Report on the IUTAM Symposium on Mobile Particulate Systems: Kinematics, Rheology, and Complex Phenomena, Bangalore, India, 2012

This report summarizes the presentations and discussions conducted during the symposium, which was held under the aegis of the International Union of Theoretical and Applied Mechanics during 23-27 January 2012 in Bangalore, India. (C) 2013 AIP Publishing LLC.

Carboxyl terminal domain basic amino acids of mycobacterial topoisomerase I bind DNA to promote strand passage

Bacterial DNA topoisomerase I (topoI) carries out relaxation of negatively supercoiled DNA through a series of orchestrated steps, DNA binding, cleavage, strand passage and religation. The N-terminal domain (NTD) of the type IA topoisomerases harbor DNA cleavage and religation activities, but the carboxyl terminal domain (CTD) is highly diverse. Most of these enzymes contain a varied number of Zn2+ finger motifs in the CTD. The Zn2+ finger motifs were found to be essential in Escherichia coli topoI but dispensable in the Thermotoga maritima enzyme. Although, the CTD of mycobacterial topoI lacks Zn2+ fingers, it is indispensable for the DNA relaxation activity of the enzyme. The divergent CTD harbors three stretches of basic amino acids needed for the strand passage step of the reaction as demonstrated by a new assay. We also show that the basic amino acids constitute an independent DNA-binding site apart from the NTD and assist the simultaneous binding of two molecules of DNA to the enzyme, as required during the catalytic step. Although the NTD binds to DNA in a site-specific fashion to carry out DNA cleavage and religation, the basic residues in CTD bind to non-scissile DNA in a sequence-independent manner to promote the crucial strand passage step during DNA relaxation. The loss of Zn2+ fingers from the mycobacterial topoI could be associated with Zn2+ export and homeostasis.

Microwave, infrared-microwave double resonance, and theoretical studies of C2H4 center dot center dot center dot H2S complex

In this manuscript, rotational spectra of four new isotopologues of the S-H center dot center dot center dot pi bonded C2H4 center dot center dot center dot H2S complex, i.e., C2D4 center dot center dot center dot H2S, C2D4 center dot center dot center dot D2S, C2D4 center dot center dot center dot HDS, and (CCH4)-C-13 center dot center dot center dot H2S have been reported and analyzed. All isotopologues except C2D4 center dot center dot center dot HDS show a four line pattern whereas a doubling of the transition frequencies was observed for C2D4 center dot center dot center dot HDS. These results together with our previous report on the title complex M. Goswami, P. K. Mandal, D. J. Ramdass, and E. Arunan, Chem. Phys. Lett. 393(1-3), 22-27 (2004)] confirm that both subunits (C2H4 and H2S) are involved in large amplitude motions leading to a splitting of each rotational transition to a quartet. Further, the results also confirm that the motions which are responsible for the observed splittings involve both monomers. Molecular symmetry group analysis, considering the interchange of equivalent H atoms in H2S and C2H4 could explain the observed four line pattern and their intensities in the microwave spectrum. In addition, hydride stretching fundamentals of the complex were measured using coherence-converted population transfer Fourier Transform Microwave-infrared (IR-MW double resonance) experiments in the S-H and C-H stretch regions. Changes in the tunneling splittings upon vibrational excitation are consistent with the isotopic dependence of pure rotational transitions. A complexation shift of 2.7-6.5 cm(-1) has been observed in the two fundamental S-H stretching modes of the H2S monomer in the complex. Vibrational pre-dissociation in the bound S-H stretch has been detected whereas the instrument-limited line-shapes in other S-H and C-H stretches indicate slower pre-dissociation rate. Some local perturbations in the vibrational spectra have been observed. Two combination bands have been observed corresponding to both the S-H stretching fundamentals and what appears to be the intermolecular stretching mode at 55 cm(-1). The tunneling splitting involved in the rotation of C2H4 unit has been deduced to be 1.5 GHz from the IR-MW results. In addition, ab initio barrier heights derived for different motions of the monomers support the experimental results and provide further insight into the motions causing the splitting. (C) 2013 AIP Publishing LLC.

Domains in complex surfaces with a noncompact automorphism group - II

Let X be an arbitrary complex surface and D subset of X a domain that has a noncompact group of holomorphic automorphisms. A characterization of those domains D that admit a smooth real analytic, finite type, boundary orbit accumulation point and whose closures are contained in a complete hyperbolic domain D' subset of X is obtained.

