Evaluation of multicast schemes in optical burst-switched networks: the case with dynamic sessions

NASA Astrophysics Data System (ADS)

Jeong, Myoungki; Qiao, Chunming; Xiong, Yijun; Vandenhoute, Marc

2000-10-01

In this paper, we evaluate the performance of several multicast schemes in optical burst-switched WDM networks taking into accounts the overheads due to control packets and guard bands (Gbs) of bursts on separate channels (wavelengths). A straightforward scheme is called Separate Multicasting (S-MCAST) where each source node constructs separate bursts for its multicast (per each multicast session) and unicast traffic. To reduce the overhead due to Gbs (and control packets), one may piggyback the multicast traffic in bursts containing unicast traffic using a scheme called Multiple Unicasting (M-UCAST). The third scheme is called Tree-Shared Multicasting (TS-MCAST) wehreby multicast traffic belonging to multiple multicast sesions can be mixed together in a burst, which is delivered via a shared multicast tree. In [1], we have evaluated several multicast schemes with static sessions at the flow level. In this paper, we perform a simple analysis for the multicast schemes and evaluate the performance of three multicast schemes, focusing on the case with dynamic sessions in terms of the link utilization, bandwidth consumption, blocking (loss) probability, goodput and the processing loads.

Extensible Interest Management for Scalable Persistent Distributed Virtual Environments

DTIC Science & Technology

1999-12-01

Calvin, Cebula et al. 1995; Morse, Bic et al. 2000) uses a two grid, with each grid cell having two multicast addresses. An entity expresses interest...Entity distribution for experimental runs 78 s I * • ...... ^..... * * a» Sis*«*»* 1 ***** Jj |r...Multiple Users and Shared Applications with VRML. VRML 97, Monterey, CA. pp. 33-40. Calvin, J. O., D. P. Cebula , et al. (1995). Data Subscription in

Maximization Network Throughput Based on Improved Genetic Algorithm and Network Coding for Optical Multicast Networks

NASA Astrophysics Data System (ADS)

Wei, Chengying; Xiong, Cuilian; Liu, Huanlin

2017-12-01

Maximal multicast stream algorithm based on network coding (NC) can improve the network's throughput for wavelength-division multiplexing (WDM) networks, which however is far less than the network's maximal throughput in terms of theory. And the existing multicast stream algorithms do not give the information distribution pattern and routing in the meantime. In the paper, an improved genetic algorithm is brought forward to maximize the optical multicast throughput by NC and to determine the multicast stream distribution by hybrid chromosomes construction for multicast with single source and multiple destinations. The proposed hybrid chromosomes are constructed by the binary chromosomes and integer chromosomes, while the binary chromosomes represent optical multicast routing and the integer chromosomes indicate the multicast stream distribution. A fitness function is designed to guarantee that each destination can receive the maximum number of decoding multicast streams. The simulation results showed that the proposed method is far superior over the typical maximal multicast stream algorithms based on NC in terms of network throughput in WDM networks.

The Impact on Quality of Service When Using Security-Enabling Filters to Provide for the Security of Run-Time Virtual Environments

DTIC Science & Technology

2002-09-01

Secure Multicast......................................................................24 i. Message Digests and Message Authentication Codes ( MACs ...that is, the needs of the VE will determine what the design will look like (e.g., reliable vs . unreliable data communications). In general, there...Molva00] and [Abdalla00]. i. Message Digests and Message Authentication Codes ( MACs ) Message digests and MACs are used for data integrity verification

Multicasting in Wireless Communications (Ad-Hoc Networks): Comparison against a Tree-Based Approach

NASA Astrophysics Data System (ADS)

Rizos, G. E.; Vasiliadis, D. C.

2007-12-01

We examine on-demand multicasting in ad hoc networks. The Core Assisted Mesh Protocol (CAMP) is a well-known protocol for multicast routing in ad-hoc networks, generalizing the notion of core-based trees employed for internet multicasting into multicast meshes that have much richer connectivity than trees. On the other hand, wireless tree-based multicast routing protocols use much simpler structures for determining route paths, using only parent-child relationships. In this work, we compare the performance of the CAMP protocol against the performance of wireless tree-based multicast routing protocols, in terms of two important factors, namely packet delay and ratio of dropped packets.

An algorithm for converting a virtual-bond chain into a complete polypeptide backbone chain

NASA Technical Reports Server (NTRS)

Luo, N.; Shibata, M.; Rein, R.

1991-01-01

A systematic analysis is presented of the algorithm for converting a virtual-bond chain, defined by the coordinates of the alpha-carbons of a given protein, into a complete polypeptide backbone. An alternative algorithm, based upon the same set of geometric parameters used in the Purisima-Scheraga algorithm but with a different "linkage map" of the algorithmic procedures, is proposed. The global virtual-bond chain geometric constraints are more easily separable from the loal peptide geometric and energetic constraints derived from, for example, the Ramachandran criterion, within the framework of this approach.

Smart-Grid Backbone Network Real-Time Delay Reduction via Integer Programming.

PubMed

Pagadrai, Sasikanth; Yilmaz, Muhittin; Valluri, Pratyush

2016-08-01

This research investigates an optimal delay-based virtual topology design using integer linear programming (ILP), which is applied to the current backbone networks such as smart-grid real-time communication systems. A network traffic matrix is applied and the corresponding virtual topology problem is solved using the ILP formulations that include a network delay-dependent objective function and lightpath routing, wavelength assignment, wavelength continuity, flow routing, and traffic loss constraints. The proposed optimization approach provides an efficient deterministic integration of intelligent sensing and decision making, and network learning features for superior smart grid operations by adaptively responding the time-varying network traffic data as well as operational constraints to maintain optimal virtual topologies. A representative optical backbone network has been utilized to demonstrate the proposed optimization framework whose simulation results indicate that superior smart-grid network performance can be achieved using commercial networks and integer programming.

Demonstration of flexible and reconfigurable WDM multicast scheme supporting downstream emergency multicast communication for WDM optical access network

NASA Astrophysics Data System (ADS)

Li, Ze; Zhang, Min; Wang, Danshi; Cui, Yue

2017-09-01

We propose a flexible and reconfigurable wavelength-division multiplexing (WDM) multicast scheme supporting downstream emergency multicast communication for WDM optical access network (WDM-OAN) via a multicast module (MM) based on four-wave mixing (FWM) in a semiconductor optical amplifier. It serves as an emergency measure to dispose of the burst, large bandwidth, and real-time multicast service with fast service provisioning and high resource efficiency. It also plays the role of physical backup in cases of big data migration or network disaster caused by invalid lasers or modulator failures. It provides convenient and reliable multicast service and emergency protection for WDM-OAN without modifying WDM-OAN structure. The strategies of an MM setting at the optical line terminal and remote node are discussed to apply this scheme to passive optical networks and active optical networks, respectively. Utilizing the proposed scheme, we demonstrate a proof-of-concept experiment in which one-to-six/eight 10-Gbps nonreturn-to-zero-differential phase-shift keying WDM multicasts in both strategies are successfully transmitted over single-mode fiber of 20.2 km. One-to-many reconfigurable WDM multicasts dealing with higher data rate and other modulation formats of multicast service are possible through the proposed scheme. It can be applied to different WDM access technologies, e.g., time-wavelength-division multiplexing-OAN and coherent WDM-OAN, and upgraded smoothly.

Degree-constrained multicast routing for multimedia communications

NASA Astrophysics Data System (ADS)

Wang, Yanlin; Sun, Yugeng; Li, Guidan

2005-02-01

Multicast services have been increasingly used by many multimedia applications. As one of the key techniques to support multimedia applications, the rational and effective multicast routing algorithms are very important to networks performance. When switch nodes in networks have different multicast capability, multicast routing problem is modeled as the degree-constrained Steiner problem. We presented two heuristic algorithms, named BMSTA and BSPTA, for the degree-constrained case in multimedia communications. Both algorithms are used to generate degree-constrained multicast trees with bandwidth and end to end delay bound. Simulations over random networks were carried out to compare the performance of the two proposed algorithms. Experimental results show that the proposed algorithms have advantages in traffic load balancing, which can avoid link blocking and enhance networks performance efficiently. BMSTA has better ability in finding unsaturated links and (or) unsaturated nodes to generate multicast trees than BSPTA. The performance of BMSTA is affected by the variation of degree constraints.

A Stateful Multicast Access Control Mechanism for Future Metro-Area-Networks.

ERIC Educational Resources Information Center

Sun, Wei-qiang; Li, Jin-sheng; Hong, Pei-lin

2003-01-01

Multicasting is a necessity for a broadband metro-area-network; however security problems exist with current multicast protocols. A stateful multicast access control mechanism, based on MAPE, is proposed. The architecture of MAPE is discussed, as well as the states maintained and messages exchanged. The scheme is flexible and scalable. (Author/AEF)

A proposed group management scheme for XTP multicast

NASA Technical Reports Server (NTRS)

Dempsey, Bert J.; Weaver, Alfred C.

1990-01-01

The purpose of a group management scheme is to enable its associated transfer layer protocol to be responsive to user determined reliability requirements for multicasting. Group management (GM) must assist the client process in coordinating multicast group membership, allow the user to express the subset of the multicast group that a particular multicast distribution must reach in order to be successful (reliable), and provide the transfer layer protocol with the group membership information necessary to guarantee delivery to this subset. GM provides services and mechanisms that respond to the need of the client process or process level management protocols to coordinate, modify, and determine attributes of the multicast group, especially membership. XTP GM provides a link between process groups and their multicast groups by maintaining a group membership database that identifies members in a name space understood by the underlying transfer layer protocol. Other attributes of the multicast group useful to both the client process and the data transfer protocol may be stored in the database. Examples include the relative dispersion, most recent update, and default delivery parameters of a group.

Optical multicast system for data center networks.

PubMed

Samadi, Payman; Gupta, Varun; Xu, Junjie; Wang, Howard; Zussman, Gil; Bergman, Keren

2015-08-24

We present the design and experimental evaluation of an Optical Multicast System for Data Center Networks, a hardware-software system architecture that uniquely integrates passive optical splitters in a hybrid network architecture for faster and simpler delivery of multicast traffic flows. An application-driven control plane manages the integrated optical and electronic switched traffic routing in the data plane layer. The control plane includes a resource allocation algorithm to optimally assign optical splitters to the flows. The hardware architecture is built on a hybrid network with both Electronic Packet Switching (EPS) and Optical Circuit Switching (OCS) networks to aggregate Top-of-Rack switches. The OCS is also the connectivity substrate of splitters to the optical network. The optical multicast system implementation requires only commodity optical components. We built a prototype and developed a simulation environment to evaluate the performance of the system for bulk multicasting. Experimental and numerical results show simultaneous delivery of multicast flows to all receivers with steady throughput. Compared to IP multicast that is the electronic counterpart, optical multicast performs with less protocol complexity and reduced energy consumption. Compared to peer-to-peer multicast methods, it achieves at minimum an order of magnitude higher throughput for flows under 250 MB with significantly less connection overheads. Furthermore, for delivering 20 TB of data containing only 15% multicast flows, it reduces the total delivery energy consumption by 50% and improves latency by 55% compared to a data center with a sole non-blocking EPS network.

Virtually-synchronous communication based on a weak failure suspector

NASA Technical Reports Server (NTRS)

Schiper, Andre; Ricciardi, Aleta

1993-01-01

Failure detectors (or, more accurately Failure Suspectors (FS)) appear to be a fundamental service upon which to build fault-tolerant, distributed applications. This paper shows that a FS with very weak semantics (i.e., that delivers failure and recovery information in no specific order) suffices to implement virtually-synchronous communication (VSC) in an asynchronous system subject to process crash failures and network partitions. The VSC paradigm is particularly useful in asynchronous systems and greatly simplifies building fault-tolerant applications that mask failures by replicating processes. We suggest a three-component architecture to implement virtually-synchronous communication: (1) at the lowest level, the FS component; (2) on top of it, a component (2a) that defines new views; and (3) a component (2b) that reliably multicasts messages within a view. The issues covered in this paper also lead to a better understanding of the various membership service semantics proposed in recent literature.

A novel WDM passive optical network architecture supporting two independent multicast data streams

NASA Astrophysics Data System (ADS)

Qiu, Yang; Chan, Chun-Kit

2012-01-01

We propose a novel scheme to perform optical multicast overlay of two independent multicast data streams on a wavelength-division-multiplexed (WDM) passive optical network. By controlling a sinusoidal clock signal and shifting the wavelength at the optical line terminal (OLT), the delivery of the two multicast data, being carried by the generated optical tones, can be independently and flexibly controlled. Simultaneous transmission of 10-Gb/s unicast downstream and upstream data as well as two independent 10-Gb/s multicast data was successfully demonstrated.

Enabling end-user network monitoring via the multicast consolidated proxy monitor

NASA Astrophysics Data System (ADS)

Kanwar, Anshuman; Almeroth, Kevin C.; Bhattacharyya, Supratik; Davy, Matthew

2001-07-01

The debugging of problems in IP multicast networks relies heavily on an eclectic set of stand-alone tools. These tools traditionally neither provide a consistent interface nor do they generate readily interpretable results. We propose the ``Multicast Consolidated Proxy Monitor''(MCPM), an integrated system for collecting, analyzing and presenting multicast monitoring results to both the end user and the network operator at the user's Internet Service Provider (ISP). The MCPM accesses network state information not normally visible to end users and acts as a proxy for disseminating this information. Functionally, through this architecture, we aim to a) provide a view of the multicast network at varying levels of granularity, b) provide end users with a limited ability to query the multicast infrastructure in real time, and c) protect the infrastructure from overwhelming amount of monitoring load through load control. Operationally, our scheme allows scaling to the ISPs dimensions, adaptability to new protocols (introduced as multicast evolves), threshold detection for crucial parameters and an access controlled, customizable interface design. Although the multicast scenario is used to illustrate the benefits of consolidated monitoring, the ultimate aim is to scale the scheme to unicast IP networks.

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains

NASA Astrophysics Data System (ADS)

Sieradzan, Adam K.; Makowski, Mariusz; Augustynowicz, Antoni; Liwo, Adam

2017-03-01

A general and systematic method for the derivation of the functional expressions for the effective energy terms in coarse-grained force fields of polymer chains is proposed. The method is based on the expansion of the potential of mean force of the system studied in the cluster-cumulant series and expanding the all-atom energy in the Taylor series in the squares of interatomic distances about the squares of the distances between coarse-grained centers, to obtain approximate analytical expressions for the cluster cumulants. The primary degrees of freedom to average about are the angles for collective rotation of the atoms contained in the coarse-grained interaction sites about the respective virtual-bond axes. The approach has been applied to the revision of the virtual-bond-angle, virtual-bond-torsional, and backbone-local-and-electrostatic correlation potentials for the UNited RESidue (UNRES) model of polypeptide chains, demonstrating the strong dependence of the torsional and correlation potentials on virtual-bond angles, not considered in the current UNRES. The theoretical considerations are illustrated with the potentials calculated from the ab initio potential-energy surface of terminally blocked alanine by numerical integration and with the statistical potentials derived from known protein structures. The revised torsional potentials correctly indicate that virtual-bond angles close to 90° result in the preference for the turn and helical structures, while large virtual-bond angles result in the preference for polyproline II and extended backbone geometry. The revised correlation potentials correctly reproduce the preference for the formation of β-sheet structures for large values of virtual-bond angles and for the formation of α-helical structures for virtual-bond angles close to 90°.

Issues in designing transport layer multicast facilities

NASA Technical Reports Server (NTRS)

Dempsey, Bert J.; Weaver, Alfred C.

1990-01-01

Multicasting denotes a facility in a communications system for providing efficient delivery from a message's source to some well-defined set of locations using a single logical address. While modem network hardware supports multidestination delivery, first generation Transport Layer protocols (e.g., the DoD Transmission Control Protocol (TCP) (15) and ISO TP-4 (41)) did not anticipate the changes over the past decade in underlying network hardware, transmission speeds, and communication patterns that have enabled and driven the interest in reliable multicast. Much recent research has focused on integrating the underlying hardware multicast capability with the reliable services of Transport Layer protocols. Here, we explore the communication issues surrounding the design of such a reliable multicast mechanism. Approaches and solutions from the literature are discussed, and four experimental Transport Layer protocols that incorporate reliable multicast are examined.

Application Layer Multicast

NASA Astrophysics Data System (ADS)

Allani, Mouna; Garbinato, Benoît; Pedone, Fernando

An increasing number of Peer-to-Peer (P2P) Internet applications rely today on data dissemination as their cornerstone, e.g., audio or video streaming, multi-party games. These applications typically depend on some support for multicast communication, where peers interested in a given data stream can join a corresponding multicast group. As a consequence, the efficiency, scalability, and reliability guarantees of these applications are tightly coupled with that of the underlying multicast mechanism.

A reliable multicast for XTP

NASA Technical Reports Server (NTRS)

Dempsey, Bert J.; Weaver, Alfred C.

1990-01-01

Multicast services needed for current distributed applications on LAN's fall generally into one of three categories: datagram, semi-reliable, and reliable. Transport layer multicast datagrams represent unreliable service in which the transmitting context 'fires and forgets'. XTP executes these semantics when the MULTI and NOERR mode bits are both set. Distributing sensor data and other applications in which application-level error recovery strategies are appropriate benefit from the efficiency in multidestination delivery offered by datagram service. Semi-reliable service refers to multicasting in which the control algorithms of the transport layer--error, flow, and rate control--are used in transferring the multicast distribution to the set of receiving contexts, the multicast group. The multicast defined in XTP provides semi-reliable service. Since, under a semi-reliable service, joining a multicast group means listening on the group address and entails no coordination with other members, a semi-reliable facility can be used for communication between a client and a server group as well as true peer-to-peer group communication. Resource location in a LAN is an important application domain. The term 'semi-reliable' refers to the fact that group membership changes go undetected. No attempt is made to assess the current membership of the group at any time--before, during, or after--the data transfer.

Issues in providing a reliable multicast facility

NASA Technical Reports Server (NTRS)

Dempsey, Bert J.; Strayer, W. Timothy; Weaver, Alfred C.

1990-01-01

Issues involved in point-to-multipoint communication are presented and the literature for proposed solutions and approaches surveyed. Particular attention is focused on the ideas and implementations that align with the requirements of the environment of interest. The attributes of multicast receiver groups that might lead to useful classifications, what the functionality of a management scheme should be, and how the group management module can be implemented are examined. The services that multicasting facilities can offer are presented, followed by mechanisms within the communications protocol that implements these services. The metrics of interest when evaluating a reliable multicast facility are identified and applied to four transport layer protocols that incorporate reliable multicast.

Simultaneous Wireless Power Transfer and Secure Multicasting in Cooperative Decode-and-Forward Relay Networks.

PubMed

Lee, Jong-Ho; Sohn, Illsoo; Kim, Yong-Hwa

2017-05-16

In this paper, we investigate simultaneous wireless power transfer and secure multicasting via cooperative decode-and-forward (DF) relays in the presence of multiple energy receivers and eavesdroppers. Two scenarios are considered under a total power budget: maximizing the minimum harvested energy among the energy receivers under a multicast secrecy rate constraint; and maximizing the multicast secrecy rate under a minimum harvested energy constraint. For both scenarios, we solve the transmit power allocation and relay beamformer design problems by using semidefinite relaxation and bisection technique. We present numerical results to analyze the energy harvesting and secure multicasting performances in cooperative DF relay networks.

Simultaneous Wireless Power Transfer and Secure Multicasting in Cooperative Decode-and-Forward Relay Networks

PubMed Central

Lee, Jong-Ho; Sohn, Illsoo; Kim, Yong-Hwa

2017-01-01

In this paper, we investigate simultaneous wireless power transfer and secure multicasting via cooperative decode-and-forward (DF) relays in the presence of multiple energy receivers and eavesdroppers. Two scenarios are considered under a total power budget: maximizing the minimum harvested energy among the energy receivers under a multicast secrecy rate constraint; and maximizing the multicast secrecy rate under a minimum harvested energy constraint. For both scenarios, we solve the transmit power allocation and relay beamformer design problems by using semidefinite relaxation and bisection technique. We present numerical results to analyze the energy harvesting and secure multicasting performances in cooperative DF relay networks. PMID:28509841

A Real-Time Executive for Multiple-Computer Clusters.

DTIC Science & Technology

1984-12-01

in a real-time environment is tantamount to speed and efficiency. By effectively co-locating real-time sensors and related processing modules, real...of which there are two ki n1 s : multicast group address - virtually any nur.,ber of node groups can be assigned a group address so they are all able...interfaceloopbark by 󈧅’b4, internal _loopback by 02"b4, clear loooback by 󈧇’b4, go offline by Ŝ"b4, eo online by 󈧍’b4, onboard _diagnostic by Oa’b4, cdr

Mobile Multicast in Hierarchical Proxy Mobile IPV6

NASA Astrophysics Data System (ADS)

Hafizah Mohd Aman, Azana; Hashim, Aisha Hassan A.; Mustafa, Amin; Abdullah, Khaizuran

2013-12-01

Mobile Internet Protocol Version 6 (MIPv6) environments have been developing very rapidly. Many challenges arise with the fast progress of MIPv6 technologies and its environment. Therefore the importance of improving the existing architecture and operations increases. One of the many challenges which need to be addressed is the need for performance improvement to support mobile multicast. Numerous approaches have been proposed to improve mobile multicast performance. This includes Context Transfer Protocol (CXTP), Hierarchical Mobile IPv6 (HMIPv6), Fast Mobile IPv6 (FMIPv6) and Proxy Mobile IPv6 (PMIPv6). This document describes multicast context transfer in hierarchical proxy mobile IPv6 (H-PMIPv6) to provide better multicasting performance in PMIPv6 domain.

Efficient Group Coordination in Multicast Trees

DTIC Science & Technology

2001-01-01

describe a novel protocol to coordinate multipoint groupwork within the IP-multicast framework. The protocol supports Internet-wide coordination for large...and highly-interactive groupwork , relying on the dissemination of coordination directives among group members across a shared end-to-end multicast

WDM Network and Multicasting Protocol Strategies

PubMed Central

Zaim, Abdul Halim

2014-01-01

Optical technology gains extensive attention and ever increasing improvement because of the huge amount of network traffic caused by the growing number of internet users and their rising demands. However, with wavelength division multiplexing (WDM), it is easier to take the advantage of optical networks and optical burst switching (OBS) and to construct WDM networks with low delay rates and better data transparency these technologies are the best choices. Furthermore, multicasting in WDM is an urgent solution for bandwidth-intensive applications. In the paper, a new multicasting protocol with OBS is proposed. The protocol depends on a leaf initiated structure. The network is composed of source, ingress switches, intermediate switches, edge switches, and client nodes. The performance of the protocol is examined with Just Enough Time (JET) and Just In Time (JIT) reservation protocols. Also, the paper involves most of the recent advances about WDM multicasting in optical networks. WDM multicasting in optical networks is given as three common subtitles: Broadcast and-select networks, wavelength-routed networks, and OBS networks. Also, in the paper, multicast routing protocols are briefly summarized and optical burst switched WDM networks are investigated with the proposed multicast schemes. PMID:24744683

Point-to-Point Multicast Communications Protocol

NASA Technical Reports Server (NTRS)

Byrd, Gregory T.; Nakano, Russell; Delagi, Bruce A.

1987-01-01

This paper describes a protocol to support point-to-point interprocessor communications with multicast. Dynamic, cut-through routing with local flow control is used to provide a high-throughput, low-latency communications path between processors. In addition multicast transmissions are available, in which copies of a packet are sent to multiple destinations using common resources as much as possible. Special packet terminators and selective buffering are introduced to avoid a deadlock during multicasts. A simulated implementation of the protocol is also described.

High-Performance, Reliable Multicasting: Foundations for Future Internet Groupware Applications

NASA Technical Reports Server (NTRS)

Callahan, John; Montgomery, Todd; Whetten, Brian

1997-01-01

Network protocols that provide efficient, reliable, and totally-ordered message delivery to large numbers of users will be needed to support many future Internet applications. The Reliable Multicast Protocol (RMP) is implemented on top of IP multicast to facilitate reliable transfer of data for replicated databases and groupware applications that will emerge on the Internet over the next decade. This paper explores some of the basic questions and applications of reliable multicasting in the context of the development and analysis of RMP.

Simultaneous multichannel wavelength multicasting and XOR logic gate multicasting for three DPSK signals based on four-wave mixing in quantum-dot semiconductor optical amplifier.

PubMed

Qin, Jun; Lu, Guo-Wei; Sakamoto, Takahide; Akahane, Kouichi; Yamamoto, Naokatsu; Wang, Danshi; Wang, Cheng; Wang, Hongxiang; Zhang, Min; Kawanishi, Tetsuya; Ji, Yuefeng

2014-12-01

In this paper, we experimentally demonstrate simultaneous multichannel wavelength multicasting (MWM) and exclusive-OR logic gate multicasting (XOR-LGM) for three 10Gbps non-return-to-zero differential phase-shift-keying (NRZ-DPSK) signals in quantum-dot semiconductor optical amplifier (QD-SOA) by exploiting the four-wave mixing (FWM) process. No additional pump is needed in the scheme. Through the interaction of the input three 10Gbps DPSK signal lights in QD-SOA, each channel is successfully multicasted to three wavelengths (1-to-3 for each), totally 3-to-9 MWM, and at the same time, three-output XOR-LGM is obtained at three different wavelengths. All the new generated channels are with a power penalty less than 1.2dB at a BER of 10(-9). Degenerate and non-degenerate FWM components are fully used in the experiment for data and logic multicasting.

Minimum Interference Channel Assignment Algorithm for Multicast in a Wireless Mesh Network.

PubMed

Choi, Sangil; Park, Jong Hyuk

2016-12-02

Wireless mesh networks (WMNs) have been considered as one of the key technologies for the configuration of wireless machines since they emerged. In a WMN, wireless routers provide multi-hop wireless connectivity between hosts in the network and also allow them to access the Internet via gateway devices. Wireless routers are typically equipped with multiple radios operating on different channels to increase network throughput. Multicast is a form of communication that delivers data from a source to a set of destinations simultaneously. It is used in a number of applications, such as distributed games, distance education, and video conferencing. In this study, we address a channel assignment problem for multicast in multi-radio multi-channel WMNs. In a multi-radio multi-channel WMN, two nearby nodes will interfere with each other and cause a throughput decrease when they transmit on the same channel. Thus, an important goal for multicast channel assignment is to reduce the interference among networked devices. We have developed a minimum interference channel assignment (MICA) algorithm for multicast that accurately models the interference relationship between pairs of multicast tree nodes using the concept of the interference factor and assigns channels to tree nodes to minimize interference within the multicast tree. Simulation results show that MICA achieves higher throughput and lower end-to-end packet delay compared with an existing channel assignment algorithm named multi-channel multicast (MCM). In addition, MICA achieves much lower throughput variation among the destination nodes than MCM.

Minimum Interference Channel Assignment Algorithm for Multicast in a Wireless Mesh Network

PubMed Central

Choi, Sangil; Park, Jong Hyuk

2016-01-01

Wireless mesh networks (WMNs) have been considered as one of the key technologies for the configuration of wireless machines since they emerged. In a WMN, wireless routers provide multi-hop wireless connectivity between hosts in the network and also allow them to access the Internet via gateway devices. Wireless routers are typically equipped with multiple radios operating on different channels to increase network throughput. Multicast is a form of communication that delivers data from a source to a set of destinations simultaneously. It is used in a number of applications, such as distributed games, distance education, and video conferencing. In this study, we address a channel assignment problem for multicast in multi-radio multi-channel WMNs. In a multi-radio multi-channel WMN, two nearby nodes will interfere with each other and cause a throughput decrease when they transmit on the same channel. Thus, an important goal for multicast channel assignment is to reduce the interference among networked devices. We have developed a minimum interference channel assignment (MICA) algorithm for multicast that accurately models the interference relationship between pairs of multicast tree nodes using the concept of the interference factor and assigns channels to tree nodes to minimize interference within the multicast tree. Simulation results show that MICA achieves higher throughput and lower end-to-end packet delay compared with an existing channel assignment algorithm named multi-channel multicast (MCM). In addition, MICA achieves much lower throughput variation among the destination nodes than MCM. PMID:27918438

MTP: An atomic multicast transport protocol

NASA Technical Reports Server (NTRS)

Freier, Alan O.; Marzullo, Keith

1990-01-01

Multicast transport protocol (MTP); a reliable transport protocol that utilizes the multicast strategy of applicable lower layer network architectures is described. In addition to transporting data reliably and efficiently, MTP provides the client synchronization necessary for agreement on the receipt of data and the joining of the group of communicants.

Link importance incorporated failure probability measuring solution for multicast light-trees in elastic optical networks

NASA Astrophysics Data System (ADS)

Li, Xin; Zhang, Lu; Tang, Ying; Huang, Shanguo

2018-03-01

The light-tree-based optical multicasting (LT-OM) scheme provides a spectrum- and energy-efficient method to accommodate emerging multicast services. Some studies focus on the survivability technologies for LTs against a fixed number of link failures, such as single-link failure. However, a few studies involve failure probability constraints when building LTs. It is worth noting that each link of an LT plays different important roles under failure scenarios. When calculating the failure probability of an LT, the importance of its every link should be considered. We design a link importance incorporated failure probability measuring solution (LIFPMS) for multicast LTs under independent failure model and shared risk link group failure model. Based on the LIFPMS, we put forward the minimum failure probability (MFP) problem for the LT-OM scheme. Heuristic approaches are developed to address the MFP problem in elastic optical networks. Numerical results show that the LIFPMS provides an accurate metric for calculating the failure probability of multicast LTs and enhances the reliability of the LT-OM scheme while accommodating multicast services.

Mobility based key management technique for multicast security in mobile ad hoc networks.

PubMed

Madhusudhanan, B; Chitra, S; Rajan, C

2015-01-01

In MANET multicasting, forward and backward secrecy result in increased packet drop rate owing to mobility. Frequent rekeying causes large message overhead which increases energy consumption and end-to-end delay. Particularly, the prevailing group key management techniques cause frequent mobility and disconnections. So there is a need to design a multicast key management technique to overcome these problems. In this paper, we propose the mobility based key management technique for multicast security in MANET. Initially, the nodes are categorized according to their stability index which is estimated based on the link availability and mobility. A multicast tree is constructed such that for every weak node, there is a strong parent node. A session key-based encryption technique is utilized to transmit a multicast data. The rekeying process is performed periodically by the initiator node. The rekeying interval is fixed depending on the node category so that this technique greatly minimizes the rekeying overhead. By simulation results, we show that our proposed approach reduces the packet drop rate and improves the data confidentiality.

Many-to-Many Multicast Routing Schemes under a Fixed Topology

PubMed Central

Ding, Wei; Wang, Hongfa; Wei, Xuerui

2013-01-01

Many-to-many multicast routing can be extensively applied in computer or communication networks supporting various continuous multimedia applications. The paper focuses on the case where all users share a common communication channel while each user is both a sender and a receiver of messages in multicasting as well as an end user. In this case, the multicast tree appears as a terminal Steiner tree (TeST). The problem of finding a TeST with a quality-of-service (QoS) optimization is frequently NP-hard. However, we discover that it is a good idea to find a many-to-many multicast tree with QoS optimization under a fixed topology. In this paper, we are concerned with three kinds of QoS optimization objectives of multicast tree, that is, the minimum cost, minimum diameter, and maximum reliability. All of three optimization problems are distributed into two types, the centralized and decentralized version. This paper uses the dynamic programming method to devise an exact algorithm, respectively, for the centralized and decentralized versions of each optimization problem. PMID:23589706

Dynamic segment shared protection for multicast traffic in meshed wavelength-division-multiplexing optical networks

NASA Astrophysics Data System (ADS)

Liao, Luhua; Li, Lemin; Wang, Sheng

2006-12-01

We investigate the protection approach for dynamic multicast traffic under shared risk link group (SRLG) constraints in meshed wavelength-division-multiplexing optical networks. We present a shared protection algorithm called dynamic segment shared protection for multicast traffic (DSSPM), which can dynamically adjust the link cost according to the current network state and can establish a primary light-tree as well as corresponding SRLG-disjoint backup segments for a dependable multicast connection. A backup segment can efficiently share the wavelength capacity of its working tree and the common resources of other backup segments based on SRLG-disjoint constraints. The simulation results show that DSSPM not only can protect the multicast sessions against a single-SRLG breakdown, but can make better use of the wavelength resources and also lower the network blocking probability.

Near-field self-interference cancellation and quality of service multicast beamforming in full-duplex

NASA Astrophysics Data System (ADS)

Wu, Fei; Shao, Shihai; Tang, Youxi

2016-10-01

To enable simultaneous multicast downlink transmit and receive operations on the same frequency band, also known as full-duplex links between an access point and mobile users. The problem of minimizing the total power of multicast transmit beamforming is considered from the viewpoint of ensuring the suppression amount of near-field line-of-sight self-interference and guaranteeing prescribed minimum signal-to-interference-plus-noise-ratio (SINR) at each receiver of the multicast groups. Based on earlier results for multicast groups beamforming, the joint problem is easily shown to be NP-hard. A semidefinite relaxation (SDR) technique with linear program power adjust method is proposed to solve the NP-hard problem. Simulation shows that the proposed method is feasible even when the local receive antenna in nearfield and the mobile user in far-filed are in the same direction.

An efficient group multicast routing for multimedia communication

NASA Astrophysics Data System (ADS)

Wang, Yanlin; Sun, Yugen; Yan, Xinfang

2004-04-01

Group multicasting is a kind of communication mechanism whereby each member of a group sends messages to all the other members of the same group. Group multicast routing algorithms capable of satisfying quality of service (QoS) requirements of multimedia applications are essential for high-speed networks. We present a heuristic algorithm for group multicast routing with end to end delay constraint. Source-specific routing trees for each member are generated in our algorithm, which satisfy member"s bandwidth and end to end delay requirements. Simulations over random network were carried out to compare proposed algorithm performance with Low and Song"s. The experimental results show that our proposed algorithm performs better in terms of network cost and ability in constructing feasible multicast trees for group members. Moreover, our algorithm achieves good performance in balancing traffic, which can avoid link blocking and enhance the network behavior efficiently.

Multicast Routing and Wavelength Assignment with Shared Protection in Multi-Fiber WDM Mesh Networks: Optimal and Heuristic Solutions

NASA Astrophysics Data System (ADS)

Woradit, Kampol; Guyot, Matthieu; Vanichchanunt, Pisit; Saengudomlert, Poompat; Wuttisittikulkij, Lunchakorn

While the problem of multicast routing and wavelength assignment (MC-RWA) in optical wavelength division multiplexing (WDM) networks has been investigated, relatively few researchers have considered network survivability for multicasting. This paper provides an optimization framework to solve the MC-RWA problem in a multi-fiber WDM network that can recover from a single-link failure with shared protection. Using the light-tree (LT) concept to support multicast sessions, we consider two protection strategies that try to reduce service disruptions after a link failure. The first strategy, called light-tree reconfiguration (LTR) protection, computes a new multicast LT for each session affected by the failure. The second strategy, called optical branch reconfiguration (OBR) protection, tries to restore a logical connection between two adjacent multicast members disconnected by the failure. To solve the MC-RWA problem optimally, we propose an integer linear programming (ILP) formulation that minimizes the total number of fibers required for both working and backup traffic. The ILP formulation takes into account joint routing of working and backup traffic, the wavelength continuity constraint, and the limited splitting degree of multicast-capable optical cross-connects (MC-OXCs). After showing some numerical results for optimal solutions, we propose heuristic algorithms that reduce the computational complexity and make the problem solvable for large networks. Numerical results suggest that the proposed heuristic yields efficient solutions compared to optimal solutions obtained from exact optimization.

Dynamic multicast routing scheme in WDM optical network

NASA Astrophysics Data System (ADS)

Zhu, Yonghua; Dong, Zhiling; Yao, Hong; Yang, Jianyong; Liu, Yibin

2007-11-01

During the information era, the Internet and the service of World Wide Web develop rapidly. Therefore, the wider and wider bandwidth is required with the lower and lower cost. The demand of operation turns out to be diversified. Data, images, videos and other special transmission demands share the challenge and opportunity with the service providers. Simultaneously, the electrical equipment has approached their limit. So the optical communication based on the wavelength division multiplexing (WDM) and the optical cross-connects (OXCs) shows great potentials and brilliant future to build an optical network based on the unique technical advantage and multi-wavelength characteristic. In this paper, we propose a multi-layered graph model with inter-path between layers to solve the problem of multicast routing wavelength assignment (RWA) contemporarily by employing an efficient graph theoretic formulation. And at the same time, an efficient dynamic multicast algorithm named Distributed Message Copying Multicast (DMCM) mechanism is also proposed. The multicast tree with minimum hops can be constructed dynamically according to this proposed scheme.

Performance investigation of optical multicast overlay system using orthogonal modulation format

NASA Astrophysics Data System (ADS)

Singh, Simranjit; Singh, Sukhbir; Kaur, Ramandeep; Kaler, R. S.

2015-03-01

We proposed a bandwidth efficient wavelength division multiplexed-passive optical network (WDM-PON) to simultaneously transmit 60 Gb/s unicast and 10 Gb/s multicast services with 10 Gb/s upstream. The differential phase shift keying (DPSK) multicast signal is superimposed onto multiplexed non-return to zero/polarization shift keying (NRZ/PolSK) orthogonal modulated data signals. Upstream amplitude shift keying (ASK) signals formed without use of any additional light source and superimposed onto received unicast NRZ/PolSK signal before being transmitted back to optical line terminal (OLT). We also investigated the proposed WDM-PON system for variable optical input power, transmission distance of single mode fiber in multicast enable and disable mode. The measured Quality factor for all unicast and multicast signal is in acceptable range (>6). The original contribution of this paper is to propose a bandwidth efficient WDM-PON system that could be projected even in high speed scenario at reduced channel spacing and expected to be more technical viable due to use of optical orthogonal modulation formats.

Scalable Multicast Protocols for Overlapped Groups in Broker-Based Sensor Networks

NASA Astrophysics Data System (ADS)

Kim, Chayoung; Ahn, Jinho

In sensor networks, there are lots of overlapped multicast groups because of many subscribers, associated with their potentially varying specific interests, querying every event to sensors/publishers. And gossip based communication protocols are promising as one of potential solutions providing scalability in P(Publish)/ S(Subscribe) paradigm in sensor networks. Moreover, despite the importance of both guaranteeing message delivery order and supporting overlapped multicast groups in sensor or P2P networks, there exist little research works on development of gossip-based protocols to satisfy all these requirements. In this paper, we present two versions of causally ordered delivery guaranteeing protocols for overlapped multicast groups. The one is based on sensor-broker as delegates and the other is based on local views and delegates representing subscriber subgroups. In the sensor-broker based protocol, sensor-broker might lead to make overlapped multicast networks organized by subscriber's interests. The message delivery order has been guaranteed consistently and all multicast messages are delivered to overlapped subscribers using gossip based protocols by sensor-broker. Therefore, these features of the sensor-broker based protocol might be significantly scalable rather than those of the protocols by hierarchical membership list of dedicated groups like traditional committee protocols. And the subscriber-delegate based protocol is much stronger rather than fully decentralized protocols guaranteeing causally ordered delivery based on only local views because the message delivery order has been guaranteed consistently by all corresponding members of the groups including delegates. Therefore, this feature of the subscriber-delegate protocol is a hybrid approach improving the inherent scalability of multicast nature by gossip-based technique in all communications.

Inertial Motion Tracking for Inserting Humans into a Networked Synthetic Environment

DTIC Science & Technology

2007-08-31

tracking methods. One method requires markers on the tracked buman body, and other method does not use nmkers. OPTOTRAK from Northem Digital Inc. is a...of using multicasting protocols. Unfortunately, most routers on the Internet are not configured for multicasting. A technique called tunneling is...used to overcome this problem. Tunneling is a software solution that m s on the end point routerslcomputers and allows multicast packets to traverse

Authenticated IGMP for Controlling Access to Multicast Distribution Tree

NASA Astrophysics Data System (ADS)

Park, Chang-Seop; Kang, Hyun-Sun

A receiver access control scheme is proposed to protect the multicast distribution tree from DoS attack induced by unauthorized use of IGMP, by extending the security-related functionality of IGMP. Based on a specific network and business model adopted for commercial deployment of IP multicast applications, a key management scheme is also presented for bootstrapping the proposed access control as well as accounting and billing for CP (Content Provider), NSP (Network Service Provider), and group members.

Mobility based multicast routing in wireless mesh networks

NASA Astrophysics Data System (ADS)

Jain, Sanjeev; Tripathi, Vijay S.; Tiwari, Sudarshan

2013-01-01

There exist two fundamental approaches to multicast routing namely minimum cost trees and shortest path trees. The (MCT's) minimum cost tree is one which connects receiver and sources by providing a minimum number of transmissions (MNTs) the MNTs approach is generally used for energy constraint sensor and mobile ad hoc networks. In this paper we have considered node mobility and try to find out simulation based comparison of the (SPT's) shortest path tree, (MST's) minimum steiner trees and minimum number of transmission trees in wireless mesh networks by using the performance metrics like as an end to end delay, average jitter, throughput and packet delivery ratio, average unicast packet delivery ratio, etc. We have also evaluated multicast performance in the small and large wireless mesh networks. In case of multicast performance in the small networks we have found that when the traffic load is moderate or high the SPTs outperform the MSTs and MNTs in all cases. The SPTs have lowest end to end delay and average jitter in almost all cases. In case of multicast performance in the large network we have seen that the MSTs provide minimum total edge cost and minimum number of transmissions. We have also found that the one drawback of SPTs, when the group size is large and rate of multicast sending is high SPTs causes more packet losses to other flows as MCTs.

The Verification-based Analysis of Reliable Multicast Protocol

NASA Technical Reports Server (NTRS)

Wu, Yunqing

1996-01-01

Reliable Multicast Protocol (RMP) is a communication protocol that provides an atomic, totally ordered, reliable multicast service on top of unreliable IP Multicasting. In this paper, we develop formal models for R.W using existing automatic verification systems, and perform verification-based analysis on the formal RMP specifications. We also use the formal models of RW specifications to generate a test suite for conformance testing of the RMP implementation. Throughout the process of RMP development, we follow an iterative, interactive approach that emphasizes concurrent and parallel progress between the implementation and verification processes. Through this approach, we incorporate formal techniques into our development process, promote a common understanding for the protocol, increase the reliability of our software, and maintain high fidelity between the specifications of RMP and its implementation.

ISIS and META projects

NASA Technical Reports Server (NTRS)

Birman, Kenneth; Cooper, Robert; Marzullo, Keith

1990-01-01

The ISIS project has developed a new methodology, virtual synchony, for writing robust distributed software. High performance multicast, large scale applications, and wide area networks are the focus of interest. Several interesting applications that exploit the strengths of ISIS, including an NFS-compatible replicated file system, are being developed. The META project is distributed control in a soft real-time environment incorporating feedback. This domain encompasses examples as diverse as monitoring inventory and consumption on a factory floor, and performing load-balancing on a distributed computing system. One of the first uses of META is for distributed application management: the tasks of configuring a distributed program, dynamically adapting to failures, and monitoring its performance. Recent progress and current plans are reported.

The reliable multicast protocol application programming interface

NASA Technical Reports Server (NTRS)

Montgomery , Todd; Whetten, Brian

1995-01-01

The Application Programming Interface for the Berkeley/WVU implementation of the Reliable Multicast Protocol is described. This transport layer protocol is implemented as a user library that applications and software buses link against.

Multicast backup reprovisioning problem for Hamiltonian cycle-based protection on WDM networks

NASA Astrophysics Data System (ADS)

Din, Der-Rong; Huang, Jen-Shen

2014-03-01

As networks grow in size and complexity, the chance and the impact of failures increase dramatically. The pre-allocated backup resources cannot provide 100% protection guarantee when continuous failures occur in a network. In this paper, the multicast backup re-provisioning problem (MBRP) for Hamiltonian cycle (HC)-based protection on WDM networks for the link-failure case is studied. We focus on how to recover the protecting capabilities of Hamiltonian cycle against the subsequent link-failures on WDM networks for multicast transmissions, after recovering the multicast trees affected by the previous link-failure. Since this problem is a hard problem, an algorithm, which consists of several heuristics and a genetic algorithm (GA), is proposed to solve it. The simulation results of the proposed method are also given. Experimental results indicate that the proposed algorithm can solve this problem efficiently.

The specification-based validation of reliable multicast protocol: Problem Report. M.S. Thesis

NASA Technical Reports Server (NTRS)

Wu, Yunqing

1995-01-01

Reliable Multicast Protocol (RMP) is a communication protocol that provides an atomic, totally ordered, reliable multicast service on top of unreliable IP multicasting. In this report, we develop formal models for RMP using existing automated verification systems, and perform validation on the formal RMP specifications. The validation analysis help identifies some minor specification and design problems. We also use the formal models of RMP to generate a test suite for conformance testing of the implementation. Throughout the process of RMP development, we follow an iterative, interactive approach that emphasizes concurrent and parallel progress of implementation and verification processes. Through this approach, we incorporate formal techniques into our development process, promote a common understanding for the protocol, increase the reliability of our software, and maintain high fidelity between the specifications of RMP and its implementation.

Flexible and re-configurable optical three-input XOR logic gate of phase-modulated signals with multicast functionality for potential application in optical physical-layer network coding.

PubMed

Lu, Guo-Wei; Qin, Jun; Wang, Hongxiang; Ji, XuYuefeng; Sharif, Gazi Mohammad; Yamaguchi, Shigeru

2016-02-08

Optical logic gate, especially exclusive-or (XOR) gate, plays important role in accomplishing photonic computing and various network functionalities in future optical networks. On the other hand, optical multicast is another indispensable functionality to efficiently deliver information in optical networks. In this paper, for the first time, we propose and experimentally demonstrate a flexible optical three-input XOR gate scheme for multiple input phase-modulated signals with a 1-to-2 multicast functionality for each XOR operation using four-wave mixing (FWM) effect in single piece of highly-nonlinear fiber (HNLF). Through FWM in HNLF, all of the possible XOR operations among input signals could be simultaneously realized by sharing a single piece of HNLF. By selecting the obtained XOR components using a followed wavelength selective component, the number of XOR gates and the participant light in XOR operations could be flexibly configured. The re-configurability of the proposed XOR gate and the function integration of the optical logic gate and multicast in single device offer the flexibility in network design and improve the network efficiency. We experimentally demonstrate flexible 3-input XOR gate for four 10-Gbaud binary phase-shift keying signals with a multicast scale of 2. Error-free operations for the obtained XOR results are achieved. Potential application of the integrated XOR and multicast function in network coding is also discussed.

Demonstration of flexible multicasting and aggregation functionality for TWDM-PON

NASA Astrophysics Data System (ADS)

Chen, Yuanxiang; Li, Juhao; Zhu, Paikun; Zhu, Jinglong; Tian, Yu; Wu, Zhongying; Peng, Huangfa; Xu, Yongchi; Chen, Jingbiao; He, Yongqi; Chen, Zhangyuan

2017-06-01

The time- and wavelength-division multiplexed passive optical network (TWDM-PON) has been recognized as an attractive solution to provide broadband access for the next-generation networks. In this paper, we propose flexible service multicasting and aggregation functionality for TWDM-PON utilizing multiple-pump four-wave-mixing (FWM) and cyclic arrayed waveguide grating (AWG). With the proposed scheme, multiple TWDM-PON links share a single optical line terminal (OLT), which can greatly reduce the network deployment expense and achieve efficient network resource utilization by load balancing among different optical distribution networks (ODNs). The proposed scheme is compatible with existing TDM-PON infrastructure with fixed-wavelength OLT transmitter, thus smooth service upgrade can be achieved. Utilizing the proposed scheme, we demonstrate a proof-of-concept experiment with 10-Gb/s OOK and 10-Gb/s QPSK orthogonal frequency division multiplexing (OFDM) signal multicasting and aggregating to seven PON links. Compared with back-to-back (BTB) channel, the newly generated multicasting OOK signal and OFDM signal have power penalty of 1.6 dB and 2 dB at the BER of 10-3, respectively. For the aggregation of multiple channels, no obvious power penalty is observed. What is more, to verify the flexibility of the proposed scheme, we reconfigure the wavelength selective switch (WSS) and adjust the number of pumps to realize flexible multicasting functionality. One to three, one to seven, one to thirteen and one to twenty-one multicasting are achieved without modifying OLT structure.

A Discontinuous Potential Model for Protein-Protein Interactions.

PubMed

Shao, Qing; Hall, Carol K

2016-01-01

Protein-protein interactions play an important role in many biologic and industrial processes. In this work, we develop a two-bead-per-residue model that enables us to account for protein-protein interactions in a multi-protein system using discontinuous molecular dynamics simulations. This model deploys discontinuous potentials to describe the non-bonded interactions and virtual bonds to keep proteins in their native state. The geometric and energetic parameters are derived from the potentials of mean force between sidechain-sidechain, sidechain-backbone, and backbone-backbone pairs. The energetic parameters are scaled with the aim of matching the second virial coefficient of lysozyme reported in experiment. We also investigate the performance of several bond-building strategies.

Digital multi-channel stabilization of four-mode phase-sensitive parametric multicasting.

PubMed

Liu, Lan; Tong, Zhi; Wiberg, Andreas O J; Kuo, Bill P P; Myslivets, Evgeny; Alic, Nikola; Radic, Stojan

2014-07-28

Stable four-mode phase-sensitive (4MPS) process was investigated as a means to enhance two-pump driven parametric multicasting conversion efficiency (CE) and signal to noise ratio (SNR). Instability of multi-beam, phase sensitive (PS) device that inherently behaves as an interferometer, with output subject to ambient induced fluctuations, was addressed theoretically and experimentally. A new stabilization technique that controls phases of three input waves of the 4MPS multicaster and maximizes CE was developed and described. Stabilization relies on digital phase-locked loop (DPLL) specifically was developed to control pump phases to guarantee stable 4MPS operation that is independent of environmental fluctuations. The technique also controls a single (signal) input phase to optimize the PS-induced improvement of the CE and SNR. The new, continuous-operation DPLL has allowed for fully stabilized PS parametric broadband multicasting, demonstrating CE improvement over 20 signal copies in excess of 10 dB.

Multicast Routing of Hierarchical Data

NASA Technical Reports Server (NTRS)

Shacham, Nachum

1992-01-01

The issue of multicast of broadband, real-time data in a heterogeneous environment, in which the data recipients differ in their reception abilities, is considered. Traditional multicast schemes, which are designed to deliver all the source data to all recipients, offer limited performance in such an environment, since they must either force the source to overcompress its signal or restrict the destination population to those who can receive the full signal. We present an approach for resolving this issue by combining hierarchical source coding techniques, which allow recipients to trade off reception bandwidth for signal quality, and sophisticated routing algorithms that deliver to each destination the maximum possible signal quality. The field of hierarchical coding is briefly surveyed and new multicast routing algorithms are presented. The algorithms are compared in terms of network utilization efficiency, lengths of paths, and the required mechanisms for forwarding packets on the resulting paths.

Multifunctional switching unit for add/drop, wavelength conversion, format conversion, and WDM multicast based on bidirectional LCoS and SOA-loop architecture.

PubMed

Wang, Danshi; Zhang, Min; Qin, Jun; Lu, Guo-Wei; Wang, Hongxiang; Huang, Shanguo

2014-09-08

We propose a multifunctional optical switching unit based on the bidirectional liquid crystal on silicon (LCoS) and semiconductor optical amplifier (SOA) architecture. Add/drop, wavelength conversion, format conversion, and WDM multicast are experimentally demonstrated. Due to the bidirectional characteristic, the LCoS device cannot only multiplex the input signals, but also de-multiplex the converted signals. Dual-channel wavelength conversion and format conversion from 2 × 25Gbps differential quadrature phase-shift-keying (DQPSK) to 2 × 12.5Gbps differential phase-shift-keying (DPSK) based on four-wave mixing (FWM) in SOA is obtained with only one pump. One-to-six WDM multicast of 25Gbps DQPSK signals with two pumps is also achieved. All of the multicast channels are with a power penalty less than 1.1 dB at FEC threshold of 3.8 × 10⁻³.

Multisites Coordination in Shared Multicast Trees

DTIC Science & Technology

1999-01-01

conferencing, distributed interactive simulations, and collaborative systems. We de- scribe a novel protocol to coordinate multipoint groupwork in the IP...multicast framework. The pro- tocol supports Internet-wide coordination for large and highly-interactive groupwork , relying on trans- mission of

Short-distance probes for protein backbone structure based on energy transfer between bimane and transition metal ions

PubMed Central

Taraska, Justin W.; Puljung, Michael C.; Zagotta, William N.

2009-01-01

The structure and dynamics of proteins underlies the workings of virtually every biological process. Existing biophysical methods are inadequate to measure protein structure at atomic resolution, on a rapid time scale, with limited amounts of protein, and in the context of a cell or membrane. FRET can measure distances between two probes, but depends on the orientation of the probes and typically works only over long distances comparable with the size of many proteins. Also, common probes used for FRET can be large and have long, flexible attachment linkers that position dyes far from the protein backbone. Here, we improve and extend a fluorescence method called transition metal ion FRET that uses energy transfer to transition metal ions as a reporter of short-range distances in proteins with little orientation dependence. This method uses a very small cysteine-reactive dye monobromobimane, with virtually no linker, and various transition metal ions bound close to the peptide backbone as the acceptor. We show that, unlike larger fluorophores and longer linkers, this donor–acceptor pair accurately reports short-range distances and changes in backbone distances. We further extend the method by using cysteine-reactive metal chelators, which allow the technique to be used in protein regions of unknown secondary structure or when native metal ion binding sites are present. This improved method overcomes several of the key limitations of classical FRET for intramolecular distance measurements. PMID:19805285

Optimization of multicast optical networks with genetic algorithm

NASA Astrophysics Data System (ADS)

Lv, Bo; Mao, Xiangqiao; Zhang, Feng; Qin, Xi; Lu, Dan; Chen, Ming; Chen, Yong; Cao, Jihong; Jian, Shuisheng

2007-11-01

In this letter, aiming to obtain the best multicast performance of optical network in which the video conference information is carried by specified wavelength, we extend the solutions of matrix games with the network coding theory and devise a new method to solve the complex problems of multicast network switching. In addition, an experimental optical network has been testified with best switching strategies by employing the novel numerical solution designed with an effective way of genetic algorithm. The result shows that optimal solutions with genetic algorithm are accordance with the ones with the traditional fictitious play method.

A Secure Multicast Framework in Large and High-Mobility Network Groups

NASA Astrophysics Data System (ADS)

Lee, Jung-San; Chang, Chin-Chen

With the widespread use of Internet applications such as Teleconference, Pay-TV, Collaborate tasks, and Message services, how to construct and distribute the group session key to all group members securely is becoming and more important. Instead of adopting the point-to-point packet delivery, these emerging applications are based upon the mechanism of multicast communication, which allows the group member to communicate with multi-party efficiently. There are two main issues in the mechanism of multicast communication: Key Distribution and Scalability. The first issue is how to distribute the group session key to all group members securely. The second one is how to maintain the high performance in large network groups. Group members in conventional multicast systems have to keep numerous secret keys in databases, which makes it very inconvenient for them. Furthermore, in case that a member joins or leaves the communication group, many involved participants have to change their own secret keys to preserve the forward secrecy and the backward secrecy. We consequently propose a novel version for providing secure multicast communication in large network groups. Our proposed framework not only preserves the forward secrecy and the backward secrecy but also possesses better performance than existing alternatives. Specifically, simulation results demonstrate that our scheme is suitable for high-mobility environments.

XML Tactical Chat (XTC): The Way Ahead for Navy Chat

DTIC Science & Technology

2007-09-01

multicast transmissions via sophisticated pruning algorithms, while allowing multicast packets to “ tunnel ” through IP routers. [Macedonia, Brutzman 1994...conference was Jabber Inc. who added some great insight into the power of Jabber. • Great features including blackberry handheld connectivity and

An FEC Adaptive Multicast MAC Protocol for Providing Reliability in WLANs

NASA Astrophysics Data System (ADS)

Basalamah, Anas; Sato, Takuro

For wireless multicast applications like multimedia conferencing, voice over IP and video/audio streaming, a reliable transmission of packets within short delivery delay is needed. Moreover, reliability is crucial to the performance of error intolerant applications like file transfer, distributed computing, chat and whiteboard sharing. Forward Error Correction (FEC) is frequently used in wireless multicast to enhance Packet Error Rate (PER) performance, but cannot assure full reliability unless coupled with Automatic Repeat Request forming what is knows as Hybrid-ARQ. While reliable FEC can be deployed at different levels of the protocol stack, it cannot be deployed on the MAC layer of the unreliable IEEE802.11 WLAN due to its inability to exchange ACKs with multiple recipients. In this paper, we propose a Multicast MAC protocol that enhances WLAN reliability by using Adaptive FEC and study it's performance through mathematical analysis and simulation. Our results show that our protocol can deliver high reliability and throughput performance.

Analysis on Multicast Routing Protocols for Mobile Ad Hoc Networks

NASA Astrophysics Data System (ADS)

Xiang, Ma

As the Mobile Ad Hoc Networks technologies face a series of challenges like dynamic changes of topological structure, existence of unidirectional channel, limited wireless transmission bandwidth, the capability limitations of mobile termination and etc, therefore, the research to mobile Ad Hoc network routings inevitablely undertake a more important task than those to other networks. Multicast is a mode of communication transmission oriented to group computing, which sends the data to a group of host computers by using single source address. In a typical mobile Ad Hoc Network environment, multicast has a significant meaning. On the one hand, the users of mobile Ad Hoc Network usually need to form collaborative working groups; on the other hand, this is also an important means of fully using the broadcast performances of wireless communication and effectively using the limited wireless channel resources. This paper summarizes and comparatively analyzes the routing mechanisms of various existing multicast routing protocols according to the characteristics of mobile Ad Hoc network.

WDM/TDM PON experiments using the AWG free spectral range periodicity to transmit unicast and multicast data

NASA Astrophysics Data System (ADS)

Bock, Carlos; Prat, Josep

2005-04-01

A hybrid WDM/TDM PON architecture implemented by means of two cascaded Arrayed Waveguide Gratings (AWG) is presented. Using the Free Spectral Range (FSR) periodicity of AWGs we transmit unicast and multicast traffic on different wavelengths to each Optical Network Unit (ONU). The OLT is equipped with two laser stacks, a tunable one for unicast transmission and a fixed one for multicast transmission. We propose the ONU to be reflective in order to avoid any light source at the Costumer Premises Equipment (CPE). Optical transmission tests demonstrate correct transmission at 2.5 Gbps up to 30 km.

Performance Evaluation of Reliable Multicast Protocol for Checkout and Launch Control Systems

NASA Technical Reports Server (NTRS)

Shu, Wei Wennie; Porter, John

2000-01-01

The overall objective of this project is to study reliability and performance of Real Time Critical Network (RTCN) for checkout and launch control systems (CLCS). The major tasks include reliability and performance evaluation of Reliable Multicast (RM) package and fault tolerance analysis and design of dual redundant network architecture.

A Low-Complexity Subgroup Formation with QoS-Aware for Enhancing Multicast Services in LTE Networks

NASA Astrophysics Data System (ADS)

Algharem, M.; Omar, M. H.; Rahmat, R. F.; Budiarto, R.

2018-03-01

The high demand of Multimedia services on in Long Term Evolution (LTE) and beyond networks forces the networks operators to find a solution that can handle the huge traffic. Along with this, subgroup formation techniques are introduced to overcome the limitations of the Conventional Multicast Scheme (CMS) by splitting the multicast users into several subgroups based on the users’ channels quality signal. However, finding the best subgroup configuration with low complexity is need more investigations. In this paper, an efficient and simple subgroup formation mechanisms are proposed. The proposed mechanisms take the transmitter MAC queue in account. The effectiveness of the proposed mechanisms is evaluated and compared with CMS in terms of throughput, fairness, delay, Block Error Rate (BLER).

Proxy-assisted multicasting of video streams over mobile wireless networks

NASA Astrophysics Data System (ADS)

Nguyen, Maggie; Pezeshkmehr, Layla; Moh, Melody

2005-03-01

This work addresses the challenge of providing seamless multimedia services to mobile users by proposing a proxy-assisted multicast architecture for delivery of video streams. We propose a hybrid system of streaming proxies, interconnected by an application-layer multicast tree, where each proxy acts as a cluster head to stream out content to its stationary and mobile users. The architecture is based on our previously proposed Enhanced-NICE protocol, which uses an application-layer multicast tree to deliver layered video streams to multiple heterogeneous receivers. We targeted the study on placements of streaming proxies to enable efficient delivery of live and on-demand video, supporting both stationary and mobile users. The simulation results are evaluated and compared with two other baseline scenarios: one with a centralized proxy system serving the entire population and one with mini-proxies each to serve its local users. The simulations are implemented using the J-SIM simulator. The results show that even though proxies in the hybrid scenario experienced a slightly longer delay, they had the lowest drop rate of video content. This finding illustrates the significance of task sharing in multiple proxies. The resulted load balancing among proxies has provided a better video quality delivered to a larger audience.

The Role of the Virtual Astronomical Observatory in the Era of Big Data

NASA Astrophysics Data System (ADS)

Berriman, G. B.; Hanisch, R. J.; Lazio, T. J.

2013-01-01

The Virtual Observatory (VO) is realizing global electronic integration of astronomy data. The rapid growth in the size and complexity of data sets is transforming the computing landscape in astronomy. One of the long-term goals of the U.S. VO project, the Virtual Astronomical Observatory (VAO), is development of an information backbone that responds to this growth. Such a backbone will, when complete, provide innovative mechanisms for fast discovery of, and access to, massive data sets, and services that enable distributed storage, publication processing of large datasets. All these services will be built so that new projects can incorporate them as part of their data management and processing plans. Services under development to date include a general purpose indexing scheme for fast access to data sets, a cross-comparison engine that operate on catalogs of 1 billion records or more, and an interface for managing distributed data sets and connecting them to data discovery and analysis tools. The VAO advises projects on technology solutions for their data access and processing needs, and recently advised the Sagan Workshop on using cloud computing to support hands-on data analysis sessions for 150+ participants. Acknowledgements: The Virtual Astronomical Observatory (VAO) is managed by the VAO, LLC, a non-profit company established as a partnership of the Associated Universities, Inc. and the Association of Universities for Research in Astronomy, Inc. The VAO is sponsored by the National Science Foundation and the National Aeronautics and Space Administration.

Multicasting based optical inverse multiplexing in elastic optical network.

PubMed

Guo, Bingli; Xu, Yingying; Zhu, Paikun; Zhong, Yucheng; Chen, Yuanxiang; Li, Juhao; Chen, Zhangyuan; He, Yongqi

2014-06-16

Optical multicasting based inverse multiplexing (IM) is introduced in spectrum allocation of elastic optical network to resolve the spectrum fragmentation problem, where superchannels could be split and fit into several discrete spectrum blocks in the intermediate node. We experimentally demonstrate it with a 1-to-7 optical superchannel multicasting module and selecting/coupling components. Also, simulation results show that, comparing with several emerging spectrum defragmentation solutions (e.g., spectrum conversion, split spectrum), IM could reduce blocking performance significantly but without adding too much system complexity as split spectrum. On the other hand, service fairness for traffic with different granularity of these schemes is investigated for the first time and it shows that IM performs better than spectrum conversion and almost as well as split spectrum, especially for smaller size traffic under light traffic intensity.

Reliable multicast protocol specifications protocol operations

NASA Technical Reports Server (NTRS)

Callahan, John R.; Montgomery, Todd; Whetten, Brian

1995-01-01

This appendix contains the complete state tables for Reliable Multicast Protocol (RMP) Normal Operation, Multi-RPC Extensions, Membership Change Extensions, and Reformation Extensions. First the event types are presented. Afterwards, each RMP operation state, normal and extended, is presented individually and its events shown. Events in the RMP specification are one of several things: (1) arriving packets, (2) expired alarms, (3) user events, (4) exceptional conditions.

Tera-node Network Technology (Task 3) Scalable Personal Telecommunications

DTIC Science & Technology

2000-03-14

Simulation results of this work may be found in http://north.east.isi.edu/spt/ audio.html. 6. Internet Research Task Force Reliable Multicast...Adaptation, 4. Multimedia Proxy Caching, 5. Experiments with the Rate Adaptation Protocol (RAP) 6. Providing leadership and innovation to the Internet ... Research Task Force (IRTF) Reliable Multicast Research Group (RMRG) 1. End-to-end Architecture for Quality-adaptive Streaming Applications over the

Bulk data transfer distributer: a high performance multicast model in ALMA ACS

NASA Astrophysics Data System (ADS)

Cirami, R.; Di Marcantonio, P.; Chiozzi, G.; Jeram, B.

