnish beta-vinylboronates by altering the ligand from a trialkylphosphine to N-heterocyclic carbene. A variety of terminal alkynes are shown to furnish the corresponding alpha- or beta-vinylboronates in good to excellent selectivity and yield. The mechanistic studies suggest that the solvent is the proton source and bromobenzene functions as an important additive in driving this reaction forward.

Pressure-induced phase transition in Bi2Se3 at 3 GPa: electronic topological transition or not?

In recent years, a low pressure transition around P similar to 3 GPa exhibited by the A(2)B(3)-type 3D topological insulators is attributed to an electronic topological transition (ETT) for which there is no direct evidence either from theory or experiments. We address this phase transition and other transitions at higher pressure in bismuth selenide (Bi2Se3) using Raman spectroscopy at pressure up to 26.2 GPa. We see clear Raman signatures of an isostructural phase transition at P similar to 2.4 GPa followed by structural transitions at similar to 10 GPa and 16 GPa. First-principles calculations reveal anomalously sharp changes in the structural parameters like the internal angle of the rhombohedral unit cell with a minimum in the c/a ratio near P similar to 3 GPa. While our calculations reveal the associated anomalies in vibrational frequencies and electronic bandgap, the calculated Z(2) invariant and Dirac conical surface electronic structure remain unchanged, showing that there is no change in the electronic topology at the lowest pressure transition.

On the issues of resolving a low melting combination as a definite eutectic or an elusive cocrystal: A critical evaluation

Cocrystals and eutectics are different yet related crystalline multi-component adducts with diverse applications in pharmaceutical and materials fields. Recently, they were shown to be alternate products of cocrystallization experiments. Whereas a cocrystal shows distinct diffraction, spectroscopic and thermal signatures as compared to parent components, the hallmark of a eutectic is its low melting nature. However, in certain cases, there can be a problem when one resorts to design a cocrystal and assess its formation vis-A -vis a eutectic. In the absence of a gold standard method to make a cocrystal, it is often difficult to judge how exhaustive should the cocrystallization trials be to ensure the accomplishment of a desired/putative cocrystal. Further, a cocrystal can manifest with intermolecular interactions and/or crystal structure similar to that of its parent compounds such that the conventional diffraction and spectroscopic techniques will be of little help to conclusively infer the formation of cocrystal in the lack of single crystals. Such situations combined with low melting behavior of a combination brings the complication of resolving the combination as a cocrystal or eutectic since now both the adducts share common features. Based on the curious case of Caffeine-Benzoic acid combination, this study aims to unfold the intricate issues related to the design, formation and characterization of cocrystals and eutectics for a way forward. The utility of heteronuclear seeding methodology in establishing a given combination as a cocrystal-forming one or a eutectic-forming one in four known systems is appraised.