Structural Insights into Saccharomyces cerevisiae Msh4-Msh5 Complex Function Using Homology Modeling

The Msh4-Msh5 protein complex in eukaryotes is involved in stabilizing Holliday junctions and its progenitors to facilitate crossing over during Meiosis I. These functions of the Msh4-Msh5 complex are essential for proper chromosomal segregation during the first meiotic division. The Msh4/5 proteins are homologous to the bacterial mismatch repair protein MutS and other MutS homologs (Msh2, Msh3, Msh6). Saccharomyces cerevisiae msh4/5 point mutants were identified recently that show two fold reduction in crossing over, compared to wild-type without affecting chromosome segregation. Three distinct classes of msh4/5 point mutations could be sorted based on their meiotic phenotypes. These include msh4/5 mutations that have a) crossover and viability defects similar to msh4/5 null mutants; b) intermediate defects in crossing over and viability and c) defects only in crossing over. The absence of a crystal structure for the Msh4-Msh5 complex has hindered an understanding of the structural aspects of Msh4-Msh5 function as well as molecular explanation for the meiotic defects observed in msh4/5 mutations. To address this problem, we generated a structural model of the S. cerevisiae Msh4-Msh5 complex using homology modeling. Further, structural analysis tailored with evolutionary information is used to predict sites with potentially critical roles in Msh4-Msh5 complex formation, DNA binding and to explain asymmetry within the Msh4-Msh5 complex. We also provide a structural rationale for the meiotic defects observed in the msh4/5 point mutations. The mutations are likely to affect stability of the Msh4/5 proteins and/or interactions with DNA. The Msh4-Msh5 model will facilitate the design and interpretation of new mutational data as well as structural studies of this important complex involved in meiotic chromosome segregation.

Does linear separability really matter? Complex visual search is explained by simple search

Visual search in real life involves complex displays with a target among multiple types of distracters, but in the laboratory, it is often tested using simple displays with identical distracters. Can complex search be understood in terms of simple searches? This link may not be straightforward if complex search has emergent properties. One such property is linear separability, whereby search is hard when a target cannot be separated from its distracters using a single linear boundary. However, evidence in favor of linear separability is based on testing stimulus configurations in an external parametric space that need not be related to their true perceptual representation. We therefore set out to assess whether linear separability influences complex search at all. Our null hypothesis was that complex search performance depends only on classical factors such as target-distracter similarity and distracter homogeneity, which we measured using simple searches. Across three experiments involving a variety of artificial and natural objects, differences between linearly separable and nonseparable searches were explained using target-distracter similarity and distracter heterogeneity. Further, simple searches accurately predicted complex search regardless of linear separability (r = 0.91). Our results show that complex search is explained by simple search, refuting the widely held belief that linear separability influences visual search.

Versatility of azide in serendipitous assembly of Copper(II) Magnetic Polyclusters

Engineering at the molecular level is one of the most exciting new developments for the generation of functional materials. However, the concept of designing polynuclear extended structures from bottom up is still not mature. Although progress has been made with secondary building units (SBUs) in metal organic frameworks (MOFs), the control seems to be just an illusion when it comes to bridging ligands such as the azide ion. When we say that the azido ligand is versatile in its bridging capabilities, what we mean is that it would be difficult to predict or control its bridging properties. However, this kind of serendipity is not always bad news. For example, scientists have shown that the azido ligand can mediate magnetic exchanges between paramagnetic metals in a predictable fashion (usually depending upon the bonding geometries). Therefore, it is a well-respected ligand in polynuclear assemblies. Serendipitous assemblies offer new magnetic structures that we may not otherwise even think about synthesizing. The azido ligand forms a variety of complexes with copper(II) using different blocking amines or pyridine based ligands. Its structural nature changes upon changing the substitution on amine, as well as the amount of blocking ligand. In principle, if we take any of these complexes and provide more coordination sites to the bridging azido ligands by removing a fraction of the blocking ligands, we can get new complexes with intricate structural networks and therefore different magnetic properties with the same components as used for the parent complex. In this Account, we mainly discuss the development of a number of new topological and magnetic exchange systems synthesized using this concept. Not all of these new complexes can be grouped according to their basic building structures or even by the ratio of the metal to blocking ligand. Therefore, we divided the discussion by the nuclearity of the basic building structures. Some of the complexes with the same nuclearities have very similar or even almost identical basic structures. However, the way these building units are joined together (by the azido bridges) to form the overall extended structures differ almost in every case. The complexes having the Cu-6 core are particularly interesting from a structural point of view. Although they have almost identical basic structures, some of them are extended in three dimensions, but two of them are extended in two dimensions by two different bridging networks. In the complexes having linear Cu-4 basic units, we find that using similar ligands does not always give the same bridging networks even within the basic building structures. These complexes have also enriched the field of molecular magnetism. One of the complexes with a Cu-3 building unit has provided us with the opportunity to study the competing behavior of two different kinds of magnetic exchange mechanism (ferromagnetic and antiferromagnetic) acting simultaneously between two metal ions. Through density functional theory calculations, we showed how they work independently and their additive nature to produce the overall effect. The exciting methodology for the generation of copper(II) polyclusters presented in this Account will provide the opportunity to explore analogous serendipitous assembly of diverse structures with interesting magnetic behavior using other transition metal ions having more than one unpaired electrons.

