Forming Networks of Strategic Agents with Desired Topologies

Many networks such as social networks and organizational networks in global companies consist of self-interested agents. The topology of these networks often plays a crucial role in important tasks such as information diffusion and information extraction. Consequently, growing a stable network having a certain topology is of interest. Motivated by this, we study the following important problem: given a certain desired network topology, under what conditions would best response (link addition/deletion) strategies played by self-interested agents lead to formation of a stable network having that topology. We study this interesting reverse engineering problem by proposing a natural model of recursive network formation and a utility model that captures many key features. Based on this model, we analyze relevant network topologies and derive a set of sufficient conditions under which these topologies emerge as pairwise stable networks, wherein no node wants to delete any of its links and no two nodes would want to create a link between them.

Graphene based E. coli sensor on flexible acetate sheet

A low cost, reagent free, Escherichia coli sensor is demonstrated with graphene, on transparent flexible acetate substrate. Graphene is grown on 100 mu m thick Cu foil, using CVD process and subsequently transferred on to a flexible acetate substrate. Gold electrodes are deposited on graphene to form a two terminal, interdigitated capacitor structure. Impedance spectroscopy (10 Hz to 100 kHz) is performed to characterize the change in impedance, as a function of E. coli concentration on graphene surface. The residual methyl groups on graphene, resulting from the transfer process, act as binding sites for E. coli. It has been observed that the resistance of graphene decreases with increasing E. coli concentration. This is due to the increased hole doping induced by negatively charged E. coli. A sensitivity of 60% is achieved for an E. coli concentration of 4.5 x 10(7) cfu/ml. An equivalent RC model is proposed to explain the sensing mechanism. (C) 2013 Elsevier B.V. All rights reserved.

Forming limit investigation of friction stir welded sheets: influence of shoulder diameter and plunge depth

The main aim of the present work is to analyze the influence of shoulder diameter and plunge depth on the formability of friction stir welded sheets. The base material used for welding and forming was AA6061-T6. Formability evaluation was performed through limiting dome height tests. The forming limit curve, FLC (only in the stretching region), thickness distribution, and strain hardening exponent of the weld region were monitored during formability studies. It is found from the work that the forming limit of friction stir welded sheets is better than unwelded sheets. In general, with an increase in shoulder diameter and plunge depth, the forming limit is found to improve considerably. With a decrease in thickness gradient severity and an increase in strain hardening exponent (n) of the weld region, the forming limit is found to increase. The increase in n value of the weld region is believed to occur because of the reduction in dislocation density. The maximum thickness difference is higher in the retreating side, rather than in the advancing side, of the weld. This is due to the differential straining and hardness levels attained by both sides during friction stir welding.

Lysis dynamics and membrane oligomerization pathways for Cytolysin A (ClyA) pore-forming toxin

Pore-forming toxins are known for their ability to efficiently form transmembrane pores which eventually leads to cell lysis. The dynamics of lysis and underlying self-assembly or oligomerization pathways leading to pore formation are incompletely understood. In this manuscript the pore-forming kinetics and lysis dynamics of Cytolysin-A (ClyA) toxins on red blood cells (RBCs) are quantified and compared with experimental lysis data. Lysis experiments are carried out on a fixed mass of RBCs, under isotonic conditions in phosphate-buffered saline, for different initial toxin concentrations ranging from 2.94-14.7 nM. Kinetic models which account for monomer binding, conformation and oligomerization to form the dodecameric ClyA pore complex are developed and lysis is assumed to occur when the number of pores per RBC (n(p)) exceeds a critical number, n(pc). By analysing the model in a sublytic regime (n(p) < n(pc)) the number of pores per RBC to initiate lysis is found to lie between 392 and 768 for the sequential oligomerization mechanism and between 5300 and 6300 for the non-sequential mechanism. Rupture rates which are first order in the number of RBCs are seen to provide the best agreement with the lysis experiments. The time constants for pore formation are estimated to lie between 1 and 20 s and monomer conformation time scales were found to be 2-4 times greater than the oligomerization times. Cell rupture takes places in 100s of seconds, and occurs predominantly with a steady number of pores ranging from 515 to 11 000 on the RBC surface for the sequential mechanism. Both the sequential irreversible and non-sequential kinetics provide similar predictions of the hemoglobin release dynamics, however the hemoglobin released as a function of the toxin concentration was accurately captured only with the sequential model. Each mechanism develops a distinct distribution of mers on the surface, providing a unique experimentally observable fingerprint to identify the underlying oligomerization pathways. Our study offers a method to quantify the extent and dynamics of lysis which is an important aspect of developing novel drug and gene delivery strategies based on pore-forming toxins.

