Backbone Connectivity Research Articles

Frequency Response of a Protein to Local Conformational Perturbations

Signals created by local perturbations are known to propagate long distances through proteins via backbone connectivity and nonbonded interactions. In the current study, signal propagation from the flexible ligand binding loop to the rest of Protein Tyrosine Phosphatase 1B (PTP1B) was investigated using frequency response techniques. Using restrained Targeted Molecular Dynamics (TMD) potential on WPD and R loops, PTP1B was driven between its crystal structure conformations at different frequencies. Propagation of the local perturbation signal was manifested via peaks at the fundamental frequency and upper harmonics of 1/f distributed spectral density of atomic variables, such as Cα atoms, dihedral angles, or polar interaction distances. Frequency of perturbation was adjusted high enough (simulation length >∼10×period of a perturbation cycle) not to be clouded by random diffusional fluctuations, and low enough (<∼0.8 ns−1) not to attenuate the propagating signal and enhance the contribution of the side-chains to the dissipation of the signals. Employing Discrete Fourier Transform (DFT) to TMD simulation trajectories of 16 cycles of conformational transitions at periods of 1.2 to 5 ns yielded Cα displacements consistent with those obtained from crystal structures. Identification of the perturbed atomic variables by statistical t-tests on log-log scale spectral densities revealed the extent of signal propagation in PTP1B, while phase angles of the filtered trajectories at the fundamental frequency were used to cluster collectively fluctuating elements. Hydrophobic interactions were found to have a higher contribution to signal transduction between side-chains compared to the role of polar interactions. Most of in-phase fluctuating residues on the signaling pathway were found to have high identity among PTP domains, and located over a wide region of PTP1B including the allosteric site. Due to its simplicity and efficiency, the suggested technique may find wide applications in identification of signaling pathways of different proteins.

Prebiotic RNA unstuck

Non-enzymatic copying of an RNA template is appealing as a transition from pre-life to an RNA world, but it has been difficult to demonstrate in the laboratory. Now, two separate studies focusing on RNA's backbone connectivity offer partial solutions to some of the problems raised with this hypothesis for the origin of life.

Transmission Range Assignment for Backbone Connectivity in Clustered Wireless Networks

In this paper, a method is proposed to assign minimum transmission ranges to the backbone nodes of a hierarchically structured multihop network, while seeking an M% probability to have end-to-end connectivity to the network's data sink. The target scenario is data collection in which cluster head (CH) nodes collect packets from cluster members and then forward them over a CH-backbone towards the sink. The proposed method reduces the energy consumption of data transmissions made by CH nodes, and hence improves the efficiency of existing node clustering protocols, which select arbitrarily large ranges for backbone communications.

Enhanced Bluetree: a mesh topology approach forming Bluetooth scatternet

This study presents the enhanced Bluetree, a mesh topology scheme for Bluetooth scatternet formation. The scatternet formation algorithm includes two phases. In the first phase, a root node begins to create a conventional tree-shaped topology. To improve the network reliability of tree topology, a return connection mechanism is introduced in the second phase to generate more connection paths and to convert the tree-shape into a mesh-shaped topology. The mechanism contains two connection models including the ‘slave/slave mesh’ (SSM) and the ‘master/slave mesh’ (MSM) models. The SSM model builds a mesh-shaped topology by interconnecting more leaf nodes, whereas the MSM model connects additional intermediate nodes to establish the backbone connection in a mesh-shaped topology. Simulation results show that the enhanced Bluetree effectively improves the performance metrics, including the piconet efficiency, path length and end-to-end delay, beyond the Bluetree with more formation packets. As a result, the enhanced Bluetree not only builds a mesh-shaped topology that improves the network reliability but also generates an efficient network with less packet delay performance than a conventional Bluetree network.

Altering the Conjugation Pathway for Improved Performance of Benzobisoxazole-Based Polymer Guest Emitters in Polymer Light-Emitting Diodes

Benzobisoxazoles (BBOs) are known to increase the electron affinities and improve the electron transporting properties of materials containing them. However, BBO copolymers generally do not perform well as emissive guests in guest–host PLEDs due to inefficient Forster resonance energy transfer (FRET) between host and guest. The incomplete FRET results in a large amount of host emission and limits the potential efficiencies of the devices. In all previously reported BBO copolymers, the conjugation pathway was through the oxazole rings. Herein we report six new BBO copolymers with backbone connectivity directly on the central benzene ring, resulting in a conjugation pathway for the polymers that is perpendicular to the previously reported pathway. Guest–host PLEDs made using these polymers show that the new conjugation pathway improves FRET between the poly(N-vinylcarbazole) host and the BBO-containing polymer guest. Because of highly efficient FRET, no host emission is observed even at lower guest concentr...

