Stabilisation of unusual simultaneous binding of four cytosine nucleobases to copper(II) by a novel network of bifurcated hydrogen bonding

The crystal structure of tetrakis(cytosine)copper(II) perchlorate dihydrate has been determined. All the hydrogen atoms were obtained from Fourier-difference synthesis. The geometry around. copper is a bicapped octahedron (4 + 2 + 2*). The adjacent cytosine rings are oriented head-to-tail with respect to each other and are roughly at right angles to the co-ordination plane. The exocyclic oxo groups form an interligand, intracomplex hydrogen-bonding network above and below the co-ordination plane with the exocyclic amino groups of alternate cytosine bases. The EPR and electronic spectra are consistent with the retention of the solid-state structure in solution. The steric effect of the C(2)=O group of cytosine is offset by the presence of the intracomplex hydrogen-bonding network. The trend in Ei values of Cu-II-Cu-I couples for 1.4 complexes of cytosine, cytodine, pyridine, 2-methylpyridine and N-methylimidazole suggests that both steric effects and pi-delocalization in imidazole and pyridine ligands and the steric effect of C(2)=O in pyrimidine ligands are important in stabilising Cu-I relative to Cu-II.

The effect of traffic shaping in efficiently providing end-to-end performance guarantees

This paper reports new results concerning the capabilities of a family of service disciplines aimed at providing per-connection end-to-end delay (and throughput) guarantees in high-speed networks. This family consists of the class of rate-controlled service disciplines, in which traffic from a connection is reshaped to conform to specific traffic characteristics, at every hop on its path. When used together with a scheduling policy at each node, this reshaping enables the network to provide end-to-end delay guarantees to individual connections. The main advantages of this family of service disciplines are their implementation simplicity and flexibility. On the other hand, because the delay guarantees provided are based on summing worst case delays at each node, it has also been argued that the resulting bounds are very conservative which may more than offset the benefits. In particular, other service disciplines such as those based on Fair Queueing or Generalized Processor Sharing (GPS), have been shown to provide much tighter delay bounds. As a result, these disciplines, although more complex from an implementation point-of-view, have been considered for the purpose of providing end-to-end guarantees in high-speed networks. In this paper, we show that through ''proper'' selection of the reshaping to which we subject the traffic of a connection, the penalty incurred by computing end-to-end delay bounds based on worst cases at each node can be alleviated. Specifically, we show how rate-controlled service disciplines can be designed to outperform the Rate Proportional Processor Sharing (RPPS) service discipline. Based on these findings, we believe that rate-controlled service disciplines provide a very powerful and practical solution to the problem of providing end-to-end guarantees in high-speed networks.

NETGEM: Network Embedded Temporal GEnerative Model for gene expression data

Background: Temporal analysis of gene expression data has been limited to identifying genes whose expression varies with time and/or correlation between genes that have similar temporal profiles. Often, the methods do not consider the underlying network constraints that connect the genes. It is becoming increasingly evident that interactions change substantially with time. Thus far, there is no systematic method to relate the temporal changes in gene expression to the dynamics of interactions between them. Information on interaction dynamics would open up possibilities for discovering new mechanisms of regulation by providing valuable insight into identifying time-sensitive interactions as well as permit studies on the effect of a genetic perturbation. Results: We present NETGEM, a tractable model rooted in Markov dynamics, for analyzing the dynamics of the interactions between proteins based on the dynamics of the expression changes of the genes that encode them. The model treats the interaction strengths as random variables which are modulated by suitable priors. This approach is necessitated by the extremely small sample size of the datasets, relative to the number of interactions. The model is amenable to a linear time algorithm for efficient inference. Using temporal gene expression data, NETGEM was successful in identifying (i) temporal interactions and determining their strength, (ii) functional categories of the actively interacting partners and (iii) dynamics of interactions in perturbed networks. Conclusions: NETGEM represents an optimal trade-off between model complexity and data requirement. It was able to deduce actively interacting genes and functional categories from temporal gene expression data. It permits inference by incorporating the information available in perturbed networks. Given that the inputs to NETGEM are only the network and the temporal variation of the nodes, this algorithm promises to have widespread applications, beyond biological systems. The source code for NETGEM is available from https://github.com/vjethava/NETGEM

