Topological Placement Research Articles

Coupled mode theory revisited: the role of the network topology and ordered directionality

We propose a theoretical correction to the coupled mode theory (CMT) to describe three or more coupled optical resonators considering the topological placement of each resonator and the light flow direction. This work allows an expansion of the CMT approximation for strong coupling and is validated by employing the transfer matrix method. A model of the three coupled resonators was studied in detail to provide evidence of the significant improvement in predicting the transmission spectrum of dark modes.

МЕТОДИКА СОЗДАНИЯ ТОПОЛОГИЧЕСКИХ ОГРАНИЧЕНИЙ ПРИ ВЫСОКОЙ УТИЛИЗАЦИИ РЕСУРСОВ ПЛИС

In the paper we consider the problem of achieving high real performance of reconfigurablecomputer systems in implementing computationally expensive tasks from various problem areas.The parameters of the programs executed on reconfigurable systems determine their real performance.The main component of these programs is the computing data processing structures implementedas FPGA configuration files. At the same time, one of the key parameters of any computingstructure is the clock frequency of its operation, which directly affects its performance. However,there are several problems concerning the achievement of high clock rates, and they cannot be solvedwith the help of modern CAD tools. The reason is the non-optimal topological placement of functionalblocks of the computing structure within the field of FPGA primitives, especially with high resourceutilization. Due to this, the load on the FPGA switching matrix is increasing, and, as a result,the connections among functionally dependent FPGA primitives turn out to be much longer than isacceptable. In addition, excessive connection length is observed when tracing connections amongprimitives that are placed on different FPGA chips or are physically separated by on-chip peripherals.In the paper we describe a methodology which provides optimization of the placement of computingstructure elements on FPGA primitives, and minimizes the length of traces among primitives,and also minimizes the number of traces among physically separated FPGA topological sections.To prove the proposed methodology, we implemented the test task "FIR-filter" on a reconfigurablecomputer "Tertius." We have demonstrated the main problems concerning reaching the target clockrate and have described a method for their solution. Owing to our methodology, it is possible toincrease the clock rate; hence, the performance of Tertius will increase by 25% without revisingthe functional circuit of the task’s computing structure. According to our current research of thesuggested methodology and its efficiency, we claim that CAD tools, used for creating topologicalrestrictions and based on our methodology, will significantly reduce the time for developing programswith the required characteristics for reconfigurable computer systems.

On closed subgroups of precompact groups

Abstract It is a theorem of W. W. Comfort and K. A. Ross that if 𝐺 is a subgroup of a compact Abelian group and 𝑆 denotes the continuous homomorphisms from 𝐺 to the one-dimensional torus, then the topology on 𝐺 is the initial topology given by 𝑆. Assume that 𝐻 is a subgroup of 𝐺. We study how the choice of 𝑆 affects the topological placement and properties of 𝐻 in 𝐺. Among other results, we have made significant progress toward the solution of the following specific questions. How many totally bounded group topologies does 𝐺 admit such that 𝐻 is a closed (dense) subgroup? If C S C_{S} denotes the poset of all subgroups of 𝐺 that are 𝑆-closed, ordered by inclusion, does C S C_{S} have a greatest (resp. smallest) element? We say that a totally bounded (topological, resp.) group is an SC group (topologically simple, resp.) if all its subgroups are closed (if 𝐺 and { e } \{e\} are its only possible closed normal subgroups, resp.) In addition, we investigate the following questions. How many SC-(topologically simple totally bounded, resp.) group topologies does an arbitrary Abelian group 𝐺 admit?

Topological Placement of Quality Sensors in Water-Distribution Networks without the Recourse to Hydraulic Modeling

AbstractThe detection of contaminant intrusion into a water-distribution network (WDN) is a difficult issue due to uncertainty related to the type of injected contaminant, source location, and intr...

DendriPeps: Expanding Dendrimer Functionality by Hybridizing Poly(amidoamine) (PAMAM) Scaffolds with Peptide Segments.

In this work, the first synthesis of poly(amidoamine) (PAMAM) dendrimers whose branches are hybridized with peptide segments (DendriPeps) is reported. The intercalation of amino acids within the branches of PAMAMs provides supplementary internal functionalities to the coronal groups. Four DendriPep prototypes are synthesized with lysine or glutamic acid as "guest" amino acids, displaying, respectively, a primary amine or a carboxyl group, on generation (G)2 and G3 PAMAMs as host scaffolds. The precise control over the number, type, and topological placement of functional groups expands the functional behavior of DendriPeps beyond current PAMAM dendrimers toward new frontiers or colloids, drug delivery vectors, and catalysis.