A Novel Design Method for SOGI-PLL for Minimum Settling Time and Low Unit Vector Distortion

Phase-locked loops (PLLs) are necessary in grid connected systems to obtain information about the frequency, amplitude and phase of the grid voltage. In stationary reference frame control, the unit vectors of PLLs are used for reference generation. It is important that the PLL performance is not affected significantly when grid voltage undergoes amplitude and frequency variations. In this paper, a novel design for the popular single-phase PLL topology, namely the second-order generalized integrator (SOGI) based PLL is proposed which achieves minimum settling time during grid voltage amplitude and frequency variations. The proposed design achieves a settling time of less than 27.7 ms. This design also ensures that the unit vectors generated by this PLL have a steady state THD of less than 1% during frequency variations of the grid voltage. The design of the SOGI-PLL based on the theoretical analysis is validated by experimental results.

Structural basis for the redox sensitivity of the Mycobacterium tuberculosis SigK-RskA sigma-anti-sigma complex

The host-pathogen interactions in Mycobacterium tuberculosis infection are significantly influenced by redox stimuli and alterations in the levels of secreted antigens. The extracyto-plasmic function (ECF) sigma factor sigma(K) governs the transcription of the serodominant antigens MPT70 and MPT83. The cellular levels of sigma(K) are regulated by the membrane-associated anti-sigma(K) (RskA) that localizes sigma(K) in an inactive complex. The crystal structure of M. tuberculosis sigma(K) in complex with the cytosolic domain of RskA (RskAcyto) revealed a disulfide bridge in the -35 promoter-interaction region of sigma(K). Biochemical experiments reveal that the redox potential of the disulfide-forming cysteines in sigma(K) is consistent with its role as a sensor. The disulfide bond in sigma(K) influences the stability of the sigma(K)-RskA(cyto) complex but does not interfere with sigma(K)-promoter DNA interactions. It is noted that these disulfide-forming cysteines are conserved across homologues, suggesting that this could be a general mechanism for redox-sensitive transcription regulation.

Sensitivity of Water Dynamics to Biologically Significant Surfaces of Monomeric Insulin: Role of Topology and Electrostatic Interactions

In addition to the biologically active monomer of the protein insulin circulating in human blood, the molecule also exists in dimeric and hexameric forms that are used as storage. The insulin monomer contains two distinct surfaces, namely, the dimer forming surface (DFS) and the hexamer forming surface (HFS), that are specifically designed to facilitate the formation of the dimer and the hexamer, respectively. In order to characterize the structural and dynamical behavior of interfacial water molecules near these two surfaces (DFS and HFS), we performed atomistic molecular dynamics simulations of insulin with explicit water. Dynamical characterization reveals that the structural relaxation of the hydrogen bonds formed between the residues of DFS and the interfacial water molecules is faster than those formed between water and that of the HFS. Furthermore, the residence times of water molecules in the protein hydration layer for both the DFS and HFS are found to be significantly higher than those for some of the other proteins studied so far, such as HP-36 and lysozyme. In particular, we find that more structured water molecules, with higher residence times (similar to 300-500 ps), are present near HFS than those near DFS. A significant slowing down is observed in the decay of associated rotational auto time correlation functions of O-H bond vector of water in the vicinity of HFS. The surface topography and the arrangement of amino acid residues work together to organize the water molecules in the hydration layer in order to provide them with a preferred orientation. HFS having a large polar solvent accessible surface area and a convex extensive nonpolar region, drives the surrounding water molecules to acquire predominantly an outward H-atoms directed, clathrate-like structure. In contrast, near the DFS, the surrounding water molecules acquire an inward H-atoms directed orientation owing to the flat curvature of hydrophobic surface and the interrupted hydrophilic residual alignment. We have followed escape trajectory of several such quasi-bound water molecules from both the surfaces that reveal the significant differences between the two hydration layers.

High Throughput, Low Latency, Memory Optimized 64K Point FFT Architecture using Novel Radix-4 Butterfly Unit

In this paper we propose a fully parallel 64K point radix-4(4) FFT processor. The radix-4(4) parallel unrolled architecture uses a novel radix-4 butterfly unit which takes all four inputs in parallel and can selectively produce one out of the four outputs. The radix-4(4) block can take all 256 inputs in parallel and can use the select control signals to generate one out of the 256 outputs. The resultant 64K point FFT processor shows significant reduction in intermediate memory but with increased hardware complexity. Compared to the state-of-art implementation 5], our architecture shows reduced latency with comparable throughput and area. The 64K point FFT architecture was synthesized using a 130nm CMOS technology which resulted in a throughput of 1.4 GSPS and latency of 47.7 mu s with a maximum clock frequency of 350MHz. When compared to 5], the latency is reduced by 303 mu s with 50.8% reduction in area.

Rare-earth carboxylates, Ln(2)(III)(mu(3)-OH)(C4H4O5)(2)(C4H2O4)]center dot 2H(2)O Ln = Ce, Pr and Nd]: synthesis, structure and properties

A new series of inorganic-organic hybrid framework compounds, Ln(2)(mu(3)-OH)(C4H4O5)(2)(C4H2O4)]center dot 2H(2)O, (Ln = Ce, Pr and Nd), have been prepared employing a hydrothermal method. Malic acid and fumaric acid form part of the structure. The malate units connect the lanthanide centers forming Ln-O-Ln two-dimensional layers, which are cross-linked by the fumarate units forming the three-dimensional structure. Extra framework water molecules form a dimer and occupy the channels. The water molecules can be reversibly adsorbed. The dehydrated structure did not show any differences in framework structure/ connectivity. The presence of lattice water provides a pathway for proton conductivity. Optical studies suggest an up-conversion behavior involving more than one photon for a neodymium compound.