A Mesh Topology Approach for Bluetooth Scatternet Formation

This paper presents the Enhanced Bluetree, a mesh topology scheme for Bluetooth scatternet formation. The scatternet formation algorithm includes two phases. In the first phase, a designated node called the root starts to create a tree-shaped topology and in the second phase the tree-shaped topology is converted into a mesh-shaped topology. In addition, a return connection mechanism is introduced in this phase to generate more connection paths among the nodes. The mechanism contains two scatternet topology models including the slave/slave mesh (SSM) model and the master/slave mesh (MSM) model. The SSM Model builds a mesh-shaped topology by interconnecting more leaf nodes. On the other hand, the MSM Model connects additional intermediate nodes to establish the backbone connection in a mesh-shaped topology. Simulation results show that both the SSM and the MSM of an Enhanced Bluetree more effectively improve the network performance than Bluetree by significantly reducing the average path length.

Dual-band selective double cross polarization for heteronuclear polarization transfer between dilute spins in solid-state MAS NMR

A sinusoidal modulation scheme is described for selective heteronuclear polarization transfer between two dilute spins in double cross polarization magic-angle-spinning nuclear magnetic resonance spectroscopy. During the second N→C cross polarization, the 13C RF amplitude is modulated sinusoidally while the 15N RF amplitude is tangent. This modulation induces an effective spin-lock field in two selective frequency bands in either side of the 13C RF carrier frequency, allowing for simultaneous polarization transfers from 15N to 13C in those two selective frequency bands. It is shown by experiments and simulations that this sinusoidal modulation allows one to selectively polarize from 15N to its covalently bonded 13Cα and 13C’ carbons in neighboring peptide planes simultaneously, which is useful for establishing the backbone connectivity between two sequential residues in protein structural elucidation. The selectivity and efficiency were experimentally demonstrated on a uniformly 13C,15N-labeled β1 immunoglobulin binding domain of protein G (GB1).

Structural Analysis of the Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) Intracellular Domain Reveals a Conserved Interaction Epitope

Plasmodium falciparum-infected red blood cells adhere to endothelial cells, thereby obstructing the microvasculature. Erythrocyte adherence is directly associated with severe malaria and increased disease lethality, and it is mediated by the PfEMP1 family. PfEMP1 clustering in knob-like protrusions on the erythrocyte membrane is critical for cytoadherence, however the molecular mechanisms behind this system remain elusive. Here, we show that the intracellular domains of the PfEMP1 family (ATS) share a unique molecular architecture, which comprises a minimal folded core and extensive flexible elements. A conserved flexible segment at the ATS center is minimally restrained by the folded core. Yeast-two-hybrid data and a novel sequence analysis method suggest that this central segment contains a conserved protein interaction epitope. Interestingly, ATS in solution fails to bind the parasite knob-associated histidine-rich protein (KAHRP), an essential cytoadherence component. Instead, we demonstrate that ATS associates with PFI1780w, a member of the Plasmodium helical interspersed sub-telomeric (PHIST) family. PHIST domains are widespread in exported parasite proteins, however this is the first specific molecular function assigned to any variant of this family. We propose that PHIST domains facilitate protein interactions, and that the conserved ATS epitope may be targeted to disrupt the parasite cytoadherence system.

GBG Approach for Connectivity and Coverage Control in Wireless Sensor Network

sensor network are used to monitor various physical environment. These environments are mostly highly asymmetric terrains. The deployment of the sensor node for coverage and connectivity cost should be optimized. Therefore, in sensor network, providing high connectivity and coverage becomes the critical issue. In the proposed work, coverage and connectivity is a minimization of cost function as square of the distance between the nodes. This has been solved for cost optimization which is based on gradient methods. This modified protocol provides a genetic framework. We assume that the backbone nodes are connected to each and they provide coverage to the sensors on the basis of fitness function. The protocol performing better on the basis of cost which is also optimizing both network coverage and backbone connectivity. Our formalization allows the design of self-organized network system, which achieves minimum cost configurations. We have presented simulation results that show the effectiveness of genetic algorithm to provide network configuration that optimize both network coverage and backbone connectivity in different scenarios. We have simulated the Genetic Based Gradient (GBG) method and the proposed work in done on MATLAB.