Mobile Data Offloading with Uniform Pricing and Overlaps

Mobile data offloading is an emerging technology to alleviate cellular network congestion and improve user service quality. In this paper, we investigate the economics of mobile data offloading through access points (APs) deployed by small cell service providers (SSPs), implementing uniform volume prices for all the mobile users (MUs) in each SSP's coverage including the overlapping area. In particular, we consider a data offloading game with a single mobile network operator (MNO) and two SSPs with overlapping coverage areas, where each SSP announces a uniform price for serving the cellular traffic within its coverage, and the MNO determines the traffic volumes to offload. We show that there is no pure Nash equilibrium (PNE) under such price competition, and determine the corresponding mixed strategy Nash equilibrium (MNE) using price randomization. As a practical solution, we propose a simple one shot auction mechanism that is easy to implement and has PNEs which is payoff equivalent with the MNE under price competition. We believe that this simple mechanism due to its simplicity of determining the equilibrium prices could be used in the negotiation between the SSPs and the MNO to determine the average service prices. Finally, we study the strategic topological infrastructure placement problem using a 1-dimension (1D, linear) user traffic flow model and a 2-dimension (2D) user traffic flow model when SSPs compete assuming uniform price competition as above. We show that the first mover in the placement problem will deploy its APs to cover more than half of the total flow volume and has an advantage to obtain a higher equilibrium payoff.

Tip-dating and the origin of Telluraves

Despite a relatively vast accumulation of molecular data, the timing of diversification of modern bird lineages remains elusive. Accurate dating of the origination of Telluraves—a clade of birds defined by their arboreality—is of particular interest, as it contains the most species-rich avian group, the passerines. Historically, neontological studies have estimated a Cretaceous origin for the group, but more recent studies have recovered Cenozoic dates, closer to the oldest known fossils for the group. We employ total-evidence dating to estimate divergence times that are expected to be both less sensitive to prior assumptions and more accurate. Specifically, we use a large collection of morphological character data from arboreal bird fossils, along with combined molecular sequence and morphological character data from extant taxa. Our analyses recover a Late Cretaceous origin for crown Telluraves, with a few lineages crossing the K-Pg boundary. Following the K-Pg boundary, our results show the group underwent rapid diversification, likely benefiting from increased ecological opportunities in the aftermath of the extinction event. We find very little confidence for the precise topological placement of many extinct taxa, possibly due to rapid diversification, paucity of character data, and rapid morphological differentiation during the early history of the group.

Gene regulatory and signaling networks exhibit distinct topological distributions of motifs.

The biological processes of cellular decision making and differentiation involve a plethora of signaling pathways and gene regulatory circuits. These networks in turn exhibit a multitude of motifs playing crucial parts in regulating network activity. Here we compare the topological placement of motifs in gene regulatory and signaling networks and observe that it suggests different evolutionary strategies in motif distribution for distinct cellular subnetworks.

Gradients of Connectivity in the Cerebral Cortex

The human neocortex is organized with distributed networks that connect distant regions together, but what determines their spatial layout? A recent study sheds light on the topological placement of regions along the cortical surface in relation to gradients of connectivity in both humans and macaques.

Community Detection in Signed Networks: the Role of Negative ties in Different Scales.

Extracting community structure of complex network systems has many applications from engineering to biology and social sciences. There exist many algorithms to discover community structure of networks. However, it has been significantly under-explored for networks with positive and negative links as compared to unsigned ones. Trying to fill this gap, we measured the quality of partitions by introducing a Map Equation for signed networks. It is based on the assumption that negative relations weaken positive flow from a node towards a community, and thus, external (internal) negative ties increase the probability of staying inside (escaping from) a community. We further extended the Constant Potts Model, providing a map spectrum for signed networks. Accordingly, a partition is selected through balancing between abridgment and expatiation of a signed network. Most importantly, multi-scale spectrum of signed networks revealed how informative are negative ties in different scales, and quantified the topological placement of negative ties between dense positive ones. Moreover, an inconsistency was found in the signed Modularity: as the number of negative ties increases, the density of positive ties is neglected more. These results shed lights on the community structure of signed networks.