2006-06-01

A high performance multicast model for the bulk data transfer mechanism in the ALMA (Atacama Large Millimeter Array) Common Software (ACS) is presented. The ALMA astronomical interferometer will consist of at least 50 12-m antennas operating at millimeter wavelength. The whole software infrastructure for ALMA is based on ACS, which is a set of application frameworks built on top of CORBA. To cope with the very strong requirements for the amount of data that needs to be transported by the software communication channels of the ALMA subsystems (a typical output data rate expected from the Correlator is of the order of 64 MB per second) and with the potential CORBA bottleneck due to parameter marshalling/de-marshalling, usage of IIOP protocol, etc., a transfer mechanism based on the ACE/TAO CORBA Audio/Video (A/V) Streaming Service has been developed. The ACS Bulk Data Transfer architecture bypasses the CORBA protocol with an out-of-bound connection for the data streams (transmitting data directly in TCP or UDP format), using at the same time CORBA for handshaking and leveraging the benefits of ACS middleware. Such a mechanism has proven to be capable of high performances, of the order of 800 Mbits per second on a 1Gbit Ethernet network. Besides a point-to-point communication model, the ACS Bulk Data Transfer provides a multicast model. Since the TCP protocol does not support multicasting and all the data must be correctly delivered to all ALMA subsystems, a distributer mechanism has been developed. This paper focuses on the ACS Bulk Data Distributer, which mimics a multicast behaviour managing data dispatching to all receivers willing to get data from the same sender.

Flexible and scalable wavelength multicast of coherent optical OFDM with tolerance against pump phase-noise using reconfigurable coherent multi-carrier pumping.

PubMed

Lu, Guo-Wei; Bo, Tianwai; Sakamoto, Takahide; Yamamoto, Naokatsu; Chan, Calvin Chun-Kit

2016-10-03

Recently the ever-growing demand for dynamic and high-capacity services in optical networks has resulted in new challenges that require improved network agility and flexibility in order for network resources to become more "consumable" and dynamic, or elastic, in response to requests from higher network layers. Flexible and scalable wavelength conversion or multicast is one of the most important technologies needed for developing agility in the physical layer. This paper will investigate how, using a reconfigurable coherent multi-carrier as a pump, the multicast scalability and the flexibility in wavelength allocation of the converted signals can be effectively improved. Moreover, the coherence in the multiple carriers prevents the phase noise transformation from the local pump to the converted signals, which is imperative for the phase-noise-sensitive multi-level single- or multi-carrier modulated signal. To verify the feasibility of the proposed scheme, we experimentally demonstrate the wavelength multicast of coherent optical orthogonal frequency division multiplexing (CO-OFDM) signals using a reconfigurable coherent multi-carrier pump, showing flexibility in wavelength allocation, scalability in multicast, and tolerance against pump phase noise. Less than 0.5 dB and 1.8 dB power penalties at a bit-error rate (BER) of 10^-3 are obtained for the converted CO-OFDM-quadrature phase-shift keying (QPSK) and CO-OFDM-16-ary quadrature amplitude modulation (16QAM) signals, respectively, even when using a distributed feedback laser (DFB) as a pump source. In contrast, with a free-running pumping scheme, the phase noise from DFB pumps severely deteriorates the CO-OFDM signals, resulting in a visible error-floor at a BER of 10^-2 in the converted CO-OFDM-16QAM signals.

Overview of AMS (CCSDS Asynchronous Message Service)

NASA Technical Reports Server (NTRS)

Burleigh, Scott

2006-01-01

This viewgraph presentation gives an overview of the Consultative Committee for Space Data Systems (CCSDS) Asynchronous Message Service (AMS). The topics include: 1) Key Features; 2) A single AMS continuum; 3) The AMS Protocol Suite; 4) A multi-continuum venture; 5) Constraining transmissions; 6) Security; 7) Fault Tolerance; 8) Performance of Reference Implementation; 9) AMS vs Multicast (1); 10) AMS vs Multicast (2); 11) RAMS testing exercise; and 12) Results.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ishihara, T

Currently, the problem at hand is in distributing identical copies of OEP and filter software to a large number of farm nodes. One of the common methods used to transfer these softwares is through unicast. Unicast protocol faces the problem of repetitiously sending the same data over the network. Since the sending rate is limited, this process poses to be a bottleneck. Therefore, one possible solution to this problem lies in creating a reliable multicast protocol. A specific type of multicast protocol is the Bulk Multicast Protocol [4]. This system consists of one sender distributing data to many receivers. Themore » sender delivers data at a given rate of data packets. In response to that, the receiver replies to the sender with a status packet which contains information about the packet loss in terms of Negative Acknowledgment. The probability of the status packet sent back to the sender is+, where N is the number of receivers. The protocol is designed to have approximately 1 status packet for each data packet sent. In this project, we were able to show that the time taken for the complete transfer of a file to multiple receivers was about 12 times faster with multicast than by the use of unicast. The implementation of this experimental protocol shows remarkable improvement in mass data transfer to a large number of farm machines.« less

Robust Group Sparse Beamforming for Multicast Green Cloud-RAN With Imperfect CSI

NASA Astrophysics Data System (ADS)

Shi, Yuanming; Zhang, Jun; Letaief, Khaled B.

2015-09-01

In this paper, we investigate the network power minimization problem for the multicast cloud radio access network (Cloud-RAN) with imperfect channel state information (CSI). The key observation is that network power minimization can be achieved by adaptively selecting active remote radio heads (RRHs) via controlling the group-sparsity structure of the beamforming vector. However, this yields a non-convex combinatorial optimization problem, for which we propose a three-stage robust group sparse beamforming algorithm. In the first stage, a quadratic variational formulation of the weighted mixed l1/l2-norm is proposed to induce the group-sparsity structure in the aggregated beamforming vector, which indicates those RRHs that can be switched off. A perturbed alternating optimization algorithm is then proposed to solve the resultant non-convex group-sparsity inducing optimization problem by exploiting its convex substructures. In the second stage, we propose a PhaseLift technique based algorithm to solve the feasibility problem with a given active RRH set, which helps determine the active RRHs. Finally, the semidefinite relaxation (SDR) technique is adopted to determine the robust multicast beamformers. Simulation results will demonstrate the convergence of the perturbed alternating optimization algorithm, as well as, the effectiveness of the proposed algorithm to minimize the network power consumption for multicast Cloud-RAN.

Hybrid digital-analog video transmission in wireless multicast and multiple-input multiple-output system

NASA Astrophysics Data System (ADS)

Liu, Yu; Lin, Xiaocheng; Fan, Nianfei; Zhang, Lin

2016-01-01

Wireless video multicast has become one of the key technologies in wireless applications. But the main challenge of conventional wireless video multicast, i.e., the cliff effect, remains unsolved. To overcome the cliff effect, a hybrid digital-analog (HDA) video transmission framework based on SoftCast, which transmits the digital bitstream with the quantization residuals, is proposed. With an effective power allocation algorithm and appropriate parameter settings, the residual gains can be maximized; meanwhile, the digital bitstream can assure transmission of a basic video to the multicast receiver group. In the multiple-input multiple-output (MIMO) system, since nonuniform noise interference on different antennas can be regarded as the cliff effect problem, ParCast, which is a variation of SoftCast, is also applied to video transmission to solve it. The HDA scheme with corresponding power allocation algorithms is also applied to improve video performance. Simulations show that the proposed HDA scheme can overcome the cliff effect completely with the transmission of residuals. What is more, it outperforms the compared WSVC scheme by more than 2 dB when transmitting under the same bandwidth, and it can further improve performance by nearly 8 dB in MIMO when compared with the ParCast scheme.

Apply network coding for H.264/SVC multicasting

NASA Astrophysics Data System (ADS)

Wang, Hui; Kuo, C.-C. Jay

2008-08-01

In a packet erasure network environment, video streaming benefits from error control in two ways to achieve graceful degradation. The first approach is application-level (or the link-level) forward error-correction (FEC) to provide erasure protection. The second error control approach is error concealment at the decoder end to compensate lost packets. A large amount of research work has been done in the above two areas. More recently, network coding (NC) techniques have been proposed for efficient data multicast over networks. It was shown in our previous work that multicast video streaming benefits from NC for its throughput improvement. An algebraic model is given to analyze the performance in this work. By exploiting the linear combination of video packets along nodes in a network and the SVC video format, the system achieves path diversity automatically and enables efficient video delivery to heterogeneous receivers in packet erasure channels. The application of network coding can protect video packets against the erasure network environment. However, the rank defficiency problem of random linear network coding makes the error concealment inefficiently. It is shown by computer simulation that the proposed NC video multicast scheme enables heterogenous receiving according to their capacity constraints. But it needs special designing to improve the video transmission performance when applying network coding.

Multicast Parametric Synchronous Sampling

DTIC Science & Technology

2011-09-01

enhancement in a parametric mixer device. Fig. 4 shows the principle of generating uniform, high quality replicas extending over previously un-attainable...critical part of the MPASS architecture and is responsible for the direct and continuous acquisition of data across all of the multicast signal copies...ii) ability to copy THz signals with impunity to tens of replicas ; (iii) all-optical delays > 1.9 us; (iv) 10’s of THz-fast all-optical sampling of

Fault recovery in the reliable multicast protocol

NASA Technical Reports Server (NTRS)

Callahan, John R.; Montgomery, Todd L.; Whetten, Brian

1995-01-01

The Reliable Multicast Protocol (RMP) provides a unique, group-based model for distributed programs that need to handle reconfiguration events at the application layer. This model, called membership views, provides an abstraction in which events such as site failures, network partitions, and normal join-leave events are viewed as group reformations. RMP provides access to this model through an application programming interface (API) that notifies an application when a group is reformed as the result of a some event. RMP provides applications with reliable delivery of messages using an underlying IP Multicast (12, 5) media to other group members in a distributed environment even in the case of reformations. A distributed application can use various Quality of Service (QoS) levels provided by RMP to tolerate group reformations. This paper explores the implementation details of the mechanisms in RMP that provide distributed applications with membership view information and fault recovery capabilities.

Specification and Design of a Fault Recovery Model for the Reliable Multicast Protocol

NASA Technical Reports Server (NTRS)

Montgomery, Todd; Callahan, John R.; Whetten, Brian

1996-01-01

The Reliable Multicast Protocol (RMP) provides a unique, group-based model for distributed programs that need to handle reconfiguration events at the application layer. This model, called membership views, provides an abstraction in which events such as site failures, network partitions, and normal join-leave events are viewed as group reformations. RMP provides access to this model through an application programming interface (API) that notifies an application when a group is reformed as the result of a some event. RMP provides applications with reliable delivery of messages using an underlying IP Multicast media to other group members in a distributed environment even in the case of reformations. A distributed application can use various Quality of Service (QoS) levels provided by RMP to tolerate group reformations. This paper explores the implementation details of the mechanisms in RMP that provide distributed applications with membership view information and fault recovery capabilities.

Reliable multicast protocol specifications flow control and NACK policy

NASA Technical Reports Server (NTRS)

Callahan, John R.; Montgomery, Todd L.; Whetten, Brian

1995-01-01

This appendix presents the flow and congestion control schemes recommended for RMP and a NACK policy based on the whiteboard tool. Because RMP uses a primarily NACK based error detection scheme, there is no direct feedback path through which receivers can signal losses through low buffer space or congestion. Reliable multicast protocols also suffer from the fact that throughput for a multicast group must be divided among the members of the group. This division is usually very dynamic in nature and therefore does not lend itself well to a priori determination. These facts have led the flow and congestion control schemes of RMP to be made completely orthogonal to the protocol specification. This allows several differing schemes to be used in different environments to produce the best results. As a default, a modified sliding window scheme based on previous algorithms are suggested and described below.

Fixed-rate layered multicast congestion control

NASA Astrophysics Data System (ADS)

Bing, Zhang; Bing, Yuan; Zengji, Liu

2006-10-01

A new fixed-rate layered multicast congestion control algorithm called FLMCC is proposed. The sender of a multicast session transmits data packets at a fixed rate on each layer, while receivers each obtain different throughput by cumulatively subscribing to deferent number of layers based on their expected rates. In order to provide TCP-friendliness and estimate the expected rate accurately, a window-based mechanism implemented at receivers is presented. To achieve this, each receiver maintains a congestion window, adjusts it based on the GAIMD algorithm, and from the congestion window an expected rate is calculated. To measure RTT, a new method is presented which combines an accurate measurement with a rough estimation. A feedback suppression based on a random timer mechanism is given to avoid feedback implosion in the accurate measurement. The protocol is simple in its implementation. Simulations indicate that FLMCC shows good TCP-friendliness, responsiveness as well as intra-protocol fairness, and provides high link utilization.

On-board B-ISDN fast packet switching architectures. Phase 2: Development. Proof-of-concept architecture definition report

NASA Technical Reports Server (NTRS)

Shyy, Dong-Jye; Redman, Wayne

1993-01-01

For the next-generation packet switched communications satellite system with onboard processing and spot-beam operation, a reliable onboard fast packet switch is essential to route packets from different uplink beams to different downlink beams. The rapid emergence of point-to-point services such as video distribution, and the large demand for video conference, distributed data processing, and network management makes the multicast function essential to a fast packet switch (FPS). The satellite's inherent broadcast features gives the satellite network an advantage over the terrestrial network in providing multicast services. This report evaluates alternate multicast FPS architectures for onboard baseband switching applications and selects a candidate for subsequent breadboard development. Architecture evaluation and selection will be based on the study performed in phase 1, 'Onboard B-ISDN Fast Packet Switching Architectures', and other switch architectures which have become commercially available as large scale integration (LSI) devices.

Agile multicasting based on cascaded χ(2) nonlinearities in a step-chirped periodically poled lithium niobate.

PubMed

Ahlawat, Meenu; Bostani, Ameneh; Tehranchi, Amirhossein; Kashyap, Raman

2013-08-01

We experimentally demonstrate the possibility of agile multicasting for wavelength division multiplexing (WDM) networks, of a single-channel to two and seven channels over the C band, also extendable to S and L bands. This is based on cascaded χ(2) nonlinear mixing processes, namely, second-harmonic generation (SHG)-sum-frequency generation (SFG) and difference-frequency generation (DFG) in a 20-mm-long step-chirped periodically poled lithium niobate crystal, specially designed and fabricated for a 28-nm-wide SH-SF bandwidth centered at around 1.55 μm. The multiple idlers are simultaneously tuned by detuning the pump wavelengths within the broad SH-SF bandwidth. By selectively tuning the pump wavelengths over less than 10 and 6 nm, respectively, multicasting into two and seven idlers is successfully achieved across ~70 WDM channels within the 50 GHz International Telecommunication Union grid spacing.

AF-TRUST, Air Force Team for Research in Ubiquitous Secure Technology

DTIC Science & Technology

2010-07-26

Charles Sutton, J. D. Tygar, and Kai Xia. Book chapter in Jeffrey J. P. Tsai and Philip S. Yu (eds.) Machine Learning in Cyber Trust: Security, Privacy...enterprise, tactical, embedded systems and command and control levels. From these studies, commissioned by Dr . Sekar Chandersekaran of the Secretary of the...Data centers avoid IP Multicast because of a series of problems with the technology. • Dr . Multicast (the MCMD), a system that maps traditional I PMC

Secure Hierarchical Multicast Routing and Multicast Internet Anonymity

DTIC Science & Technology

1998-06-01

Multimedia, Summer 94, pages 76{79, 94. [15] David Chaum . Blind signatures for untraceable payments. In Proc. Crypto󈨖, pages 199{203, 1982. [16] David L...use of digital signatures , which consist of a cryptographic hash of the message encrypted with the private key of the signer. Digitally-signed messages... signature on the request and on the certi cate it contains. Notice that the location service need not retrieve the initiator’s public key as it is contained

Remote software upload techniques in future vehicles and their performance analysis

NASA Astrophysics Data System (ADS)

Hossain, Irina

Updating software in vehicle Electronic Control Units (ECUs) will become a mandatory requirement for a variety of reasons, for examples, to update/fix functionality of an existing system, add new functionality, remove software bugs and to cope up with ITS infrastructure. Software modules of advanced vehicles can be updated using Remote Software Upload (RSU) technique. The RSU employs infrastructure-based wireless communication technique where the software supplier sends the software to the targeted vehicle via a roadside Base Station (BS). However, security is critically important in RSU to avoid any disasters due to malfunctions of the vehicle or to protect the proprietary algorithms from hackers, competitors or people with malicious intent. In this thesis, a mechanism of secure software upload in advanced vehicles is presented which employs mutual authentication of the software provider and the vehicle using a pre-shared authentication key before sending the software. The software packets are sent encrypted with a secret key along with the Message Digest (MD). In order to increase the security level, it is proposed the vehicle to receive more than one copy of the software along with the MD in each copy. The vehicle will install the new software only when it receives more than one identical copies of the software. In order to validate the proposition, analytical expressions of average number of packet transmissions for successful software update is determined. Different cases are investigated depending on the vehicle's buffer size and verification methods. The analytical and simulation results show that it is sufficient to send two copies of the software to the vehicle to thwart any security attack while uploading the software. The above mentioned unicast method for RSU is suitable when software needs to be uploaded to a single vehicle. Since multicasting is the most efficient method of group communication, updating software in an ECU of a large number of vehicles could benefit from it. However, like the unicast RSU, the security requirements of multicast communication, i.e., authenticity, confidentiality and integrity of the software transmitted and access control of the group members is challenging. In this thesis, an infrastructure-based mobile multicasting for RSU in vehicle ECUs is proposed where an ECU receives the software from a remote software distribution center using the road side BSs as gateways. The Vehicular Software Distribution Network (VSDN) is divided into small regions administered by a Regional Group Manager (RGM). Two multicast Group Key Management (GKM) techniques are proposed based on the degree of trust on the BSs named Fully-trusted (FT) and Semi-trusted (ST) systems. Analytical models are developed to find the multicast session establishment latency and handover latency for these two protocols. The average latency to perform mutual authentication of the software vendor and a vehicle, and to send the multicast session key by the software provider during multicast session initialization, and the handoff latency during multicast session is calculated. Analytical and simulation results show that the link establishment latency per vehicle of our proposed schemes is in the range of few seconds and the ST system requires few ms higher time than the FT system. The handoff latency is also in the range of few seconds and in some cases ST system requires less handoff time than the FT system. Thus, it is possible to build an efficient GKM protocol without putting too much trust on the BSs.

An Economic Case for End System Multicast

NASA Astrophysics Data System (ADS)

Analoui, Morteza; Rezvani, Mohammad Hossein

This paper presents a non-strategic model for the end-system multicast networks based on the concept of replica exchange economy. We believe that microeconomics is a good candidate to investigate the problem of selfishness of the end-users (peers) in order to maximize the aggregate throughput. In this solution concept, the decisions that a peer might make, does not affect the actions of the other peers at all. The proposed mechanism tunes the price of the service in such a way that general equilibrium holds.

Experiences with the BSCW Shared Workspace System as the Backbone of a Virtual Learning Environment for Students.

ERIC Educational Resources Information Center

Appelt, Wolfgang; Mambrey, Peter

The GMD (German National Research Center for Information Technology) has developed the BSCW (Basic Support for Cooperative Work) Shared Workspace system within the last four years with the goal of transforming the Web from a primarily passive information repository to an active cooperation medium. The BSCW system is a Web-based groupware tool for…

Information and Communication Technology in Foreign Language Teaching: Leveraging the Internet to Make Language Learning Real

ERIC Educational Resources Information Center

Watson, Etáin

2013-01-01

The internet is the largest communications network in the world. It has become the virtual backbone of all communication. Therefore, it seems natural to leverage it as a major tool in any education involving communication skills, especially language skills. This chapter outlines a practitioner's experience on how this can be done in a foreign…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ennis, G.; Lala, T.K.

This document presents the results of a study undertaken by First Pacific Networks as part of EPRI Project RP-3567-01 regarding the support of broadcast services within the EPRI Utility Communications Architecture (UCA) protocols and the use of such services by UCA applications. This report has focused on the requirements and architectural implications of broadcast within UCA. A subsequent phase of this project is to develop specific recommendations for extending CUA so as to support broadcast. The conclusions of this report are presented in Section 5. The authors summarize the major conclusions as follows: broadcast and multicast support would be verymore » useful within UCA, not only for utility-specific applications but also simply to support the network engineering of a large-scale communications system, in this regard, UCA is no different from other large network systems which have found broadcast and multicast to be of substantial benefit for a variety of system management purposes; the primary architectural impact of broadcast and multicast falls on the UCA network level (which would need to be enhanced) and the UCA application level (which would be the user of broadcast); there is a useful subset of MMS services which could take advantage of broadcast; the UCA network level would need to be enhanced both in the areas of addressing and routing so as to properly support broadcast. A subsequent analysis will be required to define the specific enhancements to UCA required to support broadcast and multicast.« less

Programming with process groups: Group and multicast semantics

NASA Technical Reports Server (NTRS)

Birman, Kenneth P.; Cooper, Robert; Gleeson, Barry

1991-01-01

Process groups are a natural tool for distributed programming and are increasingly important in distributed computing environments. Discussed here is a new architecture that arose from an effort to simplify Isis process group semantics. The findings include a refined notion of how the clients of a group should be treated, what the properties of a multicast primitive should be when systems contain large numbers of overlapping groups, and a new construct called the causality domain. A system based on this architecture is now being implemented in collaboration with the Chorus and Mach projects.

Multicasting for all-optical multifiber networks

NASA Astrophysics Data System (ADS)

Kã¶Ksal, Fatih; Ersoy, Cem

2007-02-01

All-optical wavelength-routed WDM WANs can support the high bandwidth and the long session duration requirements of the application scenarios such as interactive distance learning or on-line diagnosis of patients simultaneously in different hospitals. However, multifiber and limited sparse light splitting and wavelength conversion capabilities of switches result in a difficult optimization problem. We attack this problem using a layered graph model. The problem is defined as a k-edge-disjoint degree-constrained Steiner tree problem for routing and fiber and wavelength assignment of k multicasts. A mixed integer linear programming formulation for the problem is given, and a solution using CPLEX is provided. However, the complexity of the problem grows quickly with respect to the number of edges in the layered graph, which depends on the number of nodes, fibers, wavelengths, and multicast sessions. Hence, we propose two heuristics layered all-optical multicast algorithm [(LAMA) and conservative fiber and wavelength assignment (C-FWA)] to compare with CPLEX, existing work, and unicasting. Extensive computational experiments show that LAMA's performance is very close to CPLEX, and it is significantly better than existing work and C-FWA for nearly all metrics, since LAMA jointly optimizes routing and fiber-wavelength assignment phases compared with the other candidates, which attack the problem by decomposing two phases. Experiments also show that important metrics (e.g., session and group blocking probability, transmitter wavelength, and fiber conversion resources) are adversely affected by the separation of two phases. Finally, the fiber-wavelength assignment strategy of C-FWA (Ex-Fit) uses wavelength and fiber conversion resources more effectively than the First Fit.

Multicast Delayed Authentication For Streaming Synchrophasor Data in the Smart Grid

PubMed Central

Câmara, Sérgio; Anand, Dhananjay; Pillitteri, Victoria; Carmo, Luiz

2017-01-01

Multicast authentication of synchrophasor data is challenging due to the design requirements of Smart Grid monitoring systems such as low security overhead, tolerance of lossy networks, time-criticality and high data rates. In this work, we propose inf -TESLA, Infinite Timed Efficient Stream Loss-tolerant Authentication, a multicast delayed authentication protocol for communication links used to stream synchrophasor data for wide area control of electric power networks. Our approach is based on the authentication protocol TESLA but is augmented to accommodate high frequency transmissions of unbounded length. inf TESLA protocol utilizes the Dual Offset Key Chains mechanism to reduce authentication delay and computational cost associated with key chain commitment. We provide a description of the mechanism using two different modes for disclosing keys and demonstrate its security against a man-in-the-middle attack attempt. We compare our approach against the TESLA protocol in a 2-day simulation scenario, showing a reduction of 15.82% and 47.29% in computational cost, sender and receiver respectively, and a cumulative reduction in the communication overhead. PMID:28736582

Multicast Delayed Authentication For Streaming Synchrophasor Data in the Smart Grid.

PubMed

Câmara, Sérgio; Anand, Dhananjay; Pillitteri, Victoria; Carmo, Luiz

2016-01-01

Multicast authentication of synchrophasor data is challenging due to the design requirements of Smart Grid monitoring systems such as low security overhead, tolerance of lossy networks, time-criticality and high data rates. In this work, we propose inf -TESLA, Infinite Timed Efficient Stream Loss-tolerant Authentication, a multicast delayed authentication protocol for communication links used to stream synchrophasor data for wide area control of electric power networks. Our approach is based on the authentication protocol TESLA but is augmented to accommodate high frequency transmissions of unbounded length. inf TESLA protocol utilizes the Dual Offset Key Chains mechanism to reduce authentication delay and computational cost associated with key chain commitment. We provide a description of the mechanism using two different modes for disclosing keys and demonstrate its security against a man-in-the-middle attack attempt. We compare our approach against the TESLA protocol in a 2-day simulation scenario, showing a reduction of 15.82% and 47.29% in computational cost, sender and receiver respectively, and a cumulative reduction in the communication overhead.

On compensation of four wave mixing effect in dispersion managed hybrid WDM-OTDM multicast overlay system with optical phase conjugation modules

NASA Astrophysics Data System (ADS)

Singh, Sukhbir; Singh, Surinder

2017-11-01

This paper investigated the effect of FWM and its suppression using optical phase conjugation modules in dispersion managed hybrid WDM-OTDM multicast overlay system. Interaction between propagating wavelength signals at higher power level causes new FWM component generation that can significant limit the system performance. OPC module consists of the pump signal and 0.6 km HNLF implemented in midway of optical link to generate destructive phase FWM components. Investigation revealed that by use of even OPC module in optical link reduces the FWM power and mitigate the interaction between wavelength signals at variable signal input power, dispersion parameter (β2) and transmission distance. System performance comparison is also made between without DM-OPC module, with DM and with DM-OPC module in scenario of FWM tolerance. The BER performance of hybrid WDM-OTDM multicast system using OPC module is improved by multiplication factor of 2 as comparable to dispersion managed and coverage distance is increased by factor of 2 as in Singh and Singh (2016).

Experimental Evaluation of Unicast and Multicast CoAP Group Communication

PubMed Central

Ishaq, Isam; Hoebeke, Jeroen; Moerman, Ingrid; Demeester, Piet

2016-01-01

The Internet of Things (IoT) is expanding rapidly to new domains in which embedded devices play a key role and gradually outnumber traditionally-connected devices. These devices are often constrained in their resources and are thus unable to run standard Internet protocols. The Constrained Application Protocol (CoAP) is a new alternative standard protocol that implements the same principals as the Hypertext Transfer Protocol (HTTP), but is tailored towards constrained devices. In many IoT application domains, devices need to be addressed in groups in addition to being addressable individually. Two main approaches are currently being proposed in the IoT community for CoAP-based group communication. The main difference between the two approaches lies in the underlying communication type: multicast versus unicast. In this article, we experimentally evaluate those two approaches using two wireless sensor testbeds and under different test conditions. We highlight the pros and cons of each of them and propose combining these approaches in a hybrid solution to better suit certain use case requirements. Additionally, we provide a solution for multicast-based group membership management using CoAP. PMID:27455262

Design and development of cell queuing, processing, and scheduling modules for the iPOINT input-buffered ATM testbed

NASA Astrophysics Data System (ADS)

Duan, Haoran

1997-12-01

This dissertation presents the concepts, principles, performance, and implementation of input queuing and cell-scheduling modules for the Illinois Pulsar-based Optical INTerconnect (iPOINT) input-buffered Asynchronous Transfer Mode (ATM) testbed. Input queuing (IQ) ATM switches are well suited to meet the requirements of current and future ultra-broadband ATM networks. The IQ structure imposes minimum memory bandwidth requirements for cell buffering, tolerates bursty traffic, and utilizes memory efficiently for multicast traffic. The lack of efficient cell queuing and scheduling solutions has been a major barrier to build high-performance, scalable IQ-based ATM switches. This dissertation proposes a new Three-Dimensional Queue (3DQ) and a novel Matrix Unit Cell Scheduler (MUCS) to remove this barrier. 3DQ uses a linked-list architecture based on Synchronous Random Access Memory (SRAM) to combine the individual advantages of per-virtual-circuit (per-VC) queuing, priority queuing, and N-destination queuing. It avoids Head of Line (HOL) blocking and provides per-VC Quality of Service (QoS) enforcement mechanisms. Computer simulation results verify the QoS capabilities of 3DQ. For multicast traffic, 3DQ provides efficient usage of cell buffering memory by storing multicast cells only once. Further, the multicast mechanism of 3DQ prevents a congested destination port from blocking other less- loaded ports. The 3DQ principle has been prototyped in the Illinois Input Queue (iiQueue) module. Using Field Programmable Gate Array (FPGA) devices, SRAM modules, and integrated on a Printed Circuit Board (PCB), iiQueue can process incoming traffic at 800 Mb/s. Using faster circuit technology, the same design is expected to operate at the OC-48 rate (2.5 Gb/s). MUCS resolves the output contention by evaluating the weight index of each candidate and selecting the heaviest. It achieves near-optimal scheduling and has a very short response time. The algorithm originates from a heuristic strategy that leads to 'socially optimal' solutions, yielding a maximum number of contention-free cells being scheduled. A novel mixed digital-analog circuit has been designed to implement the MUCS core functionality. The MUCS circuit maps the cell scheduling computation to the capacitor charging and discharging procedures that are conducted fully in parallel. The design has a uniform circuit structure, low interconnect counts, and low chip I/O counts. Using 2 μm CMOS technology, the design operates on a 100 MHz clock and finds a near-optimal solution within a linear processing time. The circuit has been verified at the transistor level by HSPICE simulation. During this research, a five-port IQ-based optoelectronic iPOINT ATM switch has been developed and demonstrated. It has been fully functional with an aggregate throughput of 800 Mb/s. The second-generation IQ-based switch is currently under development. Equipped with iiQueue modules and MUCS module, the new switch system will deliver a multi-gigabit aggregate throughput, eliminate HOL blocking, provide per-VC QoS, and achieve near-100% link bandwidth utilization. Complete documentation of input modules and trunk module for the existing testbed, and complete documentation of 3DQ, iiQueue, and MUCS for the second-generation testbed are given in this dissertation.

Multicast for savings in cache-based video distribution

NASA Astrophysics Data System (ADS)

Griwodz, Carsten; Zink, Michael; Liepert, Michael; On, Giwon; Steinmetz, Ralf

1999-12-01

Internet video-on-demand (VoD) today streams videos directly from server to clients, because re-distribution is not established yet. Intranet solutions exist but are typically managed centrally. Caching may overcome these management needs, however existing web caching strategies are not applicable because they work in different conditions. We propose movie distribution by means of caching, and study the feasibility from the service providers' point of view. We introduce the combination of our reliable multicast protocol LCRTP for caching hierarchies combined with our enhancement to the patching technique for bandwidth friendly True VoD, not depending on network resource guarantees.

Hybrid ARQ Scheme with Autonomous Retransmission for Multicasting in Wireless Sensor Networks.

PubMed

Jung, Young-Ho; Choi, Jihoon

2017-02-25

A new hybrid automatic repeat request (HARQ) scheme for multicast service for wireless sensor networks is proposed in this study. In the proposed algorithm, the HARQ operation is combined with an autonomous retransmission method that ensure a data packet is transmitted irrespective of whether or not the packet is successfully decoded at the receivers. The optimal number of autonomous retransmissions is determined to ensure maximum spectral efficiency, and a practical method that adjusts the number of autonomous retransmissions for realistic conditions is developed. Simulation results show that the proposed method achieves higher spectral efficiency than existing HARQ techniques.

A Loss Tolerant Rate Controller for Reliable Multicast

NASA Technical Reports Server (NTRS)

Montgomery, Todd

1997-01-01

This paper describes the design, specification, and performance of a Loss Tolerant Rate Controller (LTRC) for use in controlling reliable multicast senders. The purpose of this rate controller is not to adapt to congestion (or loss) on a per loss report basis (such as per received negative acknowledgment), but instead to use loss report information and perceived state to decide more prudent courses of action for both the short and long term. The goal of this controller is to be responsive to congestion, but not overly reactive to spurious independent loss. Performance of the controller is verified through simulation results.

Constructing new seismograms from old earthquakes: Retrospective seismology at multiple length scales

NASA Astrophysics Data System (ADS)

Entwistle, Elizabeth; Curtis, Andrew; Galetti, Erica; Baptie, Brian; Meles, Giovanni

2015-04-01

If energy emitted by a seismic source such as an earthquake is recorded on a suitable backbone array of seismometers, source-receiver interferometry (SRI) is a method that allows those recordings to be projected to the location of another target seismometer, providing an estimate of the seismogram that would have been recorded at that location. Since the other seismometer may not have been deployed at the time the source occurred, this renders possible the concept of 'retrospective seismology' whereby the installation of a sensor at one period of time allows the construction of virtual seismograms as though that sensor had been active before or after its period of installation. Using the benefit of hindsight of earthquake location or magnitude estimates, SRI can establish new measurement capabilities closer to earthquake epicenters, thus potentially improving earthquake location estimates. Recently we showed that virtual SRI seismograms can be constructed on target sensors in both industrial seismic and earthquake seismology settings, using both active seismic sources and ambient seismic noise to construct SRI propagators, and on length scales ranging over 5 orders of magnitude from ~40 m to ~2500 km[1]. Here we present the results from earthquake seismology by comparing virtual earthquake seismograms constructed at target sensors by SRI to those actually recorded on the same sensors. We show that spatial integrations required by interferometric theory can be calculated over irregular receiver arrays by embedding these arrays within 2D spatial Voronoi cells, thus improving spatial interpolation and interferometric results. The results of SRI are significantly improved by restricting the backbone receiver array to include approximately those receivers that provide a stationary phase contribution to the interferometric integrals. We apply both correlation-correlation and correlation-convolution SRI, and show that the latter constructs virtual seismograms with fewer non-physical arrivals. Finally we reconstruct earthquake seismograms at sensors that were previously active but were subsequently removed before the earthquakes occurred; thus we create virtual earthquake seismograms at those sensors, truly retrospectively. Such SRI seismograms can be used to create a catalogue of new, virtual earthquake seismograms that are available to complement real earthquake data in future earthquake seismology studies. [1]E. Entwistle, Curtis, A., Galetti, E., Baptie, B., Meles, G., Constructing new seismograms from old earthquakes: Retrospective seismology at multiple length scales, JGR, in press.

Hybrid monitoring scheme for end-to-end performance enhancement of multicast-based real-time media

NASA Astrophysics Data System (ADS)

Park, Ju-Won; Kim, JongWon

2004-10-01

As real-time media applications based on IP multicast networks spread widely, end-to-end QoS (quality of service) provisioning for these applications have become very important. To guarantee the end-to-end QoS of multi-party media applications, it is essential to monitor the time-varying status of both network metrics (i.e., delay, jitter and loss) and system metrics (i.e., CPU and memory utilization). In this paper, targeting the multicast-enabled AG (Access Grid) a next-generation group collaboration tool based on multi-party media services, the applicability of hybrid monitoring scheme that combines active and passive monitoring is investigated. The active monitoring measures network-layer metrics (i.e., network condition) with probe packets while the passive monitoring checks both application-layer metrics (i.e., user traffic condition by analyzing RTCP packets) and system metrics. By comparing these hybrid results, we attempt to pinpoint the causes of performance degradation and explore corresponding reactions to improve the end-to-end performance. The experimental results show that the proposed hybrid monitoring can provide useful information to coordinate the performance improvement of multi-party real-time media applications.

A heuristic for efficient data distribution management in distributed simulation

NASA Astrophysics Data System (ADS)

Gupta, Pankaj; Guha, Ratan K.

2005-05-01

In this paper, we propose an algorithm for reducing the complexity of region matching and efficient multicasting in data distribution management component of High Level Architecture (HLA) Run Time Infrastructure (RTI). The current data distribution management (DDM) techniques rely on computing the intersection between the subscription and update regions. When a subscription region and an update region of different federates overlap, RTI establishes communication between the publisher and the subscriber. It subsequently routes the updates from the publisher to the subscriber. The proposed algorithm computes the update/subscription regions matching for dynamic allocation of multicast group. It provides new multicast routines that exploit the connectivity of federation by communicating updates regarding interactions and routes information only to those federates that require them. The region-matching problem in DDM reduces to clique-covering problem using the connections graph abstraction where the federations represent the vertices and the update/subscribe relations represent the edges. We develop an abstract model based on connection graph for data distribution management. Using this abstract model, we propose a heuristic for solving the region-matching problem of DDM. We also provide complexity analysis of the proposed heuristics.

Efficient Network Coding-Based Loss Recovery for Reliable Multicast in Wireless Networks

NASA Astrophysics Data System (ADS)

Chi, Kaikai; Jiang, Xiaohong; Ye, Baoliu; Horiguchi, Susumu

Recently, network coding has been applied to the loss recovery of reliable multicast in wireless networks [19], where multiple lost packets are XOR-ed together as one packet and forwarded via single retransmission, resulting in a significant reduction of bandwidth consumption. In this paper, we first prove that maximizing the number of lost packets for XOR-ing, which is the key part of the available network coding-based reliable multicast schemes, is actually a complex NP-complete problem. To address this limitation, we then propose an efficient heuristic algorithm for finding an approximately optimal solution of this optimization problem. Furthermore, we show that the packet coding principle of maximizing the number of lost packets for XOR-ing sometimes cannot fully exploit the potential coding opportunities, and we then further propose new heuristic-based schemes with a new coding principle. Simulation results demonstrate that the heuristic-based schemes have very low computational complexity and can achieve almost the same transmission efficiency as the current coding-based high-complexity schemes. Furthermore, the heuristic-based schemes with the new coding principle not only have very low complexity, but also slightly outperform the current high-complexity ones.

Fingerprint multicast in secure video streaming.

PubMed

Zhao, H Vicky; Liu, K J Ray

2006-01-01

Digital fingerprinting is an emerging technology to protect multimedia content from illegal redistribution, where each distributed copy is labeled with unique identification information. In video streaming, huge amount of data have to be transmitted to a large number of users under stringent latency constraints, so the bandwidth-efficient distribution of uniquely fingerprinted copies is crucial. This paper investigates the secure multicast of anticollusion fingerprinted video in streaming applications and analyzes their performance. We first propose a general fingerprint multicast scheme that can be used with most spread spectrum embedding-based multimedia fingerprinting systems. To further improve the bandwidth efficiency, we explore the special structure of the fingerprint design and propose a joint fingerprint design and distribution scheme. From our simulations, the two proposed schemes can reduce the bandwidth requirement by 48% to 87%, depending on the number of users, the characteristics of video sequences, and the network and computation constraints. We also show that under the constraint that all colluders have the same probability of detection, the embedded fingerprints in the two schemes have approximately the same collusion resistance. Finally, we propose a fingerprint drift compensation scheme to improve the quality of the reconstructed sequences at the decoder's side without introducing extra communication overhead.

IPTV multicast with peer-assisted lossy error control

NASA Astrophysics Data System (ADS)

Li, Zhi; Zhu, Xiaoqing; Begen, Ali C.; Girod, Bernd

2010-07-01

Emerging IPTV technology uses source-specific IP multicast to deliver television programs to end-users. To provide reliable IPTV services over the error-prone DSL access networks, a combination of multicast forward error correction (FEC) and unicast retransmissions is employed to mitigate the impulse noises in DSL links. In existing systems, the retransmission function is provided by the Retransmission Servers sitting at the edge of the core network. In this work, we propose an alternative distributed solution where the burden of packet loss repair is partially shifted to the peer IP set-top boxes. Through Peer-Assisted Repair (PAR) protocol, we demonstrate how the packet repairs can be delivered in a timely, reliable and decentralized manner using the combination of server-peer coordination and redundancy of repairs. We also show that this distributed protocol can be seamlessly integrated with an application-layer source-aware error protection mechanism called forward and retransmitted Systematic Lossy Error Protection (SLEP/SLEPr). Simulations show that this joint PARSLEP/ SLEPr framework not only effectively mitigates the bottleneck experienced by the Retransmission Servers, thus greatly enhancing the scalability of the system, but also efficiently improves the resistance to the impulse noise.

Verification and validation of a reliable multicast protocol

NASA Technical Reports Server (NTRS)

Callahan, John R.; Montgomery, Todd L.

1995-01-01

This paper describes the methods used to specify and implement a complex communications protocol that provides reliable delivery of data in multicast-capable, packet-switching telecommunication networks. The protocol, called the Reliable Multicasting Protocol (RMP), was developed incrementally by two complementary teams using a combination of formal and informal techniques in an attempt to ensure the correctness of the protocol implementation. The first team, called the Design team, initially specified protocol requirements using a variant of SCR requirements tables and implemented a prototype solution. The second team, called the V&V team, developed a state model based on the requirements tables and derived test cases from these tables to exercise the implementation. In a series of iterative steps, the Design team added new functionality to the implementation while the V&V team kept the state model in fidelity with the implementation through testing. Test cases derived from state transition paths in the formal model formed the dialogue between teams during development and served as the vehicles for keeping the model and implementation in fidelity with each other. This paper describes our experiences in developing our process model, details of our approach, and some example problems found during the development of RMP.

Algorithm for protecting light-trees in survivable mesh wavelength-division-multiplexing networks

NASA Astrophysics Data System (ADS)

Luo, Hongbin; Li, Lemin; Yu, Hongfang

2006-12-01

Wavelength-division-multiplexing (WDM) technology is expected to facilitate bandwidth-intensive multicast applications such as high-definition television. A single fiber cut in a WDM mesh network, however, can disrupt the dissemination of information to several destinations on a light-tree based multicast session. Thus it is imperative to protect multicast sessions by reserving redundant resources. We propose a novel and efficient algorithm for protecting light-trees in survivable WDM mesh networks. The algorithm is called segment-based protection with sister node first (SSNF), whose basic idea is to protect a light-tree using a set of backup segments with a higher priority to protect the segments from a branch point to its children (sister nodes). The SSNF algorithm differs from the segment protection scheme proposed in the literature in how the segments are identified and protected. Our objective is to minimize the network resources used for protecting each primary light-tree such that the blocking probability can be minimized. To verify the effectiveness of the SSNF algorithm, we conduct extensive simulation experiments. The simulation results demonstrate that the SSNF algorithm outperforms existing algorithms for the same problem.

Virtual knotting in proteins and other open curves

NASA Astrophysics Data System (ADS)

Alexander, Keith; Taylor, Alexander; Dennis, Mark

Long filaments naturally knot, from string to long-chain molecules. Knotting in a filament affects its properties, and may be very stable or disappear under slight manipulation. Knotting has been identified in protein backbones for which these mechanical constraints are of fundamental importance to their function, although they are open curves in which knots are not mathematically well defined; knotting can only be identified by closing the ends of the chain. We introduce a new method for resolving knotting in open curves using virtual knots, a wider class of topological objects that do not use a classical closure, capturing the topological ambiguity of open curves. Having analysed all proteins in the Protein Data Bank by this new scheme, we recover and extend previous knotting results, and identify topological interest in some new cases. The statistics of virtual knots in proteins are compared with those of Hamiltonian subchains on cubic lattices, identifying a regime of open curves in which the virtual knotting description is likely to be important. This work was supported by the Leverhulme Trust Programme Grant ``Scientific Properties of Complex Knots'' and the EPSRC.

A memetic optimization algorithm for multi-constrained multicast routing in ad hoc networks

PubMed Central

Hammad, Karim; El Bakly, Ahmed M.

2018-01-01

A mobile ad hoc network is a conventional self-configuring network where the routing optimization problem—subject to various Quality-of-Service (QoS) constraints—represents a major challenge. Unlike previously proposed solutions, in this paper, we propose a memetic algorithm (MA) employing an adaptive mutation parameter, to solve the multicast routing problem with higher search ability and computational efficiency. The proposed algorithm utilizes an updated scheme, based on statistical analysis, to estimate the best values for all MA parameters and enhance MA performance. The numerical results show that the proposed MA improved the delay and jitter of the network, while reducing computational complexity as compared to existing algorithms. PMID:29509760

A memetic optimization algorithm for multi-constrained multicast routing in ad hoc networks.

PubMed

Ramadan, Rahab M; Gasser, Safa M; El-Mahallawy, Mohamed S; Hammad, Karim; El Bakly, Ahmed M

2018-01-01

A mobile ad hoc network is a conventional self-configuring network where the routing optimization problem-subject to various Quality-of-Service (QoS) constraints-represents a major challenge. Unlike previously proposed solutions, in this paper, we propose a memetic algorithm (MA) employing an adaptive mutation parameter, to solve the multicast routing problem with higher search ability and computational efficiency. The proposed algorithm utilizes an updated scheme, based on statistical analysis, to estimate the best values for all MA parameters and enhance MA performance. The numerical results show that the proposed MA improved the delay and jitter of the network, while reducing computational complexity as compared to existing algorithms.

Towards Microeconomic Resource Sharing in End System Multicast Networks Based on Walrasian General Equilibrium

NASA Astrophysics Data System (ADS)

Rezvani, Mohammad Hossein; Analoui, Morteza

2010-11-01

We have designed a competitive economical mechanism for application level multicast in which a number of independent services are provided to the end-users by a number of origin servers. Each offered service can be thought of as a commodity and the origin servers and the users who relay the service to their downstream nodes can thus be thought of as producers of the economy. Also, the end-users can be viewed as consumers of the economy. The proposed mechanism regulates the price of each service in such a way that general equilibrium holds. So, all allocations will be Pareto optimal in the sense that the social welfare of the users is maximized.

High-speed free-space based reconfigurable card-to-card optical interconnects with broadcast capability.

PubMed

Wang, Ke; Nirmalathas, Ampalavanapillai; Lim, Christina; Skafidas, Efstratios; Alameh, Kamal

2013-07-01

In this paper, we propose and experimentally demonstrate a free-space based high-speed reconfigurable card-to-card optical interconnect architecture with broadcast capability, which is required for control functionalities and efficient parallel computing applications. Experimental results show that 10 Gb/s data can be broadcast to all receiving channels for up to 30 cm with a worst-case receiver sensitivity better than -12.20 dBm. In addition, arbitrary multicasting with the same architecture is also investigated. 10 Gb/s reconfigurable point-to-point link and multicast channels are simultaneously demonstrated with a measured receiver sensitivity power penalty of ~1.3 dB due to crosstalk.

Data collection framework for energy efficient privacy preservation in wireless sensor networks having many-to-many structures.

PubMed

Bahşi, Hayretdin; Levi, Albert

2010-01-01

Wireless sensor networks (WSNs) generally have a many-to-one structure so that event information flows from sensors to a unique sink. In recent WSN applications, many-to-many structures evolved due to the need for conveying collected event information to multiple sinks. Privacy preserved data collection models in the literature do not solve the problems of WSN applications in which network has multiple un-trusted sinks with different level of privacy requirements. This study proposes a data collection framework bases on k-anonymity for preventing record disclosure of collected event information in WSNs. Proposed method takes the anonymity requirements of multiple sinks into consideration by providing different levels of privacy for each destination sink. Attributes, which may identify an event owner, are generalized or encrypted in order to meet the different anonymity requirements of sinks at the same anonymized output. If the same output is formed, it can be multicasted to all sinks. The other trivial solution is to produce different anonymized outputs for each sink and send them to related sinks. Multicasting is an energy efficient data sending alternative for some sensor nodes. Since minimization of energy consumption is an important design criteria for WSNs, multicasting the same event information to multiple sinks reduces the energy consumption of overall network.

Visualization in transportation: challenges and opportunities for everyone.

PubMed

Pack, Michael L

2010-01-01

Transportation is the backbone of the civilization and the reason for the economic prosperity. There's serious money in our transportation infrastructure, research, policy, data collection, and, yes, software and other IT systems. The paper presents a highlevel introduction to current visualization research for transportation, discuss research opportunities, and encourage the CG community to get involved. It briefly covers transportation data visualization, wide-area real-time simulation, visualizing and mining archived data, massively multiplayer online games (MMOGs), and even virtual design and construction.

Distributed interactive virtual environments for collaborative experiential learning and training independent of distance over Internet2.

PubMed

Alverson, Dale C; Saiki, Stanley M; Jacobs, Joshua; Saland, Linda; Keep, Marcus F; Norenberg, Jeffrey; Baker, Rex; Nakatsu, Curtis; Kalishman, Summers; Lindberg, Marlene; Wax, Diane; Mowafi, Moad; Summers, Kenneth L; Holten, James R; Greenfield, John A; Aalseth, Edward; Nickles, David; Sherstyuk, Andrei; Haines, Karen; Caudell, Thomas P

2004-01-01

Medical knowledge and skills essential for tomorrow's healthcare professionals continue to change faster than ever before creating new demands in medical education. Project TOUCH (Telehealth Outreach for Unified Community Health) has been developing methods to enhance learning by coupling innovations in medical education with advanced technology in high performance computing and next generation Internet2 embedded in virtual reality environments (VRE), artificial intelligence and experiential active learning. Simulations have been used in education and training to allow learners to make mistakes safely in lieu of real-life situations, learn from those mistakes and ultimately improve performance by subsequent avoidance of those mistakes. Distributed virtual interactive environments are used over distance to enable learning and participation in dynamic, problem-based, clinical, artificial intelligence rules-based, virtual simulations. The virtual reality patient is programmed to dynamically change over time and respond to the manipulations by the learner. Participants are fully immersed within the VRE platform using a head-mounted display and tracker system. Navigation, locomotion and handling of objects are accomplished using a joy-wand. Distribution is managed via the Internet2 Access Grid using point-to-point or multi-casting connectivity through which the participants can interact. Medical students in Hawaii and New Mexico (NM) participated collaboratively in problem solving and managing of a simulated patient with a closed head injury in VRE; dividing tasks, handing off objects, and functioning as a team. Students stated that opportunities to make mistakes and repeat actions in the VRE were extremely helpful in learning specific principles. VRE created higher performance expectations and some anxiety among VRE users. VRE orientation was adequate but students needed time to adapt and practice in order to improve efficiency. This was also demonstrated successfully between Western Australia and UNM. We successfully demonstrated the ability to fully immerse participants in a distributed virtual environment independent of distance for collaborative team interaction in medical simulation designed for education and training. The ability to make mistakes in a safe environment is well received by students and has a positive impact on their understanding, as well as memory of the principles involved in correcting those mistakes. Bringing people together as virtual teams for interactive experiential learning and collaborative training, independent of distance, provides a platform for distributed "just-in-time" training, performance assessment and credentialing. Further validation is necessary to determine the potential value of the distributed VRE in knowledge transfer, improved future performance and should entail training participants to competence in using these tools.

Admission and Preventive Load Control for Delivery of Multicast and Broadcast Services via S-UMTS

NASA Astrophysics Data System (ADS)

Angelou, E.; Koutsokeras, N.; Andrikopoulos, I.; Mertzanis, I.; Karaliopoulos, M.; Henrio, P.

2003-07-01

An Admission Control strategy is proposed for unidirectional satellite systems delivering multicast and broadcast services to mobile users. In such systems, both the radio interface and the targeted services impose particular requirements on the RRM task. We briefly discuss the RRM requirements that stem from the services point of view and from the features of the SATIN access scheme that differentiate it from the conventional T-UMTS radio interface. The main functional entities of RRM and the alternative modes of operation are outlined and the proposed Admission Control algorithm is described in detail. The results from the simulation study that demonstrate its performance for a number of different scenarios are finally presented and conclusions derived.

Proteins analysed as virtual knots

NASA Astrophysics Data System (ADS)

Alexander, Keith; Taylor, Alexander J.; Dennis, Mark R.

2017-02-01

Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or disappear rapidly under manipulation and interaction. Knotting has been previously identified in protein backbone chains, for which these mechanical constraints are of fundamental importance to their molecular functionality, despite their being open curves in which the knots are not mathematically well defined; knotting can only be identified by closing the termini of the chain somehow. We introduce a new method for resolving knotting in open curves using virtual knots, which are a wider class of topological objects that do not require a classical closure and so naturally capture the topological ambiguity inherent in open curves. We describe the results of analysing proteins in the Protein Data Bank by this new scheme, recovering and extending previous knotting results, and identifying topological interest in some new cases. The statistics of virtual knots in protein chains are compared with those of open random walks and Hamiltonian subchains on cubic lattices, identifying a regime of open curves in which the virtual knotting description is likely to be important.

Proteins analysed as virtual knots

PubMed Central

Alexander, Keith; Taylor, Alexander J.; Dennis, Mark R.

2017-01-01

Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or disappear rapidly under manipulation and interaction. Knotting has been previously identified in protein backbone chains, for which these mechanical constraints are of fundamental importance to their molecular functionality, despite their being open curves in which the knots are not mathematically well defined; knotting can only be identified by closing the termini of the chain somehow. We introduce a new method for resolving knotting in open curves using virtual knots, which are a wider class of topological objects that do not require a classical closure and so naturally capture the topological ambiguity inherent in open curves. We describe the results of analysing proteins in the Protein Data Bank by this new scheme, recovering and extending previous knotting results, and identifying topological interest in some new cases. The statistics of virtual knots in protein chains are compared with those of open random walks and Hamiltonian subchains on cubic lattices, identifying a regime of open curves in which the virtual knotting description is likely to be important. PMID:28205562

Design of a Multicast Optical Packet Switch Based on Fiber Bragg Grating Technology for Future Networks

NASA Astrophysics Data System (ADS)

Cheng, Yuh-Jiuh; Yeh, Tzuoh-Chyau; Cheng, Shyr-Yuan

2011-09-01

In this paper, a non-blocking multicast optical packet switch based on fiber Bragg grating technology with optical output buffers is proposed. Only the header of optical packets is converted to electronic signals to control the fiber Bragg grating array of input ports and the packet payloads should be transparently destined to their output ports so that the proposed switch can reduce electronic interfaces as well as the bit rate. The modulation and the format of packet payloads may be non-standard where packet payloads could also include different wavelengths for increasing the volume of traffic. The advantage is obvious: the proposed switch could transport various types of traffic. An easily implemented architecture which can provide multicast services is also presented. An optical output buffer is designed to queue the packets if more than one incoming packet should reach to the same destination output port or including any waiting packets in optical output buffer that will be sent to the output port at a time slot. For preserving service-packet sequencing and fairness of routing sequence, a priority scheme and a round-robin algorithm are adopted at the optical output buffer. The fiber Bragg grating arrays for both input ports and output ports are designed for routing incoming packets using optical code division multiple access technology.

Space Flight Middleware: Remote AMS over DTN for Delay-Tolerant Messaging

NASA Technical Reports Server (NTRS)

Burleigh, Scott

2011-01-01

This paper describes a technique for implementing scalable, reliable, multi-source multipoint data distribution in space flight communications -- Delay-Tolerant Reliable Multicast (DTRM) -- that is fully supported by the "Remote AMS" (RAMS) protocol of the Asynchronous Message Service (AMS) proposed for standardization within the Consultative Committee for Space Data Systems (CCSDS). The DTRM architecture enables applications to easily "publish" messages that will be reliably and efficiently delivered to an arbitrary number of "subscribing" applications residing anywhere in the space network, whether in the same subnet or in a subnet on a remote planet or vehicle separated by many light minutes of interplanetary space. The architecture comprises multiple levels of protocol, each included for a specific purpose and allocated specific responsibilities: "application AMS" traffic performs end-system data introduction and delivery subject to access control; underlying "remote AMS" directs this application traffic to populations of recipients at remote locations in a multicast distribution tree, enabling the architecture to scale up to large networks; further underlying Delay-Tolerant Networking (DTN) Bundle Protocol (BP) advances RAMS protocol data units through the distribution tree using delay-tolerant storeand- forward methods; and further underlying reliable "convergence-layer" protocols ensure successful data transfer over each segment of the end-to-end route. The result is scalable, reliable, delay-tolerant multi-source multicast that is largely self-configuring.

BP-Dock: A Flexible Docking Scheme for Exploring Protein–Ligand Interactions Based on Unbound Structures

PubMed Central

Bolia, Ashini; Gerek, Z. Nevin; Ozkan, S. Banu

2016-01-01

Molecular docking serves as an important tool in modeling protein–ligand interactions. However, it is still challenging to incorporate overall receptor flexibility, especially backbone flexibility, in docking due to the large conformational space that needs to be sampled. To overcome this problem, we developed a novel flexible docking approach, BP-Dock (Backbone Perturbation-Dock) that can integrate both backbone and side chain conformational changes induced by ligand binding through a multi-scale approach. In the BP-Dock method, we mimic the nature of binding-induced events as a first-order approximation by perturbing the residues along the protein chain with a small Brownian kick one at a time. The response fluctuation profile of the chain upon these perturbations is computed using the perturbation response scanning method. These response fluctuation profiles are then used to generate binding-induced multiple receptor conformations for ensemble docking. To evaluate the performance of BP-Dock, we applied our approach on a large and diverse data set using unbound structures as receptors. We also compared the BP-Dock results with bound and unbound docking, where overall receptor flexibility was not taken into account. Our results highlight the importance of modeling backbone flexibility in docking for recapitulating the experimental binding affinities, especially when an unbound structure is used. With BP-Dock, we can generate a wide range of binding site conformations realized in nature even in the absence of a ligand that can help us to improve the accuracy of unbound docking. We expect that our fast and efficient flexible docking approach may further aid in our understanding of protein–ligand interactions as well as virtual screening of novel targets for rational drug design. PMID:24380381

Dynamic Network Selection for Multicast Services in Wireless Cooperative Networks

NASA Astrophysics Data System (ADS)

Chen, Liang; Jin, Le; He, Feng; Cheng, Hanwen; Wu, Lenan

In next generation mobile multimedia communications, different wireless access networks are expected to cooperate. However, it is a challenging task to choose an optimal transmission path in this scenario. This paper focuses on the problem of selecting the optimal access network for multicast services in the cooperative mobile and broadcasting networks. An algorithm is proposed, which considers multiple decision factors and multiple optimization objectives. An analytic hierarchy process (AHP) method is applied to schedule the service queue and an artificial neural network (ANN) is used to improve the flexibility of the algorithm. Simulation results show that by applying the AHP method, a group of weight ratios can be obtained to improve the performance of multiple objectives. And ANN method is effective to adaptively adjust weight ratios when users' new waiting threshold is generated.

Polarization-insensitive PAM-4-carrying free-space orbital angular momentum (OAM) communications.

PubMed

Liu, Jun; Wang, Jian

2016-02-22

We present a simple configuration incorporating single polarization-sensitive phase-only liquid crystal spatial light modulator (SLM) to facilitate polarization-insensitive free-space optical communications employing orbital angular momentum (OAM) modes. We experimentally demonstrate several polarization-insensitive optical communication subsystems by propagating a single OAM mode, multicasting 4 and 10 OAM modes, and multiplexing 8 OAM modes, respectively. Free-space polarization-insensitive optical communication links using OAM modes that carry four-level pulse-amplitude modulation (PAM-4) signal are demonstrated in the experiment. The observed optical signal-to-noise ratio (OSNR) penalties are less than 1 dB in both polarization-insensitive N-fold OAM modes multicasting and multiple OAM modes multiplexing at a bit-error rate (BER) of 2e-3 (enhanced forward-error correction (EFEC) threshold).

Virtual Vents: A Microbathymetrical Survey of the Niua South Hydrothermal Field, NE Lau Basin, Tonga

NASA Astrophysics Data System (ADS)

Kwasnitschka, T.; Köser, K.; Duda, A.; Jamieson, J. W.; Boschen, R.; Gartman, A.; Hannington, M. D.; Funganitao, C.

2016-12-01

At a diameter of 200 m, the 1100 m deep Niua South hydrothermal field (NE Lau Basin) was studied in an interdisciplinary approach during the SOI funded Virtual Vents cruise in March of 2016. On the grounds of a previously generated 50 cm resolution AUV multi beam map, the projects backbone is formed by a fully color textured, 5 cm resolution photogrammetrical 3D model. Several hundred smaller and about 15 chimneys larger than 3 m were surveyed including their basal mounds and surrounding environment interconnecting to each other. This model was populated through exhaustive geological, biological and fluid sampling as well as continuous Eh measurements, forming the basis for highly detailed geological structural and biological studies resulting in 3D maps of the entire field. At a reasonable effort, such surveys form the basis for repetitive time series analysis and have the potential of a new standard in seafloor monitoring.

Combined Wavelet Video Coding and Error Control for Internet Streaming and Multicast

NASA Astrophysics Data System (ADS)

Chu, Tianli; Xiong, Zixiang

2003-12-01

This paper proposes an integrated approach to Internet video streaming and multicast (e.g., receiver-driven layered multicast (RLM) by McCanne) based on combined wavelet video coding and error control. We design a packetized wavelet video (PWV) coder to facilitate its integration with error control. The PWV coder produces packetized layered bitstreams that are independent among layers while being embedded within each layer. Thus, a lost packet only renders the following packets in the same layer useless. Based on the PWV coder, we search for a multilayered error-control strategy that optimally trades off source and channel coding for each layer under a given transmission rate to mitigate the effects of packet loss. While both the PWV coder and the error-control strategy are new—the former incorporates embedded wavelet video coding and packetization and the latter extends the single-layered approach for RLM by Chou et al.—the main distinction of this paper lies in the seamless integration of the two parts. Theoretical analysis shows a gain of up to 1 dB on a channel with 20% packet loss using our combined approach over separate designs of the source coder and the error-control mechanism. This is also substantiated by our simulations with a gain of up to 0.6 dB. In addition, our simulations show a gain of up to 2.2 dB over previous results reported by Chou et al.

Exact and heuristic algorithms for Space Information Flow.

PubMed

Uwitonze, Alfred; Huang, Jiaqing; Ye, Yuanqing; Cheng, Wenqing; Li, Zongpeng

2018-01-01

Space Information Flow (SIF) is a new promising research area that studies network coding in geometric space, such as Euclidean space. The design of algorithms that compute the optimal SIF solutions remains one of the key open problems in SIF. This work proposes the first exact SIF algorithm and a heuristic SIF algorithm that compute min-cost multicast network coding for N (N ≥ 3) given terminal nodes in 2-D Euclidean space. Furthermore, we find that the Butterfly network in Euclidean space is the second example besides the Pentagram network where SIF is strictly better than Euclidean Steiner minimal tree. The exact algorithm design is based on two key techniques: Delaunay triangulation and linear programming. Delaunay triangulation technique helps to find practically good candidate relay nodes, after which a min-cost multicast linear programming model is solved over the terminal nodes and the candidate relay nodes, to compute the optimal multicast network topology, including the optimal relay nodes selected by linear programming from all the candidate relay nodes and the flow rates on the connection links. The heuristic algorithm design is also based on Delaunay triangulation and linear programming techniques. The exact algorithm can achieve the optimal SIF solution with an exponential computational complexity, while the heuristic algorithm can achieve the sub-optimal SIF solution with a polynomial computational complexity. We prove the correctness of the exact SIF algorithm. The simulation results show the effectiveness of the heuristic SIF algorithm.

Protein tyrosine phosphatases: Ligand interaction analysis and optimisation of virtual screening.

PubMed

Ghattas, Mohammad A; Atatreh, Noor; Bichenkova, Elena V; Bryce, Richard A

2014-07-01

Docking-based virtual screening is an established component of structure-based drug discovery. Nevertheless, scoring and ranking of computationally docked ligand libraries still suffer from many false positives. Identifying optimal docking parameters for a target protein prior to virtual screening can improve experimental hit rates. Here, we examine protocols for virtual screening against the important but challenging class of drug target, protein tyrosine phosphatases. In this study, common interaction features were identified from analysis of protein-ligand binding geometries of more than 50 complexed phosphatase crystal structures. It was found that two interactions were consistently formed across all phosphatase inhibitors: (1) a polar contact with the conserved arginine residue, and (2) at least one interaction with the P-loop backbone amide. In order to investigate the significance of these features on phosphatase-ligand binding, a series of seeded virtual screening experiments were conducted on three phosphatase enzymes, PTP1B, Cdc25b and IF2. It was observed that when the conserved arginine and P-loop amide interactions were used as pharmacophoric constraints during docking, enrichment of the virtual screen significantly increased in the three studied phosphatases, by up to a factor of two in some cases. Additionally, the use of such pharmacophoric constraints considerably improved the ability of docking to predict the inhibitor's bound pose, decreasing RMSD to the crystallographic geometry by 43% on average. Constrained docking improved enrichment of screens against both open and closed conformations of PTP1B. Incorporation of an ordered water molecule in PTP1B screening was also found to generally improve enrichment. The knowledge-based computational strategies explored here can potentially inform structure-based design of new phosphatase inhibitors using docking-based virtual screening. Copyright © 2014 Elsevier Inc. All rights reserved.