Modeling Architecture-OS interactions using Layered Queuing Network Models

The prevalent virtualization technologies provide QoS support within the software layers of the virtual machine monitor(VMM) or the operating system of the virtual machine(VM). The QoS features are mostly provided as extensions to the existing software used for accessing the I/O device because of which the applications sharing the I/O device experience loss of performance due to crosstalk effects or usable bandwidth. In this paper we examine the NIC sharing effects across VMs on a Xen virtualized server and present an alternate paradigm that improves the shared bandwidth and reduces the crosstalk effect on the VMs. We implement the proposed hardwaresoftware changes in a layered queuing network (LQN) model and use simulation techniques to evaluate the architecture. We find that simple changes in the device architecture and associated system software lead to application throughput improvement of up to 60%. The architecture also enables finer QoS controls at device level and increases the scalability of device sharing across multiple virtual machines. We find that the performance improvement derived using LQN model is comparable to that reported by similar but real implementations.

Packet Reordering in Network Processors

Network processors today consist of multiple parallel processors (micro engines) with support for multiple threads to exploit packet level parallelism inherent in network workloads. With such concurrency, packet ordering at the output of the network processor cannot be guaranteed. This paper studies the effect of concurrency in network processors on packet ordering. We use a validated Petri net model of a commercial network processor, Intel IXP 2400, to determine the extent of packet reordering for IPv4 forwarding application. Our study indicates that in addition to the parallel processing in the network processor, the allocation scheme for the transmit buffer also adversely impacts packet ordering. In particular, our results reveal that these packet reordering results in a packet retransmission rate of up to 61%. We explore different transmit buffer allocation schemes namely, contiguous, strided, local, and global which reduces the packet retransmission to 24%. We propose an alternative scheme, packet sort, which guarantees complete packet ordering while achieving a throughput of 2.5 Gbps. Further, packet sort outperforms the in-built packet ordering schemes in the IXP processor by up to 35%.

Network governance at local — A comparative approach

Factors influencing the effectiveness of democratic institutions and to that effect processes involved at the local governance level have been the interest in the literature, given the presence of various advocacies and networks that are context-specific. This paper is motivated to understand the adaptability issues related to governance given these complexities through a comparative analysis of diversified regions. We adopted a two-stage clustering along with regression methodology for this purpose. The results show that the formation of advocacies and networks depends on the context and institutional framework. The paper concludes by exploring different strategies and dynamics involved in network governance and insists on the importance of governing the networks for structural reformation through regional policy making.

On network coding for acyclic networks with delays

Problems related to network coding for acyclic, instantaneous networks (where the edges of the acyclic graph representing the network are assumed to have zero-delay) have been extensively dealt with in the recent past. The most prominent of these problems include (a) the existence of network codes that achieve maximum rate of transmission, (b) efficient network code constructions, and (c) field size issues. In practice, however, networks have transmission delays. In network coding theory, such networks with transmission delays are generally abstracted by assuming that their edges have integer delays. Using enough memory at the nodes of an acyclic network with integer delays can effectively simulate instantaneous behavior, which is probably why only acyclic instantaneous networks have been primarily focused on thus far. However, nulling the effect of the network delays are not always uniformly advantageous, as we will show in this work. Essentially, we elaborate on issues ((a), (b) and (c) above) related to network coding for acyclic networks with integer delays, and show that using the delay network as is (without adding memory) turns out to be advantageous, disadvantageous or immaterial, depending on the topology of the network and the problem considered i.e., (a), (b) or (c).

Enhancing Speedup in Network Processing Applications by Exploiting Instruction Reuse with Flow Aggregation

Instruction reuse is a microarchitectural technique that improves the execution time of a program by removing redundant computations at run-time. Although this is the job of an optimizing compiler, they do not succeed many a time due to limited knowledge of run-time data. In this paper we examine instruction reuse of integer ALU and load instructions in network processing applications. Specifically, this paper attempts to answer the following questions: (1) How much of instruction reuse is inherent in network processing applications?, (2) Can reuse be improved by reducing interference in the reuse buffer?, (3) What characteristics of network applications can be exploited to improve reuse?, and (4) What is the effect of reuse on resource contention and memory accesses? We propose an aggregation scheme that combines the high-level concept of network traffic i.e. "flows" with a low level microarchitectural feature of programs i.e. repetition of instructions and data along with an architecture that exploits temporal locality in incoming packet data to improve reuse. We find that for the benchmarks considered, 1% to 50% of instructions are reused while the speedup achieved varies between 1% and 24%. As a side effect, instruction reuse reduces memory traffic and can therefore be considered as a scheme for low power.