Experimental investigation of forming limit, void coalescence and crystallographic textures of aluminum alloy 8011 sheet annealed at various temperatures

In this work, a combined forming and fracture limit diagram, fractured void coalescence and texture analysis have been experimentally evaluated for the commercially available aluminum alloy Al 8011 sheet annealed at different temperatures viz. 200 degrees C, 250 degrees C, 300 degrees C and 350 degrees C. The sheets were examined at different annealing temperatures on microstructure, tensile properties, formability and void coalescence. The fractured surfaces of the formed samples were examined using scanning electron microscope (SEM) and these images were correlated with fracture behavior and formability of sheet metals. Formability of Al 8011 was studied and examined at various annealing temperatures using their bulk X-ray crystallographic textures and ODF plots. Forming limit diagrams, void coalescence parameters and crystallographic textures were correlated with normal anisotropy of the sheet metals annealed at different temperatures. (C) 2013 Politechnika Wroclawska. Published by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

Growing Length Scales and Their Relation to Timescales in Glass-Forming Liquids

The question of whether the dramatic slowing down of the dynamics of glass-forming liquids near the structural glass transition is caused by the growth of one or more correlation lengths has received much attention in recent years. Several proposals have been made for both static and dynamic length scales that may be responsible for the growth of timescales as the glass transition is approached. These proposals are critically examined with emphasis on the dynamic length scale associated with spatial heterogeneity of local dynamics and the static point-to-set or mosaic length scale of the random first order transition theory of equilibrium glass transition. Available results for these length scales, obtained mostly from simulations, are summarized, and the relation of the growth of timescales near the glass transition with the growth of these length scales is examined. Some of the outstanding questions about length scales in glass-forming liquids are discussed, and studies in which these questions may be addressed are suggested.

Propensity to Form Amyloid Fibrils Is Encoded as Excitations in the Free Energy Landscape of Monomeric Proteins

Protein aggregation, linked to many of diseases, is initiated when monomers access rogue conformations that are poised to form amyloid fibrils. We show, using simulations of src SH3 domain, that mechanical force enhances the population of the aggregation-prone (N*) states, which are rarely populated under force free native conditions but are encoded in the spectrum of native fluctuations. The folding phase diagrams of SH3 as a function of denaturant concentration (C]), mechanical force (f), and temperature exhibit an apparent two-state behavior, without revealing the presence of the elusive N* states. Interestingly, the phase boundaries separating the folded and unfolded states at all C] and f fall on a master curve, which can be quantitatively described using an analogy to superconductors in a magnetic field. The free energy profiles as a function of the molecular extension (R), which are accessible in pulling experiments, (R), reveal the presence of a native-like N* with a disordered solvent-exposed amino-terminal beta-strand. The structure of the N* state is identical with that found in Fyn SH3 by NMR dispersion experiments. We show that the timescale for fibril formation can be estimated from the population of the N* state, determined by the free energy gap separating the native structure and the N* state, a finding that can be used to assess fibril forming tendencies of proteins. The structures of the N* state are used to show that oligomer formation and likely route to fibrils occur by a domain-swap mechanism in SH3 domain. (C) 2014 Elsevier Ltd. All rights reserved.

Cu-II-Azide Polynuclear Complexes of Three Different Building Clusters with the Same Schiff-Base Ligand: Synthesis, Structures, Magnetic Behavior, and Density Functional Theory Studies

Three copper-azido complexes Cu-4(N-3)(8)(L-1)(2)(MeOH)(2)](n) (1), Cu-4(N-3)(8)(L-1)(2)] (2), and Cu-5(N-3)(10)(L-1)(2)](n) (3) L-1 is the imine resulting from the condensation of pyridine-2-carboxaldehyde with 2-(2-pyridyl)ethylamine] have been synthesized using lower molar equivalents of the Schiff base ligand with Cu(NO3)(2)center dot 3H(2)O and an excess of NaN3. Single crystal X-ray structures show that the basic unit of the complexes 1 and 2 contains Cu-4(II) building blocks; however, they have distinct basic and overall structures due to a small change in the bridging mode of the peripheral pair of copper atoms in the linear tetranudear structures. Interestingly, these changes are the result of changing the solvent system (MeOH/H2O to EtOH/H2O) used for the synthesis, without changing the proportions of the components (metal to ligand ratio 2:1). Using even lower proportions of the ligand, another unique complex was isolated with Cu-5(II) building units, forming a two-dimensional complex (3). Magnetic susceptibility measurements over a wide range of temperature exhibit the presence of both antiferromagnetic (very weak) and ferromagnetic exchanges within the tetranuclear unit structures. Density functional theory calculations (using B3LYP functional, and two different basis sets) have been performed on the complexes 1 and 2 to provide a qualitative theoretical interpretation of their overall magnetic behavior.