Designers workbench: toward real-time immersive modeling

NASA Astrophysics Data System (ADS)

Kuester, Falko; Duchaineau, Mark A.; Hamann, Bernd; Joy, Kenneth I.; Ma, Kwan-Liu

2000-05-01

This paper introduces the Designers Workbench, a semi- immersive virtual environment for two-handed modeling, sculpting and analysis tasks. The paper outlines the fundamental tools, design metaphors and hardware components required for an intuitive real-time modeling system. As companies focus on streamlining productivity to cope with global competition, the migration to computer-aided design (CAD), computer-aided manufacturing, and computer-aided engineering systems has established a new backbone of modern industrial product development. However, traditionally a product design frequently originates form a clay model that, after digitization, forms the basis for the numerical description of CAD primitives. The Designers Workbench aims at closing this technology or 'digital gap' experienced by design and CAD engineers by transforming the classical design paradigm into its fully integrate digital and virtual analog allowing collaborative development in a semi- immersive virtual environment. This project emphasizes two key components form the classical product design cycle: freeform modeling and analysis. In the freedom modeling stage, content creation in the form of two-handed sculpting of arbitrary objects using polygonal, volumetric or mathematically defined primitives is emphasized, whereas the analysis component provides the tools required for pre- and post-processing steps for finite element analysis tasks applied to the created models.

An Approach to Verification and Validation of a Reliable Multicasting Protocol

NASA Technical Reports Server (NTRS)

Callahan, John R.; Montgomery, Todd L.

1994-01-01

This paper describes the process of implementing a complex communications protocol that provides reliable delivery of data in multicast-capable, packet-switching telecommunication networks. The protocol, called the Reliable Multicasting Protocol (RMP), was developed incrementally using a combination of formal and informal techniques in an attempt to ensure the correctness of its implementation. Our development process involved three concurrent activities: (1) the initial construction and incremental enhancement of a formal state model of the protocol machine; (2) the initial coding and incremental enhancement of the implementation; and (3) model-based testing of iterative implementations of the protocol. These activities were carried out by two separate teams: a design team and a V&V team. The design team built the first version of RMP with limited functionality to handle only nominal requirements of data delivery. In a series of iterative steps, the design team added new functionality to the implementation while the V&V team kept the state model in fidelity with the implementation. This was done by generating test cases based on suspected errant or offnominal behaviors predicted by the current model. If the execution of a test was different between the model and implementation, then the differences helped identify inconsistencies between the model and implementation. The dialogue between both teams drove the co-evolution of the model and implementation. Testing served as the vehicle for keeping the model and implementation in fidelity with each other. This paper describes (1) our experiences in developing our process model; and (2) three example problems found during the development of RMP.

An approach to verification and validation of a reliable multicasting protocol

NASA Technical Reports Server (NTRS)

Callahan, John R.; Montgomery, Todd L.

1995-01-01

This paper describes the process of implementing a complex communications protocol that provides reliable delivery of data in multicast-capable, packet-switching telecommunication networks. The protocol, called the Reliable Multicasting Protocol (RMP), was developed incrementally using a combination of formal and informal techniques in an attempt to ensure the correctness of its implementation. Our development process involved three concurrent activities: (1) the initial construction and incremental enhancement of a formal state model of the protocol machine; (2) the initial coding and incremental enhancement of the implementation; and (3) model-based testing of iterative implementations of the protocol. These activities were carried out by two separate teams: a design team and a V&V team. The design team built the first version of RMP with limited functionality to handle only nominal requirements of data delivery. In a series of iterative steps, the design team added new functionality to the implementation while the V&V team kept the state model in fidelity with the implementation. This was done by generating test cases based on suspected errant or off-nominal behaviors predicted by the current model. If the execution of a test was different between the model and implementation, then the differences helped identify inconsistencies between the model and implementation. The dialogue between both teams drove the co-evolution of the model and implementation. Testing served as the vehicle for keeping the model and implementation in fidelity with each other. This paper describes (1) our experiences in developing our process model; and (2) three example problems found during the development of RMP.

VPLS: an effective technology for building scalable transparent LAN services

NASA Astrophysics Data System (ADS)

Dong, Ximing; Yu, Shaohua

2005-02-01

Virtual Private LAN Service (VPLS) is generating considerable interest with enterprises and service providers as it offers multipoint transparent LAN service (TLS) over MPLS networks. This paper describes an effective technology - VPLS, which links virtual switch instances (VSIs) through MPLS to form an emulated Ethernet switch and build Scalable Transparent Lan Services. It first focuses on the architecture of VPLS with Ethernet bridging technique at the edge and MPLS at the core, then it tries to elucidate the data forwarding mechanism within VPLS domain, including learning and aging MAC addresses on a per LSP basis, flooding of unknown frames and replication for unknown, multicast, and broadcast frames. The loop-avoidance mechanism, known as split horizon forwarding, is also analyzed. Another important aspect of VPLS service is its basic operation, including autodiscovery and signaling, is discussed. From the perspective of efficiency and scalability the paper compares two important signaling mechanism, BGP and LDP, which are used to set up a PW between the PEs and bind the PWs to a particular VSI. With the extension of VPLS and the increase of full mesh of PWs between PE devices (n*(n-1)/2 PWs in all, a n2 complete problem), VPLS instance could have a large number of remote PE associations, resulting in an inefficient use of network bandwidth and system resources as the ingress PE has to replicate each frame and append MPLS labels for remote PE. So the latter part of this paper focuses on the scalability issue: the Hierarchical VPLS. Within the architecture of HVPLS, this paper addresses two ways to cope with a possibly large number of MAC addresses, which make VPLS operate more efficiently.

Towards Scalable Cost-Effective Service and Survivability Provisioning in Ultra High Speed Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bin Wang

Optical transport networks based on wavelength division multiplexing (WDM) are considered to be the most appropriate choice for future Internet backbone. On the other hand, future DOE networks are expected to have the ability to dynamically provision on-demand survivable services to suit the needs of various high performance scientific applications and remote collaboration. Since a failure in aWDMnetwork such as a cable cut may result in a tremendous amount of data loss, efficient protection of data transport in WDM networks is therefore essential. As the backbone network is moving towards GMPLS/WDM optical networks, the unique requirement to support DOE’s sciencemore » mission results in challenging issues that are not directly addressed by existing networking techniques and methodologies. The objectives of this project were to develop cost effective protection and restoration mechanisms based on dedicated path, shared path, preconfigured cycle (p-cycle), and so on, to deal with single failure, dual failure, and shared risk link group (SRLG) failure, under different traffic and resource requirement models; to devise efficient service provisioning algorithms that deal with application specific network resource requirements for both unicast and multicast; to study various aspects of traffic grooming in WDM ring and mesh networks to derive cost effective solutions while meeting application resource and QoS requirements; to design various diverse routing and multi-constrained routing algorithms, considering different traffic models and failure models, for protection and restoration, as well as for service provisioning; to propose and study new optical burst switched architectures and mechanisms for effectively supporting dynamic services; and to integrate research with graduate and undergraduate education. All objectives have been successfully met. This report summarizes the major accomplishments of this project. The impact of the project manifests in many aspects: First, the project addressed many essential problems that arisen in current and future WDM optical networks, and provided a host of innovative solutions though there was no invention or patent filing. This project resulted in more than 2 dozens publications in major journals and conferences (including papers in IEEE Transactions and journals, as well as a book chapter). Our publications have been cited by many peer researchers. In particular, one of our conference papers was nominated for the best paper award of IEEE/Create-Net Broadnets (International Conference on Broadband Communications, Networks, and Systems) 2006. Second, the results and solutions of this project were well received by DOE Labs where presentations were given by the PI. We hope to continue the collaboration with DOE Labs in the future. Third, the project was the first to propose and extensively study multicast traffic grooming, new traffic models such as sliding scheduled traffic model and scheduled traffic model. Our research has sparkled a flurry of recent studies and publications by the research community in these areas. Fourth, the project has benefited a diverse population of students by motivating, engaging, enhancing their learning and skills. The project has been conducted in a manner conducive to the training of students both at graduate and undergraduate levels. As a result, one Ph.D., Dr. Abdur Billah, was graduated. Another Ph.D. student, Tianjian Li, will graduate in January 2007. In addition, four MS students were graduated. One undergraduate student, Jeffrey Alan Shininger, completed his university honors project. Fifth, thanks to the support of this ECPI project, the PI has obtained additional funding from the National Science Foundation, the Air Force Research Lab, and other sources. A few other proposals are pending. Finally, this project has also significantly impacted the curricula and resulted in the enhancement of courses at the graduate and undergraduate levels, therefore strengthening the bond between research and education.« less

Polling-Based High-Bit-Rate Packet Transfer in a Microcellular Network to Allow Fast Terminals

NASA Astrophysics Data System (ADS)

Hoa, Phan Thanh; Lambertsen, Gaute; Yamada, Takahiko

A microcellular network will be a good candidate for the future broadband mobile network. It is expected to support high-bit-rate connection for many fast mobile users if the handover is processed fast enough to lessen its impact on QoS requirements. One of the promising techniques is believed to use for the wireless interface in such a microcellular network is the WLAN (Wireless LAN) technique due to its very high wireless channel rate. However, the less capability of mobility support of this technique must be improved to be able to expand its utilization for the microcellular environment. The reason of its less support mobility is large handover latency delay caused by contention-based handover to the new BS (base station) and delay of re-forwarding data from the old to new BS. This paper presents a proposal of multi-polling and dynamic LMC (Logical Macro Cell) to reduce mentioned above delays. Polling frame for an MT (Mobile Terminal) is sent from every BS belonging to the same LMC — a virtual single macro cell that is a multicast group of several adjacent micro-cells in which an MT is communicating. Instead of contending for the medium of a new BS during handover, the MT responds to the polling sent from that new BS to enable the transition. Because only one BS of the LMC receives the polling ACK (acknowledgement) directly from the MT, this ACK frame has to be multicast to all BSs of the same LMC through the terrestrial network to continue sending the next polling cycle at each BS. Moreover, when an MT hands over to a new cell, its current LMC is switched over to a newly corresponding LMC to prevent the future contending for a new LMC. By this way, an MT can do handover between micro-cells of an LMC smoothly because the redundant resource is reserved for it at neighboring cells, no need to contend with others. Our simulation results using the OMNeT++ simulator illustrate the performance achievements of the multi-polling and dynamic LMC scheme in eliminating handover latency, packet loss and keeping mobile users' throughput stable in the high traffic load condition though it causes somewhat overhead on the neighboring cells.

Digital Multicasting of Multiple Audio Streams

NASA Technical Reports Server (NTRS)

Macha, Mitchell; Bullock, John

2007-01-01

The Mission Control Center Voice Over Internet Protocol (MCC VOIP) system (see figure) comprises hardware and software that effect simultaneous, nearly real-time transmission of as many as 14 different audio streams to authorized listeners via the MCC intranet and/or the Internet. The original version of the MCC VOIP system was conceived to enable flight-support personnel located in offices outside a spacecraft mission control center to monitor audio loops within the mission control center. Different versions of the MCC VOIP system could be used for a variety of public and commercial purposes - for example, to enable members of the general public to monitor one or more NASA audio streams through their home computers, to enable air-traffic supervisors to monitor communication between airline pilots and air-traffic controllers in training, and to monitor conferences among brokers in a stock exchange. At the transmitting end, the audio-distribution process begins with feeding the audio signals to analog-to-digital converters. The resulting digital streams are sent through the MCC intranet, using a user datagram protocol (UDP), to a server that converts them to encrypted data packets. The encrypted data packets are then routed to the personal computers of authorized users by use of multicasting techniques. The total data-processing load on the portion of the system upstream of and including the encryption server is the total load imposed by all of the audio streams being encoded, regardless of the number of the listeners or the number of streams being monitored concurrently by the listeners. The personal computer of a user authorized to listen is equipped with special- purpose MCC audio-player software. When the user launches the program, the user is prompted to provide identification and a password. In one of two access- control provisions, the program is hard-coded to validate the user s identity and password against a list maintained on a domain-controller computer at the MCC. In the other access-control provision, the program verifies that the user is authorized to have access to the audio streams. Once both access-control checks are completed, the audio software presents a graphical display that includes audiostream-selection buttons and volume-control sliders. The user can select all or any subset of the available audio streams and can adjust the volume of each stream independently of that of the other streams. The audio-player program spawns a "read" process for the selected stream(s). The spawned process sends, to the router(s), a "multicast-join" request for the selected streams. The router(s) responds to the request by sending the encrypted multicast packets to the spawned process. The spawned process receives the encrypted multicast packets and sends a decryption packet to audio-driver software. As the volume or muting features are changed by the user, interrupts are sent to the spawned process to change the corresponding attributes sent to the audio-driver software. The total latency of this system - that is, the total time from the origination of the audio signals to generation of sound at a listener s computer - lies between four and six seconds.

A novel unbalanced multiple description coder for robust video transmission over ad hoc wireless networks

NASA Astrophysics Data System (ADS)

Huang, Feng; Sun, Lifeng; Zhong, Yuzhuo

2006-01-01

Robust transmission of live video over ad hoc wireless networks presents new challenges: high bandwidth requirements are coupled with delay constraints; even a single packet loss causes error propagation until a complete video frame is coded in the intra-mode; ad hoc wireless networks suffer from bursty packet losses that drastically degrade the viewing experience. Accordingly, we propose a novel UMD coder capable of quickly recovering from losses and ensuring continuous playout. It uses 'peg' frames to prevent error propagation in the High-Resolution (HR) description and improve the robustness of key frames. The Low-Resolution (LR) coder works independent of the HR one, but they can also help each other recover from losses. Like many UMD coders, our UMD coder is drift-free, disruption-tolerant and able to make good use of the asymmetric available bandwidths of multiple paths. The simulation results under different conditions show that the proposed UMD coder has the highest decoded quality and lowest probability of pause when compared with concurrent UMDC techniques. The coder also has a comparable decoded quality, lower startup delay and lower probability of pause than a state-of-the-art FEC-based scheme. To provide robustness for video multicast applications, we propose non-end-to-end UMDC-based video distribution over a multi-tree multicast network. The multiplicity of parents decorrelates losses and the non-end-to-end feature increases the throughput of UMDC video data. We deploy an application-level service of LR description reconstruction in some intermediate nodes of the LR multicast tree. The principle behind this is to reconstruct the disrupted LR frames by the correctly received HR frames. As a result, the viewing experience at the downstream nodes benefits from the protection reconstruction at the upstream nodes.

Scalable Active Optical Access Network Using Variable High-Speed PLZT Optical Switch/Splitter

NASA Astrophysics Data System (ADS)

Ashizawa, Kunitaka; Sato, Takehiro; Tokuhashi, Kazumasa; Ishii, Daisuke; Okamoto, Satoru; Yamanaka, Naoaki; Oki, Eiji

This paper proposes a scalable active optical access network using high-speed Plumbum Lanthanum Zirconate Titanate (PLZT) optical switch/splitter. The Active Optical Network, called ActiON, using PLZT switching technology has been presented to increase the number of subscribers and the maximum transmission distance, compared to the Passive Optical Network (PON). ActiON supports the multicast slot allocation realized by running the PLZT switch elements in the splitter mode, which forces the switch to behave as an optical splitter. However, the previous ActiON creates a tradeoff between the network scalability and the power loss experienced by the optical signal to each user. It does not use the optical power efficiently because the optical power is simply divided into 0.5 to 0.5 without considering transmission distance from OLT to each ONU. The proposed network adopts PLZT switch elements in the variable splitter mode, which controls the split ratio of the optical power considering the transmission distance from OLT to each ONU, in addition to PLZT switch elements in existing two modes, the switching mode and the splitter mode. The proposed network introduces the flexible multicast slot allocation according to the transmission distance from OLT to each user and the number of required users using three modes, while keeping the advantages of ActiON, which are to support scalable and secure access services. Numerical results show that the proposed network dramatically reduces the required number of slots and supports high bandwidth efficiency services and extends the coverage of access network, compared to the previous ActiON, and the required computation time for selecting multicast users is less than 30msec, which is acceptable for on-demand broadcast services.

MDP: Reliable File Transfer for Space Missions

NASA Technical Reports Server (NTRS)

Rash, James; Criscuolo, Ed; Hogie, Keith; Parise, Ron; Hennessy, Joseph F. (Technical Monitor)

2002-01-01

This paper presents work being done at NASA/GSFC by the Operating Missions as Nodes on the Internet (OMNI) project to demonstrate the application of the Multicast Dissemination Protocol (MDP) to space missions to reliably transfer files. This work builds on previous work by the OMNI project to apply Internet communication technologies to space communication. The goal of this effort is to provide an inexpensive, reliable, standard, and interoperable mechanism for transferring files in the space communication environment. Limited bandwidth, noise, delay, intermittent connectivity, link asymmetry, and one-way links are all possible issues for space missions. Although these are link-layer issues, they can have a profound effect on the performance of transport and application level protocols. MDP, a UDP-based reliable file transfer protocol, was designed for multicast environments which have to address these same issues, and it has done so successfully. Developed by the Naval Research Lab in the mid 1990's, MDP is now in daily use by both the US Post Office and the DoD. This paper describes the use of MDP to provide automated end-to-end data flow for space missions. It examines the results of a parametric study of MDP in a simulated space link environment and discusses the results in terms of their implications for space missions. Lessons learned are addressed, which suggest minor enhancements to the MDP user interface to add specific features for space mission requirements, such as dynamic control of data rate, and a checkpoint/resume capability. These are features that are provided for in the protocol, but are not implemented in the sample MDP application that was provided. A brief look is also taken at the status of standardization. A version of MDP known as NORM (Neck Oriented Reliable Multicast) is in the process of becoming an IETF standard.

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. II. Backbone-local potentials of coarse-grained O 1 →4 -bonded polyglucose chains

NASA Astrophysics Data System (ADS)

Lubecka, Emilia A.; Liwo, Adam

2017-09-01

Based on the theory of the construction of coarse-grained force fields for polymer chains described in our recent work [A. K. Sieradzan et al., J. Chem. Phys. 146, 124106 (2017)], in this work effective coarse-grained potentials, to be used in the SUGRES-1P model of polysaccharides that is being developed in our laboratory, have been determined for the O ⋯O ⋯O virtual-bond angles (θ ) and for the dihedral angles for rotation about the O ⋯O virtual bonds (γ ) of 1 → 4 -linked glucosyl polysaccharides, for all possible combinations of [α ,β ]-[d,l]-glucose. The potentials of mean force corresponding to the virtual-bond angles and the virtual-bond dihedral angles were calculated from the free-energy surfaces of [α ,β ]-[d,l]-glucose pairs, determined by umbrella-sampling molecular-dynamics simulations with the AMBER12 force field, or combinations of the surfaces of two pairs sharing the overlapping residue, respectively, by integrating the respective Boltzmann factor over the dihedral angles λ for the rotation of the sugar units about the O ⋯O virtual bonds. Analytical expressions were subsequently fitted to the potentials of mean force. The virtual-bond-torsional potentials depend on both virtual-bond-dihedral angles and virtual-bond angles. The virtual-bond-angle potentials contain a single minimum at about θ =14 0° for all pairs except β -d-[α ,β ] -l-glucose, where the global minimum is shifted to θ =150° and a secondary minimum appears at θ =90°. The torsional potentials favor small negative γ angles for the α -d-glucose and extended negative angles γ for the β -d-glucose chains, as observed in the experimental structures of starch and cellulose, respectively. It was also demonstrated that the approximate expression derived based on Kubo's cluster-cumulant theory, whose coefficients depend on the identity of the disugar units comprising a trisugar unit that defines a torsional potential, fits simultaneously all torsional potentials very well, thus reducing the number of parameters significantly.

vMon-mobile provides wireless connection to the electronic patient record

NASA Astrophysics Data System (ADS)

Oliveira, Pedro P., Jr.; Rebelo, Marina; Pilon, Paulo E.; Gutierrez, Marco A.; Tachinardi, Umberto

2002-05-01

This work presents the development of a set of tools to help doctors to continuously monitor critical patients. Real-time monitoring signals are displayed via a Web Based Electronic Patient Record (Web-EPR) developed at the Heart Institute. Any computer on the Hospital's Intranet can access the Web-EPR that will open a browser plug-in called vMon. Recently vMon was adapted to wireless mobile devices providing the same real-time visualization of vital signals of its desktop counterpart. The monitoring network communicates with the hospital network through a gateway using HL7 messages and has the ability to export waveforms in real time using the multicast protocol through an API library. A dedicated ActiveX component was built that establishes the streaming of the biomedical signals under monitoring and displays them on an Internet Explorer 5.x browser. The mobile version - called vMon-mobile - will parse the browser window and deliver it to a PDA device connected to a local area network. The result is a virtual monitor presenting real-time data on a mobile device. All parameters and signals acquired from the moment the patient is connected to the monitors are stored for a few days. The most clinically relevant information is added to patient's EPR.

47 CFR 73.1201 - Station identification.

Code of Federal Regulations, 2010 CFR

2010-10-01

... offerings. Television and Class A television broadcast stations may make these announcements visually or... multicast audio programming streams, in a manner that appropriately alerts its audience to the fact that it is listening to a digital audio broadcast. No other insertion between the station's call letters and...

Back pressure based multicast scheduling for fair bandwidth allocation.

PubMed

Sarkar, Saswati; Tassiulas, Leandros

2005-09-01

We study the fair allocation of bandwidth in multicast networks with multirate capabilities. In multirate transmission, each source encodes its signal in layers. The lowest layer contains the most important information and all receivers of a session should receive it. If a receiver's data path has additional bandwidth, it receives higher layers which leads to a better quality of reception. The bandwidth allocation objective is to distribute the layers fairly. We present a computationally simple, decentralized scheduling policy that attains the maxmin fair rates without using any knowledge of traffic statistics and layer bandwidths. This policy learns the congestion level from the queue lengths at the nodes, and adapts the packet transmissions accordingly. When the network is congested, packets are dropped from the higher layers; therefore, the more important lower layers suffer negligible packet loss. We present analytical and simulation results that guarantee the maxmin fairness of the resulting rate allocation, and upper bound the packet loss rates for different layers.

Secure Multicast Tree Structure Generation Method for Directed Diffusion Using A* Algorithms

NASA Astrophysics Data System (ADS)

Kim, Jin Myoung; Lee, Hae Young; Cho, Tae Ho

The application of wireless sensor networks to areas such as combat field surveillance, terrorist tracking, and highway traffic monitoring requires secure communication among the sensor nodes within the networks. Logical key hierarchy (LKH) is a tree based key management model which provides secure group communication. When a sensor node is added or evicted from the communication group, LKH updates the group key in order to ensure the security of the communications. In order to efficiently update the group key in directed diffusion, we propose a method for secure multicast tree structure generation, an extension to LKH that reduces the number of re-keying messages by considering the addition and eviction ratios of the history data. For the generation of the proposed key tree structure the A* algorithm is applied, in which the branching factor at each level can take on different value. The experiment results demonstrate the efficiency of the proposed key tree structure against the existing key tree structures of fixed branching factors.

Context-based user grouping for multi-casting in heterogeneous radio networks

NASA Astrophysics Data System (ADS)

Mannweiler, C.; Klein, A.; Schneider, J.; Schotten, H. D.

2011-08-01

Along with the rise of sophisticated smartphones and smart spaces, the availability of both static and dynamic context information has steadily been increasing in recent years. Due to the popularity of social networks, these data are complemented by profile information about individual users. Making use of this information by classifying users in wireless networks enables targeted content and advertisement delivery as well as optimizing network resources, in particular bandwidth utilization, by facilitating group-based multi-casting. In this paper, we present the design and implementation of a web service for advanced user classification based on user, network, and environmental context information. The service employs simple and advanced clustering algorithms for forming classes of users. Available service functionalities include group formation, context-aware adaptation, and deletion as well as the exposure of group characteristics. Moreover, the results of a performance evaluation, where the service has been integrated in a simulator modeling user behavior in heterogeneous wireless systems, are presented.

Designers Workbench: Towards Real-Time Immersive Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuester, F; Duchaineau, M A; Hamann, B

2001-10-03

This paper introduces the DesignersWorkbench, a semi-immersive virtual environment for two-handed modeling, sculpting and analysis tasks. The paper outlines the fundamental tools, design metaphors and hardware components required for an intuitive real-time modeling system. As companies focus on streamlining productivity to cope with global competition, the migration to computer-aided design (CAD), computer-aided manufacturing (CAM), and computer-aided engineering (CAE) systems has established a new backbone of modern industrial product development. However, traditionally a product design frequently originates from a clay model that, after digitization, forms the basis for the numerical description of CAD primitives. The DesignersWorkbench aims at closing this technologymore » or ''digital gap'' experienced by design and CAD engineers by transforming the classical design paradigm into its filly integrated digital and virtual analog allowing collaborative development in a semi-immersive virtual environment. This project emphasizes two key components from the classical product design cycle: freeform modeling and analysis. In the freeform modeling stage, content creation in the form of two-handed sculpting of arbitrary objects using polygonal, volumetric or mathematically defined primitives is emphasized, whereas the analysis component provides the tools required for pre- and post-processing steps for finite element analysis tasks applied to the created models.« less

Australian DefenceScience. Volume 16, Number 1, Autumn

DTIC Science & Technology

2008-01-01

are carried via VOIP technology, and multicast IP traffic for audio -visual communications is also supported. The SSATIN system overall is seen to...Artificial Intelligence and Soft Computing Palma de Mallorca, Spain http://iasted.com/conferences/home-628.html 1 - 3 Sep 2008 Visualisation , Imaging and

QoS Adaptation in Multimedia Multicast Conference Applications for E-Learning Services

ERIC Educational Resources Information Center

Deusdado, Sérgio; Carvalho, Paulo

2006-01-01

The evolution of the World Wide Web service has incorporated new distributed multimedia conference applications, powering a new generation of e-learning development and allowing improved interactivity and prohuman relations. Groupware applications are increasingly representative in the Internet home applications market, however, the Quality of…

Internet technologies and requirements for telemedicine

NASA Technical Reports Server (NTRS)

Lamaster, H.; Meylor, J.; Meylor, F.

1997-01-01

Internet technologies are briefly introduced and those applicable for telemedicine are reviewed. Multicast internet technologies are described. The National Aeronautics and Space Administration (NASA) 'Telemedicine Space-bridge to Russia' project is described and used to derive requirements for internet telemedicine. Telemedicine privacy and Quality of Service (QoS) requirements are described.

47 CFR 76.66 - Satellite broadcast signal carriage.

Code of Federal Regulations, 2010 CFR

2010-10-01

... free over-the-air signal, including multicast and high definition digital signals. (c) Election cycle... first retransmission consent-mandatory carriage election cycle shall be for a four-year period... carriage election cycle, and all cycles thereafter, shall be for a period of three years (e.g. the second...

47 CFR 73.1201 - Station identification.

Code of Federal Regulations, 2014 CFR

2014-10-01

...; Provided, That the name of the licensee, the station's frequency, the station's channel number, as stated... number in the station identification must use the station's major channel number and may distinguish multicast program streams. For example, a DTV station with major channel number 26 may use 26.1 to identify...

47 CFR 73.1201 - Station identification.

Code of Federal Regulations, 2013 CFR

2013-10-01

...; Provided, That the name of the licensee, the station's frequency, the station's channel number, as stated... number in the station identification must use the station's major channel number and may distinguish multicast program streams. For example, a DTV station with major channel number 26 may use 26.1 to identify...

47 CFR 73.1201 - Station identification.

Code of Federal Regulations, 2011 CFR

2011-10-01

...; Provided, That the name of the licensee, the station's frequency, the station's channel number, as stated... number in the station identification must use the station's major channel number and may distinguish multicast program streams. For example, a DTV station with major channel number 26 may use 26.1 to identify...

47 CFR 73.1201 - Station identification.

Code of Federal Regulations, 2012 CFR

2012-10-01

...; Provided, That the name of the licensee, the station's frequency, the station's channel number, as stated... number in the station identification must use the station's major channel number and may distinguish multicast program streams. For example, a DTV station with major channel number 26 may use 26.1 to identify...

Copper(I)-induced amplification of a [2]catenane in a virtual dynamic library of macrocyclic alkenes.

PubMed

Berrocal, José Augusto; Nieuwenhuizen, Marko M L; Mandolini, Luigi; Meijer, E W; Di Stefano, Stefano

2014-08-28

Olefin cross-metathesis of diluted dichloromethane solutions (≤0.15 M) of the 28-membered macrocyclic alkene C1, featuring a 1,10-phenanthroline moiety in the backbone, as well as of catenand 1, composed of two identical interlocked C1 units, generates families of noninterlocked oligomers Ci. The composition of the libraries is strongly dependent on the monomer concentration, but independent of whether C1 or 1 is used as feedstock, as expected for truly equilibrated systems. Accordingly, the limiting value 0.022 M approached by the equilibrium concentration of C1 when the total monomer concentration approaches the critical value, as predicted by the Jacobson-Stockmayer theory, provides a reliable estimate of the thermodynamically effective molarity. Catenand 1 behaves as a virtual component of the dynamic libraries, in that there is no detectable trace of its presence in the equilibrated mixtures, but becomes the major component - in the form of its copper(I) complex - when olefin cross-metathesis is carried out in the presence of a copper(I) salt.

An Experimental Seismic Data and Parameter Exchange System for Tsunami Warning Systems

NASA Astrophysics Data System (ADS)

Hoffmann, T. L.; Hanka, W.; Saul, J.; Weber, B.; Becker, J.; Heinloo, A.; Hoffmann, M.

2009-12-01

For several years GFZ Potsdam is operating a global earthquake monitoring system. Since the beginning of 2008, this system is also used as an experimental seismic background data center for two different regional Tsunami Warning Systems (TWS), the IOTWS (Indian Ocean) and the interim NEAMTWS (NE Atlantic and Mediterranean). The SeisComP3 (SC3) software, developed within the GITEWS (German Indian Ocean Tsunami Early Warning System) project, capable to acquire, archive and process real-time data feeds, was extended for export and import of individual processing results within the two clusters of connected SC3 systems. Therefore not only real-time waveform data are routed to the attached warning centers through GFZ but also processing results. While the current experimental NEAMTWS cluster consists of SC3 systems in six designated national warning centers in Europe, the IOTWS cluster presently includes seven centers, with another three likely to join in 2009/10. For NEAMTWS purposes, the GFZ virtual real-time seismic network (GEOFON Extended Virtual Network -GEVN) in Europe was substantially extended by adding many stations from Western European countries optimizing the station distribution. In parallel to the data collection over the Internet, a GFZ VSAT hub for secured data collection of the EuroMED GEOFON and NEAMTWS backbone network stations became operational and first data links were established through this backbone. For the Southeast Asia region, a VSAT hub has been established in Jakarta already in 2006, with some other partner networks connecting to this backbone via the Internet. Since its establishment, the experimental system has had the opportunity to prove its performance in a number of relevant earthquakes. Reliable solutions derived from a minimum of 25 stations were very promising in terms of speed. For important events, automatic alerts were released and disseminated by emails and SMS. Manually verified solutions are added as soon as they become available. The results are also promising in terms of accuracy since epicenter coordinates, depth and magnitude estimates were sufficiently accurate from the very beginning, and usually do not differ substantially from the final solutions. In summary, automatic seismic event processing has shown to work well as a first step for starting a Tsunami Warning process. However, for the secured assessment of the tsunami potential of a given event, 24/7-manned regional TWCs are mandatory for reliable manual verification of the automatic seismic results. At this time, GFZ itself provides manual verification only when staff is available, not on a 24/7 basis, while the actual national tsunami warning centers have all a reliable 24/7 service.

78 FR 53757 - Information Collections Being Submitted for Review and Approval to the Office of Management and...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-30

...'s channel number, as stated on the station's license, and/or the station's network affiliation may... Stations, choosing to include the station's channel number in the station identification must use the station's major channel number and may distinguish multicast program streams. For example, a DTV station...

Multimedia C for Remote Language Teaching over SuperJANET.

ERIC Educational Resources Information Center

Matthews, E.; And Others

1996-01-01

Describes work carried out as part of a remote language teaching research investigation, which is looking into the use of multicast, multimedia conferencing over SuperJANET. The fundamental idea is to investigate the feasibility of sharing language teaching resources among universities within the United Kingdom by using the broadband SuperJANET…

37 CFR 386.2 - Royalty fee for secondary transmission by satellite carriers.

Code of Federal Regulations, 2011 CFR

2011-07-01

... BOARD, LIBRARY OF CONGRESS RATES AND TERMS FOR STATUTORY LICENSES ADJUSTMENT OF ROYALTY FEES FOR... a given month. (2) In the case of a station engaged in digital multicasting, the rates set forth in paragraph (b) of this section shall apply to each digital stream that a satellite carrier or distributor...

37 CFR 386.2 - Royalty fee for secondary transmission by satellite carriers.

Code of Federal Regulations, 2013 CFR

2013-07-01

... BOARD, LIBRARY OF CONGRESS RATES AND TERMS FOR STATUTORY LICENSES ADJUSTMENT OF ROYALTY FEES FOR... a given month. (2) In the case of a station engaged in digital multicasting, the rates set forth in paragraph (b) of this section shall apply to each digital stream that a satellite carrier or distributor...

75 FR 53198 - Rate Adjustment for the Satellite Carrier Compulsory License

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-31

... LIBRARY OF CONGRESS Copyright Royalty Board 37 CFR Part 386 [Docket No. 2010-4 CRB Satellite Rate] Rate Adjustment for the Satellite Carrier Compulsory License AGENCY: Copyright Royalty Board, Library... last day of a given month. (2) In the case of a station engaged in digital multicasting, the rates set...

37 CFR 386.2 - Royalty fee for secondary transmission by satellite carriers.

Code of Federal Regulations, 2014 CFR

2014-07-01

... BOARD, LIBRARY OF CONGRESS RATES AND TERMS FOR STATUTORY LICENSES ADJUSTMENT OF ROYALTY FEES FOR... a given month. (2) In the case of a station engaged in digital multicasting, the rates set forth in paragraph (b) of this section shall apply to each digital stream that a satellite carrier or distributor...

37 CFR 386.2 - Royalty fee for secondary transmission by satellite carriers.

Code of Federal Regulations, 2012 CFR

2012-07-01

... BOARD, LIBRARY OF CONGRESS RATES AND TERMS FOR STATUTORY LICENSES ADJUSTMENT OF ROYALTY FEES FOR... a given month. (2) In the case of a station engaged in digital multicasting, the rates set forth in paragraph (b) of this section shall apply to each digital stream that a satellite carrier or distributor...

Multipoint Multimedia Conferencing System with Group Awareness Support and Remote Management

ERIC Educational Resources Information Center

Osawa, Noritaka; Asai, Kikuo

2008-01-01

A multipoint, multimedia conferencing system called FocusShare is described that uses IPv6/IPv4 multicasting for real-time collaboration, enabling video, audio, and group awareness information to be shared. Multiple telepointers provide group awareness information and make it easy to share attention and intention. In addition to pointing with the…

Using Interactive Broadband Multicasting in a Museum Lifelong Learning Program.

ERIC Educational Resources Information Center

Steinbach, Leonard

The Cleveland Museum of Art has embarked on an innovative approach for delivering high quality video-on-demand and live interactive cultural programming, along with Web-based complementary material, to seniors in assisted living residence facilities, community-based centers, and disabled persons in their homes. The project is made possible in part…

Protocol Architecture Model Report

NASA Technical Reports Server (NTRS)

Dhas, Chris

2000-01-01

NASA's Glenn Research Center (GRC) defines and develops advanced technology for high priority national needs in communications technologies for application to aeronautics and space. GRC tasked Computer Networks and Software Inc. (CNS) to examine protocols and architectures for an In-Space Internet Node. CNS has developed a methodology for network reference models to support NASA's four mission areas: Earth Science, Space Science, Human Exploration and Development of Space (REDS), Aerospace Technology. This report applies the methodology to three space Internet-based communications scenarios for future missions. CNS has conceptualized, designed, and developed space Internet-based communications protocols and architectures for each of the independent scenarios. The scenarios are: Scenario 1: Unicast communications between a Low-Earth-Orbit (LEO) spacecraft inspace Internet node and a ground terminal Internet node via a Tracking and Data Rela Satellite (TDRS) transfer; Scenario 2: Unicast communications between a Low-Earth-Orbit (LEO) International Space Station and a ground terminal Internet node via a TDRS transfer; Scenario 3: Multicast Communications (or "Multicasting"), 1 Spacecraft to N Ground Receivers, N Ground Transmitters to 1 Ground Receiver via a Spacecraft.

Design alternatives for process group membership and multicast

NASA Technical Reports Server (NTRS)

Birman, Kenneth P.; Cooper, Robert; Gleeson, Barry

1991-01-01

Process groups are a natural tool for distributed programming, and are increasingly important in distributed computing environments. However, there is little agreement on the most appropriate semantics for process group membership and group communication. These issues are of special importance in the Isis system, a toolkit for distributed programming. Isis supports several styles of process group, and a collection of group communication protocols spanning a range of atomicity and ordering properties. This flexibility makes Isis adaptable to a variety of applications, but is also a source of complexity that limits performance. This paper reports on a new architecture that arose from an effort to simplify Isis process group semantics. Our findings include a refined notion of how the clients of a group should be treated, what the properties of a multicast primitive should be when systems contain large numbers of overlapping groups, and a new construct called the casuality domain. As an illustration, we apply the architecture to the problem of converting processes into fault-tolerant process groups in a manner that is 'transparent' to other processes in the system.

Integer-Linear-Programing Optimization in Scalable Video Multicast with Adaptive Modulation and Coding in Wireless Networks

PubMed Central

Lee, Chaewoo

2014-01-01

The advancement in wideband wireless network supports real time services such as IPTV and live video streaming. However, because of the sharing nature of the wireless medium, efficient resource allocation has been studied to achieve a high level of acceptability and proliferation of wireless multimedia. Scalable video coding (SVC) with adaptive modulation and coding (AMC) provides an excellent solution for wireless video streaming. By assigning different modulation and coding schemes (MCSs) to video layers, SVC can provide good video quality to users in good channel conditions and also basic video quality to users in bad channel conditions. For optimal resource allocation, a key issue in applying SVC in the wireless multicast service is how to assign MCSs and the time resources to each SVC layer in the heterogeneous channel condition. We formulate this problem with integer linear programming (ILP) and provide numerical results to show the performance under 802.16 m environment. The result shows that our methodology enhances the overall system throughput compared to an existing algorithm. PMID:25276862

CLON: Overlay Networks and Gossip Protocols for Cloud Environments

NASA Astrophysics Data System (ADS)

Matos, Miguel; Sousa, António; Pereira, José; Oliveira, Rui; Deliot, Eric; Murray, Paul

Although epidemic or gossip-based multicast is a robust and scalable approach to reliable data dissemination, its inherent redundancy results in high resource consumption on both links and nodes. This problem is aggravated in settings that have costlier or resource constrained links as happens in Cloud Computing infrastructures composed by several interconnected data centers across the globe.

A Security Architecture for Fault-Tolerant Systems

DTIC Science & Technology

1993-06-03

aspect of our effort to achieve better performance is integrating the system into microkernel -based operating systems. 4 Summary and discussion In...135-171, June 1983. [vRBC+92] R. van Renesse, K. Birman, R. Cooper, B. Glade, and P. Stephenson. Reliable multicast between microkernels . In...Proceedings of the USENIX Microkernels and Other Kernel Architectures Workshop, April 1992. 29

75 FR 52267 - Waiver of Statement of Account Filing Deadline for the 2010/1 Period

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-25

... available in a print format, a PDF format, and a software ``fill-in'' format created by Gralin Associates... retransmission of multicast streams. The paper and PDF versions of the form have been available to cable... recognize that the paper and PDF versions of the SOA have been available since July, many large and small...

High Performance Computing Multicast

DTIC Science & Technology

2012-02-01

responsiveness, first-tier applications often implement replicated in- memory key-value stores , using them to store state or to cache data from services...alternative that replicates data , combines agreement on update ordering with amnesia freedom, and supports both good scalability and fast response. A...alternative that replicates data , combines agreement on update ordering with amnesia freedom, and supports both good scalability and fast response

77 FR 65596 - Self-Regulatory Organizations; The NASDAQ Stock Market LLC; Notice of Filing of Proposed Rule...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-29

... to offer remote multi-cast ITCH Wave Ports for clients co-located at other third party data centers... delivery of third party market data to market center clients via a wireless network using millimeter wave... Multi- cast ITCH Wave Ports for clients co-located at other third-party data centers, through which...

Design and Implementation of Replicated Object Layer

NASA Technical Reports Server (NTRS)

Koka, Sudhir

1996-01-01

One of the widely used techniques for construction of fault tolerant applications is the replication of resources so that if one copy fails sufficient copies may still remain operational to allow the application to continue to function. This thesis involves the design and implementation of an object oriented framework for replicating data on multiple sites and across different platforms. Our approach, called the Replicated Object Layer (ROL) provides a mechanism for consistent replication of data over dynamic networks. ROL uses the Reliable Multicast Protocol (RMP) as a communication protocol that provides for reliable delivery, serialization and fault tolerance. Besides providing type registration, this layer facilitates distributed atomic transactions on replicated data. A novel algorithm called the RMP Commit Protocol, which commits transactions efficiently in reliable multicast environment is presented. ROL provides recovery procedures to ensure that site and communication failures do not corrupt persistent data, and male the system fault tolerant to network partitions. ROL will facilitate building distributed fault tolerant applications by performing the burdensome details of replica consistency operations, and making it completely transparent to the application.Replicated databases are a major class of applications which could be built on top of ROL.

Detecting and Preventing Sybil Attacks in Wireless Sensor Networks Using Message Authentication and Passing Method.

PubMed

Dhamodharan, Udaya Suriya Raj Kumar; Vayanaperumal, Rajamani

2015-01-01

Wireless sensor networks are highly indispensable for securing network protection. Highly critical attacks of various kinds have been documented in wireless sensor network till now by many researchers. The Sybil attack is a massive destructive attack against the sensor network where numerous genuine identities with forged identities are used for getting an illegal entry into a network. Discerning the Sybil attack, sinkhole, and wormhole attack while multicasting is a tremendous job in wireless sensor network. Basically a Sybil attack means a node which pretends its identity to other nodes. Communication to an illegal node results in data loss and becomes dangerous in the network. The existing method Random Password Comparison has only a scheme which just verifies the node identities by analyzing the neighbors. A survey was done on a Sybil attack with the objective of resolving this problem. The survey has proposed a combined CAM-PVM (compare and match-position verification method) with MAP (message authentication and passing) for detecting, eliminating, and eventually preventing the entry of Sybil nodes in the network. We propose a scheme of assuring security for wireless sensor network, to deal with attacks of these kinds in unicasting and multicasting.

Detecting and Preventing Sybil Attacks in Wireless Sensor Networks Using Message Authentication and Passing Method

PubMed Central

Dhamodharan, Udaya Suriya Raj Kumar; Vayanaperumal, Rajamani

2015-01-01

Wireless sensor networks are highly indispensable for securing network protection. Highly critical attacks of various kinds have been documented in wireless sensor network till now by many researchers. The Sybil attack is a massive destructive attack against the sensor network where numerous genuine identities with forged identities are used for getting an illegal entry into a network. Discerning the Sybil attack, sinkhole, and wormhole attack while multicasting is a tremendous job in wireless sensor network. Basically a Sybil attack means a node which pretends its identity to other nodes. Communication to an illegal node results in data loss and becomes dangerous in the network. The existing method Random Password Comparison has only a scheme which just verifies the node identities by analyzing the neighbors. A survey was done on a Sybil attack with the objective of resolving this problem. The survey has proposed a combined CAM-PVM (compare and match-position verification method) with MAP (message authentication and passing) for detecting, eliminating, and eventually preventing the entry of Sybil nodes in the network. We propose a scheme of assuring security for wireless sensor network, to deal with attacks of these kinds in unicasting and multicasting. PMID:26236773

Toward fidelity between specification and implementation

NASA Technical Reports Server (NTRS)

Callahan, John R.; Montgomery, Todd L.; Morrison, Jeff; Wu, Yunqing

1994-01-01

This paper describes the methods used to specify and implement a complex communications protocol that provides reliable delivery of data in multicast-capable, packet-switching telecommunication networks. The protocol, called the Reliable Multicasting Protocol (RMP), was developed incrementally by two complementary teams using a combination of formal and informal techniques in an attempt to ensure the correctness of the protocol implementation. The first team, called the Design team, initially specified protocol requirements using a variant of SCR requirements tables and implemented a prototype solution. The second team, called the V&V team, developed a state model based on the requirements tables and derived test cases from these tables to exercise the implementation. In a series of iterative steps, the Design team added new functionality to the implementation while the V&V team kept the state model in fidelity with the implementation through testing. Test cases derived from state transition paths in the formal model formed the dialogue between teams during development and served as the vehicles for keeping the model and implementation in fidelity with each other. This paper describes our experiences in developing our process model, details of our approach, and some example problems found during the development of RMP.

Guest Editor's introduction: Special issue on distributed virtual environments

NASA Astrophysics Data System (ADS)

Lea, Rodger

1998-09-01

Distributed virtual environments (DVEs) combine technology from 3D graphics, virtual reality and distributed systems to provide an interactive 3D scene that supports multiple participants. Each participant has a representation in the scene, often known as an avatar, and is free to navigate through the scene and interact with both the scene and other viewers of the scene. Changes to the scene, for example, position changes of one avatar as the associated viewer navigates through the scene, or changes to objects in the scene via manipulation, are propagated in real time to all viewers. This ensures that all viewers of a shared scene `see' the same representation of it, allowing sensible reasoning about the scene. Early work on such environments was restricted to their use in simulation, in particular in military simulation. However, over recent years a number of interesting and potentially far-reaching attempts have been made to exploit the technology for a range of other uses, including: Social spaces. Such spaces can be seen as logical extensions of the familiar text chat space. In 3D social spaces avatars, representing participants, can meet in shared 3D scenes and in addition to text chat can use visual cues and even in some cases spatial audio. Collaborative working. A number of recent projects have attempted to explore the use of DVEs to facilitate computer-supported collaborative working (CSCW), where the 3D space provides a context and work space for collaboration. Gaming. The shared 3D space is already familiar, albeit in a constrained manner, to the gaming community. DVEs are a logical superset of existing 3D games and can provide a rich framework for advanced gaming applications. e-commerce. The ability to navigate through a virtual shopping mall and to look at, and even interact with, 3D representations of articles has appealed to the e-commerce community as it searches for the best method of presenting merchandise to electronic consumers. The technology needed to support these systems crosses a number of disciplines in computer science. These include, but are certainly not limited to, real-time graphics for the accurate and realistic representation of scenes, group communications for the efficient update of shared consistent scene data, user interface modelling to exploit the use of the 3D representation and multimedia systems technology for the delivery of streamed graphics and audio-visual data into the shared scene. It is this intersection of technologies and the overriding need to provide visual realism that places such high demands on the underlying distributed systems infrastructure and makes DVEs such fertile ground for distributed systems research. Two examples serve to show how DVE developers have exploited the unique aspects of their domain. Communications. The usual tension between latency and throughput is particularly noticeable within DVEs. To ensure the timely update of multiple viewers of a particular scene requires that such updates be propagated quickly. However, the sheer volume of changes to any one scene calls for techniques that minimize the number of distinct updates that are sent to the network. Several techniques have been used to address this tension; these include the use of multicast communications, and in particular multicast in wide-area networks to reduce actual message traffic. Multicast has been combined with general group communications to partition updates to related objects or users of a scene. A less traditional approach has been the use of dead reckoning whereby a client application that visualizes the scene calculates position updates by extrapolating movement based on previous information. This allows the system to reduce the number of communications needed to update objects that move in a stable manner within the scene. Scaling. DVEs, especially those used for social spaces, are required to support large numbers of simultaneous users in potentially large shared scenes. The desire for scalability has driven different architectural designs, for example, the use of fully distributed architectures which scale well but often suffer performance costs versus centralized and hierarchical architectures in which the inverse is true. However, DVEs have also exploited the spatial nature of their domain to address scalability and have pioneered techniques that exploit the semantics of the shared space to reduce data updates and so allow greater scalability. Several of the systems reported in this special issue apply a notion of area of interest to partition the scene and so reduce the participants in any data updates. The specification of area of interest differs between systems. One approach has been to exploit a geographical notion, i.e. a regular portion of a scene, or a semantic unit, such as a room or building. Another approach has been to define the area of interest as a spatial area associated with an avatar in the scene. The five papers in this special issue have been chosen to highlight the distributed systems aspects of the DVE domain. The first paper, on the DIVE system, described by Emmanuel Frécon and Mårten Stenius explores the use of multicast and group communication in a fully peer-to-peer architecture. The developers of DIVE have focused on its use as the basis for collaborative work environments and have explored the issues associated with maintaining and updating large complicated scenes. The second paper, by Hiroaki Harada et al, describes the AGORA system, a DVE concentrating on social spaces and employing a novel communication technique that incorporates position update and vector information to support dead reckoning. The paper by Simon Powers et al explores the application of DVEs to the gaming domain. They propose a novel architecture that separates out higher-level game semantics - the conceptual model - from the lower-level scene attributes - the dynamic model, both running on servers, from the actual visual representation - the visual model - running on the client. They claim a number of benefits from this approach, including better predictability and consistency. Wolfgang Broll discusses the SmallView system which is an attempt to provide a toolkit for DVEs. One of the key features of SmallView is a sophisticated application level protocol, DWTP, that provides support for a variety of communication models. The final paper, by Chris Greenhalgh, discusses the MASSIVE system which has been used to explore the notion of awareness in the 3D space via the concept of `auras'. These auras define an area of interest for users and support a mapping between what a user is aware of, and what data update rate the communications infrastructure can support. We hope that this selection of papers will serve to provide a clear introduction to the distributed system issues faced by the DVE community and the approaches they have taken in solving them. Finally, we wish to thank Hubert Le Van Gong for his tireless efforts in pulling together all these papers and both the referees and the authors of the papers for the time and effort in ensuring that their contributions teased out the interesting distributed systems issues for this special issue. † E-mail address: rodger@arch.sel.sony.com

A Novel Group Coordination Protocol for Collaborative Multimedia Systems

DTIC Science & Technology

1998-01-01

technology have advanced considerably, ef- ficient group coordination support for applications characterized by synchronous and wide-area groupwork is...As a component within a general coordination architecture for many-to-many groupwork , floor control coexists with proto- cols for reliable ordered...multicast and media synchronization at a sub-application level. Orchestration of multiparty groupwork with fine-grained and fair floor control is an

78 FR 19051 - Self-Regulatory Organizations; The NASDAQ Stock Market LLC; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-28

... that is in test mode in excess of one. (c)-(f) No change. (g) Other Port Fees Remote Multi-cast ITCH... environment to test upcoming NASDAQ releases and product enhancements, as well as test software prior to... public in accordance with the provisions of 5 U.S.C. 552, will be available for Web site viewing and...

Multiuser Transmit Beamforming for Maximum Sum Capacity in Tactical Wireless Multicast Networks

DTIC Science & Technology

2006-08-01

commonly used extended Kalman filter . See [2, 5, 6] for recent tutorial overviews. In particle filtering , continuous distributions are approximated by...signals (using and developing associated particle filtering tools). Our work on these topics has been reported in seven (IEEE, SIAM) journal papers and...multidimensional scaling, tracking, intercept, particle filters . 16. PRICE CODE 17. SECURITY CLASSIFICATION OF REPORT 18. SECURITY CLASSIFICATION OF

Strong liquid-crystalline polymeric compositions

DOEpatents

Dowell, Flonnie

1993-01-01

Strong liquid-crystalline polymeric (LCP) compositions of matter. LCP backbones are combined with liquid crystalline (LC) side chains in a manner which maximizes molecular ordering through interdigitation of the side chains, thereby yielding materials which are predicted to have superior mechanical properties over existing LCPs. The theoretical design of LCPs having such characteristics includes consideration of the spacing distance between side chains along the backbone, the need for rigid sections in the backbone and in the side chains, the degree of polymerization, the length of the side chains, the regularity of the spacing of the side chains along the backbone, the interdigitation of side chains in sub-molecular strips, the packing of the side chains on one or two sides of the backbone to which they are attached, the symmetry of the side chains, the points of attachment of the side chains to the backbone, the flexibility and size of the chemical group connecting each side chain to the backbone, the effect of semiflexible sections in the backbone and the side chains, and the choice of types of dipolar and/or hydrogen bonding forces in the backbones and the side chains for easy alignment.

Strong liquid-crystalline polymeric compositions

DOEpatents

Dowell, F.

1993-12-07

Strong liquid-crystalline polymeric (LCP) compositions of matter are described. LCP backbones are combined with liquid crystalline (LC) side chains in a manner which maximizes molecular ordering through interdigitation of the side chains, thereby yielding materials which are predicted to have superior mechanical properties over existing LCPs. The theoretical design of LCPs having such characteristics includes consideration of the spacing distance between side chains along the backbone, the need for rigid sections in the backbone and in the side chains, the degree of polymerization, the length of the side chains, the regularity of the spacing of the side chains along the backbone, the interdigitation of side chains in sub-molecular strips, the packing of the side chains on one or two sides of the backbone to which they are attached, the symmetry of the side chains, the points of attachment of the side chains to the backbone, the flexibility and size of the chemical group connecting each side chain to the backbone, the effect of semiflexible sections in the backbone and the side chains, and the choice of types of dipolar and/or hydrogen bonding forces in the backbones and the side chains for easy alignment. 27 figures.

Enhanced Performance & Functionality of Tunable Delay Lines

DTIC Science & Technology

2012-08-01

Figure 6. Experimental setup. Transmitter is capable of generating 80-Gb/s RZ-DQPSK, 40-Gb/s RZ-DPSK and 40-Gb/s RZ-OOK modulation formats. Phase...Power penalty with respect to B2B of each channel for 2-, 4-, 8-fold multicasting. (c) Pulsewidth as a function of DGD along with eye diagrams of 2...63 Figure 99. Concept. (a) A distributed optical network ; (b) NOLMs for

Scalable Technology for a New Generation of Collaborative Applications

DTIC Science & Technology

2007-04-01

of the International Symposium on Distributed Computing (DISC), Cracow, Poland, September 2005. Classic Paxos vs. Fast Paxos: Caveat Emptor, Flavio...grou or able and fast multicast primitive to layer under high-level latency across dimensions as varied as group size [10, 17],abstractions such as...servers, networked via fast , dedicated interconnects. The system to subscribe to a fraction of the equities on the software stack running on a single

Saguaro: A Distributed Operating System Based on Pools of Servers.

DTIC Science & Technology

1988-03-25

asynchronous message passing, multicast, and semaphores are supported. We have found this flexibility to be very useful for distributed programming. The...variety of communication primitives provided by SR has facilitated the research of Stella Atkins, who was a visiting professor at Arizona during Spring...data bits in a raw communication channel to help keep the source and destination synchronized , Psync explicitly embeds timing information drawn from the

Improved Lower Bounds on the Price of Stability of Undirected Network Design Games

NASA Astrophysics Data System (ADS)

Bilò, Vittorio; Caragiannis, Ioannis; Fanelli, Angelo; Monaco, Gianpiero

Bounding the price of stability of undirected network design games with fair cost allocation is a challenging open problem in the Algorithmic Game Theory research agenda. Even though the generalization of such games in directed networks is well understood in terms of the price of stability (it is exactly H n , the n-th harmonic number, for games with n players), far less is known for network design games in undirected networks. The upper bound carries over to this case as well while the best known lower bound is 42/23 ≈ 1.826. For more restricted but interesting variants of such games such as broadcast and multicast games, sublogarithmic upper bounds are known while the best known lower bound is 12/7 ≈ 1.714. In the current paper, we improve the lower bounds as follows. We break the psychological barrier of 2 by showing that the price of stability of undirected network design games is at least 348/155 ≈ 2.245. Our proof uses a recursive construction of a network design game with a simple gadget as the main building block. For broadcast and multicast games, we present new lower bounds of 20/11 ≈ 1.818 and 1.862, respectively.

Using cheminformatics to predict cross reactivity of “designer drugs” to their currently available immunoassays

PubMed Central

2014-01-01

Background A challenge for drug of abuse testing is presented by ‘designer drugs’, compounds typically discovered by modifications of existing clinical drug classes such as amphetamines and cannabinoids. Drug of abuse screening immunoassays directed at amphetamine or methamphetamine only detect a small subset of designer amphetamine-like drugs, and those immunoassays designed for tetrahydrocannabinol metabolites generally do not cross-react with synthetic cannabinoids lacking the classic cannabinoid chemical backbone. This suggests complexity in understanding how to detect and identify whether a patient has taken a molecule of one class or another, impacting clinical care. Methods Cross-reactivity data from immunoassays specifically targeting designer amphetamine-like and synthetic cannabinoid drugs was collected from multiple published sources, and virtual chemical libraries for molecular similarity analysis were built. The virtual library for synthetic cannabinoid analysis contained a total of 169 structures, while the virtual library for amphetamine-type stimulants contained 288 compounds. Two-dimensional (2D) similarity for each test compound was compared to the target molecule of the immunoassay undergoing analysis. Results 2D similarity differentiated between cross-reactive and non-cross-reactive compounds for immunoassays targeting mephedrone/methcathinone, 3,4-methylenedioxypyrovalerone, benzylpiperazine, mephentermine, and synthetic cannabinoids. Conclusions In this study, we applied 2D molecular similarity analysis to the designer amphetamine-type stimulants and synthetic cannabinoids. Similarity calculations can be used to more efficiently decide which drugs and metabolites should be tested in cross-reactivity studies, as well as to design experiments and potentially predict antigens that would lead to immunoassays with cross reactivity for a broader array of designer drugs. PMID:24851137

Ion distribution in quaternary-ammonium-functionalized aromatic polymers: effects on the ionic clustering and conductivity of anion-exchange membranes.

PubMed

Weiber, E Annika; Jannasch, Patric

2014-09-01

A series of copoly(arylene ether sulfone)s that have precisely two, three, or four quaternary ammonium (QA) groups clustered directly on single phenylene rings along the backbone are studied as anion-exchange membranes. The copolymers are synthesized by condensation polymerizations that involve either di-, tri-, or tetramethylhydroquinone followed by virtually complete benzylic bromination using N-bromosuccinimide and quaternization with trimethylamine. This synthetic strategy allows excellent control and systematic variation of the local density and distribution of QA groups along the backbone. Small-angle X-ray scattering of these copolymers shows extensive ionic clustering, promoted by an increasing density of QA on the single phenylene rings. At an ion-exchange capacity (IEC) of 2.1 meq g(-1), the water uptake decreases with the increasing local density of QA groups. Moreover, at moderate IECs at 20 °C, the Br(-) conductivity of the densely functionalized copolymers is higher than a corresponding randomly functionalized polymer, despite the significantly higher water uptake of the latter. Thus, the location of multiple cations on single aromatic rings in the polymers facilitates the formation of a distinct percolating hydrophilic phase domain with a high ionic concentration to promote efficient anion transport, despite probable limitations by reduced ion dissociation. These findings imply a viable strategy to improve the performance of alkaline membrane fuel cells. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Predicting RNA folding thermodynamics with a reduced chain representation model

PubMed Central

CAO, SONG; CHEN, SHI-JIE

2005-01-01

Based on the virtual bond representation for the nucleotide backbone, we develop a reduced conformational model for RNA. We use the experimentally measured atomic coordinates to model the helices and use the self-avoiding walks in a diamond lattice to model the loop conformations. The atomic coordinates of the helices and the lattice representation for the loops are matched at the loop–helix junction, where steric viability is accounted for. Unlike the previous simplified lattice-based models, the present virtual bond model can account for the atomic details of realistic three-dimensional RNA structures. Based on the model, we develop a statistical mechanical theory for RNA folding energy landscapes and folding thermodynamics. Tests against experiments show that the theory can give much more improved predictions for the native structures, the thermal denaturation curves, and the equilibrium folding/unfolding pathways than the previous models. The application of the model to the P5abc region of Tetrahymena group I ribozyme reveals the misfolded intermediates as well as the native-like intermediates in the equilibrium folding process. Moreover, based on the free energy landscape analysis for each and every loop mutation, the model predicts five lethal mutations that can completely alter the free energy landscape and the folding stability of the molecule. PMID:16251382

Changing learning with new interactive and media-rich instruction environments: virtual labs case study report.

PubMed

Huang, Camillan

2003-01-01

Technology has created a new dimension for visual teaching and learning with web-delivered interactive media. The Virtual Labs Project has embraced this technology with instructional design and evaluation methodologies behind the simPHYSIO suite of simulation-based, online interactive teaching modules in physiology for the Stanford students. In addition, simPHYSIO provides the convenience of anytime web-access and a modular structure that allows for personalization and customization of the learning material. This innovative tool provides a solid delivery and pedagogical backbone that can be applied to developing an interactive simulation-based training tool for the use and management of the Picture Archiving and Communication System (PACS) image information system. The disparity in the knowledge between health and IT professionals can be bridged by providing convenient modular teaching tools to fill the gaps in knowledge. An innovative teaching method in the whole PACS is deemed necessary for its successful implementation and operation since it has become widely distributed with many interfaces, components, and customizations. This paper will discuss the techniques for developing an interactive-based teaching tool, a case study of its implementation, and a perspective for applying this approach to an online PACS training tool. Copyright 2002 Elsevier Science Ltd.

An Evaluation of the Network Efficiency Required in Order to Support Multicast and Synchronous Distributed Learning Network Traffic

DTIC Science & Technology

2003-09-01

This restriction limits the deployment to small and medium sized enterprises. The Internet cannot universally use DVMRP for this reason. In addition...20503. 1. AGENCY USE ONLY (Leave blank) 2. REPORT DATE September 2003 3. REPORT TYPE AND DATES COVERED Master’s Thesis 4. TITLE... University , 1996 Submitted in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE IN COMPUTER SCIENCE from

Traffic Generator (TrafficGen) Version 1.4.2: Users Guide

DTIC Science & Technology

2016-06-01

events, the user has to enter them manually . We will research and implement a way to better define and organize the multicast addresses so they can be...the network with Transmission Control Protocol and User Datagram Protocol Internet Protocol traffic. Each node generating network traffic in an...TrafficGen Graphical User Interface (GUI) 3 3.1 Anatomy of the User Interface 3 3.2 Scenario Configuration and MGEN Files 4 4. Working with

GUMP: Adapting Client/Server Messaging Protocols into Peer-to-Peer Serverless Environments

DTIC Science & Technology

2010-06-11

and other related metadata, such as message re- ceiver ID (for supporting multiple connections) and so forth. The Proxy consumes the message and uses...the underlying discovery subsystem and multicast to process the message and translate the request into behaviour suitable for the un- derlying...communication i.e. a chat. Jingle (XEP-0166) [26] is a related specification that de- fines an extension to the XMPP protocol for initiating and

Tactical Mobile Communications (Communications tactiques mobiles)

DTIC Science & Technology

1999-11-01

13]. randomly at the network nodes. Each multicast group Our studies do, in fact, support this conjecture. consists of the source node plus at least...Capability investigate the MMR concept in some more detail. The study was contracted to a group which Multi-role denotes the capability to support a...through the HW- and SW-resources of the frontends can be incorporated in a task-dedicated GPU. Functions can be grouped into four categories: MMR

Multimedia Data Capture with Multicast Dissemination for Online Distance Learning

DTIC Science & Technology

2001-12-01

Juan Gril and Dr. Don Brutzman to wrap the multiple videos in a user- friendly environment. The web pages also contain the original PowerPoint...this CD, Juan Gril , a volunteer for the Siggraph 2001 Online Committee, created web pages that match the style and functionality desired by the...leader. The Committee for 2001 consisted of Don Brutzman, Stephen. Matsuba, Mike Collins, Allen Dutton, Juan Gril , Mike Hunsberger, Jerry Isdale

Solution, solid phase and computational structures of apicidin and its backbone-reduced analogs.

PubMed

Kranz, Michael; Murray, Peter John; Taylor, Stephen; Upton, Richard J; Clegg, William; Elsegood, Mark R J

2006-06-01

The recently isolated broad-spectrum antiparasitic apicidin (1) is one of the few naturally occurring cyclic tetrapeptides (CTP). Depending on the solvent, the backbone of 1 exhibits two gamma-turns (in CH(2)Cl(2)) or a beta-turn (in DMSO), differing solely in the rotation of the plane of one of the amide bonds. In the X-ray crystal structure, the peptidic C==Os and NHs are on opposite sides of the backbone plane, giving rise to infinite stacks of cyclotetrapeptides connected by three intermolecular hydrogen bonds between the backbones. Conformational searches (Amber force field) on a truncated model system of 1 confirm all three backbone conformations to be low-energy states. The previously synthesized analogs of 1 containing a reduced amide bond exhibit the same backbone conformation as 1 in DMSO, which is confirmed further by the X-ray crystal structure of a model system of the desoxy analogs of 1. This similarity helps in explaining why the desoxy analogs retain some of the antiprotozoal activities of apicidin. The backbone-reduction approach designed to facilitate the cyclization step of the acyclic precursors of the CTPs seems to retain the conformational preferences of the parent peptide backbone.