Constraining complex aquifer geometry with geophysics (2-D ERT and MRS measurements) for stochastic modelling of groundwater flow

Stochastic modelling is a useful way of simulating complex hard-rock aquifers as hydrological properties (permeability, porosity etc.) can be described using random variables with known statistics. However, very few studies have assessed the influence of topological uncertainty (i.e. the variability of thickness of conductive zones in the aquifer), probably because it is not easy to retrieve accurate statistics of the aquifer geometry, especially in hard rock context. In this paper, we assessed the potential of using geophysical surveys to describe the geometry of a hard rock-aquifer in a stochastic modelling framework. The study site was a small experimental watershed in South India, where the aquifer consisted of a clayey to loamy-sandy zone (regolith) underlain by a conductive fissured rock layer (protolith) and the unweathered gneiss (bedrock) at the bottom. The spatial variability of the thickness of the regolith and fissured layers was estimated by electrical resistivity tomography (ERT) profiles, which were performed along a few cross sections in the watershed. For stochastic analysis using Monte Carlo simulation, the generated random layer thickness was made conditional to the available data from the geophysics. In order to simulate steady state flow in the irregular domain with variable geometry, we used an isoparametric finite element method to discretize the flow equation over an unstructured grid with irregular hexahedral elements. The results indicated that the spatial variability of the layer thickness had a significant effect on reducing the simulated effective steady seepage flux and that using the conditional simulations reduced the uncertainty of the simulated seepage flux. As a conclusion, combining information on the aquifer geometry obtained from geophysical surveys with stochastic modelling is a promising methodology to improve the simulation of groundwater flow in complex hard-rock aquifers. (C) 2013 Elsevier B.V. All rights reserved.

New Structural Topologies in a Series of 3d Metal Complexes with Isomeric Phenylenediacetates and 1,3,5-Tris(1-imidazolyl)benzene Ligand: Syntheses, Structures, and Magnetic and Luminescence Properties

In this article we present the syntheses, characterizations, magnetic and luminescence properties of five 3d-metal complexes, Co(tib)(1,2-phda)](n)center dot(H2O)(n) (1), Co-3(tib)(2)(1,3-phda)(3)(H2O)](n)center dot(H2O)(2n) (2), Co-5(tib)(3)(1,4-phda)(5)(H2O)(3)](n)center dot(H2O)(7n) (3), Zn-3(tib)(2)(1,3-phda)(3)](n)center dot(H2O)(4n) (4), and Mn(tib)(2)(H2O)(2)](n)center dot(1,4-phdaH)(2n)center dot(H2O)(4n) (5), obtained from the use of isomeric phenylenediacetates (phda) and the neutral 1,3,5-tris(1-imidazolyl)benzene (tib) ligand. Single crystal X-ray structures showed that 1 constitutes 3,5-connected 2-nodal nets with a double-layered two-dimensional (2D) structure, while 2 forms an interpenetrated 2D network (3,4-connected 3-nodal net). Complex 3 has a complicated three-dimensional structure with 10-nodal 3,4,5-connected nets. Complex 4, although it resembles 2 in stoichiometry and basic building structures, forms a very different overall 2D assembly. In complex 5 the dicarboxylic acid, upon losing only one of the acidic protons, does not take part in coordination; instead it forms a complicated hydrogen bonding network with water molecules. Magnetic susceptibility measurements over a wide range of temperatures revealed that the metal ions exchange very poorly through the tib ligand, but for the Co(II) complexes the effects of nonquenched orbital contributions are prominent. The 3d(10) metal complex 4 showed strong luminescence with lambda(max) = 415 nm (lambda(ex) = 360 nm).