Integrated Monitoring of Multi-Domain Backbone Connections

Novel large scale research projects often require cooperation between various different project partners that are spread among the entire world. They do not only need huge computing resources, but also a reliable network to operate on. The Large Hadron Collider (LHC) at CERN is a representative example for such a project. Its experiments result in a vast amount of data, which is interesting for researchers around the world. For transporting the data from CERN to 11 data processing and storage sites, an optical private network (OPN) has been constructed. As the experiment data is highly valuable, LHC defines very high requirements to the underlying network infrastructure. In order to fulfil those requirements, the connections have to be managed and monitored permanently. In this paper, we present the integrated monitoring solution developed for the LHCOPN. We first outline the requirements and show how they are met on the single network layers. After that, we describe, how those single measurements can be combined into an integrated view. We cover design concepts as well as tool implementation highlights.

Navigation function design for backbone connectivity in vehicle ad hoc networks

Backbone connectivity is a critical and challenging problem in vehicle ad hoc networks. Just like base stations in cellular networks, the backbones or mobile base stations in vehicle ad hoc networks play important roles in location management and engineering applications. In this paper, we discuss the one-to-one connectivity by extending the navigation functions, and present the integrated power and mobility navigation functions. Considering the interference between the backbones, we describe the interference alleviating navigation function design. We establish the control laws, describe the numerical computation, and discuss the stability of the navigation system at the end.

Towards Semiconducting Graft Copolymers: Switching from ATRP to “Click” Approach

The synthesis of two polyconjugated graft copolymers based on a poly(fluorene-phenylene) backbone and polystyrene side chains is described here. The two different approaches followed, ATRP growth of side chains from a preformed conjugated backbone and click connection of well-defined polymeric chains to the backbone, led to different results in terms of solubility and material properties. While the ATRP method seems to be responsible of a partially cross-linked and nonsoluble copolymer, the click approach provides a graft copolymer, which is completely soluble, showing atypical spectroscopic properties that are here elucidated.

Cooperation Stimulation Strategies for Peer-to-Peer Wireless Live Video-Sharing Social Networks

Human behavior analysis in video sharing social networks is an emerging research area, which analyzes the behavior of users who share multimedia content and investigates the impact of human dynamics on video sharing systems. Users watching live streaming in the same wireless network share the same limited bandwidth of backbone connection to the Internet, thus, they might want to cooperate with each other to obtain better video quality. These users form a wireless live-streaming social network. Every user wishes to watch video with high quality while paying as little as possible cost to help others. This paper focuses on providing incentives for user cooperation. We propose a game-theoretic framework to model user behavior and to analyze the optimal strategies for user cooperation simulation in wireless live streaming. We first analyze the Pareto optimality and the time-sensitive bargaining equilibrium of the two-person game. We then extend the solution to the multiuser scenario. We also consider potential selfish users' cheating behavior and malicious users' attacking behavior and analyze the performance of the proposed strategies with the existence of cheating users and malicious attackers. Both our analytical and simulation results show that the proposed strategies can effectively stimulate user cooperation, achieve cheat free and attack resistance, and help provide reliable services for wireless live streaming applications.

DBA-MAC: DYNAMIC BACKBONE-ASSISTED MEDIUM ACCESS CONTROL PROTOCOL FOR EFFICIENT BROADCAST IN VANETS

Active safety systems based on dissemination of alert messages are one of the most important applications of Vehicular ad Hoc Networks (VANETs). These systems typically require to provide efficient and reliable delivery of safety information to all the vehicles travelling over a geographical area. Reducing the delivery delay is also a crucial issue due to the real-time nature of the communication. To meet these requirements, in this paper we design a cross-layered MAC and clustering solution for the fast propagation of broadcast messages in a VANET. A distributed dynamic clustering algorithm is proposed in order to create a dynamic virtual backbone inside the vehicular network. The vehicle-members of the backbone are responsible for implementing an efficient message propagation. The backbone creation and maintenance are proactively performed aiming to balance the stability of backbone connections as well as cost/efficiency trade-off and hops-reduction when forwarding the broadcast messages. A fast multi-hop MAC forwarding scheme is defined to exploit the role of backbone vehicles, under a cross-layered approach. Simulation results show that our cross-layer scheme guarantees high message delivery ratio, reduces the delivery delay and provides efficient channel utilization when compared with other dissemination schemes for VANETs.