Chemical characteristics and antithrombotic effect of chondroitin sulfates from sturgeon skull and sturgeon backbone.

PubMed

Gui, Meng; Song, Juyi; Zhang, Lu; Wang, Shun; Wu, Ruiyun; Ma, Changwei; Li, Pinglan

2015-06-05

Chondroitin sulfates (CSs) were extracted from sturgeon skull and backbone, and their chemical composition, anticoagulant, anti-platelet and thrombolysis activities were evaluated. The average molecular weights of CS from sturgeon skull and backbone were 38.5kDa and 49.2kDa, respectively. Disaccharide analysis indicated that the sturgeon backbone CS was primarily composed of disaccharide monosulfated in position four of the GalNAc (37.8%) and disaccharide monosulfated in position six of the GalNAc (59.6%) while sturgeon skull CS was primarily composed of nonsulfated disaccharide (74.2%). Sturgeon backbone CS showed stronger antithrombotic effect than sturgeon skull CS. Sturgeon backbone CS could significantly prolong activated partial thromboplastin time (APTT) and thrombin time (TT), inhibited ADP-induced platelet aggregation and dissolved platelet plasma clots in vitro. The results suggested that sturgeon backbone CS can be explored as a functional food with antithrombotic function. Copyright © 2015 Elsevier Ltd. All rights reserved.

Triazine-Based Sequence-Defined Polymers with Side-Chain Diversity and Backbone-Backbone Interaction Motifs.

PubMed

Grate, Jay W; Mo, Kai-For; Daily, Michael D

2016-03-14

Sequence control in polymers, well-known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence-defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone-backbone interactions, including H-bonding motifs and pi-pi interactions. This architecture is arguably biomimetic while differing from sequence-defined polymers having peptide bonds. The synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone-backbone hydrogen-bonding motifs, and will thus enable new macromolecules and materials with useful functions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thin Films Formed from Conjugated Polymers with Ionic, Water-Soluble Backbones.

PubMed

Voortman, Thomas P; Chiechi, Ryan C

2015-12-30

This paper compares the morphologies of films of conjugated polymers in which the backbone (main chain) and pendant groups are varied between ionic/hydrophilic and aliphatic/hydrophobic. We observe that conjugated polymers in which the pendant groups and backbone are matched, either ionic-ionic or hydrophobic-hydrophobic, form smooth, structured, homogeneous films from water (ionic) or tetrahydrofuran (hydrophobic). Mismatched conjugated polymers, by contrast, form inhomogeneous films with rough topologies. The polymers with ionic backbone chains are conjugated polyions (conjugated polymers with closed-shell charges in the backbone), which are semiconducting materials with tunable bad-gaps, not unlike uncharged conjugated polymers.

Quantitative assessments of the distinct contributions of polypeptide backbone amides versus sidechain groups to chain expansion via chemical denaturation

PubMed Central

Holehouse, Alex S.; Garai, Kanchan; Lyle, Nicholas; Vitalis, Andreas; Pappu, Rohit V.

2015-01-01

In aqueous solutions with high concentrations of chemical denaturants such as urea and guanidinium chloride (GdmCl) proteins expand to populate heterogeneous conformational ensembles. These denaturing environments are thought to be good solvents for generic protein sequences because properties of conformational distributions align with those of canonical random coils. Previous studies showed that water is a poor solvent for polypeptide backbones and therefore backbones form collapsed globular structures in aqueous solvents. Here, we ask if polypeptide backbones can intrinsically undergo the requisite chain expansion in aqueous solutions with high concentrations of urea and GdmCl. We answer this question using a combination of molecular dynamics simulations and fluorescence correlation spectroscopy. We find that the degree of backbone expansion is minimal in aqueous solutions with high concentrations denaturants. Instead, polypeptide backbones sample conformations that are denaturant-specific mixtures of coils and globules, with a persistent preference for globules. Therefore, typical denaturing environments cannot be classified as good solvents for polypeptide backbones. How then do generic protein sequences expand in denaturing environments? To answer this question, we investigated the effects of sidechains using simulations of two archetypal sequences with amino acid compositions that are mixtures of charged, hydrophobic, and polar groups. We find that sidechains lower the effective concentration of backbone amides in water leading to an intrinsic expansion of polypeptide backbones in the absence of denaturants. Additional dilution of the effective concentration of backbone amides is achieved through preferential interactions with denaturants. These effects lead to conformational statistics in denaturing environments that are congruent with those of canonical random coils. Our results highlight the role of sidechain-mediated interactions as determinants of the conformational properties of unfolded states in water and in influencing chain expansion upon denaturation. PMID:25664638

Cost-effectiveness analysis of dolutegravir plus backbone compared with raltegravir plus backbone, darunavir+ritonavir plus backbone and efavirenz/tenofovir/emtricitabine in treatment naïve and experienced HIV-positive patients.

PubMed

Restelli, Umberto; Rizzardini, Giuliano; Antinori, Andrea; Lazzarin, Adriano; Bonfanti, Marzia; Bonfanti, Paolo; Croce, Davide

2017-01-01

In January 2014, the European Medicines Agency issued a marketing authorization for dolutegravir (DTG), a second-generation integrase strand transfer inhibitor for HIV treatment. The study aimed at determining the incremental cost-effectiveness ratio (ICER) of the use of DTG+backbone compared with raltegravir (RAL)+backbone, darunavir (DRV)+ritonavir(r)+backbone and efavirenz/tenofovir/emtricitabine (EFV/TDF/FTC) in HIV-positive treatment-naïve patients and compared with RAL+backbone in treatment-experienced patients, from the Italian National Health Service's point of view. A published Monte Carlo Individual Simulation Model (ARAMIS-DTG model) was used to perform the analysis. Patients pass through mutually exclusive health states (defined in terms of diagnosis of HIV with or without opportunistic infections [OIs] and cardiovascular disease [CVD]) and successive lines of therapy. The model considers costs (2014) and quality of life per monthly cycle in a lifetime horizon. Costs and quality-adjusted life years (QALYs) are dependent on OI, CVD, AIDS events, adverse events and antiretroviral therapies. In treatment-naïve patients, DTG dominates RAL; compared with DRV/r, the ICER obtained is of 38,586 €/QALY (6,170 €/QALY in patients with high viral load) and over EFV/TDF/FTC, DTG generates an ICER of 33,664 €/QALY. In treatment-experienced patients, DTG compared to RAL leads to an ICER of 12,074 €/QALY. The use of DTG+backbone may be cost effective in treatment-naïve and treatment-experienced patients compared with RAL+backbone and in treatment-naïve patients compared with DRV/r+backbone and EFV/TDF/FTC considering a threshold of 40,000 €/QALY.

Representing environment-induced helix-coil transitions in a coarse grained peptide model

NASA Astrophysics Data System (ADS)

Dalgicdir, Cahit; Globisch, Christoph; Sayar, Mehmet; Peter, Christine

2016-10-01

Coarse grained (CG) models are widely used in studying peptide self-assembly and nanostructure formation. One of the recurrent challenges in CG modeling is the problem of limited transferability, for example to different thermodynamic state points and system compositions. Understanding transferability is generally a prerequisite to knowing for which problems a model can be reliably used and predictive. For peptides, one crucial transferability question is whether a model reproduces the molecule's conformational response to a change in its molecular environment. This is of particular importance since CG peptide models often have to resort to auxiliary interactions that aid secondary structure formation. Such interactions take care of properties of the real system that are per se lost in the coarse graining process such as dihedral-angle correlations along the backbone or backbone hydrogen bonding. These auxiliary interactions may then easily overstabilize certain conformational propensities and therefore destroy the ability of the model to respond to stimuli and environment changes, i.e. they impede transferability. In the present paper we have investigated a short peptide with amphiphilic EALA repeats which undergoes conformational transitions between a disordered and a helical state upon a change in pH value or due to the presence of a soft apolar/polar interface. We designed a base CG peptide model that does not carry a specific (backbone) bias towards a secondary structure. This base model was combined with two typical approaches of ensuring secondary structure formation, namely a C α -C α -C α -C α pseudodihedral angle potential or a virtual site interaction that mimics hydrogen bonding. We have investigated the ability of the two resulting CG models to represent the environment-induced conformational changes in the helix-coil equilibrium of EALA. We show that with both approaches a CG peptide model can be obtained that is environment-transferable and that correctly represents the peptide's conformational response to different stimuli compared to atomistic reference simulations. The two types of auxiliary interactions lead to different kinetic behavior as well as to different structural properties for fully formed helices and folding intermediates, and we discuss the advantages and disadvantages of these approaches.

Collaboration Services: Enabling Chat in Disadvantaged Grids

DTIC Science & Technology

2014-06-01

grids in the tactical domain" [2]. The main focus of this group is to identify what we call tactical SOA foundation services. By this we mean which...Here, only IPv4 is supported, as differences relating to IPv4 and IPv6 addressing meant that this functionality was not easily extended to use IPv6 ...multicast groups. Our IPv4 implementation is fully compliant with the specification, whereas the IPv6 implementation uses our own interpretation of

Design and Implementation of the MARG Human Body Motion Tracking System

DTIC Science & Technology

2004-10-01

7803-8463-6/041$20.00 ©:!004 IEEE 625 OPTOTRAK from Northern Digital Inc. is a typical example of a marker-based system [I 0]. Another is the...technique called tunneling is :used to overcome this problem. Tunneling is a software solution that runs on the end point routers/computers and allows...multicast packets to traverse the network by putting them into unicast packets. MUTUP overcomes the tunneling problem using shared memory in the

A Secure Group Communication Architecture for a Swarm of Autonomous Unmanned Aerial Vehicles

DTIC Science & Technology

2008-03-01

members to use the same decryption key. This shared decryption key is called the Session Encryption Key ( SEK ) or Traffic Encryption Key (TEK...Since everyone shares the SEK , members need to hold additional Key Encryption Keys (KEK) that are used to securely distribute the SEK to each valid...managing this process. To preserve the secrecy of the multicast data, the SEK needs to be updated upon certain events such as a member joining and

Efficient File Sharing by Multicast - P2P Protocol Using Network Coding and Rank Based Peer Selection

NASA Technical Reports Server (NTRS)

Stoenescu, Tudor M.; Woo, Simon S.

2009-01-01

In this work, we consider information dissemination and sharing in a distributed peer-to-peer (P2P highly dynamic communication network. In particular, we explore a network coding technique for transmission and a rank based peer selection method for network formation. The combined approach has been shown to improve information sharing and delivery to all users when considering the challenges imposed by the space network environments.

Network connectivity enhancement by exploiting all optical multicast in semiconductor ring laser

NASA Astrophysics Data System (ADS)

Siraj, M.; Memon, M. I.; Shoaib, M.; Alshebeili, S.

2015-03-01

The use of smart phone and tablet applications will provide the troops for executing, controlling and analyzing sophisticated operations with the commanders providing crucial documents directly to troops wherever and whenever needed. Wireless mesh networks (WMNs) is a cutting edge networking technology which is capable of supporting Joint Tactical radio System (JTRS).WMNs are capable of providing the much needed bandwidth for applications like hand held radios and communication for airborne and ground vehicles. Routing management tasks can be efficiently handled through WMNs through a central command control center. As the spectrum space is congested, cognitive radios are a much welcome technology that will provide much needed bandwidth. They can self-configure themselves, can adapt themselves to the user requirement, provide dynamic spectrum access for minimizing interference and also deliver optimal power output. Sometimes in the indoor environment, there are poor signal issues and reduced coverage. In this paper, a solution utilizing (CR WMNs) over optical network is presented by creating nanocells (PCs) inside the indoor environment. The phenomenon of four-wave mixing (FWM) is exploited to generate all-optical multicast using semiconductor ring laser (SRL). As a result same signal is transmitted at different wavelengths. Every PC is assigned a unique wavelength. By using CR technology in conjunction with PC will not only solve network coverage issue but will provide a good bandwidth to the secondary users.

Unidata LDM-7: a Hybrid Multicast/unicast System for Highly Efficient and Reliable Real-Time Data Distribution

NASA Astrophysics Data System (ADS)

Emmerson, S. R.; Veeraraghavan, M.; Chen, S.; Ji, X.

2015-12-01

Results of a pilot deployment of a major new version of the Unidata Local Data Manager (LDM-7) are presented. The Unidata LDM was developed by the University Corporation for Atmospheric Research (UCAR) and comprises a suite of software for the distribution and local processing of data in near real-time. It is widely used in the geoscience community to distribute observational data and model output, most notably as the foundation of the Unidata Internet Data Distribution (IDD) system run by UCAR, but also in private networks operated by NOAA, NASA, USGS, etc. The current version, LDM-6, uses at least one unicast TCP connection per receiving host. With over 900 connections, the bit-rate of total outgoing IDD traffic from UCAR averages approximately 3.0 GHz, with peak data rates exceeding 6.6 GHz. Expected increases in data volume suggest that a more efficient distribution mechanism will be required in the near future. LDM-7 greatly reduces the outgoing bandwidth requirement by incorporating a recently-developed "semi-reliable" IP multicast protocol while retaining the unicast TCP mechanism for reliability. During the summer of 2015, UCAR and the University of Virginia conducted a pilot deployment of the Unidata LDM-7 among U.S. university participants with access to the Internet2 network. Results of this pilot program, along with comparisons to the existing Unidata LDM-6 system, are presented.

Molecular mechanism of extreme mechanostability in a pathogen adhesin.

PubMed

Milles, Lukas F; Schulten, Klaus; Gaub, Hermann E; Bernardi, Rafael C

2018-03-30

High resilience to mechanical stress is key when pathogens adhere to their target and initiate infection. Using atomic force microscopy-based single-molecule force spectroscopy, we explored the mechanical stability of the prototypical staphylococcal adhesin SdrG, which targets a short peptide from human fibrinogen β. Steered molecular dynamics simulations revealed, and single-molecule force spectroscopy experiments confirmed, the mechanism by which this complex withstands forces of over 2 nanonewtons, a regime previously associated with the strength of a covalent bond. The target peptide, confined in a screwlike manner in the binding pocket of SdrG, distributes forces mainly toward the peptide backbone through an intricate hydrogen bond network. Thus, these adhesins can attach to their target with exceptionally resilient mechanostability, virtually independent of peptide side chains. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Metropolitian area network services comprised of virtual local area networks running over hybrid fiber-coax and asynchronous transfer mode technologies

NASA Astrophysics Data System (ADS)

Biedron, William S.

1995-11-01

Since 1990 there has been a rapid increase in the demand for communication services, especially local and wide area network (LAN/WAN) oriented services. With the introduction of the DFB laser transmitter, hybrid-fiber-coax (HFC) cable plant designs, ATM transport technologies and rf modems, new LAN/WAN services can now be defined and marketed to residential and business customers over existing cable TV systems. The term metropolitan area network (MAN) can be used to describe this overall network. This paper discusses the technical components needed to provision these services as well as provides some perspectives on integration issues. Architecture at the headend and in the backbone is discussed, as well as specific service definitions and the technology issues associated with each. The TCP/IP protocol is suggested as a primary protocol to be used throughout the MAN.

Spray printing of organic semiconducting single crystals

NASA Astrophysics Data System (ADS)

Rigas, Grigorios-Panagiotis; Payne, Marcia M.; Anthony, John E.; Horton, Peter N.; Castro, Fernando A.; Shkunov, Maxim

2016-11-01

Single-crystal semiconductors have been at the forefront of scientific interest for more than 70 years, serving as the backbone of electronic devices. Inorganic single crystals are typically grown from a melt using time-consuming and energy-intensive processes. Organic semiconductor single crystals, however, can be grown using solution-based methods at room temperature in air, opening up the possibility of large-scale production of inexpensive electronics targeting applications ranging from field-effect transistors and light-emitting diodes to medical X-ray detectors. Here we demonstrate a low-cost, scalable spray-printing process to fabricate high-quality organic single crystals, based on various semiconducting small molecules on virtually any substrate by combining the advantages of antisolvent crystallization and solution shearing. The crystals' size, shape and orientation are controlled by the sheer force generated by the spray droplets' impact onto the antisolvent's surface. This method demonstrates the feasibility of a spray-on single-crystal organic electronics.

Activation of Reactive MALDI Adduct Ions Enables Differentiation of Dihydroxylated Vitamin D Isomers

NASA Astrophysics Data System (ADS)

Qi, Yulin; Müller, Miriam J.; Volmer, Dietrich A.

2017-12-01

Vitamin D compounds are secosteroids, which are best known for their role in bone health. More recent studies have shown that vitamin D metabolites and catabolites such as dihydroxylated species (e.g., 1,25- and 24,25-dihydroxyvitamin D3) play key roles in the pathologies of various diseases. Identification of these isomers by mass spectrometry is challenging and currently relies on liquid chromatography, as the isomers exhibit virtually identical product ion spectra under collision induced dissociation conditions. Here, we developed a simple MALDI-CID method that utilizes ion activation of reactive analyte/matrix adducts to distinguish isomeric dihydroxyvitamin D3 species, without the need for chromatography separation or chemical derivatization techniques. Specifically, reactive 1,5-diaminonaphthalene adducts of dihydroxyvitamin D3 compounds formed during MADI were activated and specific cleavages in the secosteroid's backbone structure were achieved that produced isomer-diagnostic fragment ions. [Figure not available: see fulltext.

Large-scale measurement and modeling of backbone Internet traffic

NASA Astrophysics Data System (ADS)

Roughan, Matthew; Gottlieb, Joel

2002-07-01

There is a brewing controversy in the traffic modeling community concerning how to model backbone traffic. The fundamental work on self-similarity in data traffic appears to be contradicted by recent findings that suggest that backbone traffic is smooth. The traffic analysis work to date has focused on high-quality but limited-scope packet trace measurements; this limits its applicability to high-speed backbone traffic. This paper uses more than one year's worth of SNMP traffic data covering an entire Tier 1 ISP backbone to address the question of how backbone network traffic should be modeled. Although the limitations of SNMP measurements do not permit us to comment on the fine timescale behavior of the traffic, careful analysis of the data suggests that irrespective of the variation at fine timescales, we can construct a simple traffic model that captures key features of the observed traffic. Furthermore, the model's parameters are measurable using existing network infrastructure, making this model practical in a present-day operational network. In addition to its practicality, the model verifies basic statistical multiplexing results, and thus sheds deep insight into how smooth backbone traffic really is.

Uncovering the essential links in online commercial networks

NASA Astrophysics Data System (ADS)

Zeng, Wei; Fang, Meiling; Shao, Junming; Shang, Mingsheng

2016-09-01

Recommender systems are designed to effectively support individuals' decision-making process on various web sites. It can be naturally represented by a user-object bipartite network, where a link indicates that a user has collected an object. Recently, research on the information backbone has attracted researchers' interests, which is a sub-network with fewer nodes and links but carrying most of the relevant information. With the backbone, a system can generate satisfactory recommenda- tions while saving much computing resource. In this paper, we propose an enhanced topology-aware method to extract the information backbone in the bipartite network mainly based on the information of neighboring users and objects. Our backbone extraction method enables the recommender systems achieve more than 90% of the accuracy of the top-L recommendation, however, consuming only 20% links. The experimental results show that our method outperforms the alternative backbone extraction methods. Moreover, the structure of the information backbone is studied in detail. Finally, we highlight that the information backbone is one of the most important properties of the bipartite network, with which one can significantly improve the efficiency of the recommender system.

The Virtual Insect Brain protocol: creating and comparing standardized neuroanatomy

PubMed Central

Jenett, Arnim; Schindelin, Johannes E; Heisenberg, Martin

2006-01-01

Background In the fly Drosophila melanogaster, new genetic, physiological, molecular and behavioral techniques for the functional analysis of the brain are rapidly accumulating. These diverse investigations on the function of the insect brain use gene expression patterns that can be visualized and provide the means for manipulating groups of neurons as a common ground. To take advantage of these patterns one needs to know their typical anatomy. Results This paper describes the Virtual Insect Brain (VIB) protocol, a script suite for the quantitative assessment, comparison, and presentation of neuroanatomical data. It is based on the 3D-reconstruction and visualization software Amira, version 3.x (Mercury Inc.) [1]. Besides its backbone, a standardization procedure which aligns individual 3D images (series of virtual sections obtained by confocal microscopy) to a common coordinate system and computes average intensities for each voxel (volume pixel) the VIB protocol provides an elaborate data management system for data administration. The VIB protocol facilitates direct comparison of gene expression patterns and describes their interindividual variability. It provides volumetry of brain regions and helps to characterize the phenotypes of brain structure mutants. Using the VIB protocol does not require any programming skills since all operations are carried out at an intuitively usable graphical user interface. Although the VIB protocol has been developed for the standardization of Drosophila neuroanatomy, the program structure can be used for the standardization of other 3D structures as well. Conclusion Standardizing brains and gene expression patterns is a new approach to biological shape and its variability. The VIB protocol provides a first set of tools supporting this endeavor in Drosophila. The script suite is freely available at [2] PMID:17196102

Vroom: designing an augmented environment for remote collaboration in digital cinema production

NASA Astrophysics Data System (ADS)

Margolis, Todd; Cornish, Tracy

2013-03-01

As media technologies become increasingly affordable, compact and inherently networked, new generations of telecollaborative platforms continue to arise which integrate these new affordances. Virtual reality has been primarily concerned with creating simulations of environments that can transport participants to real or imagined spaces that replace the "real world". Meanwhile Augmented Reality systems have evolved to interleave objects from Virtual Reality environments into the physical landscape. Perhaps now there is a new class of systems that reverse this precept to enhance dynamic media landscapes and immersive physical display environments to enable intuitive data exploration through collaboration. Vroom (Virtual Room) is a next-generation reconfigurable tiled display environment in development at the California Institute for Telecommunications and Information Technology (Calit2) at the University of California, San Diego. Vroom enables freely scalable digital collaboratories, connecting distributed, high-resolution visualization resources for collaborative work in the sciences, engineering and the arts. Vroom transforms a physical space into an immersive media environment with large format interactive display surfaces, video teleconferencing and spatialized audio built on a highspeed optical network backbone. Vroom enables group collaboration for local and remote participants to share knowledge and experiences. Possible applications include: remote learning, command and control, storyboarding, post-production editorial review, high resolution video playback, 3D visualization, screencasting and image, video and multimedia file sharing. To support these various scenarios, Vroom features support for multiple user interfaces (optical tracking, touch UI, gesture interface, etc.), support for directional and spatialized audio, giga-pixel image interactivity, 4K video streaming, 3D visualization and telematic production. This paper explains the design process that has been utilized to make Vroom an accessible and intuitive immersive environment for remote collaboration specifically for digital cinema production.

An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)

PubMed Central

2017-01-01

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of φ and ψ has not been completely described for both cis and trans backbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing the φ and ψ values of a peptide (e.g., is the regular peptide defined by φ = ψ =  − 100°  left-handed or right-handed?). This report provides a new metric for backbone handedness (h) based on interpreting a peptide backbone as a helix with axial displacement d and angular displacement θ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral angles φ, ψ and ω. In particular, h equals sin(θ)d∕|d|, with range [−1, 1] and negative (or positive) values indicating left(or right)-handedness. The metric h is used to characterize the handedness of every region of the Ramachandran plot for both cis (ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ, ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based on d and θ that serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone including cis and trans backbones. The intuitiveness arises from the fact that d and θ provide, at a glance, numerous aspects of the backbone including compactness, handedness, and planarity. PMID:28533975

E-nephrology.

PubMed

Manchanda, P K; Bid, H K

2011-01-01

Diagnosis of renal diseases is often delayed owing to the scarcity of trained physicians, lack of facilities, and shortage of funds limits effective management, particularly when it comes to the red zone of renal replacement therapy. The Internetis expected to open up a myriad resource of knowledge and applications for academicians, researchers and clinicians alike in all health care professions across the globe. Also, the Internet has grown rapidly over the years and will inevitably expand even more. Evolving technologies offer modern applications for information management, communications with multimedia and virtual reality. Now, these innovative technologies have opened up newer possibilities for nephrologists. As Internet is serving as a backbone for these modern technologies, it is an utmost necessity to use and refine Internet applications for future nephrologists. Increasingly easy access to Internet has dramatically reduced barriers in sharing of information among basic and clinical nephrologists. Considering the growing scope for nephrologists in the use of Internet, it is necessary to understand Internet as a source of information and backbone of modern application. This review illustrates expanding roles of the Internet for the nephrologists and provides ready to use compilation of useful academic, research, clinical resources and is expected to introduce, stimulate and guide nephrologists into the realm of the world wide web. It also investigates how Internet is supporting in growth and development of the field of nephrology and present and future scopes of Internet as a tool for professionals involved in this area as well as information about biological sciences, and it also gives information about societies in various continents working in field of nephrology and the links useful for clinicians and research scientists.

Toward Near Real-Time Tomography of the Upper Mantle

NASA Astrophysics Data System (ADS)

Debayle, E.; Dubuffet, F.

2014-12-01

We added a layer of automation to the Debayle and Ricard (2012)'s waveform modeling scheme for fundamental and higher mode surface waves in the period range 50-160s. We processed all the Rayleigh waveforms recorded on the LHZ channel by the virtual networks GSN_broadband, FDSN_all, and US_backbone between January 1996 and December 2013. Six millions of waveforms were obtained from IRIS DMC. We check that all the necessary information (instrument response, global CMT determination) is available and that each record includes a velocity window which encompasses the surface wave. Selected data must also have a signal-to-noise ratio greater than 3 in a range covering at least the periods between 50 and 100 s. About 3 millions of waveforms are selected (92% of the rejections are due to the signal to noise ratio criterion) and processed using Debayle and Ricard (2012)'s scheme, which allows the successful modeling of about 1.5 millions of waveforms. We complete this database with 60,000 waveforms recorded between 1976 and 1996 or after 1996 during various temporary experiments and with 161,730 Rayleigh waveforms analyzed at longer period, between 120 and 360 s. The whole data set is inverted using Debayle and Sambridge (2004)'s scheme to produce a 3D shear velocity model. A simple shell command "update_tomo" can then update our seismic model in an entirely automated way. Currently, this command checks from the CMT catalog what are the potential data available at the GSN_broadband, FDSN_all, and US_backbone virtual networks, uses web services to request these data from IRIS DMC and applies the processing chain described above to update our seismic model. We plan to update our seismic model on a regular basis in a near future, and to make it available on the web. Our most recent seismic model includes azimuthal anisotropy, achieves a lateral resolution of few hundred kilometers and a vertical resolution of a few tens of kilometers. The correlation with surface tectonics is very strong in the uppermost 200 km. Regions deeper than 400 km show no velocity contrasts larger than 1%, except for high velocity slabs which produce broad high velocity regions within the transition zone. The use of higher modes and long period surface waves allows us to extract the shear velocity structure down to about 1000 km depth.

Cost-effectiveness analysis of dolutegravir plus backbone compared with raltegravir plus backbone, darunavir+ritonavir plus backbone and efavirenz/tenofovir/emtricitabine in treatment naïve and experienced HIV-positive patients

PubMed Central

Restelli, Umberto; Rizzardini, Giuliano; Antinori, Andrea; Lazzarin, Adriano; Bonfanti, Marzia; Bonfanti, Paolo; Croce, Davide

2017-01-01

Background In January 2014, the European Medicines Agency issued a marketing authorization for dolutegravir (DTG), a second-generation integrase strand transfer inhibitor for HIV treatment. The study aimed at determining the incremental cost-effectiveness ratio (ICER) of the use of DTG+backbone compared with raltegravir (RAL)+backbone, darunavir (DRV)+ritonavir(r)+backbone and efavirenz/tenofovir/emtricitabine (EFV/TDF/FTC) in HIV-positive treatment-naïve patients and compared with RAL+backbone in treatment-experienced patients, from the Italian National Health Service’s point of view. Materials and methods A published Monte Carlo Individual Simulation Model (ARAMIS-DTG model) was used to perform the analysis. Patients pass through mutually exclusive health states (defined in terms of diagnosis of HIV with or without opportunistic infections [OIs] and cardiovascular disease [CVD]) and successive lines of therapy. The model considers costs (2014) and quality of life per monthly cycle in a lifetime horizon. Costs and quality-adjusted life years (QALYs) are dependent on OI, CVD, AIDS events, adverse events and antiretroviral therapies. Results In treatment-naïve patients, DTG dominates RAL; compared with DRV/r, the ICER obtained is of 38,586 €/QALY (6,170 €/QALY in patients with high viral load) and over EFV/TDF/FTC, DTG generates an ICER of 33,664 €/QALY. In treatment-experienced patients, DTG compared to RAL leads to an ICER of 12,074 €/QALY. Conclusion The use of DTG+backbone may be cost effective in treatment-naïve and treatment-experienced patients compared with RAL+backbone and in treatment-naïve patients compared with DRV/r+backbone and EFV/TDF/FTC considering a threshold of 40,000 €/QALY. PMID:28721059

Development of a Web-Based Distributed Interactive Simulation (DIS) Environment Using JavaScript

DTIC Science & Technology

2014-09-01

scripting that let users change or interact with web content depending on user input, which is in contrast with server-side scripts such as PHP, Java and...transfer, DIS usually broadcasts or multicasts its PDUs based on UDP socket. 3. JavaScript JavaScript is the scripting language of the web, and all...IDE) for developing desktop, mobile and web applications with JAVA , C++, HTML5, JavaScript and more. b. Framework The DIS implementation of

The Use of End-to-End Multicast Measurements for Characterizing Internal Network Behavior

DTIC Science & Technology

2002-08-01

dropping on the basis Random Early Detection ( RED ) [17] is another mechanism by which packet loss may become decorrelated. It remains to be seen whether...this mechanism will be widely deployed in communications networks. On the other hand, the use of RED to merely mark packets will not break correlations...Tail and Random Early Detection ( RED ) buffer discard methods, [17]. We compared the inferred loss and delay with actual probe loss and delay. We found

Optical burst switching based satellite backbone network

NASA Astrophysics Data System (ADS)

Li, Tingting; Guo, Hongxiang; Wang, Cen; Wu, Jian

2018-02-01

We propose a novel time slot based optical burst switching (OBS) architecture for GEO/LEO based satellite backbone network. This architecture can provide high speed data transmission rate and high switching capacity . Furthermore, we design the control plane of this optical satellite backbone network. The software defined network (SDN) and network slice (NS) technologies are introduced. Under the properly designed control mechanism, this backbone network is flexible to support various services with diverse transmission requirements. Additionally, the LEO access and handoff management in this network is also discussed.

Virtual Observatory Interfaces to the Chandra Data Archive

NASA Astrophysics Data System (ADS)

Tibbetts, M.; Harbo, P.; Van Stone, D.; Zografou, P.

2014-05-01

The Chandra Data Archive (CDA) plays a central role in the operation of the Chandra X-ray Center (CXC) by providing access to Chandra data. Proprietary interfaces have been the backbone of the CDA throughout the Chandra mission. While these interfaces continue to provide the depth and breadth of mission specific access Chandra users expect, the CXC has been adding Virtual Observatory (VO) interfaces to the Chandra proposal catalog and observation catalog. VO interfaces provide standards-based access to Chandra data through simple positional queries or more complex queries using the Astronomical Data Query Language. Recent development at the CDA has generalized our existing VO services to create a suite of services that can be configured to provide VO interfaces to any dataset. This approach uses a thin web service layer for the individual VO interfaces, a middle-tier query component which is shared among the VO interfaces for parsing, scheduling, and executing queries, and existing web services for file and data access. The CXC VO services provide Simple Cone Search (SCS), Simple Image Access (SIA), and Table Access Protocol (TAP) implementations for both the Chandra proposal and observation catalogs within the existing archive architecture. Our work with the Chandra proposal and observation catalogs, as well as additional datasets beyond the CDA, illustrates how we can provide configurable VO services to extend core archive functionality.

Modeling 15N NMR chemical shift changes in protein backbone with pressure

NASA Astrophysics Data System (ADS)

La Penna, Giovanni; Mori, Yoshiharu; Kitahara, Ryo; Akasaka, Kazuyuki; Okamoto, Yuko

2016-08-01

Nitrogen chemical shift is a useful parameter for determining the backbone three-dimensional structure of proteins. Empirical models for fast calculation of N chemical shift are improving their reliability, but there are subtle effects that cannot be easily interpreted. Among these, the effects of slight changes in hydrogen bonds, both intramolecular and with water molecules in the solvent, are particularly difficult to predict. On the other hand, these hydrogen bonds are sensitive to changes in protein environment. In this work, the change of N chemical shift with pressure for backbone segments in the protein ubiquitin is correlated with the change in the population of hydrogen bonds involving the backbone amide group. The different extent of interaction of protein backbone with the water molecules in the solvent is put in evidence.

An exhaustive survey of regular peptide conformations using a new metric for backbone handedness ( h )

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mannige, Ranjan V.

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral anglesφandψ(Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function ofφandψhas not been completely described for bothcisandtransbackbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing theφandψvalues of a peptide (e.g., is the regular peptide defined byφ = ψ =  - 100°  left-handed or right-handed?). This report provides a new metric for backbone handednessmore » (h) based on interpreting a peptide backbone as a helix with axial displacementdand angular displacementθ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral anglesφ,ψandω. In particular,hequals sin(θ)d/d|, with range [-1, 1] and negative (or positive) values indicating left(or right)-handedness. The metrichis used to characterize the handedness of every region of the Ramachandran plot for bothcis(ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ,ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based ondandθthat serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone includingcisandtransbackbones. The intuitiveness arises from the fact thatdandθprovide, at a glance, numerous aspects of the backbone including compactness, handedness, and planarity.« less

An exhaustive survey of regular peptide conformations using a new metric for backbone handedness ( h )

DOE PAGES

Mannige, Ranjan V.

2017-05-16

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral anglesφandψ(Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function ofφandψhas not been completely described for bothcisandtransbackbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing theφandψvalues of a peptide (e.g., is the regular peptide defined byφ = ψ =  - 100°  left-handed or right-handed?). This report provides a new metric for backbone handednessmore » (h) based on interpreting a peptide backbone as a helix with axial displacementdand angular displacementθ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral anglesφ,ψandω. In particular,hequals sin(θ)d/d|, with range [-1, 1] and negative (or positive) values indicating left(or right)-handedness. The metrichis used to characterize the handedness of every region of the Ramachandran plot for bothcis(ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ,ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based ondandθthat serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone includingcisandtransbackbones. The intuitiveness arises from the fact thatdandθprovide, at a glance, numerous aspects of the backbone including compactness, handedness, and planarity.« less

Solid state nuclear magnetic resonance investigation of polymer backbone dynamics in poly(ethylene oxide) based lithium and sodium polyether-ester-sulfonate ionomers.

PubMed

Roach, David J; Dou, Shichen; Colby, Ralph H; Mueller, Karl T

2013-05-21

Polymer backbone dynamics of single ion conducting poly(ethylene oxide) (PEO)-based ionomer samples with low glass transition temperatures (T(g)) have been investigated using solid-state nuclear magnetic resonance. Experiments detecting (13)C with (1)H decoupling under magic angle spinning (MAS) conditions identified the different components of the polymer backbone (PEO spacer and isophthalate groups) and their relative mobilities for a suite of lithium- and sodium-containing ionomer samples with varying cation contents. Variable temperature (203-373 K) (1)H-(13)C cross-polarization MAS (CP-MAS) experiments also provided qualitative assessment of the differences in the motions of the polymer backbone components as a function of cation content and identity. Each of the main backbone components exhibit distinct motions, following the trends expected for motional characteristics based on earlier Quasi Elastic Neutron Scattering and (1)H spin-lattice relaxation rate measurements. Previous (1)H and (7)Li spin-lattice relaxation measurements focused on both the polymer backbone and cation motion on the nanosecond timescale. The studies presented here assess the slower timescale motion of the polymer backbone allowing for a more comprehensive understanding of the polymer dynamics. The temperature dependences of (13)C linewidths were used to both qualitatively and quantitatively examine the effects of cation content and identity on PEO spacer mobility. Variable contact time (1)H-(13)C CP-MAS experiments were used to further assess the motions of the polymer backbone on the microsecond timescale. The motion of the PEO spacer, reported via the rate of magnetization transfer from (1)H to (13)C nuclei, becomes similar for T≳1.1 T(g) in all ionic samples, indicating that at similar elevated reduced temperatures the motions of the polymer backbones on the microsecond timescale become insensitive to ion interactions. These results present an improved picture, beyond those of previous findings, for the dependence of backbone dynamics on cation density (and here, cation identity as well) in these amorphous PEO-based ionomer systems.

A protein-dependent side-chain rotamer library.

PubMed

Bhuyan, Md Shariful Islam; Gao, Xin

2011-12-14

Protein side-chain packing problem has remained one of the key open problems in bioinformatics. The three main components of protein side-chain prediction methods are a rotamer library, an energy function and a search algorithm. Rotamer libraries summarize the existing knowledge of the experimentally determined structures quantitatively. Depending on how much contextual information is encoded, there are backbone-independent rotamer libraries and backbone-dependent rotamer libraries. Backbone-independent libraries only encode sequential information, whereas backbone-dependent libraries encode both sequential and locally structural information. However, side-chain conformations are determined by spatially local information, rather than sequentially local information. Since in the side-chain prediction problem, the backbone structure is given, spatially local information should ideally be encoded into the rotamer libraries. In this paper, we propose a new type of backbone-dependent rotamer library, which encodes structural information of all the spatially neighboring residues. We call it protein-dependent rotamer libraries. Given any rotamer library and a protein backbone structure, we first model the protein structure as a Markov random field. Then the marginal distributions are estimated by the inference algorithms, without doing global optimization or search. The rotamers from the given library are then re-ranked and associated with the updated probabilities. Experimental results demonstrate that the proposed protein-dependent libraries significantly outperform the widely used backbone-dependent libraries in terms of the side-chain prediction accuracy and the rotamer ranking ability. Furthermore, without global optimization/search, the side-chain prediction power of the protein-dependent library is still comparable to the global-search-based side-chain prediction methods.

Gel Permeation Chromatography Characterization of the Chain Length Distributions in Thiol-Acrylate Photopolymer Networks

PubMed Central

Rydholm, Amber E.; Held, Nicole L.; Bowman, Christopher N.; Anseth, Kristi S.

2008-01-01

Crosslinked, degradable networks formed from the photopolymerization of thiol and acrylate monomers are explored as potential biomaterials. The degradation behavior and material properties of these networks are influenced by the molecular weight of the nondegradable thiol-polyacrylate backbone chains that form during photopolymerization. Here, gel permeation chromatography was used to characterize the thiol-polyacrylate backbone chain lengths in degraded thiol-acrylate networks. Increasing thiol functionality from 1 to 4 increased the backbone molecular weight (M̄w = 2.3 ± 0.07 × 104 Da for monothiol and 3.6 ± 0.1 × 104 Da for tetrathiol networks). Decreasing thiol functional group concentration from 30 to 10 mol% also increased the backbone lengths (M̄w = 7.3 ± 1.1 × 104 Da for the networks containing 10 mol% thiol groups as compared to 3.6 ± 0.1 × 104 Da for 30 mol% thiol). Finally, the backbone chain lengths were probed at various stages of degradation and an increase in backbone molecular weight was observed as mass loss progressed from 10 to 70%. PMID:19079733

The Inherent Conformational Preferences of Glutamine-Containing Peptides: the Role for Side-Chain Backbone Hydrogen Bonds

NASA Astrophysics Data System (ADS)

Walsh, Patrick S.; McBurney, Carl; Gellman, Samuel H.; Zwier, Timothy S.

2015-06-01

Glutamine is widely known to be found in critical regions of peptides which readily fold into amyloid fibrils, the structures commonly associated with Alzheimer's disease and glutamine repeat diseases such as Huntington's disease. Building on previous single-conformation data on Gln-containing peptides containing an aromatic cap on the N-terminus (Z-Gln-OH and Z-Gln-NHMe), we present here single-conformation UV and IR spectra of Ac-Gln-NHBn and Ac-Ala-Gln-NHBn, with its C-terminal benzyl cap. These results point towards side-chain to backbone hydrogen bonds dominating the structures observed in the cold, isolated environment of a molecular beam. We have identified and assigned three main conformers for Ac-Gln-NHBn all involving primary side-chain to backbone interactions. Ac-Ala-Gln-NHBn extends the peptide chain by one amino acid, but affords an improvement in the conformational flexibility. Despite this increase in the flexibility, only a single conformation is observed in the gas-phase: a structure which makes use of both side-chain-to-backbone and backbone-to-backbone hydrogen bonds.

Modeling {sup 15}N NMR chemical shift changes in protein backbone with pressure

DOE Office of Scientific and Technical Information (OSTI.GOV)

La Penna, Giovanni, E-mail: glapenna@iccom.cnr.it; Mori, Yoshiharu, E-mail: ymori@ims.ac.jp; Kitahara, Ryo, E-mail: ryo@ph.ritsumei.ac.jp

2016-08-28

Nitrogen chemical shift is a useful parameter for determining the backbone three-dimensional structure of proteins. Empirical models for fast calculation of N chemical shift are improving their reliability, but there are subtle effects that cannot be easily interpreted. Among these, the effects of slight changes in hydrogen bonds, both intramolecular and with water molecules in the solvent, are particularly difficult to predict. On the other hand, these hydrogen bonds are sensitive to changes in protein environment. In this work, the change of N chemical shift with pressure for backbone segments in the protein ubiquitin is correlated with the change inmore » the population of hydrogen bonds involving the backbone amide group. The different extent of interaction of protein backbone with the water molecules in the solvent is put in evidence.« less

High-resolution protein design with backbone freedom.

PubMed

Harbury, P B; Plecs, J J; Tidor, B; Alber, T; Kim, P S

1998-11-20

Recent advances in computational techniques have allowed the design of precise side-chain packing in proteins with predetermined, naturally occurring backbone structures. Because these methods do not model protein main-chain flexibility, they lack the breadth to explore novel backbone conformations. Here the de novo design of a family of alpha-helical bundle proteins with a right-handed superhelical twist is described. In the design, the overall protein fold was specified by hydrophobic-polar residue patterning, whereas the bundle oligomerization state, detailed main-chain conformation, and interior side-chain rotamers were engineered by computational enumerations of packing in alternate backbone structures. Main-chain flexibility was incorporated through an algebraic parameterization of the backbone. The designed peptides form alpha-helical dimers, trimers, and tetramers in accord with the design goals. The crystal structure of the tetramer matches the designed structure in atomic detail.

EVER-EST: European Virtual Environment for Research in Earth Science Themes

NASA Astrophysics Data System (ADS)

Glaves, H.; Albani, M.

2016-12-01

EVER-EST is an EC Horizon 2020 project having the goal to develop a Virtual Research Environment (VRE) providing a state-of-the-art solution to allow Earth Scientists to preserve their work and publications for reference and future reuse, and to share with others. The availability of such a solution, based on an innovative concept and state of art technology infrastructure, will considerably enhance the quality of how Earth Scientists work together within their own institution and also across other organizations, regions and countries. The concept of Research Objects (ROs), used in the Earth Sciences for the first time, will form the backbone of the EVER-EST VRE infrastructure. ROs will enhance the ability to preserve, re-use and share entire or individual parts of scientific workflows and all the resources related to a specific scientific investigation. These ROs will also potentially be used as part of the scholarly publication process. EVER-EST is building on technologies developed during almost 15 years of research on Earth Science data management infrastructures. The EVER-EST VRE Service Oriented Architecture is being meticulously designed to accommodate at best the requirements of a wide range of Earth Science communities and use cases: focus is put on common requirements and on minimising the level of complexity in the EVER-EST VRE to ensure future sustainability within the user communities beyond the end of the project. The EVER-EST VRE will be validated through its customisation and deployment by four Virtual Research Communities (VRCs) from different Earth Science disciplines and will support enhanced interaction between data providers and scientists in the Earth Science domain. User community will range from bio-marine researchers (Sea Monitoring use case), to common foreign and security policy institutions and stakeholders (Land Monitoring for Security use case), natural hazards forecasting systems (Natural Hazards use case), and disaster and risk management teams (Supersites use case). The EVER-EST project will coordinate and collaborate with other relevant initiatives worldwide mainly through the Research Data Alliance (RDA) Virtual Research Environments interest group (VRE-IG).

Uganda's National Transmission Backbone Infrastructure Project: Technical Challenges and the Way Forward

NASA Astrophysics Data System (ADS)

Bulega, T.; Kyeyune, A.; Onek, P.; Sseguya, R.; Mbabazi, D.; Katwiremu, E.

2011-10-01

Several publications have identified technical challenges facing Uganda's National Transmission Backbone Infrastructure project. This research addresses the technical limitations of the National Transmission Backbone Infrastructure project, evaluates the goals of the project, and compares the results against the technical capability of the backbone. The findings of the study indicate a bandwidth deficit, which will be addressed by using dense wave division multiplexing repeaters, leasing bandwidth from private companies. Microwave links for redundancy, a Network Operation Center for operation and maintenance, and deployment of wireless interoperability for microwave access as a last-mile solution are also suggested.

Next Generation Integrated Environment for Collaborative Work Across Internets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harvey B. Newman

2009-02-24

We are now well-advanced in our development, prototyping and deployment of a high performance next generation Integrated Environment for Collaborative Work. The system, aimed at using the capability of ESnet and Internet2 for rapid data exchange, is based on the Virtual Room Videoconferencing System (VRVS) developed by Caltech. The VRVS system has been chosen by the Internet2 Digital Video (I2-DV) Initiative as a preferred foundation for the development of advanced video, audio and multimedia collaborative applications by the Internet2 community. Today, the system supports high-end, broadcast-quality interactivity, while enabling a wide variety of clients (Mbone, H.323) to participate in themore » same conference by running different standard protocols in different contexts with different bandwidth connection limitations, has a fully Web-integrated user interface, developers and administrative APIs, a widely scalable video network topology based on both multicast domains and unicast tunnels, and demonstrated multiplatform support. This has led to its rapidly expanding production use for national and international scientific collaborations in more than 60 countries. We are also in the process of creating a 'testbed video network' and developing the necessary middleware to support a set of new and essential requirements for rapid data exchange, and a high level of interactivity in large-scale scientific collaborations. These include a set of tunable, scalable differentiated network services adapted to each of the data streams associated with a large number of collaborative sessions, policy-based and network state-based resource scheduling, authentication, and optional encryption to maintain confidentiality of inter-personal communications. High performance testbed video networks will be established in ESnet and Internet2 to test and tune the implementation, using a few target application-sets.« less

Antigenic determinants of Staphylococcus aureus type 5 and type 8 capsular polysaccharide vaccines.

PubMed

Fattom, A I; Sarwar, J; Basham, L; Ennifar, S; Naso, R

1998-10-01

Bacterial capsular polysaccharides (CP) are carbohydrate polymers comprised of repeating saccharide units. Several of these CP have side chains attached to their backbone structures. The side chains may include O-acetyl, phosphate, sialic acid, and other moieties. Those moieties represent the immunodominant epitopes and the most functional ones. The clinically significant Staphylococcus aureus type 5 CP (CP 5) and type 8 CP (CP 8) are comprised of a trisaccharide repeat unit with one O-acetyl group attached to each repeat unit. The immunogenicity of these CP and the functionality of antibodies to the backbone and the O-acetyl moieties were investigated. Immunization with the native CP conjugates (CP with 75% O-acetylation) elicited a high proportion of antibodies directed against the O-acetyl moiety. Nonetheless, all of the vaccinees produced antibodies to the backbone moieties as well. Conjugate vaccines made of de-O-acetylated CP elicited backbone antibodies only. Antibodies to both backbone and O-acetyl groups were found to be opsonic against S. aureus strains which varied in their O-acetyl content. Absorption studies with O-acetylated and de-O-acetylated CP showed that (i) native CP conjugates generated antibodies to both backbone and O-acetyl groups and (ii) O-acetylated isolates were opsonized by both populations of antibodies while the non-O-acetylated strains were predominantly opsonized by the backbone antibodies. These results suggest that S. aureus CP conjugate vaccines elicit multiple populations of antibodies with diverse specificities. Moreover, the antibodies of different specificities (backbone or O-acetyl) are all functional and efficient against the variations in bacterial CP that may occur among clinically significant S. aureus pathogenic isolates.

Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein–Ligand Complexes

DOE PAGES

Pollock, Jonathan; Borkin, Dmitry; Lund, George; ...

2015-08-19

Multipolar interactions involving fluorine and the protein backbone have been frequently observed in protein–ligand complexes. Such fluorine–backbone interactions may substantially contribute to the high affinity of small molecule inhibitors. Here we found that introduction of trifluoromethyl groups into two different sites in the thienopyrimidine class of menin–MLL inhibitors considerably improved their inhibitory activity. In both cases, trifluoromethyl groups are engaged in short interactions with the backbone of menin. In order to understand the effect of fluorine, we synthesized a series of analogues by systematically changing the number of fluorine atoms, and we determined high-resolution crystal structures of the complexes withmore » menin. Here, we found that introduction of fluorine at favorable geometry for interactions with backbone carbonyls may improve the activity of menin–MLL inhibitors as much as 5- to 10-fold. In order to facilitate the design of multipolar fluorine–backbone interactions in protein–ligand complexes, we developed a computational algorithm named FMAP, which calculates fluorophilic sites in proximity to the protein backbone. We demonstrated that FMAP could be used to rationalize improvement in the activity of known protein inhibitors upon introduction of fluorine. Furthermore, FMAP may also represent a valuable tool for designing new fluorine substitutions and support ligand optimization in drug discovery projects. Analysis of the menin–MLL inhibitor complexes revealed that the backbone in secondary structures is particularly accessible to the interactions with fluorine. Lastly, considering that secondary structure elements are frequently exposed at protein interfaces, we postulate that multipolar fluorine–backbone interactions may represent a particularly attractive approach to improve inhibitors of protein–protein interactions.« less

E-Nephrology

PubMed Central

Manchanda, P. K.; Bid, H. K.

2011-01-01

Diagnosis of renal diseases is often delayed owing to the scarcity of trained physicians, lack of facilities, and shortage of funds limits effective management, particularly when it comes to the red zone of renal replacement therapy. The Internetis expected to open up a myriad resource of knowledge and applications for academicians, researchers and clinicians alike in all health care professions across the globe. Also, the Internet has grown rapidly over the years and will inevitably expand even more. Evolving technologies offer modern applications for information management, communications with multimedia and virtual reality. Now, these innovative technologies have opened up newer possibilities for nephrologists. As Internet is serving as a backbone for these modern technologies, it is an utmost necessity to use and refine Internet applications for future nephrologists. Increasingly easy access to Internet has dramatically reduced barriers in sharing of information among basic and clinical nephrologists. Considering the growing scope for nephrologists in the use of Internet, it is necessary to understand Internet as a source of information and backbone of modern application. This review illustrates expanding roles of the Internet for the nephrologists and provides ready to use compilation of useful academic, research, clinical resources and is expected to introduce, stimulate and guide nephrologists into the realm of the world wide web. It also investigates how Internet is supporting in growth and development of the field of nephrology and present and future scopes of Internet as a tool for professionals involved in this area as well as information about biological sciences, and it also gives information about societies in various continents working in field of nephrology and the links useful for clinicians and research scientists. PMID:21655161

Analysis of the Arabidopsis IRX9/IRX9-L and IRX14/IRX14-L pairs of glycosyltransferase genes reveals critical contributions to biosynthesis of the hemicellulose glucuronoxylan.

PubMed

Wu, Ai-Min; Hörnblad, Emma; Voxeur, Aline; Gerber, Lorenz; Rihouey, Christophe; Lerouge, Patrice; Marchant, Alan

2010-06-01

The hemicellulose glucuronoxylan (GX) is a major component of plant secondary cell walls. However, our understanding of GX synthesis remains limited. Here, we identify and analyze two new genes from Arabidopsis (Arabidopsis thaliana), IRREGULAR XYLEM9-LIKE (IRX9-L) and IRX14-LIKE (IRX14-L) that encode glycosyltransferase family 43 members proposed to function during xylan backbone elongation. We place IRX9-L and IRX14-L in a genetic framework with six previously described glycosyltransferase genes (IRX9, IRX10, IRX10-L, IRX14, FRAGILE FIBER8 [FRA8], and FRA8 HOMOLOG [F8H]) and investigate their function in GX synthesis. Double-mutant analysis identifies IRX9-L and IRX14-L as functional homologs of IRX9 and IRX14, respectively. Characterization of irx9 irx10 irx14 fra8 and irx9-L irx10-L irx14-L f8h quadruple mutants allows definition of a set of genes comprising IRX9, IRX10, IRX14, and FRA8 that perform the main role in GX synthesis during vegetative development. The IRX9-L, IRX10-L, IRX14-L, and F8H genes are able to partially substitute for their respective homologs and normally perform a minor function. The irx14 irx14-L double mutant virtually lacks xylan, whereas irx9 irx9-L and fra8 f8h double mutants form lowered amounts of GX displaying a greatly reduced degree of backbone polymerization. Our findings reveal two distinct sets of four genes each differentially contributing to GX biosynthesis.

Analysis of the Arabidopsis IRX9/IRX9-L and IRX14/IRX14-L Pairs of Glycosyltransferase Genes Reveals Critical Contributions to Biosynthesis of the Hemicellulose Glucuronoxylan1[C][W

PubMed Central

Wu, Ai-Min; Hörnblad, Emma; Voxeur, Aline; Gerber, Lorenz; Rihouey, Christophe; Lerouge, Patrice; Marchant, Alan

2010-01-01

The hemicellulose glucuronoxylan (GX) is a major component of plant secondary cell walls. However, our understanding of GX synthesis remains limited. Here, we identify and analyze two new genes from Arabidopsis (Arabidopsis thaliana), IRREGULAR XYLEM9-LIKE (IRX9-L) and IRX14-LIKE (IRX14-L) that encode glycosyltransferase family 43 members proposed to function during xylan backbone elongation. We place IRX9-L and IRX14-L in a genetic framework with six previously described glycosyltransferase genes (IRX9, IRX10, IRX10-L, IRX14, FRAGILE FIBER8 [FRA8], and FRA8 HOMOLOG [F8H]) and investigate their function in GX synthesis. Double-mutant analysis identifies IRX9-L and IRX14-L as functional homologs of IRX9 and IRX14, respectively. Characterization of irx9 irx10 irx14 fra8 and irx9-L irx10-L irx14-L f8h quadruple mutants allows definition of a set of genes comprising IRX9, IRX10, IRX14, and FRA8 that perform the main role in GX synthesis during vegetative development. The IRX9-L, IRX10-L, IRX14-L, and F8H genes are able to partially substitute for their respective homologs and normally perform a minor function. The irx14 irx14-L double mutant virtually lacks xylan, whereas irx9 irx9-L and fra8 f8h double mutants form lowered amounts of GX displaying a greatly reduced degree of backbone polymerization. Our findings reveal two distinct sets of four genes each differentially contributing to GX biosynthesis. PMID:20424005

Finding idle machines in a workstation-based distributed system

NASA Technical Reports Server (NTRS)

Theimer, Marvin M.; Lantz, Keith A.

1989-01-01

The authors describe the design and performance of scheduling facilities for finding idle hosts in a workstation-based distributed system. They focus on the tradeoffs between centralized and decentralized architectures with respect to scalability, fault tolerance, and simplicity of design, as well as several implementation issues of interest when multicast communication is used. They conclude that the principal tradeoff between the two approaches is that a centralized architecture can be scaled to a significantly greater degree and can more easily monitor global system statistics, whereas a decentralized architecture is simpler to implement.

Neuroprosthetics and Solutions for Restoring Sensorimotor Functions

DTIC Science & Technology

2009-12-01

system can load drug molecules in the polymer backbones and inside the nanoholes respectively. Electrical stimulation can release drugs from both the...polymer backbones and the 13 nanoholes , which significantly improves the drug load and release efficiency. Furthermore, with one drug incorporated...in the polymer backbone during electrochemical polymerization, the nanoholes inside the polymer can act as containers to store a different drug, and

Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold

DOE Office of Scientific and Technical Information (OSTI.GOV)

Azoitei, Mihai L.; Correia, Bruno E.; Ban, Yih-En Andrew

2012-02-07

The manipulation of protein backbone structure to control interaction and function is a challenge for protein engineering. We integrated computational design with experimental selection for grafting the backbone and side chains of a two-segment HIV gp120 epitope, targeted by the cross-neutralizing antibody b12, onto an unrelated scaffold protein. The final scaffolds bound b12 with high specificity and with affinity similar to that of gp120, and crystallographic analysis of a scaffold bound to b12 revealed high structural mimicry of the gp120-b12 complex structure. The method can be generalized to design other functional proteins through backbone grafting.

A new characterization of three-dimensional conductivity backbone above and below the percolation threshold

NASA Astrophysics Data System (ADS)

Skal, Asya S.

1996-08-01

A new definition of three-dimensional conductivity backbone, obtained from a distribution function of Joule heat and the Hall coefficient is introduced. The fractal dimension d fB = d - ( {g}/{v}) = 2.25 of conductivity backbone for both sides of the threshold is obtained from a critical exponent of the Hall coefficient g = 0.6. This allows one to construct, below the threshold, a new order parameter of metal-conductor transition—the two-component infinite conductivity back-bone and tested scaling relation, proposed by Alexander and Orbach [ J. Phys. Rev. Lett.43, 1982, L625] for both sides of a threshold.

Solution structure and thermodynamics of 2',5' RNA intercalation.

PubMed

Horowitz, Eric D; Lilavivat, Seth; Holladay, Benjamin W; Germann, Markus W; Hud, Nicholas V

2009-04-29

As a means to explore the influence of the nucleic acid backbone on the intercalative binding of ligands to DNA and RNA, we have determined the solution structure of a proflavine-bound 2',5'-linked octamer duplex with the sequence GCCGCGGC. This structure represents the first NMR structure of an intercalated RNA duplex, of either backbone structural isomer. By comparison with X-ray crystal structures, we have identified similarities and differences between intercalated 3',5' and 2',5'-linked RNA duplexes. First, the two forms of RNA have different sugar pucker geometries at the intercalated nucleotide steps, yet have the same interphosphate distances. Second, as in intercalated 3',5' RNA, the phosphate backbone angle zeta at the 2',5' RNA intercalation site prefers to be in the trans conformation, whereas unintercalated 2',5' and 3',5' RNA prefer the -gauche conformation. These observations provide new insights regarding the transitions required for intercalation of a phosphodiester-ribose backbone and suggest a possible contribution of the backbone to the origin of the nearest-neighbor exclusion principle. Thermodynamic studies presented for intercalation of both structural RNA isomers also reveal a surprising sensitivity of intercalator binding enthalpy and entropy to the details of RNA backbone structure.

Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank.

PubMed

Zhang, Qian; Xu, Zhijian; Shi, Jiye; Zhu, Weiliang

2017-07-24

Halogen bonds (XBs) are attracting increasing attention in biological systems. Protein Data Bank (PDB) archives experimentally determined XBs in biological macromolecules. However, no software for structure refinement in X-ray crystallography takes into account XBs, which might result in the weakening or even vanishing of experimentally determined XBs in PDB. In our previous study, we showed that side-chain XBs forming with protein side chains are underestimated in PDB on the basis of the phenomenon that the proportion of side-chain XBs to overall XBs decreases as structural resolution becomes lower and lower. However, whether the dominant backbone XBs forming with protein backbone are overlooked is still a mystery. Here, with the help of the ratio (R F ) of the observed XBs' frequency of occurrence to their frequency expected at random, we demonstrated that backbone XBs are largely overlooked in PDB, too. Furthermore, three cases were discovered possessing backbone XBs in high resolution structures while losing the XBs in low resolution structures. In the last two cases, even at 1.80 Å resolution, the backbone XBs were lost, manifesting the urgent need to consider XBs in the refinement process during X-ray crystallography study.

Molecular modeling of calmodulin: a comparison with crystallographic data

NASA Technical Reports Server (NTRS)

McDonald, J. J.; Rein, R.

1989-01-01

Two methods of side-chain placement on a modeled protein have been examined. Two molecular models of calmodulin were constructed that differ in the treatment of side chains prior to optimization of the molecule. A virtual bond analysis program developed by Purisima and Scheraga was used to determine the backbone conformation based on 2.2 angstroms resolution C alpha coordinates for the molecules. In the first model, side chains were initially constructed in an extended conformation. In the second model, a conformational grid search technique was employed. Calcium ions were treated explicitly during energy optimization using CHARMM. The models are compared to a recently published refined crystal structure of calmodulin. The results indicate that the initial choices for side-chains, but also significant effects on the main-chain conformation and supersecondary structure. The conformational differences are discussed. Analysis of these and other methods makes possible the formulation of a methodology for more appropriate side-chain placement in modeled proteins.

An Optimal CDS Construction Algorithm with Activity Scheduling in Ad Hoc Networks

PubMed Central

Penumalli, Chakradhar; Palanichamy, Yogesh

2015-01-01

A new energy efficient optimal Connected Dominating Set (CDS) algorithm with activity scheduling for mobile ad hoc networks (MANETs) is proposed. This algorithm achieves energy efficiency by minimizing the Broadcast Storm Problem [BSP] and at the same time considering the node's remaining energy. The Connected Dominating Set is widely used as a virtual backbone or spine in mobile ad hoc networks [MANETs] or Wireless Sensor Networks [WSN]. The CDS of a graph representing a network has a significant impact on an efficient design of routing protocol in wireless networks. Here the CDS is a distributed algorithm with activity scheduling based on unit disk graph [UDG]. The node's mobility and residual energy (RE) are considered as parameters in the construction of stable optimal energy efficient CDS. The performance is evaluated at various node densities, various transmission ranges, and mobility rates. The theoretical analysis and simulation results of this algorithm are also presented which yield better results. PMID:26221627

NMR resonance assignments of the lantibiotic immunity protein NisI from Lactococcus lactis.

PubMed

Hacker, Carolin; Christ, Nina Alexandra; Duchardt-Ferner, Elke; Korn, Sophie; Berninger, Lucija; Kötter, Peter; Entian, Karl-Dieter; Wöhnert, Jens

2015-10-01

The lantibiotic nisin is a small antimicrobial peptide which acts against a wide range of Gram-positive bacteria. Nisin-producing Lactococcus lactis strains express four genes for self-protection against their own antimicrobial compound. This immunity system consists of the lipoprotein NisI and the ABC transporter NisFEG. NisI is attached to the outside of the cytoplasmic membrane via a covalently linked diacylglycerol anchor. Both the lipoprotein and the ABC transporter are needed for full immunity but the exact immunity mechanism is still unclear. To gain insights into the highly specific immunity mechanism of nisin producing strains on a structural level we present here the backbone resonance assignment of NisI (25.8 kDa) as well as the virtually complete (1)H,(15)N,(13)C chemical shift assignments for the isolated 12.7 kDa N-terminal and 14.6 kDa C-terminal domains of NisI.

Backbone conformation affects duplex initiation and duplex propagation in hybridisation of synthetic H-bonding oligomers.

PubMed

Iadevaia, Giulia; Núñez-Villanueva, Diego; Stross, Alexander E; Hunter, Christopher A

2018-06-06

Synthetic oligomers equipped with complementary H-bond donor and acceptor side chains form multiply H-bonded duplexes in organic solvents. Comparison of the duplex forming properties of four families of oligomers with different backbones shows that formation of an extended duplex with three or four inter-strand H-bonds is more challenging than formation of complexes that make only two H-bonds. The stabilities of 1 : 1 complexes formed between length complementary homo-oligomers equipped with either phosphine oxide or phenol recognition modules were measured in toluene. When the backbone is very flexible (pentane-1,5-diyl thioether), the stability increases uniformly by an order of magnitude for each additional base-pair added to the duplex: the effective molarities for formation of the first intramolecular H-bond (duplex initiation) and subsequent intramolecular H-bonds (duplex propagation) are similar. This flexible system is compared with three more rigid backbones that are isomeric combinations of an aromatic ring and methylene groups. One of the rigid systems behaves in exactly the same way as the flexible backbone, but the other two do not. For these systems, the effective molarity for formation of the first intramolecular H-bond is the same as that found for the other two backbones, but additional H-bonds are not formed between the longer oligomers. The effective molarities are too low for duplex propagation in these systems, because the oligomer backbones cannot adopt conformations compatible with formation of an extended duplex.

Smectic order and backbone anisotropy of a side-chain liquid crystalline polymer by Small-Angle Neutron Scattering

NASA Astrophysics Data System (ADS)

Noirez, L.; Pépy, G.; Keller, P.; Benguigui, L.

1991-07-01

We have simultaneously measured, for the first time, the extension of the polymer backbone of a side-chain liquid crystalline polymer and the intensity of the 001 Bragg reflection, which gives the smectic order parameter Psi as a function of temperature in the smectic phase. We have qualitatively demonstrated that the more the smectic phase is ordered, the more the polymer backbone is localized between the mesogenic layers. It is shown that the Landau theory allows us to relate the radius of gyration parallel to the magnetic field of the polymer backbone to the smectic order parameter. We also show that the Renz-Warner theory is suitable at low temperatures.