Application of UPFC for system security improvement under normal and network contingencies

Electric power systems are exposed to various contingencies. Network contingencies often contribute to over-loading of network branches, unsatisfactory voltages and also leading to problems of stability/voltage collapse. To maintain security of the systems, it is desirable to estimate the effect of contingencies and plan suitable measures to improve system security/stability. This paper presents an approach for selection of unified power flow controller (UPFC) suitable locations considering normal and network contingencies after evaluating the degree of severity of the contingencies. The ranking is evaluated using composite criteria based fuzzy logic for eliminating masking effect. The fuzzy approach, in addition to real power loadings and bus voltage violations, voltage stability indices at the load buses also used as the post-contingent quantities to evaluate the network contingency ranking. The selection of UPFC suitable locations uses the criteria on the basis of improved system security/stability. The proposed approach for selection of UPFC suitable locations has been tested under simulated conditions on a few power systems and the results for a 24-node real-life equivalent EHV power network and 39-node New England (modified) test system are presented for illustration purposes.

Thermal diffusivity measurements on ternary Ge-Te-Tl glasses using Photo-thermal Deflection method: Effect of thallium addition

Photo-thermal Deflection (PTD) technique is used to investigate the thermal diffusivity (alpha) of Ge17Te83 - xTlx (0 <= x <= 13) glasses as a function of composition. The thermal diffusivity of these glasses is found to lie in the range 0.020 to 0.048 cm(2)/s, which is consistent with the memory type of electrical switching exhibited by these samples. Further, it is found that alpha shows an initial increase with Tl addition, followed by a decrease. The observed composition dependence of thermal diffusivity has been understood on the basis that the thallium atoms are incorporated as a covalent species for lower values of x, increasing the network rigidity; however, they enter as ionic species for higher x values, fragmenting the network. The initial increase in a is due to the increasing network rigidity and the subsequent decrease is because of the fragmentation of the network. Also, there is a strong correlation between the composition dependence of switching voltages observed earlier and the variation with composition of electrical resistivity and thermal diffusivity of Ge17Te83 - xTlx glasses obtained in the present study. (C) 2012 Elsevier B.V. All rights reserved.

Performance analysis of adaptive physical layer network coding for wireless two-way relaying

The performance analysis of adaptive physical layer network-coded two-way relaying scenario is presented which employs two phases: Multiple access (MA) phase and Broadcast (BC) phase. The deep channel fade conditions which occur at the relay referred as the singular fade states fall in the following two classes: (i) removable and (ii) non-removable singular fade states. With every singular fade state, we associate an error probability that the relay transmits a wrong network-coded symbol during the BC phase. It is shown that adaptive network coding provides a coding gain over fixed network coding, by making the error probabilities associated with the removable singular fade states contributing to the average Symbol Error Rate (SER) fall as SNR-2 instead of SNR-1. A high SNR upper-bound on the average end-to-end SER for the adaptive network coding scheme is derived, for a Rician fading scenario, which is found to be tight through simulations. Specifically, it is shown that for the adaptive network coding scheme, the probability that the relay node transmits a wrong network-coded symbol is upper-bounded by twice the average SER of a point-to-point fading channel, at high SNR. Also, it is shown that in a Rician fading scenario, it suffices to remove the effect of only those singular fade states which contribute dominantly to the average SER.

Study of the effect of alkali mixture on V-O bond length in Oxyfluoro Vanadate glasses using Raman spectroscopy

Raman spectroscopic study on Oxyfluoro Vanadate glasses containing various proportions of lithium fluoride and rubidium fluoride was carried out to see an effect of mixture of alkali on vanadium-oxygen (V-O) bond length. Glasses with a general formula 40V(2)O(5) - 30BaF(2) - (30 - x) LiF - xRbF (x = 0-30) were prepared. Room temperature Raman spectra of these glass samples were recorded in back scattering geometry. The data presented is in ``reduced Raman intensity'' form with maximum peak scaled to 100. We have used v = Aexp(BR), where A and B are fitting parameters, to correlate the bond length R with Raman scattering frequency v. We observed that variation in bond length and its distribution about a most probable value can be correlated to the alkali environment present in these glasses. We also observed that all rubidium environment around the network forming unit is more homogenous than all lithium environment.