A Novel Topological Genetic Algorithm-Based Phasor Measurement Unit Placement and Scheduling Methodology for Enhanced State Estimation

Phasor measurement units are emerging as a potential tool for on-line power system state estimation. Incorporation of phasor measurement units to the existing power system's monitoring system is impeded by various physical and economic constraints. This article proposes a novel topological genetic algorithm for optimal placement of phasor measurement units along with existing conventional measurement units such that state estimation can be achieved with enhanced accuracy and immunity against power grid contingencies. The proposed algorithm optimally places phasor measurement units so that complete observability of the power system is achieved through them and enhanced redundancy in measurement can be accomplished through conventional measurement units. Since practical phasor measurement unit placements are accomplished in multiple horizons, intelligent sorting and phase optimization methodologies have been presented to attain maximum observability during phasing periods. Placement of phasor measurement units with multiple channel limits has also been studied in this article. The efficacy of the proposed topological genetic algorithm for optimizing the number of phasor measurement units and enhancing state estimation under various operating conditions has been validated through extensive simulation studies conducted in IEEE standard bus systems. Practical case studies have been performed in the western and southern region Indian power grids.

Essentiality and centrality in protein interaction networks revisited

BackgroundMinimum dominating sets (MDSet) of protein interaction networks allow the control of underlying protein interaction networks through their topological placement. While essential proteins are enriched in MDSets, we hypothesize that the statistical properties of biological functions of essential genes are enhanced when we focus on essential MDSet proteins (e-MDSet).ResultsHere, we determined minimum dominating sets of proteins (MDSet) in interaction networks of E. coli, S. cerevisiae and H. sapiens, defined as subsets of proteins whereby each remaining protein can be reached by a single interaction. We compared several topological and functional parameters of essential, MDSet, and essential MDSet (e-MDSet) proteins. In particular, we observed that their topological placement allowed e-MDSet proteins to provide a positive correlation between degree and lethality, connect more protein complexes, and have a stronger impact on network resilience than essential proteins alone. In comparison to essential proteins we further found that interactions between e-MDSet proteins appeared more frequently within complexes, while interactions of e-MDSet proteins between complexes were depleted. Finally, these e-MDSet proteins classified into functional groupings that play a central role in survival and adaptability.ConclusionsThe determination of e-MDSet of an organism highlights a set of proteins that enhances the enrichment signals of biological functions of essential proteins. As a consequence, we surmise that e-MDSets may provide a new method of evaluating the core proteins of an organism.

Acoustic response of vortex breakdown modes in a coaxial isothermal unconfined swirling jet

The present experimental work is concerned with the study of amplitude dependent acoustic response of an isothermal coaxial swirling jet. The excitation amplitude is increased in five distinct steps at the burner’s Helmholtz resonator mode (i.e., 100 Hz). Two flow states are compared, namely, sub-critical and super-critical vortex breakdown (VB) that occur before and after the critical conical sheet breakdown, respectively. The geometric swirl number is varied in the range 2.14-4.03. Under the influence of external pulsing, global response characteristics are studied based on the topological changes observed in time-averaged 2D flow field. These are obtained from high resolution 2D PIV (particle image velocimetry) in the longitudinal-mid plane. PIV results also illustrate the changes in the normalized vortex core coordinates (rvcc/(rvcc)0 Hz, yvcc/(yvcc)0 Hz) of internal recirculation zone (IRZ). A strong forced response is observed at 100 Hz (excitation frequency) in the convectively unstable region which get amplified based on the magnitude of external forcing. The radial extent of this forced response region at a given excitation amplitude is represented by the acoustic response region (b). The topological placement of the responsive convectively unstable region is a function of both the intensity of imparted swirl (characterized by swirl number) and forcing amplitude. It is observed that for sub-critical VB mode, an increase in the excitation amplitude till a critical value shifts the vortex core centre (particularly, the vortex core moves downstream and radially outwards) leading to drastic fanning-out/widening of the IRZ. This is accompanied by ∼30% reduction in the recirculation velocity of the IRZ. It is also observed that b < R (R: radial distance from central axis to outer shear layer-OSL). At super-critical amplitudes, the sub-critical IRZ topology transits back (the vortex core retracts upstream and radially inwards) and finally undergoes a transverse shrinkage (rvcc/rvcc0Hz decreases by ∼20%) when b ≥ R. In contrast, the vortex core of super-critical breakdown mode consistently spreads radially outwards and is displaced further downstream. Finally, the IRZ fans-out at the threshold excitation amplitude. However, the acoustic response region b is still less than R. This is explained based on the characteristic geometric swirl number (SG) of the flow regimes. The super-critical flow mode with higher SG (hence, higher radial pressure drop due to rotational effect which scales as ΔP ∼ ρuθ2 and acts inwards towards the center line) compared to sub-critical state imposes a greater resistance to the radial outward spread of b. As a result, the acoustic energy supplied to the super-critical flow mode increases the degree of acoustic response at the pulsing frequency and energizes its harmonics (evident from power spectra). As a disturbance amplifier, the stronger convective instability mode within the flow structure of super-critical VB causes the topology to widen/fan-out severely at threshold excitation amplitude.