Electrostrictive Graft Elastomers

NASA Technical Reports Server (NTRS)

Su, Ji (Inventor); Harrison, Joycelyn S. (Inventor); St.Clair, Terry L. (Inventor)

2003-01-01

An electrostrictive graft elastomer has a backbone molecule which is a non-crystallizable, flexible macromolecular chain and a grafted polymer forming polar graft moieties with backbone molecules. The polar graft moieties have been rotated by an applied electric field, e.g., into substantial polar alignment. The rotation is sustained until the electric field is removed. In another embodiment, a process for producing strain in an elastomer includes: (a) providing a graft elastomer having a backbone molecule which is a non-crystallizable, flexible macromolecular chain and a grafted polymer forming polar graft moieties with backbone molecules; and (b) applying an electric field to the graft elastomer to rotate the polar graft moieties, e.g., into substantial polar alignment.

Increasing Sequence Diversity with Flexible Backbone Protein Design: The Complete Redesign of a Protein Hydrophobic Core

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murphy, Grant S.; Mills, Jeffrey L.; Miley, Michael J.

2015-10-15

Protein design tests our understanding of protein stability and structure. Successful design methods should allow the exploration of sequence space not found in nature. However, when redesigning naturally occurring protein structures, most fixed backbone design algorithms return amino acid sequences that share strong sequence identity with wild-type sequences, especially in the protein core. This behavior places a restriction on functional space that can be explored and is not consistent with observations from nature, where sequences of low identity have similar structures. Here, we allow backbone flexibility during design to mutate every position in the core (38 residues) of a four-helixmore » bundle protein. Only small perturbations to the backbone, 12 {angstrom}, were needed to entirely mutate the core. The redesigned protein, DRNN, is exceptionally stable (melting point >140C). An NMR and X-ray crystal structure show that the side chains and backbone were accurately modeled (all-atom RMSD = 1.3 {angstrom}).« less

Two-dimensional NMR spectroscopy reveals cation-triggered backbone degradation in polysulfone-based anion exchange membranes

PubMed Central

Arges, Christopher G.; Ramani, Vijay

2013-01-01

Anion exchange membranes (AEMs) find widespread applications as an electrolyte and/or electrode binder in fuel cells, electrodialysis stacks, flow and metal-air batteries, and electrolyzers. AEMs exhibit poor stability in alkaline media; their degradation is induced by the hydroxide ion, a potent nucleophile. We have used 2D NMR techniques to investigate polymer backbone stability (as opposed to cation stability) of the AEM in alkaline media. We report the mechanism behind a peculiar, often-observed phenomenon, wherein a demonstrably stable polysulfone backbone degrades rapidly in alkaline solutions upon derivatization with alkaline stable fixed cation groups. Using COSY and heteronuclear multiple quantum correlation spectroscopy (2D NMR), we unequivocally demonstrate that the added cation group triggers degradation of the polymer backbone in alkaline via quaternary carbon hydrolysis and ether hydrolysis, leading to rapid failure. This finding challenges the existing perception that having a stable cation moiety is sufficient to yield a stable AEM and emphasizes the importance of the often ignored issue of backbone stability. PMID:23335629

Simulation of Ames Backbone Network

NASA Technical Reports Server (NTRS)

Shahnasser, Hamid

1998-01-01

The networking demands of Ames Research Center are dramatically increasing. More and more workstations are requested to run video and audio applications on the network. These applications require a much greater bandwidth than data applications. The existing ARCLAN 2000 network bandwidth is insufficient, due to the use of FDDI as its backbone, for accommodating video applications. Operating at a maximum of 100 Mbps, FDDI can handle only a few workstations running multimedia applications. The ideal solution is to replace the current ARCLAN 2000 FDDI backbone with an ATM backbone. ATM has the capability to handle the increasing traffic loads on the ARCLAN 2000 that results from these new applications. As it can be seen from Figure 1, ARCLAN 2000 have a total of 32 routers (5 being core routers) each connected to the FDDI backbone via a 100 Mbps link. This network serves 34 different locations by using 34 hubs that are connected to secondary routers. End users are connected to the secondary routers with 10 Mbps links.

An Experimental Seismic Data and Parameter Exchange System for Interim NEAMTWS

NASA Astrophysics Data System (ADS)

Hanka, W.; Hoffmann, T.; Weber, B.; Heinloo, A.; Hoffmann, M.; Müller-Wrana, T.; Saul, J.

2009-04-01

In 2008 GFZ Potsdam has started to operate its global earthquake monitoring system as an experimental seismic background data centre for the interim NEAMTWS (NE Atlantic and Mediterranean Tsunami Warning System). The SeisComP3 (SC3) software, developed within the GITEWS (German Indian Ocean Tsunami Early Warning System) project was extended to test the export and import of individual processing results within a cluster of SC3 systems. The initiated NEAMTWS SC3 cluster consists presently of the 24/7 seismic services at IMP, IGN, LDG/EMSC and KOERI, whereas INGV and NOA are still pending. The GFZ virtual real-time seismic network (GEOFON Extended Virtual Network - GEVN) was substantially extended by many stations from Western European countries optimizing the station distribution for NEAMTWS purposes. To amend the public seismic network (VEBSN - Virtual European Broadband Seismic Network) some attached centres provided additional private stations for NEAMTWS usage. In parallel to the data collection by Internet the GFZ VSAT hub for the secured data collection of the EuroMED GEOFON and NEAMTWS backbone network stations became operational and the first data links were established. In 2008 the experimental system could already prove its performance since a number of relevant earthquakes have happened in NEAMTWS area. The results are very promising in terms of speed as the automatic alerts (reliable solutions based on a minimum of 25 stations and disseminated by emails and SMS) were issued between 2 1/2 and 4 minutes for Greece and 5 minutes for Iceland. They are also promising in terms of accuracy since epicenter coordinates, depth and magnitude estimates were sufficiently accurate from the very beginning, usually don't differ substantially from the final solutions and provide a good starting point for the operations of the interim NEAMTWS. However, although an automatic seismic system is a good first step, 24/7 manned RTWCs are mandatory for regular manual verification of the automatic seismic results and the estimation of the tsunami potential for a given event.

The APECS Virtual Poster Session: a virtual platform for science communication and discussion

NASA Astrophysics Data System (ADS)

Renner, A.; Jochum, K.; Jullion, L.; Pavlov, A.; Liggett, D.; Fugmann, G.; Baeseman, J. L.; Apecs Virtual Poster Session Working Group, T.

2011-12-01

The Virtual Poster Session (VPS) of the Association of Polar Early Career Scientists (APECS) was developed by early career scientists as an online tool for communicating and discussing science and research beyond the four walls of a conference venue. Poster sessions often are the backbone of a conference where especially early career scientists get a chance to communicate their research, discuss ideas, data, and scientific problems with their peers and senior scientists. There, they can hone their 'elevator pitch', discussion skills and presentation skills. APECS has taken the poster session one step further and created the VPS - the same idea but independent from conferences, travel, and location. All that is needed is a computer with internet access. Instead of letting their posters collect dust on the computer's hard drive, scientists can now upload them to the APECS website. There, others have the continuous opportunity to comment, give feedback and discuss the work. Currently, about 200 posters are accessible contributed by authors and co-authors from 34 countries. Since January 2010, researchers can discuss their poster with a broad international audience including fellow researchers, community members, potential colleagues and collaborators, policy makers and educators during monthly conference calls via an internet platform. Recordings of the calls are available online afterwards. Calls so far have included topical sessions on e.g. marine biology, glaciology, or social sciences, and interdisciplinary calls on Arctic sciences or polar research activities in a specific country, e.g. India or Romania. They attracted audiences of scientists at all career stages and from all continents, with on average about 15 persons participating per call. Online tools like the VPS open up new ways for creating collaborations and new research ideas and sharing different methodologies for future projects, pushing aside the boundaries of countries and nations, conferences, offices, and disciplines, and provide early career scientists with easily accessible training opportunities for their communication and outreach skills, independent of their location and funding situation.

Effect of methyl groups on conformational properties of small ionized comb-like polyelectrolytes at the atomic level.

PubMed

Zhao, Hongxia; Liu, Jiaping; Ran, Qianping; Yang, Yong; Shu, Xin

2017-03-01

Comb-like polycarboxylate ether (PCE) molecules with different content of methyl groups substituted on backbone and different location of methyl groups substituted on the side chains, respectively, were designed and were studied in explicit salt solutions by all-atom molecular dynamics simulations. Methyl groups substituted on the backbone of PCE have a great effect on the conformation of PCE. Stiffness of charged backbone was not only affected by the rotational freedom but also the electrostatic repulsion between the charged COO - groups. The interaction of counterions (Na + ) with COO - groups for PCE3 (with part of AA substituted by MAA on the backbone) was stronger and the screen effect was great, which decided the smaller size of PCE3. The interaction between water and COO - groups was strong regardless of the content of AA substituted by MAA on the backbone. The effect of methyl groups substituted on the different location of side chains on the conformation of PCE was less than that of methyl groups substituted on the backbone. The equilibrium sizes of the four PCE molecules with methyl groups substituted on the side chains were similar. Graphical Abstract Effect of methyl groups on conformational properties of small ionized comb-like polyelectrolytes at the atomic level.

Effect of oligonucleic acid (ONA) backbone features on assembly of ONA-star polymer conjugates: a coarse-grained molecular simulation study.

PubMed

Condon, Joshua E; Jayaraman, Arthi

2017-10-04

Understanding the impact of incorporating new physical and chemical features in oligomeric DNA mimics, termed generally as "oligonucleic acids" (ONAs), on their structure and thermodynamics will be beneficial in designing novel materials for a variety of applications. In this work, we conduct coarse-grained molecular simulations of ONA-star polymer conjugates with varying ONA backbone flexibility, ONA backbone charge, and number of arms in the star polymer at a constant ONA strand volume fraction to elucidate the effect of these design parameters on the thermodynamics and assembly of multi-arm ONA-star polymer conjugates. We quantify the thermo-reversible behavior of the ONA-star polymer conjugates by quantifying the hybridization of the ONA strands in the system as a function of temperature (i.e. melting curve). Additionally, we characterize the assembly of the ONA-star polymer conjugates by tracking cluster formation and percolation as a function of temperature, as well as cluster size distribution at temperatures near the assembly transition region. The key results are as follows. The melting temperature (T m ) of the ONA strands decreases upon going from a neutral to a charged ONA backbone and upon increasing flexibility of the ONA backbone. Similar behavior is seen for the assembly transition temperature (T a ) with varying ONA backbone charge and flexibility. While the number of arms in the ONA-star polymer conjugate has a negligible effect on the ONA T m in these systems, as the number of ONA-star polymer arms increase, the assembly temperature T a increases and local ordering in the assembled state improves. By understanding how factors like ONA backbone charge, backbone flexibility, and ONA-star polymer conjugate architecture impact the behavior of ONA-star polymer conjugate systems, we can better inform how the selection of ONA chemistry will influence resulting ONA-star polymer assembly.

Computational protein design with backbone plasticity

PubMed Central

MacDonald, James T.; Freemont, Paul S.

2016-01-01

The computational algorithms used in the design of artificial proteins have become increasingly sophisticated in recent years, producing a series of remarkable successes. The most dramatic of these is the de novo design of artificial enzymes. The majority of these designs have reused naturally occurring protein structures as ‘scaffolds’ onto which novel functionality can be grafted without having to redesign the backbone structure. The incorporation of backbone flexibility into protein design is a much more computationally challenging problem due to the greatly increased search space, but promises to remove the limitations of reusing natural protein scaffolds. In this review, we outline the principles of computational protein design methods and discuss recent efforts to consider backbone plasticity in the design process. PMID:27911735

Analysis of stationary availability factor of two-level backbone computer networks with arbitrary topology

NASA Astrophysics Data System (ADS)

Rahman, P. A.

2018-05-01

This scientific paper deals with the two-level backbone computer networks with arbitrary topology. A specialized method, offered by the author for calculation of the stationary availability factor of the two-level backbone computer networks, based on the Markov reliability models for the set of the independent repairable elements with the given failure and repair rates and the methods of the discrete mathematics, is also discussed. A specialized algorithm, offered by the author for analysis of the network connectivity, taking into account different kinds of the network equipment failures, is also observed. Finally, this paper presents an example of calculation of the stationary availability factor for the backbone computer network with the given topology.

Automation Hooks Architecture for Flexible Test Orchestration - Concept Development and Validation

NASA Technical Reports Server (NTRS)

Lansdowne, C. A.; Maclean, John R.; Winton, Chris; McCartney, Pat

2011-01-01

The Automation Hooks Architecture Trade Study for Flexible Test Orchestration sought a standardized data-driven alternative to conventional automated test programming interfaces. The study recommended composing the interface using multicast DNS (mDNS/SD) service discovery, Representational State Transfer (Restful) Web Services, and Automatic Test Markup Language (ATML). We describe additional efforts to rapidly mature the Automation Hooks Architecture candidate interface definition by validating it in a broad spectrum of applications. These activities have allowed us to further refine our concepts and provide observations directed toward objectives of economy, scalability, versatility, performance, severability, maintainability, scriptability and others.

Integrating security in a group oriented distributed system

NASA Technical Reports Server (NTRS)

Reiter, Michael; Birman, Kenneth; Gong, LI

1992-01-01

A distributed security architecture is proposed for incorporation into group oriented distributed systems, and in particular, into the Isis distributed programming toolkit. The primary goal of the architecture is to make common group oriented abstractions robust in hostile settings, in order to facilitate the construction of high performance distributed applications that can tolerate both component failures and malicious attacks. These abstractions include process groups and causal group multicast. Moreover, a delegation and access control scheme is proposed for use in group oriented systems. The focus is the security architecture; particular cryptosystems and key exchange protocols are not emphasized.

An approach to verification and validation of a reliable multicasting protocol: Extended Abstract

NASA Technical Reports Server (NTRS)

Callahan, John R.; Montgomery, Todd L.

1995-01-01

This paper describes the process of implementing a complex communications protocol that provides reliable delivery of data in multicast-capable, packet-switching telecommunication networks. The protocol, called the Reliable Multicasting Protocol (RMP), was developed incrementally using a combination of formal and informal techniques in an attempt to ensure the correctness of its implementation. Our development process involved three concurrent activities: (1) the initial construction and incremental enhancement of a formal state model of the protocol machine; (2) the initial coding and incremental enhancement of the implementation; and (3) model-based testing of iterative implementations of the protocol. These activities were carried out by two separate teams: a design team and a V&V team. The design team built the first version of RMP with limited functionality to handle only nominal requirements of data delivery. This initial version did not handle off-nominal cases such as network partitions or site failures. Meanwhile, the V&V team concurrently developed a formal model of the requirements using a variant of SCR-based state tables. Based on these requirements tables, the V&V team developed test cases to exercise the implementation. In a series of iterative steps, the design team added new functionality to the implementation while the V&V team kept the state model in fidelity with the implementation. This was done by generating test cases based on suspected errant or off-nominal behaviors predicted by the current model. If the execution of a test in the model and implementation agreed, then the test either found a potential problem or verified a required behavior. However, if the execution of a test was different in the model and implementation, then the differences helped identify inconsistencies between the model and implementation. In either case, the dialogue between both teams drove the co-evolution of the model and implementation. We have found that this interactive, iterative approach to development allows software designers to focus on delivery of nominal functionality while the V&V team can focus on analysis of off nominal cases. Testing serves as the vehicle for keeping the model and implementation in fidelity with each other. This paper describes (1) our experiences in developing our process model; and (2) three example problems found during the development of RMP. Although RMP has provided our research effort with a rich set of test cases, it also has practical applications within NASA. For example, RMP is being considered for use in the NASA EOSDIS project due to its significant performance benefits in applications that need to replicate large amounts of data to many network sites.

Solvation thermodynamics of amino acid side chains on a short peptide backbone

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hajari, Timir; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de

The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment. A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone. To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvationmore » free energies of nonpolar and polar side chains attached to a short peptide backbone. The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone. We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected. This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution. We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar side chain cavities in bulk water, in agreement with earlier work in the literature on analysis of cavity fluctuations at nonpolar molecular surfaces. The cavity and dispersion interaction contributions correlate quite well with the solvent accessible surface area of the nonpolar side chains attached to the backbone. This correlation however is weak for the overall solvation free energies owing to the fact that the cavity and dispersion free energy contributions are almost exactly cancelling each other.« less

Solvation thermodynamics of amino acid side chains on a short peptide backbone

NASA Astrophysics Data System (ADS)

Hajari, Timir; van der Vegt, Nico F. A.

2015-04-01

The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment. A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone. To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvation free energies of nonpolar and polar side chains attached to a short peptide backbone. The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone. We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected. This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution. We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar side chain cavities in bulk water, in agreement with earlier work in the literature on analysis of cavity fluctuations at nonpolar molecular surfaces. The cavity and dispersion interaction contributions correlate quite well with the solvent accessible surface area of the nonpolar side chains attached to the backbone. This correlation however is weak for the overall solvation free energies owing to the fact that the cavity and dispersion free energy contributions are almost exactly cancelling each other.

Backbone-only restraints for fast determination of the protein fold: The role of paramagnetism-based restraints. Cytochrome b562 as an example

NASA Astrophysics Data System (ADS)

Banci, Lucia; Bertini, Ivano; Felli, Isabella C.; Sarrou, Josephine

2005-02-01

CH α residual dipolar couplings (Δ rdc's) were measured for the oxidized cytochrome b562 from Escherichia coli as a result of its partial self-orientation in high magnetic fields due to the anisotropy of the overall magnetic susceptibility tensor. Both the low spin iron (III) heme and the four-helix bundle fold contribute to the magnetic anisotropy tensor. CH α Δ rdc's, which span a larger range than the analogous NH values (already available in the literature) sample large space variations at variance with NH Δ rdc's, which are largely isooriented within α helices. The whole structure is now significantly refined with the chemical shift index and CH α Δ rdc's. The latter are particularly useful also in defining the molecular magnetic anisotropy parameters. It is shown here that the backbone folding can be conveniently and accurately determined using backbone restraints only, which include NOEs, hydrogen bonds, residual dipolar couplings, pseudocontact shifts, and chemical shift index. All these restraints are easily and quickly determined from the backbone assignment. The calculated backbone structure is comparable to that obtained by using also side chain restraint. Furthermore, the structure obtained with backbone only restraints is, in its whole, very similar to that obtained with the complete set of restraints. The paramagnetism based restraints are shown to be absolutely relevant, especially for Δ rdc's.

Understanding traffic dynamics at a backbone POP

NASA Astrophysics Data System (ADS)

Taft, Nina; Bhattacharyya, Supratik; Jetcheva, Jorjeta; Diot, Christophe

2001-07-01

Spatial and temporal information about traffic dynamics is central to the design of effective traffic engineering practices for IP backbones. In this paper we study backbone traffic dynamics using data collected at a major POP on a tier-1 IP backbone. We develop a methodology that combines packet-level traces from access links in the POP and BGP routing information to build components of POP-to-POP traffic matrices. Our results show that there is wide disparity in the volume of traffic headed towards different egress POPs. At the same time, we find that current routing practices in the backbone tend to constrain traffic between ingress-egress POP pairs to a small number of paths. As a result, there is a wide variation in the utilization level of links in the backbone. Frequent capacity upgrades of the heavily used links are expensive; the need for such upgrades can be reduced by designing load balancing policies that will route more traffic over less utilized links. We identify traffic aggregates based on destination address prefixes and find that this set of criteria isolates a few aggregates that account for an overwhelmingly large portion of inter-POP traffic. We also demonstrate that these aggregates exhibit stability throughout the day on per-hour time scales, and thus they form a natural basis for splitting traffic over multiple paths in order to improve load balancing.

Determination of backbone chain direction of PDA using FFM

NASA Astrophysics Data System (ADS)

Jo, Sadaharu; Okamoto, Kentaro; Takenaga, Mitsuru

2010-01-01

The effect of backbone chains on friction force was investigated on both Langmuir-Blodgett (LB) films of 10,12-heptacosadiynoic acid and the (0 1 0) surfaces of single crystals of 2,4-hexadiene-1,6-diol using friction force microscopy (FFM). It was observed that friction force decreased when the scanning direction was parallel to the [0 0 1] direction in both samples. Moreover, friction force decreased when the scanning direction was parallel to the crystallographic [1 0 2], [1 0 1], [1 0 0] and [1 0 1¯] directions in only the single crystals. For the LB films, the [0 0 1] direction corresponds to the backbone chain direction of 10,12-heptacosadiynoic acid. For the single crystals, both the [0 0 1] and [1 0 1] directions correspond to the backbone chain direction, and the [1 0 2], [1 0 0] and [1 0 1¯] directions correspond to the low-index crystallographic direction. In both the LB films and single crystals, the friction force was minimized when the directions of scanning and the backbone chain were parallel.

Triazine-based sequence-defined polymers with side-chain diversity and backbone-backbone interaction motifs

DOE PAGES

Grate, Jay W.; Mo, Kai -For; Daily, Michael D.

2016-02-10

Sequence control in polymers, well-known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence-defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone–backbone interactions, including H-bonding motifs and pi–pi interactions. This architecture is arguably biomimetic while differing from sequence-defined polymers having peptide bonds. In conclusion, the synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone–backbone hydrogen-bonding motifs, and willmore » thus enable new macromolecules and materials with useful functions.« less

Triazine-based sequence-defined polymers with side-chain diversity and backbone-backbone interaction motifs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grate, Jay W.; Mo, Kai -For; Daily, Michael D.

Sequence control in polymers, well-known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence-defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone–backbone interactions, including H-bonding motifs and pi–pi interactions. This architecture is arguably biomimetic while differing from sequence-defined polymers having peptide bonds. In conclusion, the synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone–backbone hydrogen-bonding motifs, and willmore » thus enable new macromolecules and materials with useful functions.« less

Backbone assignment of the little finger domain of a Y-family DNA polymerase.

PubMed

Ma, Dejian; Fowler, Jason D; Suo, Zucai

2011-10-01

Sulfolobus solfataricus DNA polymerase IV (Dpo4), a prototype Y-family DNA polymerase, contains a unique little finger domain besides a catalytic core. Here, we report the chemical shift assignments for the backbone nitrogens, α and β carbons, and amide protons of the little finger domain of Dpo4. This work and our published backbone assignment for the catalytic core provide the basis for investigating the conformational dynamics of Dpo4 during catalysis using solution NMR spectroscopy.

Wetting of nonconserved residue-backbones: A feature indicative of aggregation associated regions of proteins.

PubMed

Pradhan, Mohan R; Pal, Arumay; Hu, Zhongqiao; Kannan, Srinivasaraghavan; Chee Keong, Kwoh; Lane, David P; Verma, Chandra S

2016-02-01

Aggregation is an irreversible form of protein complexation and often toxic to cells. The process entails partial or major unfolding that is largely driven by hydration. We model the role of hydration in aggregation using "Dehydrons." "Dehydrons" are unsatisfied backbone hydrogen bonds in proteins that seek shielding from water molecules by associating with ligands or proteins. We find that the residues at aggregation interfaces have hydrated backbones, and in contrast to other forms of protein-protein interactions, are under less evolutionary pressure to be conserved. Combining evolutionary conservation of residues and extent of backbone hydration allows us to distinguish regions on proteins associated with aggregation (non-conserved dehydron-residues) from other interaction interfaces (conserved dehydron-residues). This novel feature can complement the existing strategies used to investigate protein aggregation/complexation. © 2015 Wiley Periodicals, Inc.

Structural insights into the backbone-circularized granulocyte colony-stimulating factor containing a short connector.

PubMed

Miyafusa, Takamitsu; Shibuya, Risa; Honda, Shinya

2018-06-02

Backbone circularization is a powerful approach for enhancing the structural stability of polypeptides. Herein, we present the crystal structure of the circularized variant of the granulocyte colony-stimulating factor (G-CSF) in which the terminal helical region was circularized using a short, two-amino acid connector. The structure revealed that the N- and C-termini were indeed connected by a peptide bond. The local structure of the C-terminal region transited from an α helix to 3 10 helix with a bend close to the N-terminal region, indicating that the structural change offset the insufficient length of the connector. This is the first-ever report of a crystal structure of the backbone of a circularized protein. It will facilitate the development of backbone circularization methodology. Copyright © 2018 Elsevier Inc. All rights reserved.

Semiautomated model building for RNA crystallography using a directed rotameric approach.

PubMed

Keating, Kevin S; Pyle, Anna Marie

2010-05-04

Structured RNA molecules play essential roles in a variety of cellular processes; however, crystallographic studies of such RNA molecules present a large number of challenges. One notable complication arises from the low resolutions typical of RNA crystallography, which results in electron density maps that are imprecise and difficult to interpret. This problem is exacerbated by the lack of computational tools for RNA modeling, as many of the techniques commonly used in protein crystallography have no equivalents for RNA structure. This leads to difficulty and errors in the model building process, particularly in modeling of the RNA backbone, which is highly error prone due to the large number of variable torsion angles per nucleotide. To address this, we have developed a method for accurately building the RNA backbone into maps of intermediate or low resolution. This method is semiautomated, as it requires a crystallographer to first locate phosphates and bases in the electron density map. After this initial trace of the molecule, however, an accurate backbone structure can be built without further user intervention. To accomplish this, backbone conformers are first predicted using RNA pseudotorsions and the base-phosphate perpendicular distance. Detailed backbone coordinates are then calculated to conform both to the predicted conformer and to the previously located phosphates and bases. This technique is shown to produce accurate backbone structure even when starting from imprecise phosphate and base coordinates. A program implementing this methodology is currently available, and a plugin for the Coot model building program is under development.

Use of CID/ETD Mass Spectrometry to Analyze Glycopeptides

PubMed Central

Mechref, Yehia

2013-01-01

Collision-induced dissociation (CID) tandem mass spectrometry (MS) does not allow the characterization of glycopeptides because of the fragmentation of their glycan structures and limited fragmentation of peptide backbones. Electron-transfer dissociation (ETD) tandem MS, on the other hand, offers an alternative approach allowing the fragmentation of only peptide backbones of glycopeptides. Characterization of glycopeptides using both CID and ETD is summarized in this unit. While CID provide information related to the composition of glycan moiety attached to a peptide backbone, ETD permits de novo sequencing of peptides, since it prompts only peptide backbone fragmentation while keeping posttranslational modifications intact. Radical anions transfer of electrons to peptide backbone which induces cleavage of the N-Cα bond is observed in ETD. The glycan moiety is retained on the peptide backbone, largely unaffected by the ETD process. Accordingly, ETD allows not only the identification of the amino acid sequence of a glycopeptide, but also the unambiguous assignment of its glycosylation site. When data acquired from both fragmentation techniques are combined, it is possible to characterize comprehensively the entire glycopeptide. This is achieved using an instrument capable of alternating between CID and ETD experiments during an LC-MS/MS analysis. This unit discusses the different fragmentation of glycopeptides observed in CID and ETD. Tables of residue masses associated with oxonium ions observed in CID are provided to help in the interpretation of CID mass spectra. The utility of both CID and ETD for better characterization of glycopeptides are demonstrated for a model glycoprotein. PMID:22470127

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

PubMed Central

Zgarbová, Marie; Luque, F. Javier; Šponer, Jiří; Cheatham, Thomas E.; Otyepka, Michal; Jurečka, Petr

2013-01-01

We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as εζOL1, were derived from quantum-mechanical calculations with inclusion of conformation-dependent solvation effects according to the recently reported methodology (J. Chem. Theory Comput. 2012, 7(9), 2886-2902). The performance of the refined parameters was analyzed by means of extended molecular dynamics (MD) simulations for several representative systems. The results showed that the εζOL1 refinement improves the backbone description of B-DNA double helices and G-DNA stem. In B-DNA simulations, we observed an average increase of the helical twist and narrowing of the major groove, thus achieving better agreement with X-ray and solution NMR data. The balance between populations of BI and BII backbone substates was shifted towards the BII state, in better agreement with ensemble-refined solution experimental results. Furthermore, the refined parameters decreased the backbone RMS deviations in B-DNA MD simulations. In the antiparallel guanine quadruplex (G-DNA) the εζOL1 modification improved the description of non-canonical α/γ backbone substates, which were shown to be coupled to the ε/ζ torsion potential. Thus, the refinement is suggested as a possible alternative to the current ε/ζ torsion potential, which may enable more accurate modeling of nucleic acids. However, long-term testing is recommended before its routine application in DNA simulations. PMID:24058302

On the relationship between NMR-derived amide order parameters and protein backbone entropy changes

PubMed Central

Sharp, Kim A.; O’Brien, Evan; Kasinath, Vignesh; Wand, A. Joshua

2015-01-01

Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O2NH) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O2NH < 0.8) shows that these report both on the local flexibility of the protein and on a different component of the conformational entropy than that reported by the side chain methyl axis order parameters, O2axis. A calibration curve for backbone entropy vs. O2NH is developed which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O2NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, e.g. upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O2axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements. PMID:25739366

Antibody side chain conformations are position-dependent.

PubMed

Leem, Jinwoo; Georges, Guy; Shi, Jiye; Deane, Charlotte M

2018-04-01

Side chain prediction is an integral component of computational antibody design and structure prediction. Current antibody modelling tools use backbone-dependent rotamer libraries with conformations taken from general proteins. Here we present our antibody-specific rotamer library, where rotamers are binned according to their immunogenetics (IMGT) position, rather than their local backbone geometry. We find that for some amino acid types at certain positions, only a restricted number of side chain conformations are ever observed. Using this information, we are able to reduce the breadth of the rotamer sampling space. Based on our rotamer library, we built a side chain predictor, position-dependent antibody rotamer swapper (PEARS). On a blind test set of 95 antibody model structures, PEARS had the highest average χ 1 and χ1+2 accuracy (78.7% and 64.8%) compared to three leading backbone-dependent side chain predictors. Our use of IMGT position, rather than backbone ϕ/ψ, meant that PEARS was more robust to errors in the backbone of the model structure. PEARS also achieved the lowest number of side chain-side chain clashes. PEARS is freely available as a web application at http://opig.stats.ox.ac.uk/webapps/pears. © 2018 Wiley Periodicals, Inc.

Discrete RNA libraries from pseudo-torsional space

PubMed Central

Humphris-Narayanan, Elisabeth

2012-01-01

The discovery that RNA molecules can fold into complex structures and carry out diverse cellular roles has led to interest in developing tools for modeling RNA tertiary structure. While significant progress has been made in establishing that the RNA backbone is rotameric, few libraries of discrete conformations specifically for use in RNA modeling have been validated. Here, we present six libraries of discrete RNA conformations based on a simplified pseudo-torsional notation of the RNA backbone, comparable to phi and psi in the protein backbone. We evaluate the ability of each library to represent single nucleotide backbone conformations and we show how individual library fragments can be assembled into dinucleotides that are consistent with established RNA backbone descriptors spanning from sugar to sugar. We then use each library to build all-atom models of 20 test folds and we show how the composition of a fragment library can limit model quality. Despite the limitations inherent in using discretized libraries, we find that several hundred discrete fragments can rebuild RNA folds up to 174 nucleotides in length with atomic-level accuracy (<1.5Å RMSD). We anticipate the libraries presented here could easily be incorporated into RNA structural modeling, analysis, or refinement tools. PMID:22425640

On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.

PubMed

Sharp, Kim A; O'Brien, Evan; Kasinath, Vignesh; Wand, A Joshua

2015-05-01

Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O(2) NH ) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O(2) NH  < 0.8) shows that these report both on the local flexibility of the protein and on a different component of the conformational entropy than that reported by the side chain methyl axis order parameters, O(2) axis . A calibration curve for backbone entropy vs. O(2) NH is developed, which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O(2) NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, for example, upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O(2) axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements. © 2015 Wiley Periodicals, Inc.

Polyimide-based intracortical neural implant with improved structural stiffness

NASA Astrophysics Data System (ADS)

Lee, Kee-Keun; He, Jiping; Singh, Amarjit; Massia, Stephen; Ehteshami, Gholamreza; Kim, Bruce; Raupp, Gregory

2004-01-01

A novel structure for chronically implantable cortical electrodes using polyimide bio-polymer was devised, which provides both flexibility for micro-motion compliance between brain tissues and the skull and at the brain/implant interface and stiffness for better surgical handling. A 5-10 µm thick silicon backbone layer was attached to the tip of the electrode to enhance the structural stiffness. This stiff segment was then followed by a 1 mm flexible segment without a silicon backbone layer. The fabricated implants have tri-shanks with five recording sites (20 µm × 20 µm) and two vias of 40 µm × 40 µm on each shank. In vitro cytotoxicity tests of prototype implants revealed no adverse toxic effects on cells. Bench test impedance values were assessed, resulting in an average impedance value of ~2 MOmega at 1 KHz. For a 5 µm thick silicon backbone electrode, the stiffness of polyimide-based electrodes was increased ten times over that of electrodes without the silicon backbone layer. Furthermore, polyimide-based electrodes with 5 µm and 10 µm thick silicon backbone layer penetrated pia of rat brain without buckling that has been observed in implants without silicon reinforcement.

Tension amplification in tethered layers of bottle-brush polymers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leuty, Gary M.; Tsige, Mesfin; Grest, Gary S.

2016-02-26

In this paper, molecular dynamics simulations of a coarse-grained bead–spring model have been used to study the effects of molecular crowding on the accumulation of tension in the backbone of bottle-brush polymers tethered to a flat substrate. The number of bottle-brushes per unit surface area, Σ, as well as the lengths of the bottle-brush backbones N bb (50 ≤ N bb ≤ 200) and side chains N sc (50 ≤ N sc ≤ 200) were varied to determine how the dimensions and degree of crowding of bottle-brushes give rise to bond tension amplification along the backbone, especially near the substrate.more » From these simulations, we have identified three separate regimes of tension. For low Σ, the tension is due solely to intramolecular interactions and is dominated by the side chain repulsion that governs the lateral brush dimensions. With increasing Σ, the interactions between bottle-brush polymers induce compression of the side chains, transmitting increasing tension to the backbone. For large Σ, intermolecular side chain repulsion increases, forcing side chain extension and reorientation in the direction normal to the surface and transmitting considerable tension to the backbone.« less

An ``Alternating-Curvature'' Model for the Nanometer-scale Structure of the Nafion Ionomer, Based on Backbone Properties Detected by NMR

NASA Astrophysics Data System (ADS)

Schmidt-Rohr, Klaus; Chen, Q.

2006-03-01

The perfluorinated ionomer, Nafion, which consists of a (-CF2-)n backbone and charged side branches, is useful as a proton exchange membrane in H2/O2 fuel cells. A modified model of the nanometer-scale structure of hydrated Nafion will be presented. It features hydrated ionic clusters familiar from some previous models, but is based most prominently on pronounced backbone rigidity between branch points and limited orientational correlation of local chain axes. These features have been revealed by solid-state NMR measurements, which take advantage of fast rotations of the backbones around their local axes. The resulting alternating curvature of the backbones towards the hydrated clusters also better satisfies the requirement of dense space filling in solids. Simulations based on this ``alternating curvature'' model reproduce orientational correlation data from NMR, as well as scattering features such as the ionomer peak and the I(q) ˜ 1/q power law at small q values, which can be attributed to modulated cylinders resulting from the chain stiffness. The shortcomings of previous models, including Gierke's cluster model and more recent lamellar or bundle models, in matching all requirements imposed by the experimental data will be discussed.

Effects of counterion size and backbone rigidity on the dynamics of ionic polymer melts and glasses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fu, Yao; Bocharova, Vera; Ma, Mengze

Backbone rigidity, counterion size and the static dielectric constant affect the glass transition temperature, segmental relaxation time and decoupling between counterion and segmental dynamics in significant manners.

LETTER TO THE EDITOR: Backbones of traffic jams

NASA Astrophysics Data System (ADS)

Shikhar Gupta, Himadri; Ramaswamy, Ramakrishna

1996-11-01

We study the jam phase of the deterministic traffic model in two dimensions. Within the jam phase, there is a phase transition, from a self-organized jam (formed by initial synchronization followed by jamming), to a random-jam structure. The backbone of the jam is defined and used to analyse self-organization in the jam. The fractal dimension and interparticle correlations on the backbone indicate a continous phase transition at density 0305-4470/29/21/003/img1 with critical exponent 0305-4470/29/21/003/img2, which are characterized through simulations.

Replacement solvents for use in chemical synthesis

DOEpatents

Molnar, Linda K.; Hatton, T. Alan; Buchwald, Stephen L.

2001-05-15

Replacement solvents for use in chemical synthesis include polymer-immobilized solvents having a flexible polymer backbone and a plurality of pendant groups attached onto the polymer backbone, the pendant groups comprising a flexible linking unit bound to the polymer backbone and to a terminal solvating moiety. The polymer-immobilized solvent may be dissolved in a benign medium. Replacement solvents for chemical reactions for which tetrahydrofuran or diethyl may be a solvent include substituted tetrahydrofurfuryl ethers and substituted tetrahydro-3-furan ethers. The replacement solvents may be readily recovered from the reaction train using conventional methods.

The Impact of Acceptor-Acceptor Homocoupling on the Optoelectronic Properties and Photovoltaic Performance of PDTSQxff Low Bandgap Polymers.

PubMed

Pirotte, Geert; Kesters, Jurgen; Cardeynaels, Tom; Verstappen, Pieter; D'Haen, Jan; Lutsen, Laurence; Champagne, Benoît; Vanderzande, Dirk; Maes, Wouter

2018-04-22

Push-pull-type conjugated polymers applied in organic electronics do not always contain a perfect alternation of donor and acceptor building blocks. Misscouplings can occur, which have a noticeable effect on the device performance. In this work, the influence of homocoupling on the optoelectronic properties and photovoltaic performance of PDTSQx ff polymers is investigated, with a specific focus on the quinoxaline acceptor moieties. A homocoupled biquinoxaline segment is intentionally inserted in specific ratios during the polymerization. These homocoupled units cause a gradually blue-shifted absorption, while the highest occupied molecular orbital energy levels decrease only significantly upon the presence of 75-100% of homocouplings. Density functional theory calculations show that the homocoupled acceptor unit generates a twist in the polymer backbone, which leads to a decreased conjugation length and a reduced aggregation tendency. The virtually defect-free PDTSQx ff affords a solar cell efficiency of 5.4%, which only decreases substantially upon incorporating a homocoupling degree over 50%. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dissecting the relationship between protein structure and sequence variation

NASA Astrophysics Data System (ADS)

Shahmoradi, Amir; Wilke, Claus; Wilke Lab Team

2015-03-01

Over the past decade several independent works have shown that some structural properties of proteins are capable of predicting protein evolution. The strength and significance of these structure-sequence relations, however, appear to vary widely among different proteins, with absolute correlation strengths ranging from 0 . 1 to 0 . 8 . Here we present the results from a comprehensive search for the potential biophysical and structural determinants of protein evolution by studying more than 200 structural and evolutionary properties in a dataset of 209 monomeric enzymes. We discuss the main protein characteristics responsible for the general patterns of protein evolution, and identify sequence divergence as the main determinant of the strengths of virtually all structure-evolution relationships, explaining ~ 10 - 30 % of observed variation in sequence-structure relations. In addition to sequence divergence, we identify several protein structural properties that are moderately but significantly coupled with the strength of sequence-structure relations. In particular, proteins with more homogeneous back-bone hydrogen bond energies, large fractions of helical secondary structures and low fraction of beta sheets tend to have the strongest sequence-structure relation. BEACON-NSF center for the study of evolution in action.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, C.; Santschi, P; Roberts, K

Relatively recently, inorganic colloids have been invoked to reconcile the apparent contradictions between expectations based on classical dissolved-phase Pu transport and field observations of 'enhanced' Pu mobility (Kersting et al. Nature 1999, 397, 56-59). A new paradigm for Pu transport is mobilization and transport via biologically produced ligands. This study for the first time reports a new finding of Pu being transported, at sub-pM concentrations, by a cutin-like natural substance containing siderophore-like moieties and virtually all mobile Pu. Most likely, Pu is complexed by chelating groups derived from siderophores that are covalently bound to a backbone of cutin-derived soil degradationmore » products, thus revealing the history of initial exposure to Pu. Features such as amphiphilicity and small size make this macromolecule an ideal collector for actinides and other metals and a vector for their dispersal. Cross-linking to the hydrophobic domains (e.g., by polysaccharides) gives this macromolecule high mobility and a means of enhancing Pu transport. This finding provides a new mechanism for Pu transport through environmental systems that would not have been predicted by Pu transport models.« less

Controlled conjugated backbone twisting for an increased open-circuit voltage while having a high short-circuit current in poly(hexylthiophene) derivatives.

PubMed

Ko, Sangwon; Hoke, Eric T; Pandey, Laxman; Hong, Sanghyun; Mondal, Rajib; Risko, Chad; Yi, Yuanping; Noriega, Rodrigo; McGehee, Michael D; Brédas, Jean-Luc; Salleo, Alberto; Bao, Zhenan

2012-03-21

Conjugated polymers with nearly planar backbones have been the most commonly investigated materials for organic-based electronic devices. More twisted polymer backbones have been shown to achieve larger open-circuit voltages in solar cells, though with decreased short-circuit current densities. We systematically impose twists within a family of poly(hexylthiophene)s and examine their influence on the performance of polymer:fullerene bulk heterojunction (BHJ) solar cells. A simple chemical modification concerning the number and placement of alkyl side chains along the conjugated backbone is used to control the degree of backbone twisting. Density functional theory calculations were carried out on a series of oligothiophene structures to provide insights on how the sterically induced twisting influences the geometric, electronic, and optical properties. Grazing incidence X-ray scattering measurements were performed to investigate how the thin-film packing structure was affected. The open-circuit voltage and charge-transfer state energy of the polymer:fullerene BHJ solar cells increased substantially with the degree of twist induced within the conjugated backbone--due to an increase in the polymer ionization potential--while the short-circuit current decreased as a result of a larger optical gap and lower hole mobility. A controlled, moderate degree of twist along the poly(3,4-dihexyl-2,2':5',2''-terthiophene) (PDHTT) conjugated backbone led to a 19% enhancement in the open-circuit voltage (0.735 V) vs poly(3-hexylthiophene)-based devices, while similar short-circuit current densities, fill factors, and hole-carrier mobilities were maintained. These factors resulted in a power conversion efficiency of 4.2% for a PDHTT:[6,6]-phenyl-C(71)-butyric acid methyl ester (PC(71)BM) blend solar cell without thermal annealing. This simple approach reveals a molecular design avenue to increase open-circuit voltage while retaining the short-circuit current.

Modeling backbone flexibility to achieve sequence diversity: The design of novel alpha-helical ligands for Bcl-xL

PubMed Central

Fu, Xiaoran; Apgar, James R.; Keating, Amy E.

2007-01-01

Computational protein design can be used to select sequences that are compatible with a fixed-backbone template. This strategy has been used in numerous instances to engineer novel proteins. However, the fixed-backbone assumption severely restricts the sequence space that is accessible via design. For challenging problems, such as the design of functional proteins, this may not be acceptable. In this paper, we present a method for introducing backbone flexibility into protein design calculations and apply it to the design of diverse helical BH3 ligands that bind to the anti-apoptotic protein Bcl-xL, a member of the Bcl-2 protein family. We demonstrate how normal mode analysis can be used to sample different BH3 backbones, and show that this leads to a larger and more diverse set of low-energy solutions than can be achieved using a native high-resolution Bcl-xL complex crystal structure as a template. We tested several of the designed solutions experimentally and found that this approach worked well when normal mode calculations were used to deform a native BH3 helix structure, but less well when they were used to deform an idealized helix. A subsequent round of design and testing identified a likely source of the problem as inadequate sampling of the helix pitch. In all, we tested seventeen designed BH3 peptide sequences, including several point mutants. Of these, eight bound well to Bcl-xL and four others showed weak but detectable binding. The successful designs showed a diversity of sequences that would have been difficult or impossible to achieve using only a fixed backbone. Thus, introducing backbone flexibility via normal mode analysis effectively broadened the set of sequences identified by computational design, and provided insight into positions important for binding Bcl-xL. PMID:17597151

Efficiency of High Molecular Weight Backbone Degradable HPMA Copolymer – Prostaglandin E1 Conjugate in Promotion of Bone Formation in Ovariectomized Rats

PubMed Central

Pan, Huaizhong; Sima, Monika; Miller, Scott C.; Kopečková, Pavla; Yang, Jiyuan; Kopeček, Jindřich

2013-01-01

Multiblock, high molecular weight, linear, backbone degradable HPMA copolymer-prostaglandin E1 (PGE1) conjugate has been synthesized by RAFT polymerization mediated by a new bifunctional chain transfer agent (CTA), which contains an enzymatically degradable oligopeptide sequence flanked by two dithiobenzoate groups, followed by post-polymerization aminolysis and thiol-ene chain extension. The multiblock conjugate contains Asp8 as the bone-targeting moiety and enzymatically degradable bonds in the polymer backbone; in vivo degradation produces cleavage products that are below the renal threshold. Using an ovariectomized (OVX) rat model, the accumulation in bone and efficacy to promote bone formation was evaluated; low molecular weight conjugates served as control. The results indicated a higher accumulation in bone, greater enhancement of bone density, and higher plasma osteocalcin levels for the backbone degradable conjugate. PMID:23731780

Modeling helical proteins using residual dipolar couplings, sparse long-range distance constraints and a simple residue-based force field

PubMed Central

Eggimann, Becky L.; Vostrikov, Vitaly V.; Veglia, Gianluigi; Siepmann, J. Ilja

2013-01-01

We present a fast and simple protocol to obtain moderate-resolution backbone structures of helical proteins. This approach utilizes a combination of sparse backbone NMR data (residual dipolar couplings and paramagnetic relaxation enhancements) or EPR data with a residue-based force field and Monte Carlo/simulated annealing protocol to explore the folding energy landscape of helical proteins. By using only backbone NMR data, which are relatively easy to collect and analyze, and strategically placed spin relaxation probes, we show that it is possible to obtain protein structures with correct helical topology and backbone RMS deviations well below 4 Å. This approach offers promising alternatives for the structural determination of proteins in which nuclear Overha-user effect data are difficult or impossible to assign and produces initial models that will speed up the high-resolution structure determination by NMR spectroscopy. PMID:24639619

Small Angle Neutron Scattering (sans) Studies on "SIDE-END FIXED" and "SIDE-ON FIXED" Liquid Crystal Polymers

NASA Astrophysics Data System (ADS)

Hardouin, F.; Noirez, L.; Keller, P.; Leroux, N.; Cotton, J. P.

The following sections are included: * Introduction * Experimental * Results and discussion * Determination of the backbone conformation in the nematic and smectic A phases of "side-end fixed" L.C. polymethacrylates (PMA) or polyacrylates (PA) * Determination of the global and backbone conformation in the nematic and smectic A phases of "side-end fixed" L.C. polysiloxanes (PMS) * Determination of the backbone conformation in the unique nematic phase (without smectic A phase) or in the reentrant nematic phase (below smectic A phase) of "side-end fixed" L.C. polyacrylates (PA) * Determination of the global conformation in the nematic phase of "side-on fixed" L.C. polysiloxanes (PMS) * Determination of the global conformation in the nematic phase of "diluted side-on fixed" L.C. copolysiloxanes * Determination of the backbone conformation in the nematic phase of "side-on fixed" L.C. polyacrylates * Conclusions * References

Design of real-time voice over internet protocol system under bandwidth network

NASA Astrophysics Data System (ADS)

Zhang, Li; Gong, Lina

2017-04-01

With the increasing bandwidth of the network and network convergence accelerating, VoIP means of communication across the network is becoming increasingly popular phenomenon. The real-time identification and analysis for VOIP flow over backbone network become the urgent needs and research hotspot of network operations management. Based on this, the paper proposes a VoIP business management system over backbone network. The system first filters VoIP data stream over backbone network and further resolves the call signaling information and media voice. The system can also be able to design appropriate rules to complete real-time reduction and presentation of specific categories of calls. Experimental results show that the system can parse and process real-time backbone of the VoIP call, and the results are presented accurately in the management interface, VoIP-based network traffic management and maintenance provide the necessary technical support.

Pentopyranosyl Oligonucleotide Systems. Part 11: Systems with Shortened Backbones: D)-beta-Ribopyranosyl-(4 yields 3 )- and (L)-alpha - Lyxopyranosyl-(4 yields 3 )-oligonucleotides

NASA Technical Reports Server (NTRS)

Wippo, Harald; Reck, Folkert; Kudick, Rene; Ramaseshan, Mahesh; Ceulemans, Griet; Bolli, Martin; Krishnamurthy, Ramanarayanan; Eschenmoser, Albert

2001-01-01

The (L)-a-lyxopyranosyl-(4'yields 3')-oligonucleotide system-a member of a pentopyranosyl oligonucleotide family containing a shortened backbone-is capable of cooperative base-pairing and of cross-pairing with DNA and RNA. In contrast, corresponding (D)-beta-ribopyransoyl-(4' yields 3')-oligonucleotides do not show base-pairing under similar conditions. We conclude that oligonucleotide systems can violate the six-bonds-per-backbone-unit rule by having five bonds instead, if their vicinally bound phosphodiester bridges can assume an antiperiplanar conformation. An additional structural feature that seems relevant to the cross-pairing capability of the (L)-a-lyxopyranosyl-(4' yields 3')-oligonucleotide system is its (small) backbone/basepair axes inclination. An inclination which is similar to that in B-DNA seems to be a prerequisite for an oligonucleotide system s capability to cross-pair with DNA.

Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li+, Na+, K+ and Rb+ via Water-Mediated Hydrogen Bonding

PubMed Central

Savelyev, Alexey; MacKerell, Alexander D.

2015-01-01

Recently, we reported the differential impact of the monovalent cations Li+, Na+, K+ and Rb+ on DNA conformational properties. These were identified from variations in the calculated solution-state X-ray DNA spectra as a function of the ion type in the solvation buffer in MD simulations using our recently developed polarizable force field based on the classical Drude oscillator. Changes in the DNA structure were found to mainly involve variations in the minor groove width. Because minor groove dimensions vary significantly in protein-DNA complexes and have been shown to play a critical role in both specific and nonspecific DNA readout, understanding the origins of the observed differential DNA modulation by the first-group monovalent ions is of great biological importance. In the present study we show that the primary microscopic mechanism for the phenomenon is the formation of the water-mediated hydrogen bonds between solvated cations located inside the minor groove and simultaneously to two DNA strands, a process whose intensity and impact on DNA structure depends on both the type of the ion and DNA sequence. Additionally, it is shown that formation of such ion-DNA hydrogen bond complexes appreciably modulates the conformation of the backbone by increasing the population of the BII substate. Notably, the differential impact of the ions on DNA conformational behavior is only predicted by the Drude polarizable model for DNA, with virtually no effect observed from MD simulations utilizing the additive CHARMM36 model. Analysis of dipole moments of the water shows the Drude SWM4 model to possess high sensitivity to changes in the local environment, which indicates the important role of electronic polarization in the salt-dependent conformational properties. This also suggests that inclusion of polarization effects is required to model even relatively simple biological systems such as DNA in various ionic solutions. PMID:26575937

Complete Sequencing of pNDM-HK Encoding NDM-1 Carbapenemase from a Multidrug-Resistant Escherichia coli Strain Isolated in Hong Kong

PubMed Central

Ho, Pak Leung; Lo, Wai U.; Yeung, Man Kiu; Lin, Chi Ho; Chow, Kin Hung; Ang, Irene; Tong, Amy Hin Yan; Bao, Jessie Yun-Juan; Lok, Si; Lo, Janice Yee Chi

2011-01-01

Background The emergence of plasmid-mediated carbapenemases, such as NDM-1 in Enterobacteriaceae is a major public health issue. Since they mediate resistance to virtually all β-lactam antibiotics and there is often co-resistance to other antibiotic classes, the therapeutic options for infections caused by these organisms are very limited. Methodology We characterized the first NDM-1 producing E. coli isolate recovered in Hong Kong. The plasmid encoding the metallo-β-lactamase gene was sequenced. Principal Findings The plasmid, pNDM-HK readily transferred to E. coli J53 at high frequencies. It belongs to the broad host range IncL/M incompatibility group and is 88803 bp in size. Sequence alignment showed that pNDM-HK has a 55 kb backbone which shared 97% homology with pEL60 originating from the plant pathogen, Erwina amylovora in Lebanon and a 28.9 kb variable region. The plasmid backbone includes the mucAB genes mediating ultraviolet light resistance. The 28.9 kb region has a composite transposon-like structure which includes intact or truncated genes associated with resistance to β-lactams (bla TEM-1, bla NDM-1, Δbla DHA-1), aminoglycosides (aacC2, armA), sulphonamides (sul1) and macrolides (mel, mph2). It also harbors the following mobile elements: IS26, ISCR1, tnpU, tnpAcp2, tnpD, ΔtnpATn1 and insL. Certain blocks within the 28.9 kb variable region had homology with the corresponding sequences in the widely disseminated plasmids, pCTX-M3, pMUR050 and pKP048 originating from bacteria in Poland in 1996, in Spain in 2002 and in China in 2006, respectively. Significance The genetic support of NDM-1 gene suggests that it has evolved through complex pathways. The association with broad host range plasmid and multiple mobile genetic elements explain its observed horizontal mobility in multiple bacterial taxa. PMID:21445317

Protein backbone engineering as a strategy to advance foldamers toward the frontier of protein-like tertiary structure.

PubMed

Reinert, Zachary E; Horne, W Seth

2014-11-28

A variety of non-biological structural motifs have been incorporated into the backbone of natural protein sequences. In parallel work, diverse unnatural oligomers of de novo design (termed "foldamers") have been developed that fold in defined ways. In this Perspective article, we survey foundational studies on protein backbone engineering, with a focus on alterations made in the context of complex tertiary folds. We go on to summarize recent work illustrating the potential promise of these methods to provide a general framework for the construction of foldamer mimics of protein tertiary structures.

Protein-Backbone Thermodynamics across the Membrane Interface.

PubMed

Bereau, Tristan; Kremer, Kurt

2016-07-07

The thermodynamics of insertion of a protein in a membrane depends on the fine interplay between backbone and side-chain contributions interacting with the lipid environment. Using computer simulations, we probe how different descriptions of the backbone glycyl unit affect the thermodynamics of insertion of individual residues, dipeptides, and entire transmembrane helices. Due to the lack of reference data, we first introduce an efficient methodology to estimate atomistic potential of mean force (PMF) curves from a series of representative and uncorrelated coarse-grained (CG) snapshots. We find strong discrepancies between two CG models, Martini and PLUM, against reference atomistic PMFs and experiments. Atomistic simulations suggest a weak free energy of insertion between water and a POPC membrane for the glycyl unit, in overall agreement with experimental results despite severe assumptions in our calculations. We show that refining the backbone contribution in PLUM significantly improves the PMF of insertion of the WALP16 transmembrane peptide. An improper balance between the glycyl backbone and the attached side chain will lead to energetic artifacts, rationalizing Martini's overstabilization of WALP's adsorbed interfacial state. It illustrates difficulties associated with free-energy-based parametrizations of single-residue models, as the relevant free energy of partitioning used for force-field parametrization does not arise from the entire residue but rather the solvent-accessible chemical groups.

Effect of Backbone Chemistry on the Structure of Polyurea Films Deposited by Molecular Layer Deposition

DOE PAGES

Bergsman, David S.; Closser, Richard G.; Tassone, Christopher J.; ...

2017-01-01

An experimental investigation into the growth of polyurea films by molecular layer deposition was performed by examining trends in the growth rate, crystallinity, and orientation of chains as a function of backbone flexibility. Growth curves obtained for films containing backbones of aliphatic and phenyl groups indicate that an increase in backbone flexibility leads to a reduction in growth rate from 4 to 1 Å/cycle. Crystallinity measurements collected using grazing incidence X-ray diffraction and Fourier transform infrared spectroscopy suggest that some chains form paracrystalline, out-of-plane stacks of polymer segments with packing distances ranging from 4.4 to 3.7 Å depending on themore » monomer size. Diffraction intensity is largely a function of the homogeneity of the backbone. Near-edge X-ray absorption fine structure measurements for thin and thick samples show an average chain orientation of ~25° relative to the substrate across all samples, suggesting that changes in growth rate are not caused by differences in chain angle but instead may be caused by differences in the frequency of chain terminations. In conclusion, these results suggest a model of molecular layer deposition-based chain growth in which films consist of a mixture of upward growing chains and horizontally aligned layers of paracrystalline polymer segments.« less

The Graphical Representation of the Digital Astronaut Physiology Backbone

NASA Technical Reports Server (NTRS)

Briers, Demarcus

2010-01-01

This report summarizes my internship project with the NASA Digital Astronaut Project to analyze the Digital Astronaut (DA) physiology backbone model. The Digital Astronaut Project (DAP) applies integrated physiology models to support space biomedical operations, and to assist NASA researchers in closing knowledge gaps related to human physiologic responses to space flight. The DA physiology backbone is a set of integrated physiological equations and functions that model the interacting systems of the human body. The current release of the model is HumMod (Human Model) version 1.5 and was developed over forty years at the University of Mississippi Medical Center (UMMC). The physiology equations and functions are scripted in an XML schema specifically designed for physiology modeling by Dr. Thomas G. Coleman at UMMC. Currently it is difficult to examine the physiology backbone without being knowledgeable of the XML schema. While investigating and documenting the tags and algorithms used in the XML schema, I proposed a standard methodology for a graphical representation. This standard methodology may be used to transcribe graphical representations from the DA physiology backbone. In turn, the graphical representations can allow examination of the physiological functions and equations without the need to be familiar with the computer programming languages or markup languages used by DA modeling software.

Normal Mode Analysis of Polytheonamide B

NASA Astrophysics Data System (ADS)

Mori, Takaharu; Kokubo, Hironori; Shimizu, Hirofumi; Iwamoto, Masayuki; Oiki, Shigetoshi; Okamoto, Yuko

2007-09-01

Polytheonamide B is a linear 48-residue peptide which forms a single β-helix structure with alternating d- and l-amino acids and contains methylated and hydroxy variants of proteinogenic amino acids. To investigate the dynamical properties of polytheonamide B we perform the normal mode analysis. Root-mean-square displacements of all backbone atoms, root-mean-square fluctuations of the backbone dihedral angles (φ,\\psi), and correlation factors for the Cα atom fluctuations and for the dihedral angle fluctuations are calculated. The normal mode analysis reveals that polytheonamide B shows the elastic rod behavior in the very low-frequency regions and that librational motions of backbone amide planes have the modes with relatively low frequencies, which is relevant to the function of polytheonamide B. In addition, these librational motions occur almost independently and weakly anticorrelate with those of the hydrogen-bonded neighboring amide planes. Calculations of the backbone fluctuations show that the flexibility of polytheonamide B is roughly uniform over the entire helix. We compare our results with those of gramicidin A, the analogue of polytheonamide B, to discuss the structures and functions, and obtain some common features in the flexibilities and dynamics of the backbone atoms. These results present important clues for clarifying the function of polytheonamide B at the atomic level.

Charge transport properties of poly(dA)-poly(dT) DNA in variation of backbone disorder and amplitude of base-pair twisting motion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rahmi, Kinanti Aldilla, E-mail: kinanti.aldilla@ui.ac.id; Yudiarsah, Efta

By using tight binding Hamiltonian model, charge transport properties of poly(dA)-poly(dT) DNA in variation of backbone disorder and amplitude of base-pair twisting motion is studied. The DNA chain used is 32 base pairs long poly(dA)-poly(dT) molecule. The molecule is contacted to electrode at both ends. The influence of environment on charge transport in DNA is modeled as variation of backbone disorder. The twisting motion amplitude is taking into account by assuming that the twisting angle distributes following Gaussian distribution function with zero average and standard deviation proportional to square root of temperature and inversely proportional to the twisting motion frequency.more » The base-pair twisting motion influences both the onsite energy of the bases and electron hopping constant between bases. The charge transport properties are studied by calculating current using Landauer-Buttiker formula from transmission probabilities which is calculated by transfer matrix methods. The result shows that as the backbone disorder increases, the maximum current decreases. By decreasing the twisting motion frequency, the current increases rapidly at low voltage, but the current increases slower at higher voltage. The threshold voltage can increase or decrease with increasing backbone disorder and increasing twisting frequency.« less

Engineering botulinum neurotoxin domains for activation by toxin light chain.

PubMed

Stancombe, Patrick R; Masuyer, Geoffrey; Birch-Machin, Ian; Beard, Matthew; Foster, Keith A; Chaddock, John A; Acharya, K Ravi

2012-02-01

Targeted secretion inhibitors (TSI) are a new class of biopharmaceuticals designed from a botulinum neurotoxin protein scaffold. The backbone consists of the 50-kDa endopeptidase light chain and translocation domain (N-terminal portion of the heavy chain), lacks neuronal toxicity, but retains the ability to target cytoplasmic soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins. TSI are produced as single-chain proteins and then cleaved post-translationally to generate functional heterodimers. Precise proteolytic cleavage is essential to activate the protein to a dichain form. TSI are themselves highly specific proteases. We have exploited this activity to create self-activating enzymes by replacing the native proteolytic site with a substrate SNARE peptide for the TSI protease. We have also created cross-activating backbones. By replacing the proteolytic activation site in one backbone with the substrate SNARE peptide for another serotype, controlled activation is achieved. SNARE peptides encompassing the whole of the coiled-coil region enabled complete activation and assembly of the dichain backbone. These engineered TSI backbones are capable of translocating their enzymatic domains to target intracellular SNARE proteins. They are also investigative tools with which to further the understanding of endopeptidase activity of light chain in SNARE interactions. © 2011 Syntaxin Ltd. Journal compilation © 2011 FEBS.

Synthesis and characterization of poly-3-((2,5-hydroquinone)vinyl)-1H-pyrrole: investigation on backbone/pendant interactions in a conducting redox polymer.

PubMed

Huang, Hao; Karlsson, Christoffer; Strømme, Maria; Gogoll, Adolf; Sjödin, Martin

2017-04-19

We herein report the synthesis and electrochemical characterization of poly-3-((2,5-hydroquinone)vinyl)-1H-pyrrole, consisting of a polypyrrole backbone derivatized at the beta position by a vinyl-hydroquinone pendant group. The structure of the polymer was characterized by solid state NMR spectroscopy. The interactions between the polypyrrole backbone and the oxidized quinone or reduced hydroquinone pendant groups are probed by several in situ methods. In situ attenuated total reflectance-Fourier transform infrared spectroscopy shows a spectroscopic response from both the doping of the polymer backbone and the redox activity of the pendant groups. Using an in situ Electrochemical Quartz Crystal Microbalance we reveal that the polymer doping is unaffected by the pendant group redox chemistry, as opposed to previous reports. Despite the continuous doping the electrochemical conversion from the hydroquinone state to the quinone state results in a significant conductance drop, as observed by in situ conductivity measurements using an Interdigitated Array electrode set-up. Twisting of the conducting polymer backbone as a result of a decreased separation between pendant groups due to π-π stacking in the oxidized state is suggested as the cause of this conductance drop.

Building alternate protein structures using the elastic network model.

PubMed

Yang, Qingyi; Sharp, Kim A

2009-02-15

We describe a method for efficiently generating ensembles of alternate, all-atom protein structures that (a) differ significantly from the starting structure, (b) have good stereochemistry (bonded geometry), and (c) have good steric properties (absence of atomic overlap). The method uses reconstruction from a series of backbone framework structures that are obtained from a modified elastic network model (ENM) by perturbation along low-frequency normal modes. To ensure good quality backbone frameworks, the single force parameter ENM is modified by introducing two more force parameters to characterize the interaction between the consecutive carbon alphas and those within the same secondary structure domain. The relative stiffness of the three parameters is parameterized to reproduce B-factors, while maintaining good bonded geometry. After parameterization, violations of experimental Calpha-Calpha distances and Calpha-Calpha-Calpha pseudo angles along the backbone are reduced to less than 1%. Simultaneously, the average B-factor correlation coefficient improves to R = 0.77. Two applications illustrate the potential of the approach. (1) 102,051 protein backbones spanning a conformational space of 15 A root mean square deviation were generated from 148 nonredundant proteins in the PDB database, and all-atom models with minimal bonded and nonbonded violations were produced from this ensemble of backbone structures using the SCWRL side chain building program. (2) Improved backbone templates for homology modeling. Fifteen query sequences were each modeled on two targets. For each of the 30 target frameworks, dozens of improved templates could be produced In all cases, improved full atom homology models resulted, of which 50% could be identified blind using the D-Fire statistical potential. (c) 2008 Wiley-Liss, Inc.

Peptide models XLV: conformational properties of N-formyl-L-methioninamide and its relevance to methionine in proteins.