Mitochondria-Targeting Oxidovanadium(IV) Complex as a Near-IR Light Photocytotoxic Agent

Oxidovanadium(IV) complexes VO(L-1)(phen)]Cl (1) and VO(L-2)(L-3)]Cl (2), in which HL1 is 2-{(benzimidazol-2-yl)methylimino]-methyl}phenol (sal-ambmz), HL2 is 2-({1-(anthracen-9-yl)methyl]-benzimidazol-2-yl}methylimino)-met hyl]phenol (sal-an-ambmz), phen is 1,10-phenanthroline and L-3 is dipyrido3,2-a:2,3-c]phenazine (dppz) conjugated to a Gly-Gly-OMe dipeptide moiety, were prepared, characterized, and their DNA binding, photoinduced DNA-cleavage, and photocytotoxic properties were studied. Fluorescence microscopy studies were performed by using complex 2 in HeLa and HaCaT cells. Complex 1, structurally characterized by X-ray crystallography, has a vanadyl group in VO2N4 core with the VO2+ moiety bonded to N,N-donor phen and a N,N,O-donor Schiff base. Complex 2, having an anthracenyl fluorophore, showed fluorescence emission bands at 397, 419, and 443nm. The complexes are redox-active exhibiting the V(IV)/V(III) redox couple near -0.85V versus SCE in DMF 0.1M tetrabutylammonium perchlorate (TBAP). Complex 2, having a dipeptide moiety, showed specific binding towards poly(dAdT)(2) sequence. The dppz-Gly-Gly-OMe complex showed significant DNA photocleavage activity in red light of 705nm through a hydroxyl radical ((OH)-O-.) pathway. Complex 2 showed photocytotoxicity in HaCaT and HeLa cells in visible light (400-700nm) and red light (620-700nm), however, the complex was less toxic in the dark. Fluorescence microscopy revealed the localization of complex 2 primarily in mitochondria. Apoptosis was found to occur inside mitochondria (intrinsic pathway) caused by ROS generation.

AIPE-active green phosphorescent iridium(III) complex impregnated test strips for the vapor-phase detection of 2,4,6-trinitrotoluene (TNT)

Detection of explosives, especially trinitrotoluene (TNT), is of utmost importance due to its highly explosive nature and environmental hazard. Therefore, detection of TNT has been a matter of great concern to the scientific community worldwide. Herein, a new aggregation-induced phosphorescent emission (AIPE)-active iridium(III) bis(2-(2,4-difluorophenyl)pyridinato-NC2') (2-(2-pyridyl)benzimidazolato-N,N') complex FIrPyBiz] has been developed and serves as a molecular probe for the detection of TNT in the vapor phase, solid phase, and aqueous media. In addition, phosphorescent test strips have been constructed by impregnating Whatman filter paper with aggregates of FIrPyBiz for trace detection of TNT in contact mode, with detection limits in nanograms, by taking advantage of the excited state interaction of AIPE-active phosphorescent iridium(III) complex with that of TNT and the associated photophysical properties.

Delineating Ecological Boundaries of Hanuman Langur Species Complex in Peninsular India Using MaxEnt Modeling Approach

Hanuman langur is one of the widely distributed and extensively studied non-human diurnal primates in India. Until recently it was believed to be a single species - Semnopithecus entellus. Recent molecular and morphological studies suggest that the Hanuman langurs consists of at least three species S. entellus, S. hypoleucos and S. priam. Furthermore, morphological studies suggested that both S. hypoleucos and S. priam have at least three subspecies in each. We explored the use of ecological niche modeling (ENM) to confirm the validity of these seven taxa and an additional taxon S. johnii belonging to the same genus. MaxEnt modeling tool was used with 19 bioclimatic, 12 vegetation and 6 hydrological environmental layers. We reduced total environmental variables to 14 layers after testing for collinearity and an independent test for model prediction was done using ENMTools. A total of 196 non-overlapping data points from primary and secondary sources were used as inputs for ENM. Results showed eight distinct ecological boundaries, corroborating the eight taxa mentioned above thereby confirming validity of these eight taxa. The study, for the first time provided ecological variables that determined the ecological requirements and distribution of members of the Hanuman langur species complex in the Indian peninsula.