Effect of topological placement of memory cells in memory chips on multiplicity of cell upsets from heavy charged particles

An analysis of factors influencing operational reliability of memory chips has been performed. Different topological configurations of 6-transistors memory cells have been considered. Two configurations of cells most sensitive to the influence of multiple cell upsets (MCUs) have been identified.

Developing Domain-Knowledge Evolutionary Algorithms for Network-on-Chip Application Mapping

This paper addresses the Network-on-Chip (NoC) application mapping problem. This is an NP-hard problem that deals with the optimal topological placement of Intellectual Property cores onto the NoC tiles. Network-on-Chip application mapping Evolutionary Algorithms are developed, evaluated and optimized for minimizing the NoC communication energy. Two crossover and one mutation operators are proposed. It is analyzed how each optimization algorithm performs with every genetic operator, in terms of solution quality and convergence speed. Our proposed operators are compared with state-of-the-art genetic operators for permutation problems. Finally, the problem is approached in a multi-objective way. Besides energy minimization, it is also aimed to map the cores such that a thermally balanced Network-on-Chip design is obtained. It is shown, through simulations on real applications, that by using domain-knowledge, our developed genetic operators increase the algorithms’ performance. By comparing these Evolutionary Algorithms with an Optimized Simulated Annealing, it is shown that they perform better. In the case of two contradictory objectives, our genetic operators can still help at providing the mappings with the lowest communication energy.

Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology

BackgroundIn many protein-protein interaction (PPI) networks, densely connected hub proteins are more likely to be essential proteins. This is referred to as the "centrality-lethality rule", which indicates that the topological placement of a protein in PPI network is connected with its biological essentiality. Though such connections are observed in many PPI networks, the underlying topological properties for these connections are not yet clearly understood. Some suggested putative connections are the involvement of essential proteins in the maintenance of overall network connections, or that they play a role in essential protein clusters. In this work, we have attempted to examine the placement of essential proteins and the network topology from a different perspective by determining the correlation of protein essentiality and reverse nearest neighbor topology (RNN).ResultsThe RNN topology is a weighted directed graph derived from PPI network, and it is a natural representation of the topological dependences between proteins within the PPI network. Similar to the original PPI network, we have observed that essential proteins tend to be hub proteins in RNN topology. Additionally, essential genes are enriched in clusters containing many hub proteins in RNN topology (RNN protein clusters). Based on these two properties of essential genes in RNN topology, we have proposed a new measure; the RNN cluster centrality. Results from a variety of PPI networks demonstrate that RNN cluster centrality outperforms other centrality measures with regard to the proportion of selected proteins that are essential proteins. We also investigated the biological importance of RNN clusters.ConclusionsThis study reveals that RNN cluster centrality provides the best correlation of protein essentiality and placement of proteins in PPI network. Additionally, merged RNN clusters were found to be topologically important in that essential proteins are significantly enriched in RNN clusters, and biologically important because they play an important role in many Gene Ontology (GO) processes.

Modelling hydrological effects of wetland restoration: a differentiated view

The paper presents findings of a conjunctive hydrological and ecological study into habitat restoration and catchment hydrology. Physically-based, fully distributed hydrological modelling was coupled with spatial analysis and wetland scenario generation techniques to simulate potential effects of restoring lower, middle, and upper catchment wetlands. In the past, anthropogenic interference of this catchments' landscape for agriculture and settlement has left most wetland areas drained, and brought the natural functioning of the ecosystem into conflict with human needs. Many eco-hydrology studies conclude that such disturbances result in a more extreme hydrological regime. The study objectives were to develop and study innovative methods for habitat restoration, and understand the potential hydrological impacts of each approach. The study aims to analyze the scenarios and whether the hydrological response is influenced by the topological placement of the restoration sites. Land-use change scenarios are developed on the basis of physical characteristics and consider the credibility of transitions from current land-use. This study focused on the position of the wetlands in the catchment and hydrological typology. Wetland restoration scenarios are created for different geographical settings within the catchment. A distinction is made between groundwater dependent wetlands and wetlands that are influenced by in-stream water tables or surface water inundations. Results show that there is little effect on the total annual water budget. The results point to river valley rewetting as having the effect of decreasing the paved overland component of stream flow, and increasing the saturated zone flow component. It promoted groundwater recharge. There was no increase of peak flows due to headwater wetlands, contrary to some sources (Bullock & Acreman 2003). The catchments' actual evapotranspiration and root zone water responses were found to be varied over the analysis points, and were the consequence of a number of factors. As a second conclusion we point out the main knowledge gaps and demerits that could compromise the modelling exercise. Land-use classification for hydrological modelling is subject to important ambiguities. Different maps often have different class definitions and methods for classification. Many in-between land use/land cover types do not fit any particular class definition in map classification. Wetlands were often found to be classified as grassland, leaf forest, or open water. How do we deal with the diversity of wetland types and how to incorporate their specific hydrological behaviour in models? These issues will be thoroughly illustrated for the case of the Grote Nete and put in a larger perspective.