PubMed

Láng, András; Csizmadia, Imre G; Perczel, András

2005-02-15

The conformational space of the most biologically significant backbone folds of a suitable methionine peptide model was explored by density functional computational method. Using a medium [6-31G(d)] and a larger basis set [6-311++G(2d,2p)], the systematic exploration of low-energy backbone structures restricted for the "L-region" in the Ramachandran map of N-formyl-L-methioninamide results in conformers corresponding to the building units of an extended backbone structure (betaL), an inverse gamma-turn (gammaL), or a right-handed helical structure (alphaL). However, no poly-proline II type (epsilonL) fold was found, indicating that this conformer has no intrinsic stability, and highlighting the effect of molecular environment in stabilizing this backbone structure. This is in agreement with the abundance of the epsilonL-type backbone conformation of methionine found in proteins. Stability properties (DeltaE) and distinct backbone-side-chain interactions support the idea that specific intramolecular contacts are operative in the selection of the lowest energy conformers. Apart from the number of different folds, all stable conformers are within a 10 kcal x mol(-1) energy range, indicating the highly flexible behavior of methionine. This conformational feature can be important in supporting catalytic processes, facilitating protein folding and dimerization via metal ion binding. In both of the biological examples discussed (HIV-1 reverse transcriptase and PcoC copper-resistant protein), the conformational properties of Met residues were found to be of key importance. Spatial proximity to other types of residues or the same type of residue seems to be crucial for the structural integrity of a protein, whether Met is buried or exposed.

An efficient coordination protocol for wireless sensor networks

NASA Astrophysics Data System (ADS)

Paruchuri, Vamsi; Durresi, Arjan; Durresi, Mimoza; Barolli, Leonard

2005-10-01

Backbones infrastructures in wireless sensor networks reduce the communication overhead and energy consumption. In this paper, we present BackBone Routing (BBR), a fully distributed protocol for construction and rotation of backbone networks. BBR reduces energy consumption without significantly diminishing the capacity or connectivity of the network. Another key feature of BBR is its energy balancing nature by distributing the role of being Backbone Node among all the nodes. BBR builds on the observation that when a region of a shared-channel wireless network has a sufficient density of nodes, only a small number of them need be on at any time to forward traffic for active connections. Improvement in system lifetime due to BBR increases as the ratio of idle-to-sleep energy consumption increases, and increases as the density of the network increases. Our experiments show that BBR is more efficient in saving energy and extending network life without deteriorating network performance when compared with geographical shortest path routing.

NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A-T phosphoramidite building blocks.

PubMed

Schmidtgall, Boris; Höbartner, Claudia; Ducho, Christian

2015-01-01

Modifications of the nucleic acid backbone are essential for the development of oligonucleotide-derived bioactive agents. The NAA-modification represents a novel artificial internucleotide linkage which enables the site-specific introduction of positive charges into the otherwise polyanionic backbone of DNA oligonucleotides. Following initial studies with the introduction of the NAA-linkage at T-T sites, it is now envisioned to prepare NAA-modified oligonucleotides bearing the modification at X-T motifs (X = A, C, G). We have therefore developed the efficient and stereoselective synthesis of NAA-linked 'dimeric' A-T phosphoramidite building blocks for automated DNA synthesis. Both the (S)- and the (R)-configured NAA-motifs were constructed with high diastereoselectivities to furnish two different phosphoramidite reagents, which were employed for the solid phase-supported automated synthesis of two NAA-modified DNA oligonucleotides. This represents a significant step to further establish the NAA-linkage as a useful addition to the existing 'toolbox' of backbone modifications for the design of bioactive oligonucleotide analogues.

Interaction Enthalpy of Side Chain and Backbone Amides in Polyglutamine Solution Monomers and Fibrils.

PubMed

Punihaole, David; Jakubek, Ryan S; Workman, Riley J; Asher, Sanford A

2018-04-19

We determined an empirical correlation that relates the amide I vibrational band frequencies of the glutamine (Q) side chain to the strength of hydrogen bonding, van der Waals, and Lewis acid-base interactions of its primary amide carbonyl. We used this correlation to determine the Q side chain carbonyl interaction enthalpy (Δ H int ) in monomeric and amyloid-like fibril conformations of D 2 Q 10 K 2 (Q10). We independently verified these Δ H int values through molecular dynamics simulations that showed excellent agreement with experiments. We found that side chain-side chain and side chain-peptide backbone interactions in fibrils and monomers are more enthalpically favorable than are Q side chain-water interactions. Q10 fibrils also showed a more favorable Δ H int for side chain-side chain interactions compared to backbone-backbone interactions. This work experimentally demonstrates that interamide side chain interactions are important in the formation and stabilization of polyQ fibrils.

Conformations of peptoids in nanosheets result from the interplay of backbone energetics and intermolecular interactions.

PubMed

Edison, John R; Spencer, Ryan K; Butterfoss, Glenn L; Hudson, Benjamin C; Hochbaum, Allon I; Paravastu, Anant K; Zuckermann, Ronald N; Whitelam, Stephen

2018-05-29

The conformations adopted by the molecular constituents of a supramolecular assembly influence its large-scale order. At the same time, the interactions made in assemblies by molecules can influence their conformations. Here we study this interplay in extended flat nanosheets made from nonnatural sequence-specific peptoid polymers. Nanosheets exist because individual polymers can be linear and untwisted, by virtue of polymer backbone elements adopting alternating rotational states whose twists oppose and cancel. Using molecular dynamics and quantum mechanical simulations, together with experimental data, we explore the design space of flat nanostructures built from peptoids. We show that several sets of peptoid backbone conformations are consistent with their being linear, but the specific combination observed in experiment is determined by a combination of backbone energetics and the interactions made within the nanosheet. Our results provide a molecular model of the peptoid nanosheet consistent with all available experimental data and show that its structure results from a combination of intra- and intermolecular interactions.

Life estimation and analysis of dielectric strength, hydrocarbon backbone and oxidation of high voltage multi stressed EPDM composites

NASA Astrophysics Data System (ADS)

Khattak, Abraiz; Amin, Muhammad; Iqbal, Muhammad; Abbas, Naveed

2018-02-01

Micro and nanocomposites of ethylene propylene diene monomer (EPDM) are recently studied for different characteristics. Study on life estimation and effects of multiple stresses on its dielectric strength and backbone scission and oxidation is also vital for endorsement of these composites for high voltage insulation and other outdoor applications. In order to achieve these goals, unfilled EPDM and its micro and nanocomposites are prepared at 23 phr micro silica and 6 phr nanosilica loadings respectively. Prepared samples are energized at 2.5 kV AC voltage and subjected for a long time to heat, ultraviolet radiation, acid rain, humidity and salt fog in accelerated manner in laboratory. Dielectric strength, leakage current and intensity of saturated backbone and carbonyl group are periodically measured. Loss in dielectric strength, increase in leakage current and backbone degradation and oxidation were observed in all samples. These effects were least in the case of EPDM nanocomposite. The nanocomposite sample also demonstrated longest shelf life.

Electron-impact total ionization cross sections of DNA sugar-phosphate backbone and an additivity principle

NASA Technical Reports Server (NTRS)

Huo, Winifred M.; Dateo, Christopher E.

2005-01-01

The improved binary-encounter dipole (iBED) model [W.M. Huo, Phys. Rev. A64, 042719-1 (2001)l is used to study the total ionization cross sections of the DNA sugar-phosphate backbone by electron impact. Calculations using neutral fragments found that the total ionization cross sections of C3' - and C5', -deoxyribose-phospate, two conformers of the sugar-phosphate backbone, are close to each other. Furthermore, the sum of the ionization cross sections of the separate deoxyribose and phosphate fragments is in close agreement with the C3' - and C5" -deoxyribose-phospate cross sections, differing by less than 10%. The result implies that certain properties of the-DNA, like the total singly ionization cross section, are localized properties and a building-up or additivity principle may apply. This allows us to obtain accurate properties of larger molecular systems built up from the results of smaller subsystem fragments. Calculations are underway using a negatively charged sugar-phosphate backbone with a metal counter-ion.

No-Enclave Percolation Corresponds to Holes in the Cluster Backbone.

PubMed

Hu, Hao; Ziff, Robert M; Deng, Youjin

2016-10-28

The no-enclave percolation (NEP) model introduced recently by Sheinman et al. can be mapped to a problem of holes within a standard percolation backbone, and numerical measurements of such holes give the same size-distribution exponent τ=1.82(1) as found for the NEP model. An argument is given that τ=1+d_{B}/2≈1.822 for backbone holes, where d_{B} is the backbone dimension. On the other hand, a model of simple holes within a percolation cluster yields τ=1+d_{f}/2=187/96≈1.948, where d_{f} is the fractal dimension of the cluster, and this value is consistent with the experimental results of gel collapse of Sheinman et al., which give τ=1.91(6). This suggests that the gel clusters are of the universality class of percolation cluster holes. Both models give a discontinuous maximum hole size at p_{c}, signifying explosive percolation behavior.

Combining Digital Archives Content with Serious Game Approach to Create a Gamified Learning Experience

NASA Astrophysics Data System (ADS)

Shih, D.-T.; Lin, C. L.; Tseng, C.-Y.

2015-08-01

This paper presents an interdisciplinary to develop content-aware application that combines game with learning on specific categories of digital archives. The employment of content-oriented game enhances the gamification and efficacy of learning in culture education on architectures and history of Hsinchu County, Taiwan. The gamified form of the application is used as a backbone to support and provide a strong stimulation to engage users in learning art and culture, therefore this research is implementing under the goal of "The Digital ARt/ARchitecture Project". The purpose of the abovementioned project is to develop interactive serious game approaches and applications for Hsinchu County historical archives and architectures. Therefore, we present two applications, "3D AR for Hukou Old " and "Hsinchu County History Museum AR Tour" which are in form of augmented reality (AR). By using AR imaging techniques to blend real object and virtual content, the users can immerse in virtual exhibitions of Hukou Old Street and Hsinchu County History Museum, and to learn in ubiquitous computing environment. This paper proposes a content system that includes tools and materials used to create representations of digitized cultural archives including historical artifacts, documents, customs, religion, and architectures. The Digital ARt / ARchitecture Project is based on the concept of serious game and consists of three aspects: content creation, target management, and AR presentation. The project focuses on developing a proper approach to serve as an interactive game, and to offer a learning opportunity for appreciating historic architectures by playing AR cards. Furthermore, the card game aims to provide multi-faceted understanding and learning experience to help user learning through 3D objects, hyperlinked web data, and the manipulation of learning mode, and then effectively developing their learning levels on cultural and historical archives in Hsinchu County.

(Z)-2-(3-Chlorobenzylidene)-3,4-dihydro-N-(2-methoxyethyl)-3-oxo-2H-benzo[b][1,4]oxazine-6-carboxamide as GSK-3β inhibitor: Identification by virtual screening and its validation in enzyme- and cell-based assay.

PubMed

Joshi, Prashant; Gupta, Mehak; Vishwakarma, Ram A; Kumar, Ajay; Bharate, Sandip B

2017-06-01

Glycogen synthase kinase 3β (GSK-3β) is a widely investigated molecular target for numerous diseases including Alzheimer's disease, cancer, and diabetes mellitus. The present study was aimed to discover new scaffolds for GSK-3β inhibition, through protein structure-guided virtual screening approach. With the availability of large number of GSK-3β crystal structures with varying degree of RMSD in protein backbone and RMSF in side chain geometry, herein appropriate crystal structures were selected based on the characteristic ROC curve and percentage enrichment of actives. The validated docking protocol was employed to screen a library of 50,000 small molecules using molecular docking and binding affinity calculations. Based on the GLIDE docking score, Prime MMGB/SA binding affinity, and interaction pattern analysis, the top 50 ligands were selected for GSK-3β inhibition. (Z)-2-(3-chlorobenzylidene)-3,4-dihydro-N-(2-methoxyethyl)-3-oxo-2H-benzo[b][1,4]oxazine-6-carboxamide (F389-0663, 7) was identified as a potent inhibitor of GSK-3β with an IC 50 value of 1.6 μm. Further, GSK-3β inhibition activity was then investigated in cell-based assay. The treatment of neuroblastoma N2a cells with 12.5 μm of F389-0663 resulted in the significant increase in GSK-3β Ser9 levels, which is indicative of the GSK-3β inhibitory activity of a compound. The molecular dynamic simulations were carried out to understand the interactions of F389-0663 with GSK-3β protein. © 2016 John Wiley & Sons A/S.

ATM encryption testing

NASA Astrophysics Data System (ADS)

Capell, Joyce; Deeth, David

1996-01-01

This paper describes why encryption was selected by Lockheed Martin Missiles & Space as the means for securing ATM networks. The ATM encryption testing program is part of an ATM network trial provided by Pacific Bell under the California Research Education Network (CalREN). The problem being addressed is the threat to data security which results when changing from a packet switched network infrastructure to a circuit switched ATM network backbone. As organizations move to high speed cell-based networks, there is a break down in the traditional security model which is designed to protect packet switched data networks from external attacks. This is due to the fact that most data security firewalls filter IP packets, restricting inbound and outbound protocols, e.g. ftp. ATM networks, based on cell-switching over virtual circuits, does not support this method for restricting access since the protocol information is not carried by each cell. ATM switches set up multiple virtual connections, thus there is no longer a single point of entry into the internal network. The problem is further complicated by the fact that ATM networks support high speed multi-media applications, including real time video and video teleconferencing which are incompatible with packet switched networks. The ability to restrict access to Lockheed Martin networks in support of both unclassified and classified communications is required before ATM network technology can be fully deployed. The Lockheed Martin CalREN ATM testbed provides the opportunity to test ATM encryption prototypes with actual applications to assess the viability of ATM encryption methodologies prior to installing large scale ATM networks. Two prototype ATM encryptors are being tested: (1) `MILKBUSH' a prototype encryptor developed by NSA for transmission of government classified data over ATM networks, and (2) a prototype ATM encryptor developed by Sandia National Labs in New Mexico, for the encryption of proprietary data.

The Completely Sequenced Plasmid pEST4011 Contains a Novel IncP1 Backbone and a Catabolic Transposon Harboring tfd Genes for 2,4-Dichlorophenoxyacetic Acid Degradation

PubMed Central

Vedler, Eve; Vahter, Merle; Heinaru, Ain

2004-01-01

The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium Achromobacter xylosoxidans subsp. denitrificans strain EST4002 contains plasmid pEST4011. This plasmid ensures its host a stable 2,4-D+ phenotype. We determined the complete 76,958-bp nucleotide sequence of pEST4011. This plasmid is a deletion and duplication derivative of pD2M4, the 95-kb highly unstable laboratory ancestor of pEST4011, and was self-generated during different laboratory manipulations performed to increase the stability of the 2,4-D+ phenotype of the original strain, strain D2M4(pD2M4). The 47,935-bp catabolic region of pEST4011 forms a transposon-like structure with identical copies of the hybrid insertion element IS1071::IS1471 at the two ends. The catabolic regions of pEST4011 and pJP4, the best-studied 2,4-D-degradative plasmid, both contain homologous, tfd-like genes for complete 2,4-D degradation, but they have little sequence similarity other than that. The backbone genes of pEST4011 are most similar to the corresponding genes of broad-host-range self-transmissible IncP1 plasmids. The backbones of the other three IncP1 catabolic plasmids that have been sequenced (the 2,4-D-degradative plasmid pJP4, the haloacetate-catabolic plasmid pUO1, and the atrazine-catabolic plasmid pADP-1) are nearly identical to the backbone of R751, the archetype plasmid of the IncP1 β subgroup. We show that despite the overall similarity in plasmid organization, the pEST4011 backbone is sufficiently different (51 to 86% amino acid sequence identity between individual backbone genes) from the backbones of members of the three IncP1 subgroups (the α, β, and γ subgroups) that it belongs to a new IncP1subgroup, the δ subgroup. This conclusion was also supported by a phylogenetic analysis of the trfA2, korA, and traG gene products of different IncP1 plasmids. PMID:15489427

Polyolefin backbone substitution in binders for low temperature powder injection moulding feedstocks.

PubMed

Hausnerova, Berenika; Kuritka, Ivo; Bleyan, Davit

2014-02-27

This paper reports the substitution of polyolefin backbone binder components with low melting temperature carnauba wax for powder injection moulding applications. The effect of various binder compositions of Al₂O₃ feedstock on thermal degradation parameters is investigated by thermogravimetric analysis. Within the experimental framework 29 original feedstock compositions were prepared and the superiority of carnauba wax over the polyethylene binder backbone was demonstrated in compositions containing polyethylene glycol as the initial opening agent and governing the proper mechanism of the degradation process. Moreover, the replacement of synthetic polymer by the natural wax contributes to an increase of environmental sustainability of modern industrial technologies.

A discrete search algorithm for finding the structure of protein backbones and side chains.

PubMed

Sallaume, Silas; Martins, Simone de Lima; Ochi, Luiz Satoru; Da Silva, Warley Gramacho; Lavor, Carlile; Liberti, Leo

2013-01-01

Some information about protein structure can be obtained by using Nuclear Magnetic Resonance (NMR) techniques, but they provide only a sparse set of distances between atoms in a protein. The Molecular Distance Geometry Problem (MDGP) consists in determining the three-dimensional structure of a molecule using a set of known distances between some atoms. Recently, a Branch and Prune (BP) algorithm was proposed to calculate the backbone of a protein, based on a discrete formulation for the MDGP. We present an extension of the BP algorithm that can calculate not only the protein backbone, but the whole three-dimensional structure of proteins.

Effect of Pendant Side-Chain Sterics and Dipole Forces on Short Range Ordering in Random Polyelectrolytes

NASA Astrophysics Data System (ADS)

Nwosu, Chinomso; Pandey, Tara; Herring, Andrew; Coughlin, Edward; University of Massachusetts, Amherst Collaboration; Colorado School of Mines Collaboration

Backbone-to-backbone spacing in polymers is known to be dictated by the length of the pendant side-chains. Dipole forces in random polyelectrolytes lead to ionic clusters with a characteristic spacing that can be observed by SAXS. Repulsion due to side-chain sterics will compete with dipole forces driving cluster formation in random polyelectrolytes. A model study on short range order in anion exchange membranes (AEMs) of quaternized P4VP-ran-PI is presented. Quaternization of P4VP with alkyl bromides having different numbers of carbons, CnBr, introduces pendant side-chains as well as charges. X-ray scattering performed on PQ4VP-ran-PI(CnBr) show that when n <5 the dipole forces dominate leading to the formation of ionic clusters. However, when n >4, the chains remain separated due to sterics, forming a distinct backbone-to-backbone spacing morphology. For n=3, both dipole clustering and backbone spacing can coexist. Crosslinking of the isoprene units increased the coexistence window from n=3 to n=6. Impedance measurements show that a maximum conductivity of 110mS/cm was obtained for PQ4VP-ran-PI(C3Br). A discussion on short range order due to competition, or counter balancing, of steric repulsion and dipole forces will be presented. US Army MURI project (W911NF1010520).

Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis

NASA Astrophysics Data System (ADS)

Naritomi, Yusuke; Fuchigami, Sotaro

2013-12-01

We recently proposed the method of time-structure based independent component analysis (tICA) to examine the slow dynamics involved in conformational fluctuations of a protein as estimated by molecular dynamics (MD) simulation [Y. Naritomi and S. Fuchigami, J. Chem. Phys. 134, 065101 (2011)]. Our previous study focused on domain motions of the protein and examined its dynamics by using rigid-body domain analysis and tICA. However, the protein changes its conformation not only through domain motions but also by various types of motions involving its backbone and side chains. Some of these motions might occur on a slow time scale: we hypothesize that if so, we could effectively detect and characterize them using tICA. In the present study, we investigated slow dynamics of the protein backbone using MD simulation and tICA. The selected target protein was lysine-, arginine-, ornithine-binding protein (LAO), which comprises two domains and undergoes large domain motions. MD simulation of LAO in explicit water was performed for 1 μs, and the obtained trajectory of Cα atoms in the backbone was analyzed by tICA. This analysis successfully provided us with slow modes for LAO that represented either domain motions or local movements of the backbone. Further analysis elucidated the atomic details of the suggested local motions and confirmed that these motions truly occurred on the expected slow time scale.

Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis.

PubMed

Hamelberg, Donald; Shen, Tongye; McCammon, J Andrew

2005-02-16

The presence of serine/threonine-proline motifs in proteins provides a conformational switching mechanism of the backbone through the cis/trans isomerization of the peptidyl-prolyl (omega) bond. The reversible phosphorylation of the serine/threonine modulates this switching in regulatory proteins to alter signaling and transcription. However, the mechanism is not well understood. This is partly because cis/trans isomerization is a very slow process and, hence, difficult to study. We have used our accelerated molecular dynamics method to study the cis/trans proline isomerization, preferred backbone conformation of a serine-proline motif, and the effects of phosphorylation of the serine residue. We demonstrate that, unlike normal molecular dynamics, the accelerated molecular dynamics allows for the system to escape very easily from the trans isomer to cis isomer, and vice versa. Moreover, for both the unphosphorylated and phosphorylated peptides, the statistical thermodynamic properties are recaptured, and the results are consistent with experimental values. Isomerization of the proline omega bond is shown to be asymmetric and strongly dependent on the psi backbone angle before and after phosphorylation. The rates of escape decrease after phosphorylation. Also, the alpha-helical backbone conformation is more favored after phosphorylation. This accelerated molecular dynamics approach provides a general approach for enhancing the conformational transitions of molecular systems without having prior knowledge of the location of the minima and barriers on the potential-energy landscape.

ROMP- and RAFT-Based Guanidinium-Containing Polymers as Scaffolds for Protein Mimic Synthesis.

PubMed

Sarapas, Joel M; Backlund, Coralie M; deRonde, Brittany M; Minter, Lisa M; Tew, Gregory N

2017-05-17

Cell-penetrating peptides are an important class of molecules with promising applications in bioactive cargo delivery. A diverse series of guanidinium-containing polymeric cell-penetrating peptide mimics (CPPMs) with varying backbone chemistries was synthesized and assessed for delivery of both GFP and fluorescently tagged siRNA. Specifically, we examined CPPMs based on norbornene, methacrylate, and styrene backbones to determine how backbone structure impacted internalization of these two cargoes. Either charge content or degree of polymerization was held constant at 20, with diguanidinium norbornene molecules being polymerized to both 10 and 20 repeat units. Generally, homopolymer CPPMs delivered low amounts of siRNA into Jurkat T cells, with no apparent backbone dependence; however, by adding a short hydrophobic methyl methacrylate block to the guanidinium-rich methacrylate polymer, siRNA delivery to nearly the entire cell population was achieved. Protein internalization yielded similar results for most of the CPPMs, though the block polymer was unable to deliver proteins. In contrast, the styrene-based CPPM yielded the highest internalization for GFP (≈40 % of cells affected), showing that indeed backbone chemistry impacts protein delivery, specifically through the incorporation of an aromatic group. These results demonstrate that an understanding of how polymer structure affects cargo-dependent internalization is critical to designing new, more effective CPPMs. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multimedia And Internetworking Architecture Infrastructure On Interactive E-Learning System

NASA Astrophysics Data System (ADS)

Indah, K. A. T.; Sukarata, G.

2018-01-01

Interactive e-learning is a distance learning method that involves information technology, electronic system or computer as one means of learning system used for teaching and learning process that is implemented without having face to face directly between teacher and student. A strong dependence on emerging technologies greatly influences the way in which the architecture is designed to produce a powerful interactive e-learning network. In this paper analyzed an architecture model where learning can be done interactively, involving many participants (N-way synchronized distance learning) using video conferencing technology. Also used broadband internet network as well as multicast techniques as a troubleshooting method for bandwidth usage can be efficient.

Animals without Backbones: The Invertebrate Story. Grade Level 5-9.

ERIC Educational Resources Information Center

Jerome, Brian; Fuqua, Paul

This guide, when used in tandem with the videotape "Animals Without Backbones," helps students learn about invertebrates. These materials promote hands-on discovery and learning. The guide is composed of six curriculum-based teaching units: (1) "Getting Started"; (2) "Porifera"; (3) "Cnidarians"; (4) "Worms"; (5) "Mollusks"; (6) "Arthropods"; and…

ExScal Backbone Network Architecture

DTIC Science & Technology

2005-01-01

802.11 battery powered nodes was laid over the sensor network. We adopted the Stargate platform for the backbone tier to serve as the basis for...its head. XSS Hardware and Network: XSS stands for eXtreme Scaling Stargate . A stargate is a linux-based single board computer. It has a 400 MHz

Southwest Virginia Community College Technology Master Plan.

ERIC Educational Resources Information Center

Pruett, Teresa

This document describes Southwest Virginia Community College's (SVCC's) general technology plan. Goals include: (1) connecting all on-campus buildings with a fiber backbone; (2) connecting all user spaces to this backbone with high-speed lines to form an integrated information infrastructure known as SVCCNet; (3) providing workstations for college…

Heterogeneity to Homogeneity: Synthesis, Base Pairing, and Ligation Studies of 4',3'-XyluloNA/RNA and TNA/RNA Chimeric Sequences

NASA Astrophysics Data System (ADS)

Bhowmik, S.; Stoop, M.; Krishnamurthy, R.

2017-07-01

Based on the reality of "prebiotic clutter," we herein present an alternate model for pre-RNA to RNA transition, which starts, not with homogeneous-backbone system, but rather with mixtures of heterogeneous-backbone of chimeric "pre-RNA/RNA."

Conformational diversity and computational enzyme design

PubMed Central

Lassila, Jonathan K.

2010-01-01

The application of computational protein design methods to the design of enzyme active sites offers potential routes to new catalysts and new reaction specificities. Computational design methods have typically treated the protein backbone as a rigid structure for the sake of computational tractability. However, this fixed-backbone approximation introduces its own special challenges for enzyme design and it contrasts with an emerging picture of natural enzymes as dynamic ensembles with multiple conformations and motions throughout a reaction cycle. This review considers the impact of conformational variation and dynamics on computational enzyme design and it highlights new approaches to addressing protein conformational diversity in enzyme design including recent advances in multistate design, backbone flexibility, and computational library design. PMID:20829099

Using Excel To Study The Relation Between Protein Dihedral Angle Omega And Backbone Length

NASA Astrophysics Data System (ADS)

Shew, Christopher; Evans, Samari; Tao, Xiuping

How to involve the uninitiated undergraduate students in computational biophysics research? We made use of Microsoft Excel to carry out calculations of bond lengths, bond angles and dihedral angles of proteins. Specifically, we studied protein backbone dihedral angle omega by examining how its distribution varies with the length of the backbone length. It turns out Excel is a respectable tool for this task. An ordinary current-day desktop or laptop can handle the calculations for midsized proteins in just seconds. Care has to be taken to enter the formulas for the spreadsheet column after column to minimize the computing load. Supported in part by NSF Grant #1238795.

Oligonucleotide labeling methods. 3. Direct labeling of oligonucleotides employing a novel, non-nucleosidic, 2-aminobutyl-1,3-propanediol backbone.

PubMed Central

Nelson, P S; Kent, M; Muthini, S

1992-01-01

Novel CE-phosphoramidite (7a-e) and CPG (8a, c, d, e) reagents have been prepared from a unique 2-aminobutyl-1,3-propanediol backbone. The reagents have been used to directly label oligonucleotides with fluorescein, acridine, and biotin via automated DNA synthesis. The versatile 2-aminobutyl-1,3-propanediol backbone allows for labeling at any position (5', internal, and 3') during solid phase oligonucleotide synthesis. Multiple labels can be achieved by repetitive coupling cycles. Furthermore, the 3-carbon atom internucleotide phosphate distance is retained when inserted internally. Using this method, individual oligonucleotides possessing two and three different reporter molecules have been prepared. PMID:1475185

Mesoscopic description of random walks on combs

NASA Astrophysics Data System (ADS)

Méndez, Vicenç; Iomin, Alexander; Campos, Daniel; Horsthemke, Werner

2015-12-01

Combs are a simple caricature of various types of natural branched structures, which belong to the category of loopless graphs and consist of a backbone and branches. We study continuous time random walks on combs and present a generic method to obtain their transport properties. The random walk along the branches may be biased, and we account for the effect of the branches by renormalizing the waiting time probability distribution function for the motion along the backbone. We analyze the overall diffusion properties along the backbone and find normal diffusion, anomalous diffusion, and stochastic localization (diffusion failure), respectively, depending on the characteristics of the continuous time random walk along the branches, and compare our analytical results with stochastic simulations.

Negative Differential Conductance in Polyporphyrin Oligomers with Nonlinear Backbones.

PubMed

Kuang, Guowen; Chen, Shi Zhang; Yan, Linghao; Chen, Ke Qiu; Shang, Xuesong; Liu, Pei Nian; Lin, Nian

2018-01-17

We study negative differential conductance (NDC) effects in polyporphyrin oligomers with nonlinear backbones. Using a low-temperature scanning tunneling microscope, we selectively controlled the charge transport path in single oligomer wires. We observed robust NDC when charge passed through a T-shape junction, bistable NDC when charge passed through a 90° kink and no NDC when charge passed through a 120° kink. Aided by density functional theory with nonequilibrium Green's functions simulations, we attributed this backbone-dependent NDC to bias-modulated hybridization of the electrode states with the resonant transport molecular orbital. We argue this mechanism is generic in molecular systems, which opens a new route of designing molecular NDC devices.

Ultraviolet absorbing copolymers

DOEpatents

Gupta, Amitava; Yavrouian, Andre H.

1982-01-01

Photostable and weather stable absorping copolymers have been prepared from acrylic esters such as methyl methacrylate containing 0.1 to 5% of an 2-hydroxy-allyl benzophenone, preferably the 4,4' dimethoxy derivative thereof. The pendant benzophenone chromophores protect the acrylic backbone and when photoexcited do not degrade the ester side chain, nor abstract hydrogen from the backbone.

Effect of Backbone Design on Hybridization Thermodynamics of Oligo-nucleic Acids: A Coarse-Grained Molecular Dynamics Simulation Study

NASA Astrophysics Data System (ADS)

Ghobadi, Ahmadreza F.; Jayaraman, Arthi

DNA hybridization is the basis of various bio-nano technologies, such as DNA origami and assembly of DNA-functionalized nanoparticles. A hybridized double stranded (ds) DNA is formed when complementary nucleobases on hybridizing strands exhibit specific and directional hydrogen bonds through canonical Watson-Crick base-pairing interactions. In recent years, the need for cheaper alternatives and significant synthetic advances have driven design of DNA mimics with new backbone chemistries. However, a fundamental understanding of how these backbone modifications in the oligo-nucleic acids impact the hybridization and melting behavior of the duplex is still lacking. In this talk, we present our recent findings on impact of varying backbone chemistry on hybridization of oligo-nucleic acid duplexes. We use coarse-grained molecular dynamics simulations to isolate the effect of strand flexibility, electrostatic interactions and nucleobase spacing on the melting curves for duplexes with various strand sequences and concentrations. Since conjugation of oligo-nucleic acids with polymers serve as building blocks for thermo-responsive polymer networks and gels, we also present the effect of such conjugation on hybridization thermodynamics and polymer conformation.

Combined quantum-mechanics/molecular-mechanics dynamics simulation of A-DNA double strands irradiated by ultra-low-energy carbon ions

NASA Astrophysics Data System (ADS)

Ngaojampa, C.; Nimmanpipug, P.; Yu, L. D.; Anuntalabhochai, S.; Lee, V. S.

2011-02-01

In order to promote understanding of the fundamentals of ultra-low-energy ion interaction with DNA, molecular dynamics simulations using combined quantum-mechanics/molecular-mechanics of poly-AT and poly-GC A-DNA double strands irradiated by <200 eV carbon ions were performed to investigate the molecular implications of mutation bias. The simulations were focused on the responses of the DNA backbones and nitrogenous bases to irradiation. Analyses of the root mean square displacements of the backbones and non-hydrogen atoms of base rings of the simulated DNA structure after irradiation revealed a potential preference of DNA double strand separation, dependent on the irradiating energy. The results show that for the backbones, the large difference in the displacement between poly-GC and poly-AT in the initial time period could be the reason for the backbone breakage; for the nitrogenous base pairs, A-T is 30% more sensitive or vulnerable to ion irradiation than G-C, demonstrating a preferential, instead of random, effect of irradiation-induced mutation.

Oxygen K edge scattering from bulk comb diblock copolymer reveals extended, ordered backbones above lamellar order-disorder transition

DOE PAGES

Kortright, Jeffrey Barrett; Sun, Jing; Spencer, Ryan K.; ...

2016-12-14

The evolution of molecular morphology in bulk samples of comb diblock copolymer pNdc 12-b-pNte 21 across the lamellar order-disorder transition (ODT) is studied using resonant x-ray scattering at the oxygen K edge, with the goal of determining whether the molecules remain extended or collapse above the ODT. The distinct spectral resonances of carbonyl oxygen on the backbone and ether oxygen in the pNte side chains combine with their different site symmetry within the molecule to yield strong differences in bulk structural sensitivity at all temperatures. Comparison with simple models for the disordered phase clearly reveals that disordering at the ODTmore » corresponds to loss of positional order of molecules with extended backbones that retain orientational order, rather than backbone collapse into a locally isotropic disordered phase. This conclusion is facilitated directly by the distinct structural sensitivity at the two resonances. Lastly, we discuss the roles of depolarized scattering in enhancing this sensitivity, and background fluorescence in limiting dynamic range, in oxygen resonant scattering.« less

Integrating quantum key distribution with classical communications in backbone fiber network.

PubMed

Mao, Yingqiu; Wang, Bi-Xiao; Zhao, Chunxu; Wang, Guangquan; Wang, Ruichun; Wang, Honghai; Zhou, Fei; Nie, Jimin; Chen, Qing; Zhao, Yong; Zhang, Qiang; Zhang, Jun; Chen, Teng-Yun; Pan, Jian-Wei

2018-03-05

Quantum key distribution (QKD) provides information-theoretic security based on the laws of quantum mechanics. The desire to reduce costs and increase robustness in real-world applications has motivated the study of coexistence between QKD and intense classical data traffic in a single fiber. Previous works on coexistence in metropolitan areas have used wavelength-division multiplexing, however, coexistence in backbone fiber networks remains a great experimental challenge, as Tbps data of up to 20 dBm optical power is transferred, and much more noise is generated for QKD. Here we present for the first time, to the best of our knowledge, the integration of QKD with a commercial backbone network of 3.6 Tbps classical data at 21 dBm launch power over 66 km fiber. With 20 GHz pass-band filtering and large effective core area fibers, real-time secure key rates can reach 4.5 kbps and 5.1 kbps for co-propagation and counter-propagation at the maximum launch power, respectively. This demonstrates feasibility and represents an important step towards building a quantum network that coexists with the current backbone fiber infrastructure of classical communications.

Golden rule for buttressing vulnerable soluble proteins.

PubMed

Fernández, Ariel; Berry, R Stephen

2010-05-07

Local weaknesses in the structure of soluble proteins have received little attention. The structure may be inherently weak at sites where hydration of the protein backbone is locally hampered by formation of an intramolecular hydrogen bond which in turn is not fully stabilized through burial within a hydrophobic environment. The result is insufficient compensation for the thermodynamic cost of dehydrating the backbone polar groups. This work shows that these structural deficiencies, the unburied backbone hydrogen bonds, are compensated in natural proteins by disulfide bonds that are needed to maintain the structural integrity. Examination of all PDB-reported soluble structures reveals that, after suitable normalization, the number of disulfide bonds, X, correlates tightly with the number of unburied backbone hydrogen bonds, Y, beyond the baseline level Y = 20, revealing a simple balance relation: Y = 5X + 20. This equation introduces a 1:5 ratio associated with the buttressing of soluble proteins with structural deficiencies. The results are justified on thermodynamic grounds and have implications for biomolecular engineering as they introduce two constants of universal applicability determining the architecture of soluble proteins.

Direct observation of the oxidation of DNA bases by phosphate radicals formed under radiation: a model of the backbone-to-base hole transfer.

PubMed

Ma, Jun; Marignier, Jean-Louis; Pernot, Pascal; Houée-Levin, Chantal; Kumar, Anil; Sevilla, Michael D; Adhikary, Amitava; Mostafavi, Mehran

2018-05-30

In irradiated DNA, by the base-to-base and backbone-to-base hole transfer processes, the hole (i.e., the unpaired spin) localizes on the most electropositive base, guanine. Phosphate radicals formed via ionization events in the DNA-backbone must play an important role in the backbone-to-base hole transfer process. However, earlier studies on irradiated hydrated DNA, on irradiated DNA-models in frozen aqueous solution and in neat dimethyl phosphate showed the formation of carbon-centered radicals and not phosphate radicals. Therefore, to model the backbone-to-base hole transfer process, we report picosecond pulse radiolysis studies of the reactions between H2PO4˙ with the DNA bases - G, A, T, and C in 6 M H3PO4 at 22 °C. The time-resolved observations show that in 6 M H3PO4, H2PO4˙ causes the one-electron oxidation of adenine, guanine and thymine, by forming the cation radicals via a single electron transfer (SET) process; however, the rate constant of the reaction of H2PO4˙ with cytosine is too low (<107 L mol-1 s-1) to be measured. The rates of these reactions are influenced by the protonation states and the reorganization energies of the base radicals and of the phosphate radical in 6 M H3PO4.

Cooperative UAV-Based Communications Backbone for Sensor Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roberts, R S

2001-10-07

The objective of this project is to investigate the use of unmanned air vehicles (UAVs) as mobile, adaptive communications backbones for ground-based sensor networks. In this type of network, the UAVs provide communication connectivity to sensors that cannot communicate with each other because of terrain, distance, or other geographical constraints. In these situations, UAVs provide a vertical communication path for the sensors, thereby mitigating geographic obstacles often imposed on networks. With the proper use of UAVs, connectivity to a widely disbursed sensor network in rugged terrain is readily achieved. Our investigation has focused on networks where multiple cooperating UAVs aremore » used to form a network backbone. The advantage of using multiple UAVs to form the network backbone is parallelization of sensor connectivity. Many widely spaced or isolated sensors can be connected to the network at once using this approach. In these networks, the UAVs logically partition the sensor network into sub-networks (subnets), with one UAV assigned per subnet. Partitioning the network into subnets allows the UAVs to service sensors in parallel thereby decreasing the sensor-to-network connectivity. A UAV services sensors in its subnet by flying a route (path) through the subnet, uplinking data collected by the sensors, and forwarding the data to a ground station. An additional advantage of using multiple UAVs in the network is that they provide redundancy in the communications backbone, so that the failure of a single UAV does not necessarily imply the loss of the network.« less

Orientation Preferences of Backbone Secondary Amide Functional Groups in Peptide Nucleic Acid Complexes: Quantum Chemical Calculations Reveal an Intrinsic Preference of Cationic D-Amino Acid-Based Chiral PNA Analogues for the P-form

PubMed Central

Topham, Christopher M.; Smith, Jeremy C.

2007-01-01

Geometric descriptions of nonideal interresidue hydrogen bonding and backbone-base water bridging in the minor groove are established in terms of polyamide backbone carbonyl group orientation from analyses of residue junction conformers in experimentally determined peptide nucleic acid (PNA) complexes. Two types of interresidue hydrogen bonding are identified in PNA conformers in heteroduplexes with nucleic acids that adopt A-like basepair stacking. Quantum chemical calculations on the binding of a water molecule to an O2 base atom in glycine-based PNA thymine dimers indicate that junctions modeled with P-form backbone conformations are lower in energy than a dimer comprising the predominant conformation observed in A-like helices. It is further shown in model systems that PNA analogs based on D-lysine are better able to preorganize in a conformation exclusive to P-form helices than is glycine-based PNA. An intrinsic preference for this conformation is also exhibited by positively charged chiral PNA dimers carrying 3-amino-D-alanine or 4-aza-D-leucine residue units that provide for additional rigidity by side-chain hydrogen bonding to the backbone carbonyl oxygen. Structural modifications stabilizing P-form helices may obviate the need for large heterocycles to target DNA pyrimidine bases via PNA·DNA-PNA triplex formation. Quantum chemical modeling methods are used to propose candidate PNA Hoogsteen strand designs. PMID:17071666

Identification of critical regulatory genes in cancer signaling network using controllability analysis

NASA Astrophysics Data System (ADS)

Ravindran, Vandana; Sunitha, V.; Bagler, Ganesh

2017-05-01

Cancer is characterized by a complex web of regulatory mechanisms which makes it difficult to identify features that are central to its control. Molecular integrative models of cancer, generated with the help of data from experimental assays, facilitate use of control theory to probe for ways of controlling the state of such a complex dynamic network. We modeled the human cancer signaling network as a directed graph and analyzed it for its controllability, identification of driver nodes and their characterization. We identified the driver nodes using the maximum matching algorithm and classified them as backbone, peripheral and ordinary based on their role in regulatory interactions and control of the network. We found that the backbone driver nodes were key to driving the regulatory network into cancer phenotype (via mutations) as well as for steering into healthy phenotype (as drug targets). This implies that while backbone genes could lead to cancer by virtue of mutations, they are also therapeutic targets of cancer. Further, based on their impact on the size of the set of driver nodes, genes were characterized as indispensable, dispensable and neutral. Indispensable nodes within backbone of the network emerged as central to regulatory mechanisms of control of cancer. In addition to probing the cancer signaling network from the perspective of control, our findings suggest that indispensable backbone driver nodes could be potentially leveraged as therapeutic targets. This study also illustrates the application of structural controllability for studying the mechanisms underlying the regulation of complex diseases.

Conjugated-Backbone Effect of Organic Small Molecules for n-Type Thermoelectric Materials with ZT over 0.2.

PubMed

Huang, Dazhen; Yao, Huiying; Cui, Yutao; Zou, Ye; Zhang, Fengjiao; Wang, Chao; Shen, Hongguang; Jin, Wenlong; Zhu, Jia; Diao, Ying; Xu, Wei; Di, Chong-An; Zhu, Daoben

2017-09-20

Conjugated backbones play a fundamental role in determining the electronic properties of organic semiconductors. On the basis of two solution-processable dihydropyrrolo[3,4-c]pyrrole-1,4-diylidenebis(thieno[3,2-b]thiophene) derivatives with aromatic and quinoid structures, we have carried out a systematic study of the relationship between the conjugated-backbone structure and the thermoelectric properties. In particular, a combination of UV-vis-NIR spectra, photoemission spectroscopy, and doping optimization are utilized to probe the interplay between energy levels, chemical doping, and thermoelectric performance. We found that a moderate change in the conjugated backbone leads to varied doping mechanisms and contributes to dramatic changes in the thermoelectric performance. Notably, the chemically doped A-DCV-DPPTT, a small molecule with aromatic structure, exhibits an electrical conductivity of 5.3 S cm -1 and a high power factor (PF 373 K ) up to 236 μW m -1 K -2 , which is 50 times higher than that of Q-DCM-DPPTT with a quinoid structure. More importantly, the low thermal conductivity enables A-DCV-DPPTT to possess a figure of merit (ZT) of 0.23 ± 0.03, which is the highest value reported to date for thermoelectric materials based on organic small molecules. These results demonstrate that the modulation of the conjugated backbone represents a powerful strategy for tuning the electronic structure and mobility of organic semiconductors toward a maximum thermoelectric performance.

DDS as middleware of the Southern African Large Telescope control system

NASA Astrophysics Data System (ADS)

Maartens, Deneys S.; Brink, Janus D.

2016-07-01

The Southern African Large Telescope (SALT) software control system1 is realised as a distributed control system, implemented predominantly in National Instruments' LabVIEW. The telescope control subsystems communicate using cyclic, state-based messages. Currently, transmitting a message is accomplished by performing an HTTP PUT request to a WebDAV directory on a centralised Apache web server, while receiving is based on polling the web server for new messages. While the method works, it presents a number of drawbacks; a scalable distributed communication solution with minimal overhead is a better fit for control systems. This paper describes our exploration of the Data Distribution Service (DDS). DDS is a formal standard specification, defined by the Object Management Group (OMG), that presents a data-centric publish-subscribe model for distributed application communication and integration. It provides an infrastructure for platform- independent many-to-many communication. A number of vendors provide implementations of the DDS standard; RTI, in particular, provides a DDS toolkit for LabVIEW. This toolkit has been evaluated against the needs of SALT, and a few deficiencies have been identified. We have developed our own implementation that interfaces LabVIEW to DDS in order to address our specific needs. Our LabVIEW DDS interface implementation is built against the RTI DDS Core component, provided by RTI under their Open Community Source licence. Our needs dictate that the interface implementation be platform independent. Since we have access to the RTI DDS Core source code, we are able to build the RTI DDS libraries for any of the platforms on which we require support. The communications functionality is based on UDP multicasting. Multicasting is an efficient communications mechanism with low overheads which avoids duplicated point-to-point transmission of data on a network where there are multiple recipients of the data. In the paper we present a performance evaluation of DDS against the current HTTP-based implementation as well as the historical DataSocket implementation. We conclude with a summary and describe future work.

Web server for priority ordered multimedia services

NASA Astrophysics Data System (ADS)

Celenk, Mehmet; Godavari, Rakesh K.; Vetnes, Vermund

2001-10-01

In this work, our aim is to provide finer priority levels in the design of a general-purpose Web multimedia server with provisions of the CM services. The type of services provided include reading/writing a web page, downloading/uploading an audio/video stream, navigating the Web through browsing, and interactive video teleconferencing. The selected priority encoding levels for such operations follow the order of admin read/write, hot page CM and Web multicasting, CM read, Web read, CM write and Web write. Hot pages are the most requested CM streams (e.g., the newest movies, video clips, and HDTV channels) and Web pages (e.g., portal pages of the commercial Internet search engines). Maintaining a list of these hot Web pages and CM streams in a content addressable buffer enables a server to multicast hot streams with lower latency and higher system throughput. Cold Web pages and CM streams are treated as regular Web and CM requests. Interactive CM operations such as pause (P), resume (R), fast-forward (FF), and rewind (RW) have to be executed without allocation of extra resources. The proposed multimedia server model is a part of the distributed network with load balancing schedulers. The SM is connected to an integrated disk scheduler (IDS), which supervises an allocated disk manager. The IDS follows the same priority handling as the SM, and implements a SCAN disk-scheduling method for an improved disk access and a higher throughput. Different disks are used for the Web and CM services in order to meet the QoS requirements of CM services. The IDS ouput is forwarded to an Integrated Transmission Scheduler (ITS). The ITS creates a priority ordered buffering of the retrieved Web pages and CM data streams that are fed into an auto regressive moving average (ARMA) based traffic shaping circuitry before being transmitted through the network.

Energies and 2'-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations.

PubMed

Mládek, Arnošt; Banáš, Pavel; Jurečka, Petr; Otyepka, Michal; Zgarbová, Marie; Šponer, Jiří

2014-01-14

Sugar-phosphate backbone is an electronically complex molecular segment imparting RNA molecules high flexibility and architectonic heterogeneity necessary for their biological functions. The structural variability of RNA molecules is amplified by the presence of the 2'-hydroxyl group, capable of forming multitude of intra- and intermolecular interactions. Bioinformatics studies based on X-ray structure database revealed that RNA backbone samples at least 46 substates known as rotameric families. The present study provides a comprehensive analysis of RNA backbone conformational preferences and 2'-hydroxyl group orientations. First, we create a benchmark database of estimated CCSD(T)/CBS relative energies of all rotameric families and test performance of dispersion-corrected DFT-D3 methods and molecular mechanics in vacuum and in continuum solvent. The performance of the DFT-D3 methods is in general quite satisfactory. The B-LYP-D3 method provides the best trade-off between accuracy and computational demands. B3-LYP-D3 slightly outperforms the new PW6B95-D3 and MPW1B95-D3 and is the second most accurate density functional of the study. The best agreement with CCSD(T)/CBS is provided by DSD-B-LYP-D3 double-hybrid functional, although its large-scale applications may be limited by high computational costs. Molecular mechanics does not reproduce the fine energy differences between the RNA backbone substates. We also demonstrate that the differences in the magnitude of the hyperconjugation effect do not correlate with the energy ranking of the backbone conformations. Further, we investigated the 2'-hydroxyl group orientation preferences. For all families, we conducted a QM and MM hydroxyl group rigid scan in gas phase and solvent. We then carried out set of explicit solvent MD simulations of folded RNAs and analyze 2'-hydroxyl group orientations of different backbone families in MD. The solvent energy profiles determined primarily by the sugar pucker match well with the distribution data derived from the simulations. The QM and MM energy profiles predict the same 2'-hydroxyl group orientation preferences. Finally, we demonstrate that the high energy of unfavorable and rarely sampled 2'-hydroxyl group orientations can be attributed to clashes between occupied orbitals.

Stereoscopic Movies for Teaching and Learning of Astronomy

NASA Astrophysics Data System (ADS)

Hayashi, Mitsuru; Kato, Tsunehiko N.; Takeda, Takaaaki; Kokubo, Eiichiro; Miura, Hitoshi; Takahei, Toshiyuki; Miyama, Shoken M.; Kaifu, Norio

To attract the interest of the public in astronomy we visualize data obtained through simulations by using super computers and observations by using state-of -the-art facilities for example the SUBARU Telescope in the virtual reality system. The system is composed of three soft screens. We use two PC's two DLP projectors with circular polarization filters and one mirror for each screen to realize stereoscopic projection. By wearing glasses of circular polarization filters we can experience immersiveness in the system. Six PC's are connected by using optical fiber cable(1Gbps). Especially we developed the software for synchronization and realized stereoscopic movies(15-30 frames per second). In addition to teaching and learning of astronomy we also utilize the system above for public relations and science itself in NAO Mitaka. The system can provide scientists with the point of view we cannot realize on the earth. We are planning to improve the contents easier for the public to understand and distribute the contents to museums and educational institutions through networks for example Super SINET(the internet backbone connects institutes at 10Gbps) in 2003 in addition to monthly exhibition in NAOMitaka

Colloidal cutin-like substances cross-linked to siderophore decomposition products mobilizing plutonium from contaminated soils.

PubMed

Xu, C; Santschi, P H; Zhong, J Y; Hatcher, P G; Francis, A J; Dodge, C J; Roberts, K A; Hung, C C; Honeyman, B D

2008-11-15

Relatively recently, inorganic colloids have been invoked to reconcile the apparent contradictions between expectations based on classical dissolved-phase Pu transport and field observations of "enhanced" Pu mobility (Kersting et al. Nature 1999, 397, 56-59). A new paradigm for Pu transport is mobilization and transport via biologically produced ligands. This study for the first time reports a new finding of Pu being transported, at sub-pM concentrations, by a cutin-like natural substance containing siderophore-like moieties and virtually all mobile Pu. Most likely, Pu is complexed by chelating groups derived from siderophores that are covalently bound to a backbone of cutin-derived soil degradation products, thus revealing the history of initial exposure to Pu. Features such as amphiphilicity and small size make this macromolecule an ideal collector for actinides and other metals and a vector for their dispersal. Cross-linking to the hydrophobic domains (e.g., by polysaccharides) gives this macromolecule high mobility and a means of enhancing Pu transport. This finding provides a new mechanism for Pu transport through environmental systems that would not have been predicted by Pu transport models.

Secure and Resilient Functional Modeling for Navy Cyber-Physical Systems

DTIC Science & Technology

2017-05-24

Functional Modeling Compiler (SCCT) FM Compiler and Key Performance Indicators (KPI) May 2018 Pending. Model Management Backbone (SCCT) MMB Demonstration...implement the agent- based distributed runtime. - KPIs for single/multicore controllers and temporal/spatial domains. - Integration of the model management ...Distributed Runtime (UCI) Not started. Model Management Backbone (SCCT) Not started. Siemens Corporation Corporate Technology Unrestricted

A Simpler Nucleic Acid

NASA Technical Reports Server (NTRS)

Orgel, Leslie

2000-01-01

It has been supposed that for a nucleic acid analog to pair with RNA it must, like RNA, have a backbone with at least a sixatom repeat; a shorter backbone presumably would not stretch far enough to bind RNA properly. The Eschenmoser group has shown, however, that this first impression is incorrect.As they report in their new paper, Eschenmoser and co-workers ( I ) have now synthesized a substantial number of these polymers, which are called (L)-a-threofuranosyl oligonucleotides or TNAs. They are composed of bases linked to a threose sugar-phosphate backbone, with phosphodiester bonds connecting the nucleotides. The investigators discovered that pairs of complementary TNAs do indeed form stable Watson-Crick double helices and, perhaps more importantly, that TNAs form stable double helices with complementary RNAs and DNAs.

¹⁵N, ¹³C and ¹H resonance assignments and secondary structure determination of a variable heavy domain of a heavy chain antibody.

PubMed

Prosser, Christine E; Waters, Lorna C; Muskett, Frederick W; Veverka, Vaclav; Addis, Philip W; Griffin, Laura M; Baker, Terry S; Lawson, Alastair D G; Wernery, Ulrich; Kinne, Jorg; Henry, Alistair J; Taylor, Richard J; Carr, Mark D

2014-04-01

Heavy chain antibodies differ in structure to conventional antibodies lacking both the light chain and the first heavy chain constant domain (CH1). Characteristics of the antigen-binding variable heavy domain of the heavy chain antibody (VHH) including the smaller size, high solubility and stability make them an attractive alternative to more traditional antibody fragments for detailed NMR-based structural analysis. Here we report essentially complete backbone and side chain (15)N, (13)C and (1)H assignments for a free VHH. Analysis of the backbone chemical shift data obtained indicates that the VHH is comprised predominantly of β-sheets corresponding to nearly 60% of the protein backbone.

Representation and Integration of Scientific Information

NASA Technical Reports Server (NTRS)

1998-01-01

The objective of this Joint Research Interchange with NASA-Ames was to investigate how the Tsimmis technology could be used to represent and integrate scientific information. The main goal of the Tsimmis project is to allow a decision maker to find information of interest from such sources, fuse it, and process it (e.g., summarize it, visualize it, discover trends). Another important goal is the easy incorporation of new sources, as well the ability to deal with sources whose structure or services evolve. During the Interchange we had research meetings approximately every month or two. The funds provided by NASA supported work that lead to the following two papers: Fusion Queries over Internet Databases; Efficient Query Subscription Processing in a Multicast Environment.

RIACS

NASA Technical Reports Server (NTRS)

Oliger, Joseph

1997-01-01

Topics considered include: high-performance computing; cognitive and perceptual prostheses (computational aids designed to leverage human abilities); autonomous systems. Also included: development of a 3D unstructured grid code based on a finite volume formulation and applied to the Navier-stokes equations; Cartesian grid methods for complex geometry; multigrid methods for solving elliptic problems on unstructured grids; algebraic non-overlapping domain decomposition methods for compressible fluid flow problems on unstructured meshes; numerical methods for the compressible navier-stokes equations with application to aerodynamic flows; research in aerodynamic shape optimization; S-HARP: a parallel dynamic spectral partitioner; numerical schemes for the Hamilton-Jacobi and level set equations on triangulated domains; application of high-order shock capturing schemes to direct simulation of turbulence; multicast technology; network testbeds; supercomputer consolidation project.

Security Enhancement Using Cache Based Reauthentication in WiMAX Based E-Learning System

PubMed Central

Rajagopal, Chithra; Bhuvaneshwaran, Kalaavathi

2015-01-01

WiMAX networks are the most suitable for E-Learning through their Broadcast and Multicast Services at rural areas. Authentication of users is carried out by AAA server in WiMAX. In E-Learning systems the users must be forced to perform reauthentication to overcome the session hijacking problem. The reauthentication of users introduces frequent delay in the data access which is crucial in delaying sensitive applications such as E-Learning. In order to perform fast reauthentication caching mechanism known as Key Caching Based Authentication scheme is introduced in this paper. Even though the cache mechanism requires extra storage to keep the user credentials, this type of mechanism reduces the 50% of the delay occurring during reauthentication. PMID:26351658

Security Enhancement Using Cache Based Reauthentication in WiMAX Based E-Learning System.

PubMed

Rajagopal, Chithra; Bhuvaneshwaran, Kalaavathi

2015-01-01

WiMAX networks are the most suitable for E-Learning through their Broadcast and Multicast Services at rural areas. Authentication of users is carried out by AAA server in WiMAX. In E-Learning systems the users must be forced to perform reauthentication to overcome the session hijacking problem. The reauthentication of users introduces frequent delay in the data access which is crucial in delaying sensitive applications such as E-Learning. In order to perform fast reauthentication caching mechanism known as Key Caching Based Authentication scheme is introduced in this paper. Even though the cache mechanism requires extra storage to keep the user credentials, this type of mechanism reduces the 50% of the delay occurring during reauthentication.

Application of the fractional Fourier transform to the design of LCOS based optical interconnects and fiber switches.

PubMed

Robertson, Brian; Zhang, Zichen; Yang, Haining; Redmond, Maura M; Collings, Neil; Liu, Jinsong; Lin, Ruisheng; Jeziorska-Chapman, Anna M; Moore, John R; Crossland, William A; Chu, D P

2012-04-20

It is shown that reflective liquid crystal on silicon (LCOS) spatial light modulator (SLM) based interconnects or fiber switches that use defocus to reduce crosstalk can be evaluated and optimized using a fractional Fourier transform if certain optical symmetry conditions are met. Theoretically the maximum allowable linear hologram phase error compared to a Fourier switch is increased by a factor of six before the target crosstalk for telecom applications of -40 dB is exceeded. A Gerchberg-Saxton algorithm incorporating a fractional Fourier transform modified for use with a reflective LCOS SLM is used to optimize multi-casting holograms in a prototype telecom switch. Experiments are in close agreement to predicted performance.

Modelling and temporal performances evaluation of networked control systems using (max, +) algebra

NASA Astrophysics Data System (ADS)

Ammour, R.; Amari, S.

2015-01-01

In this paper, we address the problem of temporal performances evaluation of producer/consumer networked control systems. The aim is to develop a formal method for evaluating the response time of this type of control systems. Our approach consists on modelling, using Petri nets classes, the behaviour of the whole architecture including the switches that support multicast communications used by this protocol. (max, +) algebra formalism is then exploited to obtain analytical formulas of the response time and the maximal and minimal bounds. The main novelty is that our approach takes into account all delays experienced at the different stages of networked automation systems. Finally, we show how to apply the obtained results through an example of networked control system.

Distributed Ship Navigation Control System Based on Dual Network

NASA Astrophysics Data System (ADS)

Yao, Ying; Lv, Wu

2017-10-01

Navigation system is very important for ship’s normal running. There are a lot of devices and sensors in the navigation system to guarantee ship’s regular work. In the past, these devices and sensors were usually connected via CAN bus for high performance and reliability. However, as the development of related devices and sensors, the navigation system also needs the ability of high information throughput and remote data sharing. To meet these new requirements, we propose the communication method based on dual network which contains CAN bus and industrial Ethernet. Also, we import multiple distributed control terminals with cooperative strategy based on the idea of synchronizing the status by multicasting UDP message contained operation timestamp to make the system more efficient and reliable.

Improving the accuracy of protein stability predictions with multistate design using a variety of backbone ensembles.

PubMed

Davey, James A; Chica, Roberto A

2014-05-01

Multistate computational protein design (MSD) with backbone ensembles approximating conformational flexibility can predict higher quality sequences than single-state design with a single fixed backbone. However, it is currently unclear what characteristics of backbone ensembles are required for the accurate prediction of protein sequence stability. In this study, we aimed to improve the accuracy of protein stability predictions made with MSD by using a variety of backbone ensembles to recapitulate the experimentally measured stability of 85 Streptococcal protein G domain β1 sequences. Ensembles tested here include an NMR ensemble as well as those generated by molecular dynamics (MD) simulations, by Backrub motions, and by PertMin, a new method that we developed involving the perturbation of atomic coordinates followed by energy minimization. MSD with the PertMin ensembles resulted in the most accurate predictions by providing the highest number of stable sequences in the top 25, and by correctly binning sequences as stable or unstable with the highest success rate (≈90%) and the lowest number of false positives. The performance of PertMin ensembles is due to the fact that their members closely resemble the input crystal structure and have low potential energy. Conversely, the NMR ensemble as well as those generated by MD simulations at 500 or 1000 K reduced prediction accuracy due to their low structural similarity to the crystal structure. The ensembles tested herein thus represent on- or off-target models of the native protein fold and could be used in future studies to design for desired properties other than stability. Copyright © 2013 Wiley Periodicals, Inc.

Exploring the Parameters Controlling the Crystallinity-Conductivity Correlation of PFSA Ionomers

NASA Astrophysics Data System (ADS)

Kusoglu, Ahmet; Shi, Shouwen; Weber, Adam

Perfluorosulfonic-acid (PFSA) ionomers are the most commonly used solid-electrolyte in electrochemical energy devices because of their remarkable conductivity and chemical/mechanical stability, with the latter imparted by their semi-crystalline fluorocarbon backbone. PFSAs owe this unique combination of transport/stability functionalities to their phase-separated morphology of conductive hydrophilic ionic domains and the non-conductive hydrophobic backbone, which are connected via pendant chains. Thus, phase-separation is governed by fractions of backbone and ionic groups, which is controlled by the equivalent weight (EW). Therefore, EW, along with the pendant chain chemistry, directly impact the conductive vs non-conductive regions, and consequently the interrelation between transport and stability. Driven by the need to achieve higher conductivities without disrupting the crystallinity, various pendant-chain chemistries have been developed. In this talk, we will report the results of a systematic investigation on hydration, conductivity, mechanical properties and crystallinity of various types and EWs of PFSA ionomers to (i) develop a structure/property map, and (ii) identify the key parameters controlling morphology and properties. It will be discussed how the pendant-chain and backbone lengths affect the conductivity and crystallinity, respectively. Lastly, the data set will be analyzed to explore universal structure/property relationships for PFSAs.

Self-assembly of diphenylalanine backbone homologues and their combination with functionalized carbon nanotubes.

PubMed

Dinesh, Bhimareddy; Squillaci, Marco A; Ménard-Moyon, Cécilia; Samorì, Paolo; Bianco, Alberto

2015-10-14

The integration of carbon nanotubes (CNTs) into organized nanostructures is of great interest for applications in materials science and biomedicine. In this work we studied the self-assembly of β and γ homologues of diphenylalanine peptides under different solvent and pH conditions. We aimed to investigate the role of peptide backbone in tuning the formation of different types of nanostructures alone or in combination with carbon nanotubes. In spite of having the same side chain, β and γ peptides formed distinctively different nanofibers, a clear indication of the role played by the backbone homologation on the self-assembly. The variation of the pH allowed to transform the nanofibers into spherical structures. Moreover, the co-assembly of β and γ peptides with carbon nanotubes covalently functionalized with the same peptide generated unique dendritic assemblies. This comparative study on self-assembly using diphenylalanine backbone homologues and of the co-assembly with CNT covalent conjugates is the first example exploring the capacity of β and γ peptides to adopt precise nanostructures, particularly in combination with carbon nanotubes. The dendritic organization obtained by mixing carbon nanotubes and peptides might find interesting applications in tissue engineering and neuronal interfacing.

Knowledge-Guided Docking of WW Domain Proteins and Flexible Ligands

NASA Astrophysics Data System (ADS)

Lu, Haiyun; Li, Hao; Banu Bte Sm Rashid, Shamima; Leow, Wee Kheng; Liou, Yih-Cherng

Studies of interactions between protein domains and ligands are important in many aspects such as cellular signaling. We present a knowledge-guided approach for docking protein domains and flexible ligands. The approach is applied to the WW domain, a small protein module mediating signaling complexes which have been implicated in diseases such as muscular dystrophy and Liddle’s syndrome. The first stage of the approach employs a substring search for two binding grooves of WW domains and possible binding motifs of peptide ligands based on known features. The second stage aligns the ligand’s peptide backbone to the two binding grooves using a quasi-Newton constrained optimization algorithm. The backbone-aligned ligands produced serve as good starting points to the third stage which uses any flexible docking algorithm to perform the docking. The experimental results demonstrate that the backbone alignment method in the second stage performs better than conventional rigid superposition given two binding constraints. It is also shown that using the backbone-aligned ligands as initial configurations improves the flexible docking in the third stage. The presented approach can also be applied to other protein domains that involve binding of flexible ligand to two or more binding sites.

Structural test of the parameterized-backbone method for protein design.

PubMed

Plecs, Joseph J; Harbury, Pehr B; Kim, Peter S; Alber, Tom

2004-09-03

Designing new protein folds requires a method for simultaneously optimizing the conformation of the backbone and the side-chains. One approach to this problem is the use of a parameterized backbone, which allows the systematic exploration of families of structures. We report the crystal structure of RH3, a right-handed, three-helix coiled coil that was designed using a parameterized backbone and detailed modeling of core packing. This crystal structure was determined using another rationally designed feature, a metal-binding site that permitted experimental phasing of the X-ray data. RH3 adopted the intended fold, which has not been observed previously in biological proteins. Unanticipated structural asymmetry in the trimer was a principal source of variation within the RH3 structure. The sequence of RH3 differs from that of a previously characterized right-handed tetramer, RH4, at only one position in each 11 amino acid sequence repeat. This close similarity indicates that the design method is sensitive to the core packing interactions that specify the protein structure. Comparison of the structures of RH3 and RH4 indicates that both steric overlap and cavity formation provide strong driving forces for oligomer specificity.