Making ordered DNA and protein structures from computer‐printed transparency film cut‐outs

Instructions are given for building physical scale models of ordered structures of B-form DNA, protein α-helix, and parallel and antiparallel protein β-pleated sheets made from colored computer printouts designed for transparency film sheets. Cut-outs from these sheets are easily assembled. Conventional color coding for atoms are used for both types of biopolymers. Arrows facilitate following chain direction for the polypeptides. For DNA, the 5' to 3' direction is guided by a 5' phosphate group and a free hydroxyl group. Important chiral centers, for example, α-carbon, deoxyribose C1', are easily made. The main advantages of this version of DNA are the proportional major and minor grooves as in the actual molecule. More importantly, because of transparency of the film one can see successive base-pair stacking very clearly and also the sense of relative base-pair rotation. Because of the introduction of two central metal wire axes, the model of B-form DNA can be twisted to give a rather good representation of A-form and even a semblance of a left-handed helix. The models of secondary structure of protein allow a better insight into the axial alignment of side chains, the formation of hydrogen bond, the handedness of the α-helix, and the backbone connection between the β-strands. Students taught by these models understand 3D features of the biopolymers better than from textbook illustrations, computer graphic representations, and even common paper and plastic versions.

LÉvy Flights and Fractal Modeling of Internet Traffic

The relation between burstiness and self-similarity of network traffic was identified in numerous papers in the past decade. These papers suggested that the widely used Poisson based models were not suitable for modeling bursty, local-area and wide-area network traffic. Poisson models were abandoned as unrealistic and simplistic characterizations of network traffic. Recent papers have challenged the accuracy of these results in today's networks. Authors of these papers believe that it is time to reexamine the Poisson traffic assumption. The explanation is that as the amount of Internet traffic grows dramatically, any irregularity of the network traffic, such as burstiness, might cancel out because of the huge number of different multiplexed flows. Some of these results are based on analyses of particular OC48 Internet backbone connections and other historical traffic traces. We analyzed the same traffic traces and applied new methods to characterize them in terms of packet interarrival times and packet lengths. The major contribution of the paper is the application of two new analytical methods. We apply the theory of smoothly truncated Levy flights and the linear fractal model in examining the variability of Internet traffic from self-similar to Poisson. The paper demonstrates that the series of interarrival times is still close to a self-similar process, but the burstiness of the packet lengths decreases significantly compared to earlier traces.

Autonomous reconfiguration and control in directional mobile ad hoc networks

Requirements for increasingly complex, scalable, and dynamic wireless networks, which provide assured end-to-end broadband connectivity in a wide range of scenarios, have been emerging. In this context, we have been investigating wireless technologies that provide extremely high data rates through the use of narrow-beam free space optical (FSO) and/or radio-frequency (RF) point-to-point links. The use of directional wireless communications to form flexible backbone networks, which provide broadband connectivity to capacity- limited wireless networks or hosts using omnidirectional transmission, promises to circumvent the scalability limitations of traditional flat wireless networks. We have been investigating backbones of base stations, in which topologies and mobility can be controlled for purposes of assured communications. We refer to these as Directional Mobile Ad Hoc Networks (DMANET). Our work considers the use of topology control to assure robust end-to-end broadband connectivity in heterogeneous and dynamic environments. Topology control is defined as the autonomous network capability to dynamically reconfigure its physical topology. In the case of directional wireless backbone (DWB) networks, the physical topology can be reconfigured through: Autonomous 1) Topology Reconfiguration (ATR): dynamic redirection of point-to-point links using heuristic algorithms for creating new topologies and pointing, acquisition and tracking of links. Topology reconfiguration algorithms, which compute minimum energy configurations by determining optimal link assignments between backbone nodes, are presented. The pointing, acquisition and tracking (PAT) process needed to physically redirect point-to-point links is also addressed. 2) Mobility Control (MC): dynamic reposition and "morphing" of backbone nodes. In this model, communication links define physical interactions between network nodes. Control mechanisms are designed to mimic physical systems' natural reaction to external excitations, which drive the network topology to minimum energy configurations Using both ATR and MC, networks are completely selforganizing. They can autonomously adapt their physical topology to maximize coverage to terminals or hosts while maintaining robust backbone connectivity. In this paper, we present the design, implementation and evaluation of our novel approaches to autonomous reconfiguration and control.