An integrated bandwidth allocation and admission control framework for the support of heterogeneous real-time traffic in class-based IP networks

The support of real-time traffic in class-based IP networks requires the reservation of resources in all the links along the end-to-end paths through appropriate queuing and forwarding mechanisms. This resource allocation should be accompanied by appropriate admission control procedures in order to guarantee that newly admitted real-time traffic flows do not cause any violation to the Quality of Service (QoS) experienced by the already established real-time traffic flows. In this paper we initially aim to highlight certain issues with respect to the areas of bandwidth allocation and admission control for the support of real-time traffic in class-based IP networks. We investigate the implications of topological placement of both the bandwidth allocation and admission control schemes. We show that the performance of bandwidth allocation and admission control schemes depends highly on the location of the employed procedures with respect to the end-users requesting the services and the various network boundaries (access, metro, core, etc.). Based on our results we conclude that the strategies for applying these schemes should be location-aware, because the performance of bandwidth allocation and admission control at different points in a class-based IP network, and for the same traffic load, can be quite different and can deviate greatly from the expected performance. Through simulations we also try to provide a quantitative view of the aforementioned deviations. Taking the implications of this “location-awareness” into account, we subsequently present a new Measurement-based Admission Control (MBAC) scheme for real-time traffic that uses measurements of aggregate bandwidth only, without keeping the state of any per-flow information. In this scheme there is no assumption made on the nature of the traffic characteristics of the real-time traffic flows, which can be of heterogeneous nature. Through simulations we show that the admission control scheme is robust with respect to traffic heterogeneity and measurement errors. We also show that our scheme compares favorably against other admission control schemes in the literature.

Molecular phylogenetics and asexuality in the brine shrimp Artemia

Explaining cases of long-term persistence of parthenogenesis has proven an arduous task for evolutionary biologists. Interpreting sexual–asexual interactions though has recently advanced owing to methodological design, increased taxon sampling and choice of model organisms. We inferred the phylogeny of Artemia, a halophilic branchiopod genus of sexual and parthenogenetic forms with cosmopolitan distribution, marked geographic patterns and ecological partitioning. Joint analysis of newly derived ITS1 sequences and 16S RFLP markers from global isolates indicates significant interspecific divergence as well as pronounced diversity for parthenogens, matching that of sexual ancestors. Maximum parsimony, maximum likelihood, and Bayesian methods were largely congruent in reconstructing the phylogeny of the genus. Given the current sampling, at least four independent origins of parthenogenesis are deduced. Molecular clock calibrations based on biogeographic landmarks indicate that the lineage leading to A. persimilis diverged from the common ancestor of all Artemia species between 80 and 90 MYA at the time of separation of Africa from South America, whereas parthenogenesis first appeared at least 3 MYA. Common mitochondrial DNA haplotypes delineate A. urmiana and A. tibetiana as possible maternal parents of several clonal lineages. A novel topological placement of A. franciscana as a sister clade to all Asian Artemia and parthenogenetic forms is proposed and also supported by ITS1 length and other existing data.

A comparison of heterogeneous video multicast schemes: Layered encoding or stream replication

The heterogeneity of the Internet's transmission resources and end system capability makes it difficult to agree on acceptable traffic characteristics among the multiple receivers of a multicast video stream. Three basic approaches have been proposed to deal with this problem: 1) multicasting the replicated video streams at different rates; 2) multicasting the video encoded in cumulative layers; and 3) multicasting the video encoded in noncumulative layers. Even though there is a common belief that the layering approach is better than the replicated stream approach, there have been no studies that compare these schemes. This paper is devoted to such a systematic comparison. Our starting point is an observation (substantiated by results in the literature) that a bandwidth overhead is incurred by encoding a video stream in layers. We argue that a fair comparison of these schemes needs to take into account this overhead, as well as the specifics of the encoding used in each scheme, protocol complexity, and the topological placement of the video source and the receivers relative to each other. Our results show that the believed superiority of layered multicast transmission relative to replicated stream multicasting is not as clear cut as is widely believed and that there are indeed scenarios where replicated stream multicasting is the preferred approach.