Impact of aggregation on scaling behavior of Internet backbone traffic

NASA Astrophysics Data System (ADS)

Zhang, Zhi-Li; Ribeiro, Vinay J.; Moon, Sue B.; Diot, Christophe

2002-07-01

We study the impact of aggregation on the scaling behavior of Internet backbone tra ffic, based on traces collected from OC3 and OC12 links in a tier-1 ISP. We make two striking observations regarding the sub-second small time scaling behaviors of Internet backbone traffic: 1) for a majority of these traces, the Hurst parameters at small time scales (1ms - 100ms) are fairly close to 0.5. Hence the traffic at these time scales are nearly uncorrelated; 2) the scaling behaviors at small time scales are link-dependent, and stay fairly invariant over changing utilization and time. To understand the scaling behavior of network traffic, we develop analytical models and employ them to demonstrate how traffic composition -- aggregation of traffic with different characteristics -- affects the small-time scalings of network traffic. The degree of aggregation and burst correlation structure are two major factors in traffic composition. Our trace-based data analysis confirms this. Furthermore, we discover that traffic composition on a backbone link stays fairly consistent over time and changing utilization, which we believe is the cause for the invariant small-time scalings we observe in the traces.

Design of HIV-1 Protease Inhibitors with Amino-bis-tetrahydrofuran Derivatives as P2-Ligands to Enhance Backbone-Binding Interactions. Synthesis, Biological Evaluation, and Protein-Ligand X-ray Studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghosh, Arun K.; Martyr, Cuthbert D.; Osswald, Heather L.

Structure-based design, synthesis, and biological evaluation of a series of very potent HIV-1 protease inhibitors are described. In an effort to improve backbone ligand–binding site interactions, we have incorporated basic-amines at the C4 position of the bis-tetrahydrofuran (bis-THF) ring. We speculated that these substituents would make hydrogen bonding interactions in the flap region of HIV-1 protease. Synthesis of these inhibitors was performed diastereoselectively. A number of inhibitors displayed very potent enzyme inhibitory and antiviral activity. Inhibitors 25f, 25i, and 25j were evaluated against a number of highly-PI-resistant HIV-1 strains, and they exhibited improved antiviral activity over darunavir. Two high resolutionmore » X-ray structures of 25f- and 25g-bound HIV-1 protease revealed unique hydrogen bonding interactions with the backbone carbonyl group of Gly48 as well as with the backbone NH of Gly48 in the flap region of the enzyme active site. These ligand–binding site interactions are possibly responsible for their potent activity.« less

Preparation and characterization of conjugated polymers made by postpolymerization reactions of alternating polyketones.

PubMed

Cheng, Chen; Guironnet, Damien; Barborak, James; Brookhart, Maurice

2011-06-29

Conjugated polymers possessing a poly(2,5-dimethylene-2,5-dihydrofuran) backbone were prepared through postpolymerization reaction of styrenic polyketones with bromine in one-pot reactions. The modification is proposed to proceed via condensation of two repeating units to form a fully characterized polymer with a poly(2,5-dimethylenetetrahydrofuran) backbone. Subsequent bromination and elimination of HBr yield a polymer with a fully conjugated carbon backbone. The new conjugated polymers were characterized by NMR, IR, and UV-vis spectroscopies and by CV. These polymers have strong absorption in the visible region, with the absorption peaks shifted to the NIR region upon doping with acids. The ease of the synthesis of the starting polyketone and of the modifications allows large-scale preparation of those conjugated polymers.

Structural dependence of MEH-PPV chromism in solution.

PubMed

de Magalhães, Carlos E T; Savedra, Ranylson M L; Dias, Karina S; Ramos, Rodrigo; Siqueira, Melissa F

2017-03-01

The chromism observed in the MEH-PPV polymer in tetrahydrofuran (THF) solution is discussed as a function of the structural morphology of the backbone chains. To evaluate this phenomenon, we carried out simulations employing a hybrid methodology using molecular dynamics and quantum mechanical approaches. Our results support the hypothesis that the morphological order-disorder transition is related to the change from red to blue phase observed experimentally. The morphological disorder is associated with total or partial twisted arrangements in the polymer backbone, which induces an electronic conjugation length more confined to shorter segments. In addition, the main band of the MEH-PPV UV-Vis spectrum at the lower wavelength is related to the blue phase, in contrast to the red phase found for the more planar backbone chains.

Fluorous Peptide Nucleic Acids: PNA Analogues with Fluorine in Backbone (γ-CF2-apg-PNA) Enhance Cellular Uptake.

PubMed

Ellipilli, Satheesh; Ganesh, Krishna N

2015-09-18

Fluorous PNA analogues possessing fluorine as inherent part of aminopropylglycine (apg) backbone (γ-CF2-apg PNA) have been synthesized and evaluated for biophysical and cell penetrating properties. These form duplexes of higher thermal stability with cRNA than cDNA, although destabilized compared to duplexes of standard aeg-PNA. Cellular uptake of the fluorinated γ-CF2-apg PNAs in NIH 3T3 and HeLa cells was 2-3-fold higher compared to that of nonfluorinated apg PNA, with NIH 3T3 cells showing better permeability compared to HeLa cells. The backbone fluorinated PNAs, which are first in this class, when combined with other chemical modifications may have potential for future PNA-based antisense agents.

Elastic Backbone Defines a New Transition in the Percolation Model

NASA Astrophysics Data System (ADS)

Sampaio Filho, Cesar I. N.; Andrade, José S.; Herrmann, Hans J.; Moreira, André A.

2018-04-01

The elastic backbone is the set of all shortest paths. We found a new phase transition at peb above the classical percolation threshold at which the elastic backbone becomes dense. At this transition in 2D, its fractal dimension is 1.750 ±0.003 , and one obtains a novel set of critical exponents βeb=0.50 ±0.02 , γeb=1.97 ±0.05 , and νeb=2.00 ±0.02 , fulfilling consistent critical scaling laws. Interestingly, however, the hyperscaling relation is violated. Using Binder's cumulant, we determine, with high precision, the critical probabilities peb for the triangular and tilted square lattice for site and bond percolation. This transition describes a sudden rigidification as a function of density when stretching a damaged tissue.

Neutron scattering studies of molecular conformations in liquid crystal polymers

NASA Astrophysics Data System (ADS)

Noirez, L.; Moussa, F.; Cotton, J. P.; Keller, P.; Pépy, G.

1991-03-01

A comblike liquid crystal polymer (LPC) is a polymer on which mesogenic molecules have been grafted. It exhibits a succession of liquid crystal phases. Usually the equilibrium conformation of an ordinary polymeric chain corresponds to a maximum entropy, i.e., to an isotropic spherical coil. How does the backbone of a LCP behave in the nematic and smectic field? Small-angle neutron scattering may answer this question. Such measurements are presented here on four different polymers as a function of temperature. An anisotropy of the backbone conformation is found in all these studied compounds, much more pronounced in the smectic phase than in the nematic phase: the backbone spreads more or less perpendicularly to its hanging cores. A comparison with existing theories and a discussion of these results is outlined.

Conversion of polymers of methyl- and vinylsilane to Si-C ceramics

NASA Technical Reports Server (NTRS)

Hurwitz, Frances I.; Kacik, Terrance A.; Bu, Xin-Ya; Masnovi, John; Heimann, Paula J.; Beyene, Kassahun

1994-01-01

Poly(methylsilane) and poly(vinylsilane) were synthesized using a titanocene catalyst, and their pyrolytic conversion to ceramics was followed using a combination of thermal analysis and infrared spectroscopy. The two polymers have distinctly different backbone structures, as determined by Si NMR; methylsilane polymerizes to a polysilane, while vinylsilane polymers have predominately polycarbosilane backbone, with some polysilane structure as well. The pyrolysis path and char yield were dependent primarily on backbone structure, with little influence of polymer molecular weight. The majority of the weight loss on conversion occurs below 650 degrees C, although bond rearrangement continues to 1400 degrees C. Poly(vinylsilane) produced a C-rich Si-C ceramic in which the carbon was dispersed on a sufficiently fine level to show resistance to oxidation on heating in air to 1400 degrees C.

Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly.

PubMed

Aliev, Abil E; Courtier-Murias, Denis

2010-09-30

Experimental NMR verification of MD simulations using 12 different force fields (AMBER, CHARMM, GROMOS, and OPLS-AA) and 5 different water models has been undertaken to identify reliable MD protocols for structure and dynamics elucidations of small open chain peptides containing Gly and Pro. A conformationally flexible tetrapeptide Gly-Pro-Gly-Gly was selected for NMR (3)J-coupling, chemical shift, and internuclear distance measurements, followed by their calculations using 2 μs long MD simulations in water. In addition, Ramachandran population maps for Pro-2 and Gly-3 residues of GPGG obtained from MD simulations were used for detailed comparisons with similar maps from the protein data bank (PDB) for large number of Gly and Pro residues in proteins. The MD simulations revealed strong dependence of the populations and geometries of preferred backbone and side chain conformations, as well as the time scales of the peptide torsional transitions on the force field used. On the basis of the analysis of the measured and calculated data, AMBER99SB is identified as the most reliable force field for reproducing NMR measured parameters, which are dependent on the peptide backbone and the Pro side chain geometries and dynamics. Ramachandran maps showing the dependence of conformational populations as a function of backbone ϕ/ψ angles for Pro-2 and Gly-3 residues of GPGG from MD simulations using AMBER99SB, AMBER03, and CHARMM were found to resemble similar maps for Gly and Pro residues from the PDB survey. Three force fields (AMBER99, AMBER99ϕ, and AMBER94) showed the least satisfactory agreement with both the solution NMR and the PDB survey data. The poor performance of these force fields is attributed to their propensity to overstabilize helical peptide backbone conformations at the Pro-2 and Gly-3 residues. On the basis of the similarity of the MD and PDB Ramachandran plots, the following sequence of transitions is suggested for the Gly backbone conformation: α(L) ⇆ β(PR) ⇆ β(S) ⇆ β(P) ⇆ α, where backbone secondary structures α(L) and α are associated with helices and turns, β(P) and β(PR) correspond to the left- and right-handed polyproline II structures and β(S) denotes the fully stretched backbone conformation. Compared to the force field dependence, less significant, but noteworthy, variations in the populations of the peptide backbone conformations were observed. For different solvent models considered, a correlation was noted between the number of torsional transitions in GPGG and the water self-diffusion coefficient on using TIP3P, TIP4P, and TIP5P models. In addition to MD results, we also report DFT derived Karplus relationships for Gly and Pro residues using B972 and B3LYP functionals.

Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform.

PubMed

Mládek, Arnošt; Sponer, Judit E; Kulhánek, Petr; Lu, Xiang-Jun; Olson, Wilma K; Sponer, Jiřĺ

2012-01-10

Folded RNA molecules are shaped by an astonishing variety of highly conserved noncanonical molecular interactions and backbone topologies. The dinucleotide platform is a widespread recurrent RNA modular building submotif formed by the side-by-side pairing of bases from two consecutive nucleotides within a single strand, with highly specific sequence preferences. This unique arrangement of bases is cemented by an intricate network of noncanonical hydrogen bonds and facilitated by a distinctive backbone topology. The present study investigates the gas-phase intrinsic stabilities of the three most common RNA dinucleotide platforms - 5'-GpU-3', ApA, and UpC - via state-of-the-art quantum-chemical (QM) techniques. The mean stability of base-base interactions decreases with sequence in the order GpU > ApA > UpC. Bader's atoms-in-molecules analysis reveals that the N2(G)…O4(U) hydrogen bond of the GpU platform is stronger than the corresponding hydrogen bonds in the other two platforms. The mixed-pucker sugar-phosphate backbone conformation found in most GpU platforms, in which the 5'-ribose sugar (G) is in the C2'-endo form and the 3'-sugar (U) in the C3'-endo form, is intrinsically more stable than the standard A-RNA backbone arrangement, partially as a result of a favorable O2'…O2P intra-platform interaction. Our results thus validate the hypothesis of Lu et al. (Lu Xiang-Jun, et al. Nucleic Acids Res. 2010, 38, 4868-4876), that the superior stability of GpU platforms is partially mediated by the strong O2'…O2P hydrogen bond. In contrast, ApA and especially UpC platform-compatible backbone conformations are rather diverse and do not display any characteristic structural features. The average stabilities of ApA and UpC derived backbone conformers are also lower than those of GpU platforms. Thus, the observed structural and evolutionary patterns of the dinucleotide platforms can be accounted for, to a large extent, by their intrinsic properties as described by modern QM calculations. In contrast, we show that the dinucleotide platform is not properly described in the course of atomistic explicit-solvent simulations. Our work also gives methodological insights into QM calculations of experimental RNA backbone geometries. Such calculations are inherently complicated by rather large data and refinement uncertainties in the available RNA experimental structures, which often preclude reliable energy computations.

Tension Amplification in Molecular Brushes in Solutions and on Substrates

PubMed Central

Panyukov, Sergey; Zhulina, Ekaterina B.; Sheiko, Sergei S.; Randall, Greg C.; Brock, James; Rubinstein, Michael

2009-01-01

Molecular bottle-brushes are highly branched macromolecules with side chains densely grafted to a long polymer backbone. The brush-like architecture allows focusing of the side-chain tension to the backbone and its amplification from the picoNewton to nanoNewton range. The backbone tension depends on the overall molecular conformation and the surrounding environment. Here we study the relation between the tension and conformation of the molecular brushes in solutions, melts, and on substrates. In solutions, we find that the backbone tension in dense brushes with side chains attached to every backbone monomer is on the order of f0N3/8 in athermal solvents, f0N1/3 in θ-solvents, and f0 in poor solvents and melts, where N is the degree of polymerization of side chains, f0≃ kBT/b is the maximum tension in side chains, b is the Kuhn length, kB is Boltzmann constant, and T is absolute temperature. Depending on the side chain length and solvent quality, molecular brushes in solutions develop tension on the order of 10–100 picoNewtons, which is sufficient to break hydrogen bonds. Significant amplification of tension occurs upon adsorption of brushes onto a substrate. On a strongly attractive substrate, maximum tension in the brush backbone is ~ f0N, reaching values on the order of several nanoNewtons which exceed the strength of a typical covalent bond. At low grafting density and high spreading parameter the cross-sectional profile of adsorbed molecular brush is approximately rectangular with thicknes ~bA/S, where A is the Hamaker constant and S is the spreading parameter. At a very high spreading parameter (S > A), the brush thickness saturates at monolayer ~ b. At a low spreading parameter, the cross-sectional profile of adsorbed molecular brush has triangular tent-like shape. In the cross-over between these two opposite cases, covering a wide range of parameter space, the adsorbed molecular brush consists of two layers. Side chains in the lower layer gain surface energy due to the direct interaction with the substrate, while the second layer spreads on the top of the first layer. Scaling theory predicts that this second layer has a triangular cross-section with width R ~ N3/5 and height h ~ N2/5. Using self-consistent field theory we calculate the cap profile y (x) = h (1 − x2/R2)2, where x is the transverse distance from the backbone. The predicted cap shape is in excellent agreement with both computer simulation and experiment. PMID:19673133

Poly(carbonate-imide) polymer

NASA Technical Reports Server (NTRS)

St. Clair, Terry L. (Inventor); Maudgal, Shubha (Inventor); Pratt, J. Richard (Inventor)

1987-01-01

A novel series of polymers and copolymers based on a polyimide backbone with the incorporation of carbonate moieties along the backbone. The process for preparing these polymers and copolymers is also disclosed as is a novel series of dinitrodiphenyl carbonates and diaminodiphenyl carbonates. The novel polymers and copolymers exhibit high temperature capability and because of the carbonate unit, many exhibit a high degree of order and/or crystallinity.

Poly (Carbonate-Mide) Polymer

NASA Technical Reports Server (NTRS)

St.clair, T. L. (Inventor); Maudgal, S. (Inventor); Pratt, J. R. (Inventor)

1986-01-01

A novel series of polymers and copolymers based on a polymide backbone with the incorporation of carbonate moieties along the backbone is presented. The preparation process for the polymers and copolymers is disclosed together with a novel series of dinitrodiphenyl carbonates and diaminodiphenyl carbonates. The novel polyners and copolymers exhibit high temperature capability and because of the carbonate unit, many exhibit a high degree of order and/or crystallinity.

The extension of a DNA double helix by an additional Watson-Crick base pair on the same backbone.

PubMed

Kumar, Pawan; Sharma, Pawan K; Madsen, Charlotte S; Petersen, Michael; Nielsen, Poul

2013-06-17

Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ambient noise levels in the continental United States

USGS Publications Warehouse

McNamara, D.E.; Buland, R.P.

2004-01-01

The results of our noise analysis are useful for characterizing the performance of existing broadband stations and for detecting operational problems and should be relevant to the future siting of ANSS backbone stations. The noise maps at body-wave frequencies should be useful for estimating the magnitude threshold for the ANSS backbone and regional networks or conversely for optimizing the distribution of regional network stations.

Short and long-term genome stability analysis of prokaryotic genomes.

PubMed

Brilli, Matteo; Liò, Pietro; Lacroix, Vincent; Sagot, Marie-France

2013-05-08

Gene organization dynamics is actively studied because it provides useful evolutionary information, makes functional annotation easier and often enables to characterize pathogens. There is therefore a strong interest in understanding the variability of this trait and the possible correlations with life-style. Two kinds of events affect genome organization: on one hand translocations and recombinations change the relative position of genes shared by two genomes (i.e. the backbone gene order); on the other, insertions and deletions leave the backbone gene order unchanged but they alter the gene neighborhoods by breaking the syntenic regions. A complete picture about genome organization evolution therefore requires to account for both kinds of events. We developed an approach where we model chromosomes as graphs on which we compute different stability estimators; we consider genome rearrangements as well as the effect of gene insertions and deletions. In a first part of the paper, we fit a measure of backbone gene order conservation (hereinafter called backbone stability) against phylogenetic distance for over 3000 genome comparisons, improving existing models for the divergence in time of backbone stability. Intra- and inter-specific comparisons were treated separately to focus on different time-scales. The use of multiple genomes of a same species allowed to identify genomes with diverging gene order with respect to their conspecific. The inter-species analysis indicates that pathogens are more often unstable with respect to non-pathogens. In a second part of the text, we show that in pathogens, gene content dynamics (insertions and deletions) have a much more dramatic effect on genome organization stability than backbone rearrangements. In this work, we studied genome organization divergence taking into account the contribution of both genome order rearrangements and genome content dynamics. By studying species with multiple sequenced genomes available, we were able to explore genome organization stability at different time-scales and to find significant differences for pathogen and non-pathogen species. The output of our framework also allows to identify the conserved gene clusters and/or partial occurrences thereof, making possible to explore how gene clusters assembled during evolution.

Force Field for Peptides and Proteins based on the Classical Drude Oscillator

PubMed Central

Lopes, Pedro E.M.; Huang, Jing; Shim, Jihyun; Luo, Yun; Li, Hui; Roux, Benoît; MacKerell, Alexander D.

2013-01-01

Presented is a polarizable force field based on a classical Drude oscillator framework, currently implemented in the programs CHARMM and NAMD, for modeling and molecular dynamics (MD) simulation studies of peptides and proteins. Building upon parameters for model compounds representative of the functional groups in proteins, the development of the force field focused on the optimization of the parameters for the polypeptide backbone and the connectivity between the backbone and side chains. Optimization of the backbone electrostatic parameters targeted quantum mechanical conformational energies, interactions with water, molecular dipole moments and polarizabilities and experimental condensed phase data for short polypeptides such as (Ala)5. Additional optimization of the backbone φ, ψ conformational preferences included adjustments of the tabulated two-dimensional spline function through the CMAP term. Validation of the model included simulations of a collection of peptides and proteins. This 1st generation polarizable model is shown to maintain the folded state of the studied systems on the 100 ns timescale in explicit solvent MD simulations. The Drude model typically yields larger RMS differences as compared to the additive CHARMM36 force field (C36) and shows additional flexibility as compared to the additive model. Comparison with NMR chemical shift data shows a small degradation of the polarizable model with respect to the additive, though the level of agreement may be considered satisfactory, while for residues shown to have significantly underestimated S2 order parameters in the additive model, improvements are calculated with the polarizable model. Analysis of dipole moments associated with the peptide backbone and tryptophan side chains show the Drude model to have significantly larger values than those present in C36, with the dipole moments of the peptide backbone enhanced to a greater extent in sheets versus helices and the dipoles of individual moieties observed to undergo significant variations during the MD simulations. Although there are still some limitations, the presented model, termed Drude-2013, is anticipated to yield a molecular picture of peptide and protein structure and function that will be of increased physical validity and internal consistency in a computationally accessible fashion. PMID:24459460

Conformational analysis investigation into the influence of nano-porosity of ultra-permeable ultra-selective polyimides on its diffusivity as potential membranes for use in the "green" separation of natural gases

NASA Astrophysics Data System (ADS)

Madkour, Tarek M.

2013-08-01

Nano-porous polymers of intrinsic microporosity, PIM, have exhibited excellent permeability and selectivity characteristics that could be utilized in an environmentally friendly gas separation process. A full understanding of the mechanism through which these membranes effectively and selectively allow for the permeation of specific gases will lead to further development of these membranes. Three factors obviously influenced the conformational behavior of these polymers, which are the presence of electronegative atoms, the presence of non-linearity in the polymeric backbones (backbone kinks) and the presence of bulky side groups on the polymeric chains. The dipole moment increased sharply with the presence of backbone kinks more than any other factor. Replacing the fluorine atoms with bulky alkyl groups didn't influence the dipole moment greatly indicating that the size of the side chains had much less dramatic influence on the dipole moment than having a bent backbone. Similarly, the presence of the backbone kinks in the polymeric chains influenced the polymeric chains to assume less extended configuration causing the torsional angles around the interconnecting bonds unable to cross the high potential energy barriers. The presence of the bulky side groups also caused the energy barriers of the cis-configurations to increase dramatically, which prevented the polymeric segments from experiencing full rotation about the connecting bonds. For these polymers, it was clear that the fully extended configurations are the preferred configurations in the absence of strong electronegative atoms, backbones kinks or bulky side groups. The addition of any of these factors to the polymeric structures resulted in the polymeric chains being forced to assume less extended configurations. Rather interestingly, the length or bulkiness of the side groups didn't affect the end-to-end distance distribution to a great deal since the presence of quite large bulky side chain such as the pentyl group has caused the polymeric chains to revert back to the fully extended configurations possibly due to the quite high potential energy barriers that the chains have to cross to reach the less extended configurational states.

Sulfation and cation effects on the conformational properties of the glycan backbone of chondroitin sulfate disaccharides.

PubMed

Faller, Christina E; Guvench, Olgun

2015-05-21

Chondroitin sulfate (CS) is one of several glycosaminoglycans that are major components of proteoglycans. A linear polymer consisting of repeats of the disaccharide -4GlcAβ1-3GalNAcβ1-, CS undergoes differential sulfation resulting in five unique sulfation patterns. Because of the dimer repeat, the CS glycosidic "backbone" has two distinct sets of conformational degrees of freedom defined by pairs of dihedral angles: (ϕ1, ψ1) about the β1-3 glycosidic linkage and (ϕ2, ψ2) about the β1-4 glycosidic linkage. Differential sulfation and the possibility of cation binding, combined with the conformational flexibility and biological diversity of CS, complicate experimental efforts to understand CS three-dimensional structures at atomic resolution. Therefore, all-atom explicit-solvent molecular dynamics simulations with Adaptive Biasing Force sampling of the CS backbone were applied to obtain high-resolution, high-precision free energies of CS disaccharides as a function of all possible backbone geometries. All 10 disaccharides (β1-3 vs β1-4 linkage × five different sulfation patterns) were studied; additionally, ion effects were investigated by considering each disaccharide in the presence of either neutralizing sodium or calcium cations. GlcAβ1-3GalNAc disaccharides have a single, broad, thermodynamically important free-energy minimum, whereas GalNAcβ1-4GlcA disaccharides have two such minima. Calcium cations but not sodium cations bind to the disaccharides, and binding is primarily to the GlcA -COO(-) moiety as opposed to sulfate groups. This binding alters the glycan backbone thermodynamics in instances where a calcium cation bound to -COO(-) can act to bridge and stabilize an interaction with an adjacent sulfate group, whereas, in the absence of this cation, the proximity of a sulfate group to -COO(-) results in two like charges being both desolvated and placed adjacent to each other and is found to be destabilizing. In addition to providing information on sulfation and cation effects, the present results can be applied to building models of CS polymers and as a point of comparison in studies of CS polymer backbone dynamics and thermodynamics.

Conservation and Divergence in the Candida Species Biofilm Matrix Mannan-Glucan Complex Structure, Function, and Genetic Control.

PubMed

Dominguez, Eddie; Zarnowski, Robert; Sanchez, Hiram; Covelli, Antonio S; Westler, William M; Azadi, Parastoo; Nett, Jeniel; Mitchell, Aaron P; Andes, David R

2018-04-03

Candida biofilms resist the effects of available antifungal therapies. Prior studies with Candida albicans biofilms show that an extracellular matrix mannan-glucan complex (MGCx) contributes to antifungal sequestration, leading to drug resistance. Here we implement biochemical, pharmacological, and genetic approaches to explore a similar mechanism of resistance for the three most common clinically encountered non- albicans Candida species (NAC). Our findings reveal that each Candida species biofilm synthesizes a mannan-glucan complex and that the antifungal-protective function of this complex is conserved. Structural similarities extended primarily to the polysaccharide backbone (α-1,6-mannan and β-1,6-glucan). Surprisingly, biochemical analysis uncovered stark differences in the branching side chains of the MGCx among the species. Consistent with the structural analysis, similarities in the genetic control of MGCx production for each Candida species also appeared limited to the synthesis of the polysaccharide backbone. Each species appears to employ a unique subset of modification enzymes for MGCx synthesis, likely accounting for the observed side chain diversity. Our results argue for the conservation of matrix function among Candida spp. While biogenesis is preserved at the level of the mannan-glucan complex backbone, divergence emerges for construction of branching side chains. Thus, the MGCx backbone represents an ideal drug target for effective pan- Candida species biofilm therapy. IMPORTANCE Candida species, the most common fungal pathogens, frequently grow as a biofilm. These adherent communities tolerate extremely high concentrations of antifungal agents, due in large part, to a protective extracellular matrix. The present studies define the structural, functional, and genetic similarities and differences in the biofilm matrix from the four most common Candida species. Each species synthesizes an extracellular mannan-glucan complex (MGCx) which contributes to sequestration of antifungal drug, shielding the fungus from this external assault. Synthesis of a common polysaccharide backbone appears conserved. However, subtle structural differences in the branching side chains likely rely upon unique modification enzymes, which are species specific. Our findings identify MGCx backbone synthesis as a potential pan- Candida biofilm therapeutic target. Copyright © 2018 Dominguez et al.

TANGLE: Two-Level Support Vector Regression Approach for Protein Backbone Torsion Angle Prediction from Primary Sequences

PubMed Central

Song, Jiangning; Tan, Hao; Wang, Mingjun; Webb, Geoffrey I.; Akutsu, Tatsuya

2012-01-01

Protein backbone torsion angles (Phi) and (Psi) involve two rotation angles rotating around the Cα-N bond (Phi) and the Cα-C bond (Psi). Due to the planarity of the linked rigid peptide bonds, these two angles can essentially determine the backbone geometry of proteins. Accordingly, the accurate prediction of protein backbone torsion angle from sequence information can assist the prediction of protein structures. In this study, we develop a new approach called TANGLE (Torsion ANGLE predictor) to predict the protein backbone torsion angles from amino acid sequences. TANGLE uses a two-level support vector regression approach to perform real-value torsion angle prediction using a variety of features derived from amino acid sequences, including the evolutionary profiles in the form of position-specific scoring matrices, predicted secondary structure, solvent accessibility and natively disordered region as well as other global sequence features. When evaluated based on a large benchmark dataset of 1,526 non-homologous proteins, the mean absolute errors (MAEs) of the Phi and Psi angle prediction are 27.8° and 44.6°, respectively, which are 1% and 3% respectively lower than that using one of the state-of-the-art prediction tools ANGLOR. Moreover, the prediction of TANGLE is significantly better than a random predictor that was built on the amino acid-specific basis, with the p-value<1.46e-147 and 7.97e-150, respectively by the Wilcoxon signed rank test. As a complementary approach to the current torsion angle prediction algorithms, TANGLE should prove useful in predicting protein structural properties and assisting protein fold recognition by applying the predicted torsion angles as useful restraints. TANGLE is freely accessible at http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/TANGLE/. PMID:22319565

Kr-86 Ion-Beam Irradiation of Hydrated DNA: Free Radical and Unaltered Base Yields

PubMed Central

Becker, David; Adhikary, Amitava; Tetteh, Smedley T.; Bull, Arthur W.; Sevilla, Michael D.

2012-01-01

This work reports an ESR and product analysis investigation of Kr-86 ion-beam irradiation of hydrated DNA at 77 K. The irradiation results in the formation and trapping of both base radicals and sugar phosphate radicals (DNA backbone radicals). The absolute yields (G, μmol/J) of the base radicals are smaller than the yields found in similarly prepared γ-irradiated DNA samples, and the relative yields of backbone radicals relative to base radicals are much higher than that found in γ-irradiated samples. From these results, we have elaborated our radiation chemical model of the track structure for ion-beam irradiated DNA as it applies to krypton ion-beams. The base radicals, which are trapped as ion radicals or reversibly protonated or deprotonated ion radicals, are formed almost entirely in the track penumbra, a region in which radiation chemical effects are similar to those found in γ-irradiated samples. By comparing the yields of base radicals in ion-beam samples to the yields of the same radicals in γ-irradiated samples, the partition of energy between the low-LET region (penumbra) and the core is experimentally determined. The neutral sugar and other backbone radicals, which are not as susceptible to recombination as are ion radicals, are formed largely in the track core. The backbone radicals show a linear dose response up to very high doses. Unaltered base release yields in Kr-86 irradiated hydrated DNA are equal to sugar radical yields within experimental error limits, consistent with radiation-chemical processes in which all base release originates with sugar radicals. Two phosphorus-centered radicals from fragmentation of the DNA backbone are found in low yields. PMID:23106211

Generation of Marker- and/or Backbone-Free Transgenic Wheat Plants via Agrobacterium-Mediated Transformation.

PubMed

Wang, Gen-Ping; Yu, Xiu-Dao; Sun, Yong-Wei; Jones, Huw D; Xia, Lan-Qin

2016-01-01

Horizontal transfer of antibiotic resistance genes to animals and vertical transfer of herbicide resistance genes to the weedy relatives are perceived as major biosafety concerns in genetically modified (GM) crops. In this study, five novel vectors which used gusA and bar as a reporter gene and a selection marker gene, respectively, were constructed based on the pCLEAN dual binary vector system. Among these vectors, 1G7B and 5G7B carried two T-DNAs located on two respective plasmids with 5G7B possessing an additional virGwt gene. 5LBTG154 and 5TGTB154 carried two T-DNAs in the target plasmid with either one or double right borders, and 5BTG154 carried the selectable marker gene on the backbone outside of the T-DNA left border in the target plasmid. In addition, 5BTG154, 5LBTG154, and 5TGTB154 used pAL154 as a helper plasmid which contains Komari fragment to facilitate transformation. These five dual binary vector combinations were transformed into Agrobacterium strain AGL1 and used to transform durum wheat cv Stewart 63. Evaluation of the co-transformation efficiencies, the frequencies of marker-free transgenic plants, and integration of backbone sequences in the obtained transgenic lines indicated that two vectors (5G7B and 5TGTB154) were more efficient in generating marker-free transgenic wheat plants with no or minimal integration of backbone sequences in the wheat genome. The vector series developed in this study for generation of marker- and/or backbone-free transgenic wheat plants via Agrobacterium -mediated transformation will be useful to facilitate the creation of "clean" GM wheat containing only the foreign genes of agronomic importance.

Direct observation of backbone planarization via side-chain alignment in single bulky-substituted polythiophenes

NASA Astrophysics Data System (ADS)

Raithel, Dominic; Simine, Lena; Pickel, Sebastian; Schötz, Konstantin; Panzer, Fabian; Baderschneider, Sebastian; Schiefer, Daniel; Lohwasser, Ruth; Köhler, Jürgen; Thelakkat, Mukundan; Sommer, Michael; Köhler, Anna; Rossky, Peter J.; Hildner, Richard

2018-03-01

The backbone conformation of conjugated polymers affects, to a large extent, their optical and electronic properties. The usually flexible substituents provide solubility and influence the packing behavior of conjugated polymers in films or in bad solvents. However, the role of the side chains in determining and potentially controlling the backbone conformation, and thus the optical and electronic properties on the single polymer level, is currently under debate. Here, we investigate directly the impact of the side chains by studying the bulky-substituted poly(3-(2,5-dioctylphenyl)thiophene) (PDOPT) and the common poly(3-hexylthiophene) (P3HT), both with a defined molecular weight and high regioregularity, using low-temperature single-chain photoluminescence (PL) spectroscopy and quantum-classical simulations. Surprisingly, the optical transition energy of PDOPT is significantly (˜2,000 cm‑1 or 0.25 eV) red-shifted relative to P3HT despite a higher static and dynamic disorder in the former. We ascribe this red shift to a side-chain induced backbone planarization in PDOPT, supported by temperature-dependent ensemble PL spectroscopy. Our atomistic simulations reveal that the bulkier 2,5-dioctylphenyl side chains of PDOPT adopt a clear secondary helical structural motif and thus protect conjugation, i.e., enforce backbone planarity, whereas, for P3HT, this is not the case. These different degrees of planarity in both thiophenes do not result in different conjugation lengths, which we found to be similar. It is rather the stronger electronic coupling between the repeating units in the more planar PDOPT which gives rise to the observed spectral red shift as well as to a reduced calculated electron‑hole polarization.

Kr-86 ion-beam irradiation of hydrated DNA: free radical and unaltered base yields.

PubMed

Becker, David; Adhikary, Amitava; Tetteh, Smedley T; Bull, Arthur W; Sevilla, Michael D

2012-12-01

This work reports an ESR and product analysis investigation of Kr-86 ion-beam irradiation of hydrated DNA at 77 K. The irradiation results in the formation and trapping of both base radicals and sugar phosphate radicals (DNA backbone radicals). The absolute yields (G, μmol/J) of the base radicals are smaller than the yields found in similarly prepared γ-irradiated DNA samples, and the relative yields of backbone radicals relative to base radicals are much higher than that found in γ-irradiated samples. From these results, we have elaborated our radiation chemical model of the track structure for ion-beam irradiated DNA as it applies to krypton ion-beams. The base radicals, which are trapped as ion radicals or reversibly protonated or deprotonated ion radicals, are formed almost entirely in the track penumbra, a region in which radiation chemical effects are similar to those found in γ-irradiated samples. By comparing the yields of base radicals in ion-beam samples to the yields of the same radicals in γ-irradiated samples, the partition of energy between the low-LET region (penumbra) and the core is experimentally determined. The neutral sugar and other backbone radicals, which are not as susceptible to recombination as are ion radicals, are formed largely in the track core. The backbone radicals show a linear dose response up to very high doses. Unaltered base release yields in Kr-86 irradiated hydrated DNA are equal to sugar radical yields within experimental error limits, consistent with radiation-chemical processes in which all base release originates with sugar radicals. Two phosphorus-centered radicals from fragmentation of the DNA backbone are found in low yields.

Overcoming deep roots, fast rates, and short internodes to resolve the ancient rapid radiation of eupolypod II ferns.

PubMed

Rothfels, Carl J; Larsson, Anders; Kuo, Li-Yaung; Korall, Petra; Chiou, Wen-Liang; Pryer, Kathleen M

2012-05-01

Backbone relationships within the large eupolypod II clade, which includes nearly a third of extant fern species, have resisted elucidation by both molecular and morphological data. Earlier studies suggest that much of the phylogenetic intractability of this group is due to three factors: (i) a long root that reduces apparent levels of support in the ingroup; (ii) long ingroup branches subtended by a series of very short backbone internodes (the "ancient rapid radiation" model); and (iii) significantly heterogeneous lineage-specific rates of substitution. To resolve the eupolypod II phylogeny, with a particular emphasis on the backbone internodes, we assembled a data set of five plastid loci (atpA, atpB, matK, rbcL, and trnG-R) from a sample of 81 accessions selected to capture the deepest divergences in the clade. We then evaluated our phylogenetic hypothesis against potential confounding factors, including those induced by rooting, ancient rapid radiation, rate heterogeneity, and the Bayesian star-tree paradox artifact. While the strong support we inferred for the backbone relationships proved robust to these potential problems, their investigation revealed unexpected model-mediated impacts of outgroup composition, divergent effects of methods for countering the star-tree paradox artifact, and gave no support to concerns about the applicability of the unrooted model to data sets with heterogeneous lineage-specific rates of substitution. This study is among few to investigate these factors with empirical data, and the first to compare the performance of the two primary methods for overcoming the Bayesian star-tree paradox artifact. Among the significant phylogenetic results is the near-complete support along the eupolypod II backbone, the demonstrated paraphyly of Woodsiaceae as currently circumscribed, and the well-supported placement of the enigmatic genera Homalosorus, Diplaziopsis, and Woodsia.

TROSY of side-chain amides in large proteins

PubMed Central

Liu, Aizhuo; Yao, Lishan; Li, Yue; Yan, Honggao

2012-01-01

By using the mixed solvent of 50% H2O/50% D2O and employing deuterium decoupling, TROSY experiments exclusively detect NMR signals from semideuterated isotopomers of carboxamide groups with high sensitivities for proteins with molecular weights up to 80 kDa. This isotopomer-selective strategy extends TROSY experiments from exclusively detecting backbone to both backbone and side-chain amides, particularly in large proteins. Because of differences in both TROSY effect and dynamics between 15N–HE{DZ} and 15N–HZ{DE} isotopomers of the same carboxamide, the 15N transverse magnetization of the latter relaxes significantly faster than that of the former, which provides a direct and reliable stereospecific distinction between the two configurations. The TROSY effects on the 15N–HE{DZ} isotopomers of side-chain amides are as significant as on backbone amides. PMID:17347000

Copoly(imide-amides) containing hexafluoroisopropylidene

NASA Technical Reports Server (NTRS)

Irvin, David J.; Cassidy, Patrick E.; Cameron, Mitch L.

1990-01-01

The incorporation of the hexafluoroisopropylidene (HFIP or 6F) group into polymer backbones brings about important and useful changes in properties. These differences include increased thermal and environmental resistance and solubility and decreased dielectric constant and color. Several types of backbones have been substrates for the inclusion of HFIP and all results have reflected impressive property benefits. This project involved the incorporation of 6F groups into a poly(imide-amide) backbone by the condensation of a 6F-containing dianhydride with 4-aminobenzoic acid to yield a diimide terminated with two carboxylic acid groups. This diacid trimer was then polymerized with various diamines. The polymers were obtained in yields of 86-94 percent and with viscosities of 0.90-2.26 dL/g. They were stable to above 500 C and clear, colorless films could be cast from DMAc.

Charge delocalization characteristics of regioregular high mobility polymers

DOE PAGES

Coughlin, J. E.; Zhugayevych, A.; Wang, M.; ...

2017-01-01

Controlling the regioregularity among the structural units of narrow bandgap conjugated polymer backbones has led to improvements in optoelectronic properties, for example in the mobilities observed in field effect transistor devices. To investigate how the regioregularity affects quantities relevant to hole transport, regioregular and regiorandom oligomers representative of polymeric structures were studied using density functional theory. Several structural and electronic characteristics of the oligomers were compared, including chain planarity, cation spin density, excess charges on molecular units and internal reorganizational energy. The main difference between the regioregular and regiorandom oligomers is found to be the conjugated backbone planarity, while themore » reorganizational energies calculated are quite similar across the molecular family. Lastly, this work constitutes the first step on understanding the complex interplay of atomistic changes and an oligomer backbone structure toward modeling the charge transport properties.« less

A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream

DOE PAGES

Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.; ...

2016-01-01

Chemical restraints are a fundamental part of crystallographic protein structure refinement. In response to mounting evidence that conventional restraints have shortcomings, it has previously been documented that using backbone restraints that depend on the protein backbone conformation helps to address these shortcomings and improves the performance of refinements [Moriartyet al.(2014),FEBS J.281, 4061–4071]. It is important that these improvements be made available to all in the protein crystallography community. Toward this end, a change in the default geometry library used byPhenixis described here. Tests are presented showing that this change will not generate increased numbers of outliers during validation, or depositionmore » in the Protein Data Bank, during the transition period in which some validation tools still use the conventional restraint libraries.« less

A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.

Chemical restraints are a fundamental part of crystallographic protein structure refinement. In response to mounting evidence that conventional restraints have shortcomings, it has previously been documented that using backbone restraints that depend on the protein backbone conformation helps to address these shortcomings and improves the performance of refinements [Moriartyet al.(2014),FEBS J.281, 4061–4071]. It is important that these improvements be made available to all in the protein crystallography community. Toward this end, a change in the default geometry library used byPhenixis described here. Tests are presented showing that this change will not generate increased numbers of outliers during validation, or depositionmore » in the Protein Data Bank, during the transition period in which some validation tools still use the conventional restraint libraries.« less

Unusual Internal Electron Transfer in Conjugated Radical Polymers.

PubMed

Li, Fei; Gore, Danielle N; Wang, Shaoyang; Lutkenhaus, Jodie L

2017-08-07

Nitroxide-containing organic radical polymers (ORPs) have captured attention for their high power and fast redox kinetics. Yet a major challenge is the polymer's aliphatic backbone, resulting in a low electronic conductivity. Recent attempts that replace the aliphatic backbone with a conjugated one have not met with success. The reason for this is not understood until now. We examine a family of polythiophenes bearing nitroxide radical groups, showing that while both species are electrochemically active, there exists an internal electron transfer mechanism that interferes with stabilization of the polymer's fully oxidized form. This finding directs the future design of conjugated radical polymers in energy storage and electronics, where careful attention to the redox potential of the backbone relative to the organic radical species is needed. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Conduction in Polydiacetylene Bilayers.

DTIC Science & Technology

1979-12-04

bilayers. The basic apparatus for doping is shown in figure 2. The process consists of passing dry nitrogen over crystalline iodine and then over the...This indicates that the polymer backbone has little effect in the conduction machanism of a dark undoped sample but only comes into play upon...almost none to doping. This indicates that the polymer backbone has little effect in the conduction machanism of a dark undoped sample but only comes into

Semi-Autonomous Control with Cyber-Pain for Artificial Muscles and Smart Structures

DTIC Science & Technology

2010-09-15

avoid some key failure modes. Our approach has built on our developments in dynamic self-sensing and realistic simulation of DEA electromechanics...local controller) to avoid some key failure modes. Our approach has built on our developments in dynamic self-sensing and realistic simulation of DEA...strains [4]. In its natural state long polymer backbones are entangled with intermittent cross-links tying neighbouring backbones together. The soft

21st Century Truck Partnership 2013 Fall Meeting Summary Report

DTIC Science & Technology

2014-01-14

unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Medium - and heavy-duty vehicles serve as the backbone of America?s economy playing a vital role in moving...related to medium -duty and heavy-duty truck efficiency safety, and emissions by pursuing collaborative research and development among government and...Statement A. Approved for public release. 2   ACKNOWLEDGEMENTS Medium - and heavy-duty vehicles serve as the backbone of America’s economy

The backbone N-(4-azidobutyl) linker for the preparation of peptide chimera.

PubMed

Fernández-Llamazares, Ana I; García, Jesús; Adan, Jaume; Meunier, David; Mitjans, Francesc; Spengler, Jan; Albericio, Fernando

2013-09-06

A robust synthetic strategy for the introduction of the N-(4-azidobutyl) linker into peptides using standard SPPS techniques is described. Based on the example of Cilengitide it is shown that the N-(4-azidobutyl) group exerts similar conformational restraints as a backbone N-Me group and allows conjugation of a desired molecule either via click chemistry or-after azide reduction-via acylation or reductive alkylation.

Carboxylated hyperbranched poly(glycidol)s for preparation of pH-sensitive liposomes.

PubMed

Yuba, Eiji; Harada, Atsushi; Sakanishi, Yuichi; Kono, Kenji

2011-01-05

Previous reports by the authors described intracellular delivery using liposomes modified with various carboxylated poly(glycidol) derivatives. These linear polymer-modified liposomes exhibited a pH-dependent membrane fusion behavior in cellular acidic compartments. However, the effect of the backbone structure on membrane fusion activity remains unknown. Therefore, this study specifically investigated the backbone structure to obtain pH-sensitive polymers with much higher fusogenic activity and to reveal the effect of the polymer backbone structure on the interaction with the membrane. Hyperbranched poly(glycidol) (HPG) derivatives were prepared as a new type of pH-sensitive polymer and used for the modification of liposomes. The resultant HPG derivatives exhibited high hydrophobicity and intensive interaction with the membrane concomitantly with the increasing degree of polymerization (DP). Furthermore, HPG derivatives showed a stronger interaction with the membrane than the linear polymers show. Liposomes modified with HPG derivatives of high DP delivered contents into the cytosol of DC2.4 cells, a dendritic cell line, more effectively than the linear polymer-modified liposomes do. Results show that the backbone structure of pH-sensitive polymers affected their pH-sensitivity and interaction with liposomal and cellular membranes. Copyright © 2010 Elsevier B.V. All rights reserved.

Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools.

PubMed

Monleón, Daniel; Colson, Kimberly; Moseley, Hunter N B; Anklin, Clemens; Oswald, Robert; Szyperski, Thomas; Montelione, Gaetano T

2002-01-01

Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.

Geometry motivated alternative view on local protein backbone structures.

PubMed

Zacharias, Jan; Knapp, Ernst Walter

2013-11-01

We present an alternative to the classical Ramachandran plot (R-plot) to display local protein backbone structure. Instead of the (φ, ψ)-backbone angles relating to the chemical architecture of polypeptides generic helical parameters are used. These are the rotation or twist angle ϑ and the helical rise parameter d. Plots with these parameters provide a different view on the nature of local protein backbone structures. It allows to display the local structures in polar (d, ϑ)-coordinates, which is not possible for an R-plot, where structural regimes connected by periodicity appear disconnected. But there are other advantages, like a clear discrimination of the handedness of a local structure, a larger spread of the different local structure domains--the latter can yield a better separation of different local secondary structure motives--and many more. Compared to the R-plot we are not aware of any major disadvantage to classify local polypeptide structures with the (d, ϑ)-plot, except that it requires some elementary computations. To facilitate usage of the new (d, ϑ)-plot for protein structures we provide a web application (http://agknapp.chemie.fu-berlin.de/secsass), which shows the (d, ϑ)-plot side-by-side with the R-plot. © 2013 The Protein Society.

Toward structural dynamics: protein motions viewed by chemical shift modulations and direct detection of C'N multiple-quantum relaxation.

PubMed

Mori, Mirko; Kateb, Fatiha; Bodenhausen, Geoffrey; Piccioli, Mario; Abergel, Daniel

2010-03-17

Multiple quantum relaxation in proteins reveals unexpected relationships between correlated or anti-correlated conformational backbone dynamics in alpha-helices or beta-sheets. The contributions of conformational exchange to the relaxation rates of C'N coherences (i.e., double- and zero-quantum coherences involving backbone carbonyl (13)C' and neighboring amide (15)N nuclei) depend on the kinetics of slow exchange processes, as well as on the populations of the conformations and chemical shift differences of (13)C' and (15)N nuclei. The relaxation rates of C'N coherences, which reflect concerted fluctuations due to slow chemical shift modulations (CSMs), were determined by direct (13)C detection in diamagnetic and paramagnetic proteins. In well-folded proteins such as lanthanide-substituted calbindin (CaLnCb), copper,zinc superoxide dismutase (Cu,Zn SOD), and matrix metalloproteinase (MMP12), slow conformational exchange occurs along the entire backbone. Our observations demonstrate that relaxation rates of C'N coherences arising from slow backbone dynamics have positive signs (characteristic of correlated fluctuations) in beta-sheets and negative signs (characteristic of anti-correlated fluctuations) in alpha-helices. This extends the prospects of structure-dynamics relationships to slow time scales that are relevant for protein function and enzymatic activity.

Impact of lignin polymer backbone esters on ionic liquid pretreatment of poplar

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Kwang Ho; Dutta, Tanmoy; Ralph, John

Biomass pretreatment remains an essential step in lignocellulosic biofuel production, largely to facilitate the efficient removal of lignin and increase enzyme accessibility to the polysaccharides. In recent years, there have been significant efforts in planta to reduce lignin content or modify its composition to overcome the inherent recalcitrance that it imposes on lignocellulosic biomass during processing. Here, transgenic poplar lines in which monolignol ferulate conjugates were synthesized during cell wall development to introduce, during lignification, readily cleavable ester linkages into the lignin polymer backbone (i.e., "zip lignin"), along with wild-type (WT) controls, were pretreated with different ionic liquids (ILs). Themore » strategic introduction of ester bonds into the lignin backbone resulted in increased pretreatment efficiency and released more carbohydrates with lower energy input. After pretreatment with any of three different ILs, and after limited saccharification, the transgenic poplars, especially those with relatively higher amounts of incorporated monolignol ferulate conjugates, yielded up to 23% higher sugar levels compared to WT plants. Our findings clearly demonstrate that the introduction of ester linkages into the lignin polymer backbone decreases biomass recalcitrance in poplar has the potential to reduce the energy and/or amount of IL required for effective pretreatment, and could enable the development of an economically viable and sustainable biorefinery process.« less

Impact of lignin polymer backbone esters on ionic liquid pretreatment of poplar

DOE PAGES

Kim, Kwang Ho; Dutta, Tanmoy; Ralph, John; ...

2017-04-20

Biomass pretreatment remains an essential step in lignocellulosic biofuel production, largely to facilitate the efficient removal of lignin and increase enzyme accessibility to the polysaccharides. In recent years, there have been significant efforts in planta to reduce lignin content or modify its composition to overcome the inherent recalcitrance that it imposes on lignocellulosic biomass during processing. Here, transgenic poplar lines in which monolignol ferulate conjugates were synthesized during cell wall development to introduce, during lignification, readily cleavable ester linkages into the lignin polymer backbone (i.e., "zip lignin"), along with wild-type (WT) controls, were pretreated with different ionic liquids (ILs). Themore » strategic introduction of ester bonds into the lignin backbone resulted in increased pretreatment efficiency and released more carbohydrates with lower energy input. After pretreatment with any of three different ILs, and after limited saccharification, the transgenic poplars, especially those with relatively higher amounts of incorporated monolignol ferulate conjugates, yielded up to 23% higher sugar levels compared to WT plants. Our findings clearly demonstrate that the introduction of ester linkages into the lignin polymer backbone decreases biomass recalcitrance in poplar has the potential to reduce the energy and/or amount of IL required for effective pretreatment, and could enable the development of an economically viable and sustainable biorefinery process.« less

Flexible Xxx–Asp/Asn and Gly–Xxx Residues of Equine Cytochrome c in Matrix-Assisted Laser Desorption/Ionization In-Source Decay Mass Spectrometry

PubMed Central

Takayama, Mitsuo

2012-01-01

The backbone flexibility of a protein has been studied from the standpoint of the susceptibility of amino acid residues to in-source decay (ISD) in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). Residues more susceptible to MALDI-ISD, namely Xxx–Asp/Asn and Gly–Xxx, were identified from the discontinuous intense peak of c′-ions originating from specific cleavage at N–Cα bonds of the backbone of equine cytochrome c. The identity of the residues susceptible to ISD was consistent with the known flexible backbone amides as estimated by hydrogen/deuterium exchange (HDX) experiments. The identity of these flexible amino acid residues (Asp, Asn, and Gly) is consistent with the fact that these residues are preferred in flexible secondary structure free from intramolecular hydrogen-bonded structures such as α-helix and β-sheet. The MALDI-ISD spectrum of equine cytochrome c gave not only intense N-terminal side c′-ions originating from N–Cα bond cleavage at Xxx–Asp/Asn and Gly–Xxx residues, but also C-terminal side complement z′-ions originating from the same cleavage sites. The present study implies that MALDI-ISD can give information about backbone flexibility of proteins, comparable with the protection factors estimated by HDX. PMID:24349908

Flexible xxx-asp/asn and gly-xxx residues of equine cytochrome C in matrix-assisted laser desorption/ionization in-source decay mass spectrometry.

PubMed

Takayama, Mitsuo

2012-01-01

The backbone flexibility of a protein has been studied from the standpoint of the susceptibility of amino acid residues to in-source decay (ISD) in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). Residues more susceptible to MALDI-ISD, namely Xxx-Asp/Asn and Gly-Xxx, were identified from the discontinuous intense peak of c'-ions originating from specific cleavage at N-Cα bonds of the backbone of equine cytochrome c. The identity of the residues susceptible to ISD was consistent with the known flexible backbone amides as estimated by hydrogen/deuterium exchange (HDX) experiments. The identity of these flexible amino acid residues (Asp, Asn, and Gly) is consistent with the fact that these residues are preferred in flexible secondary structure free from intramolecular hydrogen-bonded structures such as α-helix and β-sheet. The MALDI-ISD spectrum of equine cytochrome c gave not only intense N-terminal side c'-ions originating from N-Cα bond cleavage at Xxx-Asp/Asn and Gly-Xxx residues, but also C-terminal side complement z'-ions originating from the same cleavage sites. The present study implies that MALDI-ISD can give information about backbone flexibility of proteins, comparable with the protection factors estimated by HDX.

Mutation of charged residues to neutral ones accelerates urea denaturation of HP-35.

PubMed

Wei, Haiyan; Yang, Lijiang; Gao, Yi Qin

2010-09-16

Following the studies of urea denaturation of β-hairpins using molecular dynamics, in this paper, molecular dynamics simulations of two peptides, a 35 residue three helix bundle villin headpiece protein HP-35 and its doubly norleucine-substituent mutant (Lys24Nle/Lys29Nle) HP-35 NleNle, were undertaken in urea solutions to understand the molecular mechanism of urea denaturation of α-helices. The mutant HP-35 NleNle was found to denature more easily than the wild type. During the expansion of the small hydrophobic core, water penetration occurs first, followed by that of urea molecules. It was also found that the initial hydration of the peptide backbone is achieved through water hydrogen bonding with the backbone CO groups during the denaturation of both polypeptides. The mutation of the two charged lysine residues to apolar norleucine enhances the accumulation of urea near the hydrophobic core and facilitates the denaturation process. Urea also interacts directly with the peptide backbone as well as side chains, thereby stabilizing nonnative conformations. The mechanism revealed here is consistent with the previous study on secondary structure of β-hairpin polypeptide, GB1, PEPTIDE 1, and TRPZIP4, suggesting that there is a general mechanism in the denaturation of protein backbone hydrogen bonds by urea.

Closer insight into the structure of moderate to densely branched comb polymers by combining modelling and linear rheological measurements.

PubMed

Ahmadi, Mostafa; Pioge, Sandie; Fustin, Charles-Andre; Gohy, Jean-Francois; van Ruymbeke, Evelyne

2017-02-07

Synthesis of combs with well-entangled backbones and long branches with high densities has always been a challenge. Steric hindrance frequently leads to coupling of chains and structural imperfections that cannot be easily distinguished by traditional characterization methods. Research studies have therefore tried to use a combination of different methods to obtain more information on the actual microstructures. In this work, a grafting-from approach is used to synthesize poly(n-butyl acrylate) combs using atom transfer radical polymerization (ATRP) in three steps including the synthesis of a backbone, cleavage of protecting groups and growth of side branches. We have compared the linear viscoelastic properties theoretically predicted by a time marching algorithm (TMA) tube based model with the measured rheological behaviour to provide a better insight into the actual microstructure formed during synthesis. For combs with branches smaller than an entanglement, no discernible hierarchical relaxation can be distinguished, while for those with longer branches, a high frequency plateau made by entangled branches can be separated from backbone's relaxation. Dilution of the backbone, after relaxation of side branches, may accelerate the final relaxation, while extra friction can delay it especially for longer branches. Such a comparison provides a better assessment of the microstructure formed in combs.

A Protocol for Scalable Loop-Free Multicast Routing

DTIC Science & Technology

1997-01-01

N ÁŜ+@"B�tQDVO:(#ÄŜ+ÄIO8+@D@DÀiÄq/"VÂaÀi:!8A:<B?V+B3/"V+I 8AQ "kVÄDV|¾VO¾K/"VO:J;¬K�@ÄDVNt�QDV:(𔄂+:=V|QD@D:zV+8cI#ඝ/RöV> Ä...8@DVOK¶Å�)/"Ài:�:zÀcQDÄzVO:yø|K¶@.W¢K¶ÅiQD:=Vù iIc5�T�@*(@�QR¾7/"VO:�ÀA :=VS8c;qÀi@"ILÀcQRÃMBqŜOWV I 8AQ "kV+B7¸qî�÷ï ½�ÄzÀ�8A:z:=K�WVI

Optical signal processing techniques and applications of optical phase modulation in high-speed communication systems

NASA Astrophysics Data System (ADS)

Deng, Ning

In recent years, optical phase modulation has attracted much research attention in the field of fiber optic communications. Compared with the traditional optical intensity-modulated signal, one of the main merits of the optical phase-modulated signal is the better transmission performance. For optical phase modulation, in spite of the comprehensive study of its transmission performance, only a little research has been carried out in terms of its functions, applications and signal processing for future optical networks. These issues are systematically investigated in this thesis. The research findings suggest that optical phase modulation and its signal processing can greatly facilitate flexible network functions and high bandwidth which can be enjoyed by end users. In the thesis, the most important physical-layer technology, signal processing and multiplexing, are investigated with optical phase-modulated signals. Novel and advantageous signal processing and multiplexing approaches are proposed and studied. Experimental investigations are also reported and discussed in the thesis. Optical time-division multiplexing and demultiplexing. With the ever-increasing demand on communication bandwidth, optical time division multiplexing (OTDM) is an effective approach to upgrade the capacity of each wavelength channel in current optical systems. OTDM multiplexing can be simply realized, however, the demultiplexing requires relatively complicated signal processing and stringent timing control, and thus hinders its practicability. To tackle this problem, in this thesis a new OTDM scheme with hybrid DPSK and OOK signals is proposed. Experimental investigation shows this scheme can greatly enhance the demultiplexing timing misalignment and improve the demultiplexing performance, and thus make OTDM more practical and cost effective. All-optical signal processing. In current and future optical communication systems and networks, the data rate per wavelength has been approaching the speed limitation of electronics. Thus, all-optical signal processing techniques are highly desirable to support the necessary optical switching functionalities in future ultrahigh-speed optical packet-switching networks. To cope with the wide use of optical phase-modulated signals, in the thesis, an all-optical logic for DPSK or PSK input signals is developed, for the first time. Based on four-wave mixing in semiconductor optical amplifier, the structure of the logic gate is simple, compact, and capable of supporting ultrafast operation. In addition to the general logic processing, a simple label recognition scheme, as a specific signal processing function, is proposed for phase-modulated label signals. The proposed scheme can recognize any incoming label pattern according to the local pattern, and is potentially capable of handling variable-length label patterns. Optical access network with multicast overlay and centralized light sources. In the arena of optical access networks, wavelength division multiplexing passive optical network (WDM-PON) is a promising technology to deliver high-speed data traffic. However, most of proposed WDM-PONs only support conventional point-to-point service, and cannot meet the requirement of increasing demand on broadcast and multicast service. In this thesis, a simple network upgrade is proposed based on the traditional PON architecture to support both point-to-point and multicast service. In addition, the two service signals are modulated on the same lightwave carrier. The upstream signal is also remodulated on the same carrier at the optical network unit, which can significantly relax the requirement on wavelength management at the network unit.

Interacting With A Near Real-Time Urban Digital Watershed Using Emerging Geospatial Web Technologies

NASA Astrophysics Data System (ADS)

Liu, Y.; Fazio, D. J.; Abdelzaher, T.; Minsker, B.

2007-12-01

The value of real-time hydrologic data dissemination including river stage, streamflow, and precipitation for operational stormwater management efforts is particularly high for communities where flash flooding is common and costly. Ideally, such data would be presented within a watershed-scale geospatial context to portray a holistic view of the watershed. Local hydrologic sensor networks usually lack comprehensive integration with sensor networks managed by other agencies sharing the same watershed due to administrative, political, but mostly technical barriers. Recent efforts on providing unified access to hydrological data have concentrated on creating new SOAP-based web services and common data format (e.g. WaterML and Observation Data Model) for users to access the data (e.g. HIS and HydroSeek). Geospatial Web technology including OGC sensor web enablement (SWE), GeoRSS, Geo tags, Geospatial browsers such as Google Earth and Microsoft Virtual Earth and other location-based service tools provides possibilities for us to interact with a digital watershed in near-real-time. OGC SWE proposes a revolutionary concept towards a web-connected/controllable sensor networks. However, these efforts have not provided the capability to allow dynamic data integration/fusion among heterogeneous sources, data filtering and support for workflows or domain specific applications where both push and pull mode of retrieving data may be needed. We propose a light weight integration framework by extending SWE with open source Enterprise Service Bus (e.g., mule) as a backbone component to dynamically transform, transport, and integrate both heterogeneous sensor data sources and simulation model outputs. We will report our progress on building such framework where multi-agencies" sensor data and hydro-model outputs (with map layers) will be integrated and disseminated in a geospatial browser (e.g. Microsoft Virtual Earth). This is a collaborative project among NCSA, USGS Illinois Water Science Center, Computer Science Department at UIUC funded by the Adaptive Environmental Infrastructure Sensing and Information Systems initiative at UIUC.

Polyarylether composition and membrane

DOEpatents

Hung, Joyce; Brunelle, Daniel Joseph; Harmon, Marianne Elisabeth; Moore, David Roger; Stone, Joshua James; Zhou, Hongyi; Suriano, Joseph Anthony

2010-11-09

A composition including a polyarylether copolymer is provided. The copolymer includes a polyarylether backbone; and a sulfonated oligomeric group bonded to the polyarylether suitable for use as a cation conducting membrane. Method of bonding a sulfonated oligomeric group to the polyarylether backbone to form a polyarylether copolymer. The membrane may be formed from the polyarylether copolymer composition. The chain length of the sulfonated oligomeric group may be controlled to affect or control the ion conductivity of the membrane.

Electrochemical impedance study of the interaction of metal ions with unlabeled PNA.

PubMed

Gao, Lan; Li, Congjuan; Li, Xiaohong; Kraatz, Heinz-Bernhard

2010-09-14

The interactions of the metal ions Mg(2+), Zn(2+), Ni(2+), and Co(2+) with thin films of peptide nucleic acids (PNAs) were studied by electrochemical impedance spectroscopy (EIS), and the results show that Zn(2+), Ni(2+) and Co(2+) interacted favorably with the PNA film involving the backbone and the nucleobases with the exception of Mg(2+) for which the interaction with the backbone appears to be dominant.

Solid-Phase Synthesis of RNA Analogs Containing Phosphorodithioate Linkages.

PubMed

Yang, Xianbin

2017-09-18

The oligoribonucleotide phosphorodithioate (PS2-RNA) modification uses two sulfur atoms to replace two non-bridging oxygen atoms at an internucleotide phosphorodiester backbone linkage. Like a natural phosphodiester RNA backbone linkage, a PS2-modified backbone linkage is achiral at phosphorus. PS2-RNAs are highly stable to nucleases and several in vitro assays have demonstrated their biological activity. For example, PS2-RNAs silenced mRNA in vitro and bound to protein targets in the form of PS2-aptamers (thioaptamers). Thus, the interest in and promise of PS2-RNAs has drawn attention to synthesizing, isolating, and characterizing these compounds. RNA-thiophosphoramidite monomers are commercially available from AM Biotechnologies and this unit describes an effective methodology for solid-phase synthesis, deprotection, and purification of RNAs having PS2 internucleotide linkages. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Preparation of metallic cation conducting polymers based on sterically hindered phenols containing polymeric systems

DOEpatents

Skotheim, Terje A.; Okamoto, Yoshiyuki; Lee, Hung S.

1989-01-01

The present invention relates to ion-conducting solvent-free polymeric systems characterized as being cationic single ion conductors. The solvent-free polymer electrolytes comprise a flexible polymer backbone to which is attached a metal salt, such as a lithium, sodium or potassium salt, of a sterically hindered phenol. The solid polymer electrolyte may be prepared either by (1) attaching the hindered phenol directly to a flexible polymeric backbone, followed by neutralization of the phenolic OH's or (2) reacting the hindered phenol with a polymer precursor which is then polymerized to form a flexible polymer having phenolic OH's which are subsequently neutralized. Preferably the hindered phenol-modified polymeric backbone contains a polyether segment. The ionic conductivity of these solvent-free polymer electrolytes has been measured to be in the range of 10.sup.-4 to 10.sup.-7 S cm.sup.-1 at room temperature.