EFFECT OF CORE-SHELL STRUCTURE OF HYDROGEL BEADS ON THE THRESHOLD CONCENTRATION OF WATER FOR SWELLING AND ITS PH SENSITIVITY

In this paper we investigate the effect of core-shell structure of Sodium Alginate based hydrogel beads and their size on certain activation threshold concentration of water for applications in swelling and pH sensing. This type of hydrogel experiences diffusive pressure due to transport of certain free charges across its interface with a solvent or electrolyte. This process is essentially a dynamic equilibrium of the electric force field, stress in the polymeric network with cage like structure and molecular diffusion including phase transformation due to pressure imbalance between the hydrogel and its surroundings. The effect of pH of the solvant on the swelling rate of these beads has been studied experimentally. A mathematical model of the swelling process has been developed by considering Nernst-Planck equation representing the migration of mobile ions and Er ions, Poisson equation representing the equilibrium of the electric field and mechanical field equation representing swelling of the gel. An attempt has been made to predict the experimentally observed phenomena using these numerical simulations. It is observed experimentally that certain minimum concentration called activation threshold concentration of the water molecules must be present in the hydrogel in order to activate the swelling process. For the required activation threshold concentration of water in the beads, the pH induced change in the rate of swelling is also investigated. This effect is analyzed for various different core-shell structures of the beads.

Wireless network-coded three-way relaying using Latin Cubes

The design of modulation schemes for the physical layer network-coded three-way wireless relaying scenario is considered. The protocol employs two phases: Multiple Access (MA) phase and Broadcast (BC) phase with each phase utilizing one channel use. For the two-way relaying scenario, it was observed by Koike-Akino et al. [4], that adaptively changing the network coding map used at the relay according to the channel conditions greatly reduces the impact of multiple access interference which occurs at the relay during the MA phase and all these network coding maps should satisfy a requirement called exclusive law. This paper does the equivalent for the three-way relaying scenario. We show that when the three users transmit points from the same 4-PSK constellation, every such network coding map that satisfies the exclusive law can be represented by a Latin Cube of Second Order. The network code map used by the relay for the BC phase is explicitly obtained and is aimed at reducing the effect of interference at the MA stage.

Performance analysis of adaptive physical layer network coding for wireless two-way Relaying

The analysis of modulation schemes for the physical layer network-coded two way relaying scenario is presented which employs two phases: Multiple access (MA) phase and Broadcast (BC) phase. Depending on the signal set used at the end nodes, the minimum distance of the effective constellation seen at the relay becomes zero for a finite number of channel fade states referred as the singular fade states. The singular fade states fall into the following two classes: (i) the ones which are caused due to channel outage and whose harmful effect cannot be mitigated by adaptive network coding called the non-removable singular fade states and (ii) the ones which occur due to the choice of the signal set and whose harmful effects can be removed called the removable singular fade states. In this paper, we derive an upper bound on the average end-to-end Symbol Error Rate (SER), with and without adaptive network coding at the relay, for a Rician fading scenario. It is shown that without adaptive network coding, at high Signal to Noise Ratio (SNR), the contribution to the end-to-end SER comes from the following error events which fall as SNR-1: the error events associated with the removable and nonremovable singular fade states and the error event during the BC phase. In contrast, for the adaptive network coding scheme, the error events associated with the removable singular fade states fall as SNR-2, thereby providing a coding gain over the case when adaptive network coding is not used. Also, it is shown that for a Rician fading channel, the error during the MA phase dominates over the error during the BC phase. Hence, adaptive network coding, which improves the performance during the MA phase provides more gain in a Rician fading scenario than in a Rayleigh fading scenario. Furthermore, it is shown that for large Rician factors, among those removable singular fade states which have the same magnitude, those which have the least absolute value of the phase - ngle alone contribute dominantly to the end-to-end SER and it is sufficient to remove the effect of only such singular fade states.