Adiabatic Eigenfunction Based Approach to Coherent Transfer: Application to the Fenna-Matthews-Olson (FMO) Complex and the Role of Correlations in the Efficiency of Energy Transfer

We have recently suggested a method (Pallavi Bhattacharyya and K. L. Sebastian, Physical Review E 2013, 87, 062712) for the analysis of coherence in finite-level systems that are coupled to the surroundings and used it to study the process of energy transfer in the Fenna-Matthews-Olson (FMO) complex. The method makes use of adiabatic eigenstates of the Hamiltonian, with a subsequent transformation of the Hamiltonian into a form where the terms responsible for decoherence and population relaxation could be separated out at the lowest order. Thus one can account for decoherence nonperturbatively, and a Markovian type of master equation could be used for evaluating the population relaxation. In this paper, we apply this method to a two-level system as well as to a seven-level system. Comparisons with exact numerical results show that the method works quite well and is in good agreement with numerical calculations. The technique can be applied with ease to systems with larger numbers of levels as well. We also investigate how the presence of correlations among the bath degrees of freedom of the different bacteriochlorophyll a molecules of the FMO Complex affect the rate of energy transfer. Surprisingly, in the cases that we studied, our calculations suggest that the presence of anticorrelations, in contrast to correlations, make the excitation transfer more facile.

Delineating Ecological Boundaries of Hanuman Langur Species Complex in Peninsular India Using MaxEnt Modeling Approach

Hanuman langur is one of the widely distributed and extensively studied non-human diurnal primates in India. Until recently it was believed to be a single species - Semnopithecus entellus. Recent molecular and morphological studies suggest that the Hanuman langurs consists of at least three species S. entellus, S. hypoleucos and S. priam. Furthermore, morphological studies suggested that both S. hypoleucos and S. priam have at least three subspecies in each. We explored the use of ecological niche modeling (ENM) to confirm the validity of these seven taxa and an additional taxon S. johnii belonging to the same genus. MaxEnt modeling tool was used with 19 bioclimatic, 12 vegetation and 6 hydrological environmental layers. We reduced total environmental variables to 14 layers after testing for collinearity and an independent test for model prediction was done using ENMTools. A total of 196 non-overlapping data points from primary and secondary sources were used as inputs for ENM. Results showed eight distinct ecological boundaries, corroborating the eight taxa mentioned above thereby confirming validity of these eight taxa. The study, for the first time provided ecological variables that determined the ecological requirements and distribution of members of the Hanuman langur species complex in the Indian peninsula.

Basic studies on the role of components of Bacillus megaterium as flotation biocollectors in sulphide mineral separation

Studies were carried out to assess the utility of the cellular and extracellular constituents of Bacillus megaterium for the flotation of sphalerite and galena minerals. Based on the flotation results on the individual minerals, it was observed that sphalerite was preferentially floated compared to galena. A maximum selectivity index (SI) value of 11.7 was achieved in the presence of the soluble fraction of the thermolysed cells, which was higher than that obtained with the intact cells (SI of 6.5) and the insoluble fraction of the thermolysed cells (SI of 9.6). The results of the various enzymatic treatment tests revealed that extracellular DNA played a vital role in the selective flotation of sphalerite. A noteworthy finding was that the single-stranded DNA (ssDNA) had a higher biocollector capacity vis-A -vis the double-stranded DNA (dsDNA), leading to better flotation efficiency. About 95 % recovery of sphalerite could be achieved from the mineral mixture by the combined addition of the ssDNA with the non-DNA components of the bacterial cells, resulting in a maximum SI of 19.1. Calcium and phosphate components of the nutrient media were found to be essential for better selectivity of separation of sphalerite. The mechanisms of microbe-mineral interaction are discussed.