Preparation of metallic cation conducting polymers based on sterically hindered phenols containing polymeric systems

DOEpatents

Skotheim, T.A.; Okamoto, Yoshiyuki; Lee, H.S.

1989-11-21

The present invention relates to ion-conducting solvent-free polymeric systems characterized as being cationic single ion conductors. The solvent-free polymer electrolytes comprise a flexible polymer backbone to which is attached a metal salt, such as a lithium, sodium or potassium salt, of a sterically hindered phenol. The solid polymer electrolyte may be prepared either by (1) attaching the hindered phenol directly to a flexible polymeric backbone, followed by neutralization of the phenolic OH's or (2) reacting the hindered phenol with a polymer precursor which is then polymerized to form a flexible polymer having phenolic OH's which are subsequently neutralized. Preferably the hindered phenol-modified polymeric backbone contains a polyether segment. The ionic conductivity of these solvent-free polymer electrolytes has been measured to be in the range of 10[sup [minus]4] to 10[sup [minus]7] S cm[sup [minus]1] at room temperature.

Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

PubMed Central

Shen, Yang; Bax, Ad

2013-01-01

A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, ≥ 90% fraction of the residues, with an error rate smaller than ca 3.5%, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed (φ,ψ) torsion angles of ca 12°. TALOS-N also reports sidechain χ1 rotameric states for about 50% of the residues, and a consistency with reference structures of 89%. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts. PMID:23728592

Nonribosomal biosynthesis of backbone-modified peptides

NASA Astrophysics Data System (ADS)

Niquille, David L.; Hansen, Douglas A.; Mori, Takahiro; Fercher, David; Kries, Hajo; Hilvert, Donald

2018-03-01

Biosynthetic modification of nonribosomal peptide backbones represents a potentially powerful strategy to modulate the structure and properties of an important class of therapeutics. Using a high-throughput assay for catalytic activity, we show here that an L-Phe-specific module of an archetypal nonribosomal peptide synthetase can be reprogrammed to accept and process the backbone-modified amino acid (S)-β-Phe with near-native specificity and efficiency. A co-crystal structure with a non-hydrolysable aminoacyl-AMP analogue reveals the origins of the 40,000-fold α/β-specificity switch, illuminating subtle but precise remodelling of the active site. When the engineered catalyst was paired with downstream module(s), (S)-β-Phe-containing peptides were produced at preparative scale in vitro (~1 mmol) and high titres in vivo (~100 mg l-1), highlighting the potential of biosynthetic pathway engineering for the construction of novel nonribosomal β-frameworks.

Uranyl mediated photofootprinting reveals strong E. coli RNA polymerase--DNA backbone contacts in the +10 region of the DeoP1 promoter open complex.

PubMed Central

Jeppesen, C; Nielsen, P E

1989-01-01

Employing a newly developed uranyl photofootprinting technique (Nielsen et al. (1988) FEBS Lett. 235, 122), we have analyzed the structure of the E. coli RNA polymerase deoP1 promoter open complex. The results show strong polymerase DNA backbone contacts in the -40, -10, and most notably in the +10 region. These results suggest that unwinding of the -12 to +3 region of the promoter in the open complex is mediated through polymerase DNA backbone contacts on both sides of this region. The pattern of bases that are hyperreactive towards KMnO4 or uranyl within the -12 to +3 region furthermore argues against a model in which this region is simply unwound and/or single stranded. The results indicate specific protein contacts and/or a fixed DNA conformation within the -12 to +3 region. Images PMID:2503811

Self-Assembly of Narrowly Dispersed Brush Diblock Copolymers with Domain Spacing more than 100 nm

NASA Astrophysics Data System (ADS)

Gu, Weiyin; Sveinbjornsson, Benjamin; Hong, Sung Woo; Grubbs, Robert; Russell, Thomas

2012-02-01

Self-assembled structures of high molecular weight (MW), narrow molecular weight distribution brush block copolymers containing polylactic acid (PLA) and polystyrene (PS) side chains with similar MWs were studied in both the melt and thin films. The polynorbornene-backbone-based brush diblock copolymers containing approximately equal volume fractions of each block self-assembled into highly ordered lamellae with domain spacing over 100 nm, as revealed by SAXS, GISAXS and AFM. The domain size increased approximately linearly with backbone length, which indicated an extended conformation of the backbone in the ordered state. The length of side chains also played a significant role in terms of controlling the domain size. As the degree of polymerization (DP) increased, the symmetric brush diblock copolymers with longer side chains tended to form larger lamellar microdomains in comparison to those that have the same DP but shorter side chains.

Nonlinear model identification and spectral submanifolds for multi-degree-of-freedom mechanical vibrations

NASA Astrophysics Data System (ADS)

Szalai, Robert; Ehrhardt, David; Haller, George

2017-06-01

In a nonlinear oscillatory system, spectral submanifolds (SSMs) are the smoothest invariant manifolds tangent to linear modal subspaces of an equilibrium. Amplitude-frequency plots of the dynamics on SSMs provide the classic backbone curves sought in experimental nonlinear model identification. We develop here, a methodology to compute analytically both the shape of SSMs and their corresponding backbone curves from a data-assimilating model fitted to experimental vibration signals. This model identification utilizes Taken's delay-embedding theorem, as well as a least square fit to the Taylor expansion of the sampling map associated with that embedding. The SSMs are then constructed for the sampling map using the parametrization method for invariant manifolds, which assumes that the manifold is an embedding of, rather than a graph over, a spectral subspace. Using examples of both synthetic and real experimental data, we demonstrate that this approach reproduces backbone curves with high accuracy.

The September 11 attack: A percolation of individual passive support

NASA Astrophysics Data System (ADS)

Galam, S.

2002-04-01

A model to terrorism is presented using the theory of percolation. Terrorism power is related to the spontaneous formation of random backbones of people who are sympathetic to terrorism but without being directly involved in it. They just don't oppose in case they could. In the past such friendly-to-terrorism backbones have been always existing but were of finite size and localized to a given geographical area. The September 11 terrorist attack on the US has revealed for the first time the existence of a world wide spread extension. It is argued to have result from a sudden world percolation of otherwise unconnected and dormant world spread backbones of passive supporters. The associated strategic question is then to determine if collecting ground information could have predict and thus avoid such a transition. Our results show the answer is no, voiding the major criticism against intelligence services. To conclude the impact of military action is discussed.

Fused electron deficient semiconducting polymers for air stable electron transport.

PubMed

Onwubiko, Ada; Yue, Wan; Jellett, Cameron; Xiao, Mingfei; Chen, Hung-Yang; Ravva, Mahesh Kumar; Hanifi, David A; Knall, Astrid-Caroline; Purushothaman, Balaji; Nikolka, Mark; Flores, Jean-Charles; Salleo, Alberto; Bredas, Jean-Luc; Sirringhaus, Henning; Hayoz, Pascal; McCulloch, Iain

2018-01-29

Conventional semiconducting polymer synthesis typically involves transition metal-mediated coupling reactions that link aromatic units with single bonds along the backbone. Rotation around these bonds contributes to conformational and energetic disorder and therefore potentially limits charge delocalisation, whereas the use of transition metals presents difficulties for sustainability and application in biological environments. Here we show that a simple aldol condensation reaction can prepare polymers where double bonds lock-in a rigid backbone conformation, thus eliminating free rotation along the conjugated backbone. This polymerisation route requires neither organometallic monomers nor transition metal catalysts and offers a reliable design strategy to facilitate delocalisation of frontier molecular orbitals, elimination of energetic disorder arising from rotational torsion and allowing closer interchain electronic coupling. These characteristics are desirable for high charge carrier mobilities. Our polymers with a high electron affinity display long wavelength NIR absorption with air stable electron transport in solution processed organic thin film transistors.

The structure and dynamics in solution of Cu(I) pseudoazurin from Paracoccus pantotrophus.

PubMed Central

Thompson, G. S.; Leung, Y. C.; Ferguson, S. J.; Radford, S. E.; Redfield, C.

2000-01-01

The solution structure and backbone dynamics of Cu(I) pseudoazurin, a 123 amino acid electron transfer protein from Paracoccus pantotrophus, have been determined using NMR methods. The structure was calculated to high precision, with a backbone RMS deviation for secondary structure elements of 0.35+/-0.06 A, using 1,498 distance and 55 torsion angle constraints. The protein has a double-wound Greek-key fold with two alpha-helices toward its C-terminus, similar to that of its oxidized counterpart determined by X-ray crystallography. Comparison of the Cu(I) solution structure with the X-ray structure of the Cu(II) protein shows only small differences in the positions of some of the secondary structure elements. Order parameters S2, measured for amide nitrogens, indicate that the backbone of the protein is rigid on the picosecond to nanosecond timescale. PMID:10850794

Introduction to multiprotocol over ATM (MPOA)

NASA Astrophysics Data System (ADS)

Fredette, Andre N.

1997-10-01

Multiprotocol over ATM (MPOA) is a new protocol specified by the ATM Forum. MPOA provides a framework for effectively synthesizing bridging and routing with ATM in an environment of diverse protocols and network technologies. The primary goal of MPOA is the efficient transfer of inter-subnet unicast data in a LAN Emulation (LANE) environment. MPOA integrates LANE and the next hop resolution protocol (NHRP) to preserve the benefits of LAN Emulation, while allowing inter-subnet, internetwork layer protocol communication over ATM VCCs without requiring routers in the data path. It reduces latency and the internetwork layer forwarding load on backbone routers by enabling direct connectivity between ATM-attached edge devices (i.e., shortcuts). To establish these shortcuts, MPOA uses both routing and bridging information to locate the edge device closest to the addressed end station. By integrating LANE and NHRP, MPOA allows the physical separation of internetwork layer route calculation and forwarding, a technique known as virtual routing. This separation provides a number of key benefits including enhanced manageability and reduced complexity of internetwork layer capable edge devices. This paper provides an overview of MPOA that summarizes the goals, architecture, and key attributes of the protocol. In presenting this overview, the salient attributes of LANE and NHRP are described as well.

Dielectric relaxation of alkyl chains in graphite oxide and n-alkylammonium halides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ai, Xiaoqian; Tian, Yuchen; Gu, Min, E-mail: mgu@nju.edu.cn

2016-05-15

The dynamic of n-alkylammonium halides and n-alkylammonium cations (n = 12, 14, 16, 18) intercalated in graphite oxide (GO) have been investigated with complex impedance spectroscopy. X-ray diffraction, X-ray photoelectron spectroscopy, Fourier-transform infrared spectroscopy, elemental analysis and thermogravimetry served to characterize the materials. The intercalated alkylammonium cations distributes as monolayers (when n = 12, 14 or 16) or bilayers (when n = 18), with their long axis parallel to GO layers, and with cations of headgroups bonded ionically to C-O{sup -} groups of GO; backbones of the confined molecules remain free. All halides and intercalation compounds suffer dielectric loss atmore » low temperature. Arrhenius plots of the thermal dependence of the loss peaks, which are asymmetric, produce apparent activation energies that rise with increasing n. Ngai’s correlated-state model helps to correct for effects of dipole-dipole interaction, leading to virtually identical values for actual activation energy of 110 meV ± 5%; the values are also almost the same as the barrier energy for internal rotation in the alkyl macromolecule. We conclude that the relaxation of the alkylammonium cations arises not from C{sub 3} reorientation of the CH{sub 3} at its headgroup, but from small-angle wobbling around its major axis, an intrinsic motion.« less

Identification of Potent Virtual Leads Specific to S1' Loop of ADAMTS4: Pharmacophore Modeling, 3D-QSAR, Molecular Docking and Dynamic Studies.

PubMed

Suganya, P Rathi; Kalva, Sukesh; Saleena, Lilly M

2016-01-01

ADAMTS4 (Aggrecanase-1) is an important enzyme, which belongs to ADAMTS family. Aggrecanase-1 is involved in aggrecan degradation of articular cartilage in osteoarthritis and rheumatoid arthritis. Overall variability of S1' domain of ADAMTS4 has been the main selectivity determinant to design the unique inhibitors. 34 inhibitors from Binding database and literature were used to develop the pharmacophore model. The five featured pharmacophore model AHHRR had the best survival score of 3.493 and post-hoc score of 2.545, indicating that the model is highly reliable. The 3D-QSAR acquired had excellent r(2) value of 0.99 and GH score of 0.839. The validated pharmacophore model was used for insilico screening of Asinex and ZINC database for finding the potential lead compounds. ZINC00987406 and ASN04459656 which pose high glide score i.e >7 Kcal/mol and H-bond and hydrophobic interactions in the S1'loop residues of ADAMTS4 were subjected to Molecular Dynamics Simulation studies. Molecular dynamic simulation result indicates that the RMSD and RMSF of backbone atoms for the above complexes were within the limit of 2.0 A˚. These compounds can be potential candidates for osteoarthritis by inhibiting ADAMTS4.

Base excision repair: NMR backbone assignments of Escherichia coli formamidopyrimidine-DNA glycosylase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buchko, Garry W.; Wallace, Susan S.; Kennedy, Michael A.

2002-03-01

Oxidative damage is emerging as one of the most important mechanisms responsible for mutagenesis, carcinogenesis, aging, and various diseases (Farr and Kogma, 1991). One of the potential targets for oxidation is cellular DNA. While exposure to exogenous agents, such as ionizing radiation and chemicals, contributes to damaging DNA, the most important oxidative agents are endogenous, such as the reactive free radicals produced during normal oxidative metabolism (Adelman et., 1988). To mitigate the potentially deleterious effects of oxidative DNA damage virtually all aerobic organisms have developed complex repair mechanisms (Petit and Sancar, 1999). One repair mechanism, base excision repair (BER), appearsmore » to be responsible for replacing most oxidative DNA damage (David and Williams, 1998). Formamidopyrimidine-DNA glycosylase (Fpg), a 269-residue metalloprotein with a molecular weight of 30.2 kDa, is a key BER enzyme in prokaryotes (Boiteaux et al., 1987). Substrates recognized and released by Fpg include 7,8-dihydro-8-oxoguanine (8-oxoG), 2,6 diamino-4-hydroxy-5-formamido pyrimidine (Fapy-G), the adenine equivalents 8-oxoA and Fapy-A, 5-hydroxycytosine, 5-hydroxyuracil, B ureidoisobutiric acid, and a-R-hydroxy-B-ureidoisobutiric acid (Freidberg et al., 1995). In vitro Fpg bind double-stranded DNA and performs three catalytic activities: (i) DNA glycosylase, (ii) AP lyase, and (iii) deoxyribophosphodiesterase.« less

Conformational analysis of (1. -->. 4)-. beta. -D-mannan triacetate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deslandes, Y.; Marchessault, R.H.; Bluhm, T.L.

1983-01-01

In wood, algae, and tubers, glucomannans have varying mannose-to-glucose ratios (M/G). Since diffraction on glucomannans of widely varying M/G do not show significant change in unit-cell base plane dimensions, the authors have suggested that isomorphous replacement may occur in glucomannans. To further investigate this point, it has been undertaken conformational analysis of glucomannan triacetate in which the X-ray fiber diagram suggests that two nonequivalent residues make up the asymmetric unit. X-ray fiber diagrams of the triacetate of glucomannan from Tubera salep show twofold symmetry along the chain axis with a fiber repeat of 1.6 nm. This implies that the asymmetricmore » unit is composed of two pyranose rings since the virtual bond length of a single pyranose ring cannot be greater than approximately 0.54 nm. By using empirical potential functions, it could be shown that the minimum internal energy of a mannan triacetate chain corresponds to a state where contiguous mannose triacetate units are not conformationally equivalent. This supports the hypothesis of mannobiose hexaacetate as the asymmetric unit. Furthermore, introduction of glucose triacetate into the backbone did not change the minimum energy conformation, thereby lending support to the isomorphous replacement concept in crystalline glucomannans. 19 references, 13 figures, 2 tables.« less

Effective screening strategy using ensembled pharmacophore models combined with cascade docking: application to p53-MDM2 interaction inhibitors.

PubMed

Xue, Xin; Wei, Jin-Lian; Xu, Li-Li; Xi, Mei-Yang; Xu, Xiao-Li; Liu, Fang; Guo, Xiao-Ke; Wang, Lei; Zhang, Xiao-Jin; Zhang, Ming-Ye; Lu, Meng-Chen; Sun, Hao-Peng; You, Qi-Dong

2013-10-28

Protein-protein interactions (PPIs) play a crucial role in cellular function and form the backbone of almost all biochemical processes. In recent years, protein-protein interaction inhibitors (PPIIs) have represented a treasure trove of potential new drug targets. Unfortunately, there are few successful drugs of PPIIs on the market. Structure-based pharmacophore (SBP) combined with docking has been demonstrated as a useful Virtual Screening (VS) strategy in drug development projects. However, the combination of target complexity and poor binding affinity prediction has thwarted the application of this strategy in the discovery of PPIIs. Here we report an effective VS strategy on p53-MDM2 PPI. First, we built a SBP model based on p53-MDM2 complex cocrystal structures. The model was then simplified by using a Receptor-Ligand complex-based pharmacophore model considering the critical binding features between MDM2 and its small molecular inhibitors. Cascade docking was subsequently applied to improve the hit rate. Based on this strategy, we performed VS on NCI and SPECS databases and successfully discovered 6 novel compounds from 15 hits with the best, compound 1 (NSC 5359), K(i) = 180 ± 50 nM. These compounds can serve as lead compounds for further optimization.

The laminated layer: Recent advances and insights into Echinococcus biology and evolution.

PubMed

Díaz, Álvaro; Fernández, Cecilia; Pittini, Álvaro; Seoane, Paula I; Allen, Judith E; Casaravilla, Cecilia

2015-11-01

The laminated layer is the unique mucin-based extracellular matrix that protects Echinococcus larvae, and thus to an important extent, shapes host-parasite relationships in the larval echinococcoses. In 2011, we published twin reviews summarizing what was known about this structure. Since then, important advances have been made. Complete genomes and some RNAseq data are now available for E. multilocularis and E. granulosus, leading to the inference that the E. multilocularis LL is probably formed by a single type of mucin backbone, while a second apomucin subfamily additionally contributes to the E. granulosus LL. Previously suspected differences between E. granulosus and E. multilocularis in mucin glycan size have been confirmed and pinned down to the virtual absence of Galβ1-3 chains in E. multilocularis. The LL carbohydrates from both species have been found to interact selectively with the Kupffer cell receptor expressed in rodent liver macrophages, highlighting the ancestral adaptations to rodents as intermediate hosts and to the liver as infection site. Finally, LL particles have been shown to possess carbohydrate-independent mechanisms profoundly conditioning non-liver-specific dendritic cells and macrophages. These advances are discussed in an integrated way, and in the context of the newly determined phylogeny of Echinococcus and its taenid relatives. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Kinematic decomposition and classification of octopus arm movements.

PubMed

Zelman, Ido; Titon, Myriam; Yekutieli, Yoram; Hanassy, Shlomi; Hochner, Binyamin; Flash, Tamar

2013-01-01

The octopus arm is a muscular hydrostat and due to its deformable and highly flexible structure it is capable of a rich repertoire of motor behaviors. Its motor control system uses planning principles and control strategies unique to muscular hydrostats. We previously reconstructed a data set of octopus arm movements from records of natural movements using a sequence of 3D curves describing the virtual backbone of arm configurations. Here we describe a novel representation of octopus arm movements in which a movement is characterized by a pair of surfaces that represent the curvature and torsion values of points along the arm as a function of time. This representation allowed us to explore whether the movements are built up of elementary kinematic units by decomposing each surface into a weighted combination of 2D Gaussian functions. The resulting Gaussian functions can be considered as motion primitives at the kinematic level of octopus arm movements. These can be used to examine underlying principles of movement generation. Here we used combination of such kinematic primitives to decompose different octopus arm movements and characterize several movement prototypes according to their composition. The representation and methodology can be applied to the movement of any organ which can be modeled by means of a continuous 3D curve.

Kinematic decomposition and classification of octopus arm movements

PubMed Central

Zelman, Ido; Titon, Myriam; Yekutieli, Yoram; Hanassy, Shlomi; Hochner, Binyamin; Flash, Tamar

2013-01-01

The octopus arm is a muscular hydrostat and due to its deformable and highly flexible structure it is capable of a rich repertoire of motor behaviors. Its motor control system uses planning principles and control strategies unique to muscular hydrostats. We previously reconstructed a data set of octopus arm movements from records of natural movements using a sequence of 3D curves describing the virtual backbone of arm configurations. Here we describe a novel representation of octopus arm movements in which a movement is characterized by a pair of surfaces that represent the curvature and torsion values of points along the arm as a function of time. This representation allowed us to explore whether the movements are built up of elementary kinematic units by decomposing each surface into a weighted combination of 2D Gaussian functions. The resulting Gaussian functions can be considered as motion primitives at the kinematic level of octopus arm movements. These can be used to examine underlying principles of movement generation. Here we used combination of such kinematic primitives to decompose different octopus arm movements and characterize several movement prototypes according to their composition. The representation and methodology can be applied to the movement of any organ which can be modeled by means of a continuous 3D curve. PMID:23745113

Comparison of neuronal spike exchange methods on a Blue Gene/P supercomputer.

PubMed

Hines, Michael; Kumar, Sameer; Schürmann, Felix

2011-01-01

For neural network simulations on parallel machines, interprocessor spike communication can be a significant portion of the total simulation time. The performance of several spike exchange methods using a Blue Gene/P (BG/P) supercomputer has been tested with 8-128 K cores using randomly connected networks of up to 32 M cells with 1 k connections per cell and 4 M cells with 10 k connections per cell, i.e., on the order of 4·10(10) connections (K is 1024, M is 1024(2), and k is 1000). The spike exchange methods used are the standard Message Passing Interface (MPI) collective, MPI_Allgather, and several variants of the non-blocking Multisend method either implemented via non-blocking MPI_Isend, or exploiting the possibility of very low overhead direct memory access (DMA) communication available on the BG/P. In all cases, the worst performing method was that using MPI_Isend due to the high overhead of initiating a spike communication. The two best performing methods-the persistent Multisend method using the Record-Replay feature of the Deep Computing Messaging Framework DCMF_Multicast; and a two-phase multisend in which a DCMF_Multicast is used to first send to a subset of phase one destination cores, which then pass it on to their subset of phase two destination cores-had similar performance with very low overhead for the initiation of spike communication. Departure from ideal scaling for the Multisend methods is almost completely due to load imbalance caused by the large variation in number of cells that fire on each processor in the interval between synchronization. Spike exchange time itself is negligible since transmission overlaps with computation and is handled by a DMA controller. We conclude that ideal performance scaling will be ultimately limited by imbalance between incoming processor spikes between synchronization intervals. Thus, counterintuitively, maximization of load balance requires that the distribution of cells on processors should not reflect neural net architecture but be randomly distributed so that sets of cells which are burst firing together should be on different processors with their targets on as large a set of processors as possible.

Simultaneous polarization-insensitive phase-space trans-multiplexing and wavelength multicasting via cross-phase modulation in a photonic crystal fiber at 10 GBd

NASA Astrophysics Data System (ADS)

Cannon, Brice M.

This thesis investigates the all-optical combination of amplitude and phase modulated signals into one unified multi-level phase modulated signal, utilizing the Kerr nonlinearity of cross-phase modulation (XPM). Predominantly, the first experimental demonstration of simultaneous polarization-insensitive phase-transmultiplexing and multicasting (PI-PTMM) will be discussed. The PI-PTMM operation combines the data of a single 10-Gbaud carrier-suppressed return-to-zero (CSRZ) on-off keyed (OOK) pump signal and 4x10-Gbaud return-to-zero (RZ) binary phase-shift keyed (BPSK) probe signals to generate 4x10-GBd RZ-quadrature phase-shift keyed (QPSK) signals utilizing a highly nonlinear, birefringent photonic crystal fiber (PCF). Since XPM is a highly polarization dependent nonlinearity, a polarization sensitivity reduction technique was used to alleviate the fluctuations due to the remotely generated signals' unpredictable states of polarization (SOP). The measured amplified spontaneous emission (ASE) limited receiver sensitivity optical signal-to-noise ratio (OSNR) penalty of the PI-PTMM signal relative to the field-programmable gate array (FPGA) pre-coded RZ-DQPSK baseline at a forward-error correction (FEC) limit of 10-3 BER was ≈ 0.3 dB. In addition, the OSNR of the remotely generated CSRZ-OOK signal could be degraded to ≈ 29 dB/0.1nm, before the bit error rate (BER) performance of the PI-PTMM operation began to exponentially degrade. A 138-km dispersion-managed recirculating loop system with a 100-GHz, 13-channel mixed-format dense-wavelength-division multiplexed (DWDM) transmitter was constructed to investigate the effect of metro/long-haul transmission impairments. The PI-PTMM DQPSK and the FPGA pre-coded RZ-DQPSK baseline signals were transmitted 1,900 km and 2,400 km in the nonlinearity-limited transmission regime before reaching the 10-3 BER FEC limit. The relative reduction in transmission distance for the PI-PTMM signal was due to the additional transmitter impairments in the PCF that interact negatively with the transmission fiber.

Tritium containing polymers having a polymer backbone substantially void of tritium

DOEpatents

Jensen, G.A.; Nelson, D.A.; Molton, P.M.

1992-03-31

A radioluminescent light source comprises a solid mixture of a phosphorescent substance and a tritiated polymer. The solid mixture forms a solid mass having length, width, and thickness dimensions, and is capable of self-support. In one aspect of the invention, the phosphorescent substance comprises solid phosphor particles supported or surrounded within a solid matrix by a tritium containing polymer. The tritium containing polymer comprises a polymer backbone which is essentially void of tritium. 2 figs.

Tritium containing polymers having a polymer backbone substantially void of tritium

DOEpatents

Jensen, George A.; Nelson, David A.; Molton, Peter M.

1992-01-01

A radioluminescent light source comprises a solid mixture of a phosphorescent substance and a tritiated polymer. The solid mixture forms a solid mass having length, width, and thickness dimensions, and is capable of self-support. In one aspect of the invention, the phosphorescent substance comprises solid phosphor particles supported or surrounded within a solid matrix by a tritium containing polymer. The tritium containing polymer comprises a polymer backbone which is essentially void of tritium.

Reducing Electroosmotic Flow Enables DNA Separations in Ultrathin Channels.

DTIC Science & Technology

1998-08-01

Chemical structure of DNA bases 2 Figure 1-2: Schematic diagram of DNA base pairing 5 Figure 1-3: Schematic diagram of the capillary and the...hydrogen atoms near one of the Figure 1-1: A. Chemical structure of the DNA backbone. B. Chemical structure of DNA bases . The DNA backbone consists...of pentose sugar (deoxyribose) held together by phosphodiester bonds. The DNA bases that are derivatives of purine are adenine (A) and guanine (G

Small molecule-mediated duplex formation of nucleic acids with 'incompatible' backbones.

PubMed

Cafferty, Brian J; Musetti, Caterina; Kim, Keunsoo; Horowitz, Eric D; Krishnamurthy, Ramanarayanan; Hud, Nicholas V

2016-04-07

Proflavine, a known intercalator of DNA and RNA, promotes duplex formation by nucleic acids with natural and non-natural backbones that otherwise form duplexes with low thermal stability, and even some that show no sign of duplex formation in the absence of proflavine. These findings demonstrate the potential for intercalators to be used as cofactors for the assembly of rationally designed nucleic acid structures, and could provide fundamental insights regarding intercalation of natural nucleic acid duplexes.

Bracing the Infantry’s Backbone for 21st Century Operations

DTIC Science & Technology

2010-04-27

TERMS Strategic Corporal, NCO Training and Education, Enlisted Retention. 16 . SECURITY CLASSIFICATION OF: 17. LIMITATION OF 18. NUMBER ABSTRACT OF...Demographics and Why We Must Change .......... 9 Building the Backbone One Vertebrae at a Time: Fixing NCO Training and Education .. 16 Don’t Let a Good Thing...scorn of nearly everything on earth. .... They were the Leathernecks, the Old Timers: collected from ship’s guards and shore stations all over the

The Synthesis of Potentially Catalytic Bimetallic Systems.

DTIC Science & Technology

1982-11-29

a synthetic sequence to the double metal system shown in Figure XIV (p. 19) which incorporates ferrocene as the backbone of the molecule. Such systems...diketone intermediate 1-benzoyl-1’-o-chlorobenzoyl- ferrocene (over) \\/ DO I ?,S 1473 EDITION orI Nov6II s OSETe UNCLASSIFIEDj S/N 0102. LF 014- 6601...to the double metal system shown in Figure XIV (p. 19) which incorporates ferrocene as the backbone of the molecule. Such systems have the potential

Conservation and Divergence in the Candida Species Biofilm Matrix Mannan-Glucan Complex Structure, Function, and Genetic Control

PubMed Central

Dominguez, Eddie; Zarnowski, Robert; Sanchez, Hiram; Covelli, Antonio S.; Westler, William M.; Azadi, Parastoo; Nett, Jeniel

2018-01-01

ABSTRACT Candida biofilms resist the effects of available antifungal therapies. Prior studies with Candida albicans biofilms show that an extracellular matrix mannan-glucan complex (MGCx) contributes to antifungal sequestration, leading to drug resistance. Here we implement biochemical, pharmacological, and genetic approaches to explore a similar mechanism of resistance for the three most common clinically encountered non-albicans Candida species (NAC). Our findings reveal that each Candida species biofilm synthesizes a mannan-glucan complex and that the antifungal-protective function of this complex is conserved. Structural similarities extended primarily to the polysaccharide backbone (α-1,6-mannan and β-1,6-glucan). Surprisingly, biochemical analysis uncovered stark differences in the branching side chains of the MGCx among the species. Consistent with the structural analysis, similarities in the genetic control of MGCx production for each Candida species also appeared limited to the synthesis of the polysaccharide backbone. Each species appears to employ a unique subset of modification enzymes for MGCx synthesis, likely accounting for the observed side chain diversity. Our results argue for the conservation of matrix function among Candida spp. While biogenesis is preserved at the level of the mannan-glucan complex backbone, divergence emerges for construction of branching side chains. Thus, the MGCx backbone represents an ideal drug target for effective pan-Candida species biofilm therapy. PMID:29615504

Temperature dependence of fast carbonyl backbone dynamics in chicken villin headpiece subdomain

PubMed Central

Vugmeyster, Liliya; Ostrovsky, Dmitry

2012-01-01

Temperature-dependence of protein dynamics can provide information on details of the free energy landscape by probing the characteristics of the potential responsible for the fluctuations. We have investigated the temperature-dependence of picosecond to nanosecond backbone dynamics at carbonyl carbon sites in chicken villin headpiece subdomain protein using a combination of three NMR relaxation rates: 13C′ longitudinal rate, and two cross-correlated rates involving dipolar and chemical shift anisotropy (CSA) relaxation mechanisms, 13C′/13C′−13Cα CSA/dipolar and 13C′/13C′−15N CSA/dipolar. Order parameters have been extracted using the Lipari-Szabo model-free approach assuming a separation of the time scales of internal and molecular motions in the 2–16°C temperature range. There is a gradual deviation from this assumption from lower to higher temperatures, such that above 16°C the separation of the time scales is inconsistent with the experimental data and, thus, the Lipari-Szabo formalism can not be applied. While there are variations among the residues, on the average the order parameters indicate a markedly steeper temperature dependence at backbone carbonyl carbons compared to that probed at amide nitrogens in an earlier study. This strongly advocates for probing sites other than amide nitrogen for accurate characterization of the potential and other thermodynamics characteristics of protein backbone. PMID:21416162

Solution structures and backbone dynamics of Escherichia coli rhodanese PspE in its sulfur-free and persulfide-intermediate forms: implications for the catalytic mechanism of rhodanese.

PubMed

Li, Hongwei; Yang, Fan; Kang, Xue; Xia, Bin; Jin, Changwen

2008-04-15

Rhodanese catalyzes the sulfur-transfer reaction that transfers sulfur from thiosulfate to cyanide by a double-displacement mechanism, in which an active cysteine residue plays a central role. Previous studies indicated that the phage-shock protein E (PspE) from Escherichia coli is a rhodanese composed of a single active domain and is the only accessible rhodanese among the three single-domain rhodaneses in E. coli. To understand the catalytic mechanism of rhodanese at the molecular level, we determined the solution structures of the sulfur-free and persulfide-intermediate forms of PspE by nuclear magnetic resonance (NMR) spectroscopy and identified the active site by NMR titration experiments. To obtain further insights into the catalytic mechanism, we studied backbone dynamics by NMR relaxation experiments. Our results demonstrated that the overall structures in both sulfur-free and persulfide-intermediate forms are highly similar, suggesting that no significant conformational changes occurred during the catalytic reaction. However, the backbone dynamics revealed that the motional properties of PspE in its sulfur-free form are different from the persulfide-intermediate state. The conformational exchanges are largely enhanced in the persulfide-intermediate form of PspE, especially around the active site. The present structural and biochemical studies in combination with backbone dynamics provide further insights in understanding the catalytic mechanism of rhodanese.

Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity.

PubMed

Ollikainen, Noah; de Jong, René M; Kortemme, Tanja

2015-01-01

Interactions between small molecules and proteins play critical roles in regulating and facilitating diverse biological functions, yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited. One main difficulty, in addition to inaccuracies in energy functions, is the exquisite sensitivity of protein-ligand interactions to subtle conformational changes, coupled with the computational problem of sampling the large conformational search space of degrees of freedom of ligands, amino acid side chains, and the protein backbone. Here, we describe two benchmarks for evaluating the accuracy of computational approaches for re-engineering protein-ligand interactions: (i) prediction of enzyme specificity altering mutations and (ii) prediction of sequence tolerance in ligand binding sites. After finding that current state-of-the-art "fixed backbone" design methods perform poorly on these tests, we develop a new "coupled moves" design method in the program Rosetta that couples changes to protein sequence with alterations in both protein side-chain and protein backbone conformations, and allows for changes in ligand rigid-body and torsion degrees of freedom. We show significantly increased accuracy in both predicting ligand specificity altering mutations and binding site sequences. These methodological improvements should be useful for many applications of protein-ligand design. The approach also provides insights into the role of subtle conformational adjustments that enable functional changes not only in engineering applications but also in natural protein evolution.

Peierls-Nabarro barrier and protein loop propagation

NASA Astrophysics Data System (ADS)

Sieradzan, Adam K.; Niemi, Antti; Peng, Xubiao

2014-12-01

When a self-localized quasiparticle excitation propagates along a discrete one-dimensional lattice, it becomes subject to a dissipation that converts the kinetic energy into lattice vibrations. Eventually the kinetic energy no longer enables the excitation to cross over the minimum energy barrier between neighboring sites, and the excitation becomes localized within a lattice cell. In the case of a protein, the lattice structure consists of the Cα backbone. The self-localized quasiparticle excitation is the elemental building block of loops. It can be modeled by a kink that solves a variant of the discrete nonlinear Schrödinger equation. We study the propagation of such a kink in the case of the protein G related albumin-binding domain, using the united residue coarse-grained molecular-dynamics force field. We estimate the height of the energy barriers that the kink needs to cross over in order to propagate along the backbone lattice. We analyze how these barriers give rise to both stresses and reliefs, which control the kink movement. For this, we deform a natively folded protein structure by parallel translating the kink along the backbone away from its native position. We release the transposed kink, and we follow how it propagates along the backbone toward the native location. We observe that the dissipative forces that are exerted on the kink by the various energy barriers have a pivotal role in determining how a protein folds toward its native state.

Hydration of non-polar anti-parallel β-sheets

NASA Astrophysics Data System (ADS)

Urbic, Tomaz; Dias, Cristiano L.

2014-04-01

In this work we focus on anti-parallel β-sheets to study hydration of side chains and polar groups of the backbone using all-atom molecular dynamics simulations. We show that: (i) water distribution around the backbone does not depend significantly on amino acid sequence, (ii) more water molecules are found around oxygen than nitrogen atoms of the backbone, and (iii) water molecules around nitrogen are highly localized in the planed formed by peptide backbones. To study hydration around side chains we note that anti-parallel β-sheets exhibit two types of cross-strand pairing: Hydrogen-Bond (HB) and Non-Hydrogen-Bond (NHB) pairing. We show that distributions of water around alanine, leucine, and valine side chains are very different at HB compared to NHB faces. For alanine pairs, the space between side chains has a higher concentration of water if residues are located in the NHB face of the β-sheet as opposed to the HB face. For leucine residues, the HB face is found to be dry while the space between side chains at the NHB face alternates between being occupied and non-occupied by water. Surprisingly, for valine residues the NHB face is dry, whereas the HB face is occupied by water. We postulate that these differences in water distribution are related to context dependent propensities observed for β-sheets.

Hydration of non-polar anti-parallel β-sheets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Urbic, Tomaz; Dias, Cristiano L., E-mail: cld@njit.edu

2014-04-28

In this work we focus on anti-parallel β-sheets to study hydration of side chains and polar groups of the backbone using all-atom molecular dynamics simulations. We show that: (i) water distribution around the backbone does not depend significantly on amino acid sequence, (ii) more water molecules are found around oxygen than nitrogen atoms of the backbone, and (iii) water molecules around nitrogen are highly localized in the planed formed by peptide backbones. To study hydration around side chains we note that anti-parallel β-sheets exhibit two types of cross-strand pairing: Hydrogen-Bond (HB) and Non-Hydrogen-Bond (NHB) pairing. We show that distributions ofmore » water around alanine, leucine, and valine side chains are very different at HB compared to NHB faces. For alanine pairs, the space between side chains has a higher concentration of water if residues are located in the NHB face of the β-sheet as opposed to the HB face. For leucine residues, the HB face is found to be dry while the space between side chains at the NHB face alternates between being occupied and non-occupied by water. Surprisingly, for valine residues the NHB face is dry, whereas the HB face is occupied by water. We postulate that these differences in water distribution are related to context dependent propensities observed for β-sheets.« less

The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis.

PubMed

Improta, Roberto; Vitagliano, Luigi; Esposito, Luciana

2015-11-01

The elucidation of the mutual influence between peptide bond geometry and local conformation has important implications for protein structure refinement, validation, and prediction. To gain insights into the structural determinants and the energetic contributions associated with protein/peptide backbone plasticity, we here report an extensive analysis of the variability of the peptide bond angles by combining statistical analyses of protein structures and quantum mechanics calculations on small model peptide systems. Our analyses demonstrate that all the backbone bond angles strongly depend on the peptide conformation and unveil the existence of regular trends as function of ψ and/or φ. The excellent agreement of the quantum mechanics calculations with the statistical surveys of protein structures validates the computational scheme here employed and demonstrates that the valence geometry of protein/peptide backbone is primarily dictated by local interactions. Notably, for the first time we show that the position of the H(α) hydrogen atom, which is an important parameter in NMR structural studies, is also dependent on the local conformation. Most of the trends observed may be satisfactorily explained by invoking steric repulsive interactions; in some specific cases the valence bond variability is also influenced by hydrogen-bond like interactions. Moreover, we can provide a reliable estimate of the energies involved in the interplay between geometry and conformations. © 2015 Wiley Periodicals, Inc.

From Comb-like Polymers to Bottle-Brushes

NASA Astrophysics Data System (ADS)

Liang, Heyi; Cao, Zhen; Dobrynin, Andrey; Sheiko, Sergei

We use a combination of the coarse-grained molecular dynamics simulations and scaling analysis to study conformations of bottle-brushes and comb-like polymers in a melt. Our analysis show that bottle-brushes and comb-like polymers can be in four different conformation regimes depending on the number of monomers between grafted side chains and side chain degree of polymerization. In loosely-grafted comb regime (LC) the degree of polymerization between side chains is longer than side chain degree of polymerization, such that the side chains belonging to the same macromolecule do not overlap. Crossover to a new densely-grafted comb regime (DC) takes place when side chains begin to overlap reducing interpenetration of side chains belonging to different macromolecules. In these two regimes both side-chains and backbone behave as unperturbed linear chains with the effective Kuhn length of the backbone being close to that of linear chain. Further decrease spacer degree of polymerization results in crossover to loosely-grafted bottle-brush regime (LB). In this regime, the bottle-brush backbone is stretched while the side-chains still maintain ideal chain conformation. Finally, for even shorter spacer between grafted side chains, which corresponds to densely-grafted bottle-brush regime (DB), the backbone adopts a fully extended chain conformation, and side-chains begin to stretch to maintain a constant monomer density. NSF DMR-1409710, DMR-1407645, DMR-1624569, DMR-1436201.

Computer Simulations of Bottlebrush Melts and Soft Networks

NASA Astrophysics Data System (ADS)

Cao, Zhen; Carrillo, Jan-Michael; Sheiko, Sergei; Dobrynin, Andrey

We have studied dense bottlebrush systems in a melt and network state using a combination of the molecular dynamics simulations and analytical calculations. Our simulations show that the bottlebrush macromolecules in a melt behave as ideal chains with the effective Kuhn length bK. The bottlebrush induced bending rigidity is due to redistribution of the side chains upon backbone bending. Kuhn length of the bottlebrushes increases with increasing the side-chain degree of polymerization nsc as bK ~nsc0 . 46 . This model of bottlebrush macromolecules is extended to describe mechanical properties of bottlebrush networks in linear and nonlinear deformation regimes. In the linear deformation regime, the network shear modulus scales with the degree of polymerization of the side chains as G0 ~nsc + 1 - 1 as long as the ratio of the Kuhn length to the size of the fully extended bottlebrush backbone between crosslinks, Rmax, is smaller than unity, bK /Rmax < < 1 . Bottlebrush networks with bK /Rmax ~ 1 demonstrate behavior similar to that of networks of semiflexible chains with G0 ~nsc- 0 . 5 . In the nonlinear deformation regime, the deformation dependent shear modulus is a universal function of the first strain invariant I1 and bottlebrush backbone deformation ratio β describing stretching ability of the bottlebrush backbone between crosslinks. Nsf DMR-1409710 DMR-1436201.

Community Resilience, the Foundation for Earth Science and the ESIP Federation: Bouncing Forward with Collective Impact

NASA Astrophysics Data System (ADS)

Robinson, E.

2015-12-01

The Federal Government has a long history of cross-community coordination between the Scientific Research community, and the Earth Observations and Data Provider communities. Since 1998, the Federation of Earth Science Information Partners (ESIP), organically organized using a collective impact approach that fostered these interactions primarily around Earth science interoperability problems. Unlike most collaborations, collective impact initiatives named in 2011 by the Stanford Social Innovation Review, involve a backbone infrastructure, a dedicated staff, and a structured process that leads to a common agenda, shared measurement, continuous communication, and mutually reinforcing activities among all participants. Over the last ten years, the Foundation for Earth Science (FES) has a proven track record of providing backbone support to ESIP. This presentation will cover FES's general approach to providing backbone support that enables communities to define shared agenda and then will show these practices in two case studies: (1) ESIP at-large as a mature network of developed partnerships and (2) a new project, the Local Community Resilience cluster. This new cluster aims to bridge the gap from the established ESIP network to engage local communities in order to equip citizens, professionals, and other decision-makers with the scientific underpinning necessary to make informed decisions (bounce forward) for society by leveraging the strong existing ESIP community, the backbone capabilities of FES and extending Federal Earth Science, Technology and Innovation Investments.

Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases

PubMed Central

Haupt, V. Joachim; Schroeder, Michael; Labudde, Dirk

2018-01-01

The origin of the machinery that realizes protein biosynthesis in all organisms is still unclear. One key component of this machinery are aminoacyl tRNA synthetases (aaRS), which ligate tRNAs to amino acids while consuming ATP. Sequence analyses revealed that these enzymes can be divided into two complementary classes. Both classes differ significantly on a sequence and structural level, feature different reaction mechanisms, and occur in diverse oligomerization states. The one unifying aspect of both classes is their function of binding ATP. We identified Backbone Brackets and Arginine Tweezers as most compact ATP binding motifs characteristic for each Class. Geometric analysis shows a structural rearrangement of the Backbone Brackets upon ATP binding, indicating a general mechanism of all Class I structures. Regarding the origin of aaRS, the Rodin-Ohno hypothesis states that the peculiar nature of the two aaRS classes is the result of their primordial forms, called Protozymes, being encoded on opposite strands of the same gene. Backbone Brackets and Arginine Tweezers were traced back to the proposed Protozymes and their more efficient successors, the Urzymes. Both structural motifs can be observed as pairs of residues in contemporary structures and it seems that the time of their addition, indicated by their placement in the ancient aaRS, coincides with the evolutionary trace of Proto- and Urzymes. PMID:29659563

NMR studies of the backbone flexibility and structure of human growth hormone: a comparison of high and low pH conformations.

PubMed

Kasimova, Marina R; Kristensen, Søren M; Howe, Peter W A; Christensen, Thorkild; Matthiesen, Finn; Petersen, Jørgen; Sørensen, Hans H; Led, Jens J

2002-05-03

(15)N NMR relaxation parameters and amide (1)H/(2)H-exchange rates have been used to characterize the structural flexibility of human growth hormone (rhGH) at neutral and acidic pH. Our results show that the rigidity of the molecule is strongly affected by the solution conditions. At pH 7.0 the backbone dynamics parameters of rhGH are uniform along the polypeptide chain and their values are similar to those of other folded proteins. In contrast, at pH 2.7 the overall backbone flexibility increases substantially compared to neutral pH and the average order parameter approaches the lower limit expected for a folded protein. However, a significant variation of the backbone dynamics through the molecule indicates that under acidic conditions the mobility of the residues becomes more dependent on their location within the secondary structure units. In particular, the order parameters of certain loop regions decrease dramatically and become comparable to those found in unfolded proteins. Furthermore, the HN-exchange rates at low pH reveal that the residues most protected from exchange are clustered at one end of the helical bundle, forming a stable nucleus. We suggest that this nucleus maintains the overall fold of the protein under destabilizing conditions. We therefore conclude that the acid state of rhGH consists of a structurally conserved, but dynamically more flexible helical core surrounded by an aura of highly mobile, unstructured loops. However, in spite of its prominent flexibility the acid state of rhGH cannot be considered a "molten globule" state because of its high stability. It appears from our work that under certain conditions, a protein can tolerate a considerable increase in flexibility of its backbone, along with an increased penetration of water into its core, while still maintaining a stable folded conformation.

Cloned cDNA of A/swine/Iowa/15/1930 internal genes as a candidate backbone for reverse genetics vaccine against influenza A viruses

PubMed Central

Lekcharoensuk, Porntippa; Wiriyarat, Witthawat; Petcharat, Nuntawan; Lekcharoensuk, Chalermpol; Auewarakul, Prasert; Richt, Juergen A

2012-01-01

Reverse genetics viruses for influenza vaccine production usually utilize the internal genes of the egg-adapted A/Puerto Rico/8/34 (PR8) strain. This egg-adapted strain provides high production yield in embryonated eggs but does not necessarily give the best yield in mammalian cell culture. In order to generate a reverse genetics viral backbone that is well-adapted to high growth in mammalian cell culture, a swine influenza isolate (A/swine/Iowa/15/30 (H1N1) (rg1930) that was shown to give high yield in Madin-Darby Canine Kidney (MDCK) cells was used as the internal gene donor for reverse genetics plasmids. In this report, the internal genes from rg1930 were used for construction of reverse genetics viruses carrying a cleavage site-modified hemagglutinin (HA) gene and neuraminidase (NA) gene from a highly pathogenic H5N1 virus. The resulting virus (rg1930H5N1) was low pathogenic in vivo. Inactivated rg1930H5N1 vaccine completely protected chickens from morbidity and mortality after challenge with highly pathogenic H5N1. Protective immunity was obtained when chickens were immunized with an inactivated vaccine consisting of at least 29 HA units of the rg1930H5N1 virus. In comparison to the PR8-based reverse genetics viruses carrying the same HA and NA genes from an H5N1 virus, rg1930 based viruses yielded higher viral titers in MDCK and Vero cells. In addition, the reverse genetics derived H3N2 and H5N2 viruses with the rg1930 backbone replicated in MDCK cells better than the cognate viruses with the rgPR8 backbone. It is concluded that this newly established reverse genetics backbone system could serve as a candidate for a master donor strain for development of inactivated influenza vaccines in cell-based systems. PMID:22230579

Characterization of a backbone cleavage product of BMS-196854 (Oncostatin M), a recombinant anti-inflammatory cytokine.

PubMed

Zhao, F; Stein, D J; Paborji, M; Cash, P W; Root, B J; Wei, Z; Knupp, C J

2001-01-01

BMS-196843 (Oncostatin M) is a therapeutic recombinant protein in development. Scale-up process changes led to unexpected instability of the bulk drug substance solution during storage. A product with an apparent higher MW than the parent protein was observed by the size-exclusion chromatography (SEC). This study was aimed to fully characterize the product and to identify a solution to stabilize the protein. SEC, SDS-PAGE, tryptic mapping, and N-terminal sequencing were performed to characterize the unknown product. The effect of pH, temperature, bulk concentration, and immobilized trypsin inhibitor on the degradation rate was studied to elucidate the mechanism and to identify stabilization strategies. Despite the apparent high MW indicated initially by SEC, the unknown was characterized to be a degradation product resulted from a backbone cleavage between residues Arg145-Gly146. The resulting fragments from the backbone cleavage were, however, still linked through an intramolecular disulfide bond. Thus, the final product had a more open structure with an increased hydrodynamic radius compared to the parent protein, which explains the initial SEC results. The site-specific backbone cleavage was suspected to be catalyzed by trypsin-like protease impurities in the bulk solution. The bulk drug substance solution was subsequently treated with immobilized soybean trypsin inhibitor, and the degradation rate was significantly reduced. Furthermore, increasing the solution pH from 5 to 8 led to an increase in the degradation rate, which was consistent with the expected pH dependency of trypsin activity. In addition, the effect of bulk concentration also supported the involvement of protease impurities rather than a spontaneous peptide bond hydrolysis reaction. Trace trypsin-like protease impurities led to an unusual site-specific backbone cleavage of BMS-196854. The proteolytic degradation can be minimized by treating the bulk solution with immobilized soybean trypsin inhibitor and/or controlling the solution pH and storage temperature.

Hydrophilic and Cell-Penetrable Pyrrolidinyl Peptide Nucleic Acid via Post-synthetic Modification with Hydrophilic Side Chains.

PubMed

Pansuwan, Haruthai; Ditmangklo, Boonsong; Vilaivan, Chotima; Jiangchareon, Banphot; Pan-In, Porntip; Wanichwecharungruang, Supason; Palaga, Tanapat; Nuanyai, Thanesuan; Suparpprom, Chaturong; Vilaivan, Tirayut

2017-09-20

Peptide nucleic acid (PNA) is a nucleic acid mimic in which the deoxyribose-phosphate was replaced by a peptide-like backbone. The absence of negative charge in the PNA backbone leads to several unique behaviors including a stronger binding and salt independency of the PNA-DNA duplex stability. However, PNA possesses poor aqueous solubility and cannot directly penetrate cell membranes. These are major obstacles that limit in vivo applications of PNA. In previous strategies, the PNA can be conjugated to macromolecular carriers or modified with positively charged side chains such as guanidinium groups to improve the aqueous solubility and cell permeability. In general, a preformed modified PNA monomer was required. In this study, a new approach for post-synthetic modification of PNA backbone with one or more hydrophilic groups was proposed. The PNA used in this study was the conformationally constrained pyrrolidinyl PNA with prolyl-2-aminocyclopentanecarboxylic acid dipeptide backbone (acpcPNA) that shows several advantages over the conventional PNA. The aldehyde modifiers carrying different linkers (alkylene and oligo(ethylene glycol)) and end groups (-OH, -NH 2 , and guanidinium) were synthesized and attached to the backbone of modified acpcPNA by reductive alkylation. The hybrids between the modified acpcPNAs and DNA exhibited comparable or superior thermal stability with base-pairing specificity similar to those of unmodified acpcPNA. Moreover, the modified apcPNAs also showed the improvement of aqueous solubility (10-20 folds compared to unmodified PNA) and readily penetrate cell membranes without requiring any special delivery agents. This study not only demonstrates the practicality of the proposed post-synthetic modification approach for PNA modification, which could be readily applied to other systems, but also opens up opportunities for using pyrrolidinyl PNA in various applications such as intracellular RNA sensing, specific gene detection, and antisense and antigene therapy.

Backbone resonance assignments of the PRYSPRY domain of TRIM25.

PubMed

Kong, Chen; Penumutchu, Srinivasa R; Hung, Kuo-Wei; Huang, Huiying; Lin, Tianwei; Yu, Chin

2015-10-01

TRIM25 is a member of the tripartite motif (TRIM) family and has been implicated in the regulation of innate immune signaling via the RIG-I (retinoic acid-inducible gene-I) pathway for antiviral defense. As the essential first step towards the structural and functional characterization of the TRIM25/RIG-I interaction, the backbone resonance of the PRYSPRY domain of TRIM25 is assigned here based on triple-resonance experiments using uniformly [(2)H, (13)C, (15)N]-labeled protein.

Evaluation of retro-inverso modifications of HTLV-1 protease inhibitors containing a hydroxyethylamine isoster.

PubMed

Tatsumi, Tadashi; Awahara, Chiyuki; Naka, Hiromi; Aimoto, Saburo; Konno, Hiroyuki; Nosaka, Kazuto; Akaji, Kenichi

2010-04-01

Effects of retro-inverso (RI) modifications of HTLV-1 protease inhibitors containing a hydroxyethylamine isoster backbone were clarified. Construction of the isoster backbone was achieved by a stereoselective aldol reaction. Four diastereomers with different configurations at the isoster hydroxyl site and the scissile site substituent were synthesized. Inhibitory activities of the new inhibitors suggest that partially modified RI inhibitors would interact with HTLV-1 protease in the same manner as the parent hydroxyethylamine inhibitor. Copyright 2010 Elsevier Ltd. All rights reserved.

Ductile Glass of Polyrotaxane Toughened by Stretch-Induced Intramolecular Phase Separation.

PubMed

Kato, Kazuaki; Nemoto, Kaito; Mayumi, Koichi; Yokoyama, Hideaki; Ito, Kohzo

2017-09-27

A new class of ductile glasses is created from a thermoplastic polyrotaxane. The hard glass, which has a Young's modulus of 1 GPa, shows crazing, necking, and strain hardening with a total elongation of 330%. Stress concentration is prevented through a unique stretch-induced intramolecular phase separation of the cyclic components and the exposed backbone. In situ synchrotron X-ray scattering studies indicate that the backbone polymer chains slip through the cyclic components in the regions where the stress is concentrated.

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

PubMed Central

Huang, Po-Ssu; Ban, Yih-En Andrew; Richter, Florian; Andre, Ingemar; Vernon, Robert; Schief, William R.; Baker, David

2011-01-01

We describe RosettaRemodel, a generalized framework for flexible protein design that provides a versatile and convenient interface to the Rosetta modeling suite. RosettaRemodel employs a unified interface, called a blueprint, which allows detailed control over many aspects of flexible backbone protein design calculations. RosettaRemodel allows the construction and elaboration of customized protocols for a wide range of design problems ranging from loop insertion and deletion, disulfide engineering, domain assembly, loop remodeling, motif grafting, symmetrical units, to de novo structure modeling. PMID:21909381

Functionalized polymers for binding to solutes in aqueous solutions

DOEpatents

Smith, Barbara F.; Robison, Thomas W.

2006-11-21

A functionalized polymer for binding a dissolved molecule in an aqueous solution is presented. The polymer has a backbone polymer to which one or more functional groups are covalently linked. The backbone polymer can be such polymers as polyethylenimine, polyvinylamine, polyallylamine, and polypropylamine. These polymers are generally water-soluble, but can be insoluble when cross-linked. The functional group can be for example diol derivatives, polyol derivatives, thiol and dithiol derivatives, guest-host groups, affinity groups, beta-diphosphonic acids, and beta-diamides

Solid oxide fuel cells having porous cathodes infiltrated with oxygen-reducing catalysts

DOEpatents

Liu, Meilin; Liu, Ze; Liu, Mingfei; Nie, Lifang; Mebane, David Spencer; Wilson, Lane Curtis; Surdoval, Wayne

2014-08-12

Solid-oxide fuel cells include an electrolyte and an anode electrically coupled to a first surface of the electrolyte. A cathode is provided, which is electrically coupled to a second surface of the electrolyte. The cathode includes a porous backbone having a porosity in a range from about 20% to about 70%. The porous backbone contains a mixed ionic-electronic conductor (MIEC) of a first material infiltrated with an oxygen-reducing catalyst of a second material different from the first material.

NASA Exhibits

NASA Technical Reports Server (NTRS)

Deardorff, Glenn; Djomehri, M. Jahed; Freeman, Ken; Gambrel, Dave; Green, Bryan; Henze, Chris; Hinke, Thomas; Hood, Robert; Kiris, Cetin; Moran, Patrick;

Optical network scaling: roles of spectral and spatial aggregation.

PubMed

Arık, Sercan Ö; Ho, Keang-Po; Kahn, Joseph M

2014-12-01

As the bit rates of routed data streams exceed the throughput of single wavelength-division multiplexing channels, spectral and spatial traffic aggregation become essential for optical network scaling. These aggregation techniques reduce network routing complexity by increasing spectral efficiency to decrease the number of fibers, and by increasing switching granularity to decrease the number of switching components. Spectral aggregation yields a modest decrease in the number of fibers but a substantial decrease in the number of switching components. Spatial aggregation yields a substantial decrease in both the number of fibers and the number of switching components. To quantify routing complexity reduction, we analyze the number of multi-cast and wavelength-selective switches required in a colorless, directionless and contentionless reconfigurable optical add-drop multiplexer architecture. Traffic aggregation has two potential drawbacks: reduced routing power and increased switching component size.

The influence of chain rigidity and the degree of sulfonation on the morphology of block copolymers as nano reactor

NASA Astrophysics Data System (ADS)

Hong, K.; Zhang, X.

2005-03-01

Polyelectrolyte block copolymer was used to form an ordered domain of ionic block as a ``nanoreactor'' due to its ability to bind oppositely charged metal ion, Zn^2+, Fe^2+ etc. The purpose of our research is to investigate the controllability of the size and morphology of domains (inorganic nano particles) by changing backbone stiffness, the charge density and the volume fraction of ionic block. Poly(styrene sulfonate) (PSS), which backbone is flexible, and poly(cyclohexadiene sulfonate) (PCHDS), which backbone is ``semiflexible'', were used as ionic blocks. We synthesized PtBS-PSS and PS-PCHDS with various degree of sulfonation and the volume fraction. Zinc oxide (ZnO) nano particles successfully formed in the ionic domain of microphase separated block copolymers. We used SANS to characterize the morphology of block copolymers and TEM for block copolymer containing ZnO nano particles. Our experimental results show that the chemistry of ``sulfonation'' of block copolymers can be successfully used to synthesize nano composite materials.

Protein Structural Information Derived from NMR Chemical Shift with the Neural Network Program TALOS-N

PubMed Central

Shen, Yang; Bax, Ad

2015-01-01

Summary Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors and the artificial neural network based TALOS-N program has been trained to extract backbone and sidechain torsion angles from 1H, 15N and 13C shifts. The program is quite robust, and typically yields backbone torsion angles for more than 90% of the residues, and sidechain χ1 rotamer information for about half of these, in addition to reliably predicting secondary structure. The use of TALOS-N is illustrated for the protein DinI, and torsion angles obtained by TALOS-N analysis from the measured chemical shifts of its backbone and 13Cβ nuclei are compared to those seen in a prior, experimentally determined structure. The program is also particularly useful for generating torsion angle restraints, which then can be used during standard NMR protein structure calculations. PMID:25502373

Understanding the length dependence of molecular junction thermopower.

PubMed

Karlström, Olov; Strange, Mikkel; Solomon, Gemma C

2014-01-28

Thermopower of molecular junctions is sensitive to details in the junction and may increase, decrease, or saturate with increasing chain length, depending on the system. Using McConnell's theory for exponentially suppressed transport together with a simple and easily interpretable tight binding model, we show how these different behaviors depend on the molecular backbone and its binding to the contacts. We distinguish between resonances from binding groups or undercoordinated electrode atoms, and those from the periodic backbone. It is demonstrated that while the former gives a length-independent contribution to the thermopower, possibly changing its sign, the latter determines its length dependence. This means that the question of which orbitals from the periodic chain that dominate the transport should not be inferred from the sign of the thermopower but from its length dependence. We find that the same molecular backbone can, in principle, show four qualitatively different thermopower trends depending on the binding group: It can be positive or negative for short chains, and it can either increase or decrease with length.

VCD Robustness of the Amide-I and Amide-II Vibrational Modes of Small Peptide Models.

PubMed

Góbi, Sándor; Magyarfalvi, Gábor; Tarczay, György

2015-09-01

The rotational strengths and the robustness values of amide-I and amide-II vibrational modes of For(AA)n NHMe (where AA is Val, Asn, Asp, or Cys, n = 1-5 for Val and Asn; n = 1 for Asp and Cys) model peptides with α-helix and β-sheet backbone conformations were computed by density functional methods. The robustness results verify empirical rules drawn from experiments and from computed rotational strengths linking amide-I and amide-II patterns in the vibrational circular dichroism (VCD) spectra of peptides with their backbone structures. For peptides with at least three residues (n ≥ 3) these characteristic patterns from coupled amide vibrational modes have robust signatures. For shorter peptide models many vibrational modes are nonrobust, and the robust modes can be dependent on the residues or on their side chain conformations in addition to backbone conformations. These robust VCD bands, however, provide information for the detailed structural analysis of these smaller systems. © 2015 Wiley Periodicals, Inc.

Photo-oxidative doping in π-conjugated zig-zag chain of carbon atoms with sulfur-functional group

NASA Astrophysics Data System (ADS)

Ikeura-Sekiguchi, Hiromi; Sekiguchi, Tetsuhiro

2017-12-01

Photo-oxidative doping processes were studied for the trans-polyacetylene backbone with the -SCH3 side group as a chemically representative of the precisely controlled S-functionalized zig-zag graphene nanoribbon edge. Sulfur K-edge X-ray absorption near edge structure (XANES) spectroscopy indicates that photochemical reaction of S-CH3 with atmospheric O2 forms selectively oxidized products such as -S(O)CH3 and -SO3- bound to the polyacetylene (PA) backbone. Using the correlation between the oxidation states of sulfur and the XANES peak positions, the partial charge distribution of CH3Sδ+-PAδ- has been estimated. Such positively charged sulfur atoms can attract higher electronegative oxygen atoms and expect to enhance the photooxidization capabilities. The formation of the -SO3- side group is evidently responsible for hole doping into the PA backbone. The results can provide some strategy for area-selective and controllable doping processes of atomic-scale molecular systems with the assistance of UV light.

α/β coiled coils

PubMed Central

Hartmann, Marcus D; Mendler, Claudia T; Bassler, Jens; Karamichali, Ioanna; Ridderbusch, Oswin; Lupas, Andrei N; Hernandez Alvarez, Birte

2016-01-01

Coiled coils are the best-understood protein fold, as their backbone structure can uniquely be described by parametric equations. This level of understanding has allowed their manipulation in unprecedented detail. They do not seem a likely source of surprises, yet we describe here the unexpected formation of a new type of fiber by the simple insertion of two or six residues into the underlying heptad repeat of a parallel, trimeric coiled coil. These insertions strain the supercoil to the breaking point, causing the local formation of short β-strands, which move the path of the chain by 120° around the trimer axis. The result is an α/β coiled coil, which retains only one backbone hydrogen bond per repeat unit from the parent coiled coil. Our results show that a substantially novel backbone structure is possible within the allowed regions of the Ramachandran space with only minor mutations to a known fold. DOI: http://dx.doi.org/10.7554/eLife.11861.001 PMID:26771248

Solution-processable ambipolar diketopyrrolopyrrole-selenophene polymer with unprecedentedly high hole and electron mobilities.

PubMed

Lee, Junghoon; Han, A-Reum; Kim, Jonggi; Kim, Yiho; Oh, Joon Hak; Yang, Changduk

2012-12-26

There is a fast-growing demand for polymer-based ambipolar thin-film transistors (TFTs), in which both n-type and p-type transistor operations are realized in a single layer, while maintaining simplicity in processing. Research progress toward this end is essentially fueled by molecular engineering of the conjugated backbones of the polymers and the development of process architectures for device fabrication, which has recently led to hole and electron mobilities of more than 1.0 cm(2) V(-1) s(-1). However, ambipolar polymers with even higher performance are still required. By taking into account both the conjugated backbone and side chains of the polymer component, we have developed a dithienyl-diketopyrrolopyrrole (TDPP) and selenophene containing polymer with hybrid siloxane-solubilizing groups (PTDPPSe-Si). A synergistic combination of rational polymer backbone design, side-chain dynamics, and solution processing affords an enormous boost in ambipolar TFT performance, resulting in unprecedentedly high hole and electron mobilities of 3.97 and 2.20 cm(2) V(-1) s(-1), respectively.