A quadratic optimization method for connectivity and coverage control in backbone-based wireless networks

The use of directional wireless communications to form flexible mesh backbone networks, which provide broadband connectivity to capacity-limited wireless networks or hosts, promises to circumvent the scalability limitations of traditional homogeneous wireless networks. The main challenge in the design of directional wireless backbone (DWB) networks is to assure backbone network requirements such as coverage and connectivity in a dynamic wireless environment. This paper considers the use of mobility control, as the dynamic reposition of backbone nodes, to provide assured coverage-connectivity in dynamic environments. This paper presents a novel approach to the joint coverage-connectivity optimization problem by formulating it as a quadratic minimization problem. Quadratic cost functions for network coverage and backbone connectivity are defined in terms of the square distance between neighbor nodes, which are related to the actual energy usage of the network system. Our formulation allows the design of self-organized network systems which autonomously achieve energy minimizing configurations driven by local forces exerted on network nodes. The net force on a backbone node is defined as the negative energy gradient at the location of the backbone node. A completely distributed algorithm is presented that allows backbone nodes to adjust their positions based on information about neighbors’ position only. We present initial simulation results that show the effectiveness of our force-based mobility control algorithm to provide network configurations that optimize both network coverage and backbone connectivity in different scenarios. Our algorithm is shown to be adaptive, scalable and self-organized.

Effect of covalent links on the structure, spectra, and redox properties of myeloperoxidase – A density functional study

The enzyme myeloperoxidase shows several unusual properties compared to other peroxidases, e.g. a red-shifted absorption spectrum and a peroxidase activity towards chloride. It has been suggested that this is caused by the unusual covalent links between the heme group and the surrounding protein, but whether it is caused by the two ester links to Glu-242 and Asp-94 or the sulfonium ion linkage to Met-243 is unclear. To investigate these suggestions, we have used density functional theory to study the structure, spectra, and reduction potential of 25 models of myeloperoxidase in the reduced (Fe II) and oxidized (Fe III) states, as well as in the compound I (formally Fe VO) and II (Fe IVO or Fe IVOH) states, using appropriate models of the linkages to the Asp, Glu, and Met residues (including the back-bone connection between Glu-242 and Met-243) in varying combinations. The calculated spectral shifts indicate that both the ester and sulfonium linkages play a role in the spectral shift. On the other hand, the sulfonium linkage seems to be mainly responsible for the high positive reduction potential for the both ferric/ferrous and compound I/II couples of myeloperoxidase.

Tandem Mass Spectrometry Characteristics of Silver-Cationized Polystyrenes: Internal Energy, Size, and Chain End versus Backbone Substituent Effects

The Ag(+) adducts of polystyrene (PS) oligomers with different sizes (6-19 repeat units) and initiating (alpha) or terminating (omega) end groups mainly decompose via free radical chemistry pathways upon collisionally activated dissociation. This reactivity is observed for ions formed by matrix-assisted laser desorption/ionization as well as electrospray ionization. With end groups lacking weak bonds (robust end groups), dissociation starts with random homolytic C-C bond cleavages along the PS chain, which lead to primary and benzylic radical ions containing either of the chain ends. The primary radical ions mainly depolymerize by successive beta C-C bond scissions. For the benzylic radical ions, two major pathways are in competition, namely, depolymerization by successive beta C-C bond scissions and backbiting via 1,5-H rearrangement followed by beta C-C bond scissions. The extent of backbiting decreases with internal energy. With short PS chains, the primary radical ions also undergo backbiting involving 1,4- and 1,6-H rearrangements; however, this process becomes negligible with longer chains. If the polystyrene contains a labile substituent at a chain end, this substituent is eliminated easily and, thus, not contained in the majority of observed fragments. Changes in the PS backbone structure can have a dramatic effect on the resulting dissociation chemistry. This is demonstrated for poly(alpha-methylstyrene), in which backbiting is obstructed due to the lack of benzylic H atoms; instead, this backbone connectivity promotes 1,2-phenyl shifts in the primary radical ions formed after initial C-C bond homolyses as well as H atom transfers between the incipient primary and benzylic radicals emerging from these homolyses.