MOTIVATION: Queueing theory can be effective in simulating biochemical reactions taking place in living cells, and the article paves a step toward development of a comprehensive model of cell metabolism. Such a model could help to accelerate and reduce costs for developing and testing investigational drugs reducing number of laboratory animals needed to evaluate drugs. RESULTS: The article presents a Krebs cycle model based on queueing theory. The model allows for tracking of metabolites concentration changes in real time. To validate the model, a drug-induced inhibition affecting activity of enzymes involved in Krebs cycle was simulated and compared with available experimental data. AVAILABILITYAND IMPLEMENTATION: The source code is freely available for download at https://github.com/UTP-WTIiE/KrebsCycleUsingQueueingTheory, implemented in C# supported in Linux or MS Windows. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Communications, in general, involve delivery of information from a source to a sink. At nano-scale, an example of a man-made communications involving interfacing with biological systems at intra-cellular level is non-viral gene delivery. From a telecommunications engineering perspective, important end-to-end parameters of such a system are: the end-to-end delay, system capacity, and packet loss rate. There are neither known methods to estimate those parameters theoretically nor they are ready available from standard measurements. The paper provides estimates for those parameters based on the simulation of non-viral gene delivery system based on the queuing theory. The simulator used has been validated through the series of in-vitro laboratory experiments.

In a multiple-input multiple-output (MIMO), multiband orthogonal frequency division multiplexing (MB-OFDM) ultra-wideband (UWB) system, coherent detection requires the transmission of a large number of symbols for channel estimation, thus reducing the bandwidth efficiency. For the first time, this paper proposes unitary differential space-time-frequency codes (DSTFCs) for MB-OFDM UWB communications, which increase the system bandwidth efficiency because no channel state information (CSI) is required. The proposed system would be useful when CSI is unavailable at the receiver, such as when the transmission of multiple channel estimation symbols is impractical or uneconomical. The coding and decoding algorithms for the proposed DSTFCs are then derived for both constant envelope modulation scheme, such as PSK (phase shift keying) and 4QAM (quadrature amplitude modulation), and multi-dimensional modulation scheme, such as DCM (dual carrier modulation). The paper also quantifies for the first time the diversity order of a DSTFC MB-OFDM system. Simulation results show that the application of DSTFCs can significantly improve the bit error performance of conventional differential MB-OFDM system (without MIMO), and even provide much better bit error performance than the conventional coherent MB-OFDM system (without MIMO) at high signal-to-noise ratios.

In a Cognitive Radio (CR) enabled network, Secondary Users (SUs) have an impact on the Quality-of-Service (QoS), and ultimately the revenue of the PU Primary User (PU) license holders. An important metric of an investor's economic welfare is the ratio of mean returns to the volatility of returns (Sharpe ratio). Numerous CR access schemes have been proposed that fail to account for the economic welfare of PUs when SUs access their spectrum. In this paper we consider the PU's spectrum license as an investment and analyze the impact of CR activity on the PU's economic welfare, in order to derive a cost of production of spectrum access rights such that the PU's economic welfare is not degraded. This creates an incentive for PUs to permit CR access in their spectrum bands, by ensuring that the characteristics of returns on the substantial investment made in spectrum licenses are preserved. However, under any instantaneous or spot pricing scheme, the risk of price volatility is introduced. We also propose a framework to alleviate the risk to SUs from a volatile CR rights spot price, by introducing the concept of forward pricing and hedging of CR rights. This reduces the variability of cash-flow associated with the purchase of CR rights, ensuring that the QoS provided by an SU network remains unaffected by a high CR access price. We also illustrate the leverage effect, where a PU will achieve a higher mean return- on-investment with SU operation, albeit with a higher variance of returns.

The use of licensed spectrum by Cognitive Radio (CR) enabled secondary users (SUs) impacts the Quality-of-Service (QoS) and ultimately, the revenue earned by Primary User (PU) license holders. It is therefore important to find appropriate pricing models for pricing spectrum for access by CR-based networks. Pricing of CR access rights can be modeled as an investment problem, which raises the issue of PU economic welfare preservation in the context of returns on its investment in spectrum licenses. By analyzing the impact of CR activity on the reward-to-variability ratio (Sharpe ratio) of returns on the spectrum investment, the degradation in economic welfare experienced by the PU as a result of SU activity can be quantified. In this paper, we examine the impact of a multiple PU environment and variable traffic characteristics on the dynamics of the Sharpe Ratio based pricing strategy. Numerical results indicate that with multiple spectrum license holders, the Sharpe Ratio based pricing framework will continue to maintain PU economic welfare but results in a reduced access price for SUs.

Complex orthogonal designs (CODs) have been successfully implemented in wireless systems as complex orthogonal space-time block codes (COSTBCs). Certain properties of the underlying CODs affect the performance of the codes. In addition to the main properties of a COD's rate and decoding delay, a third consideration is whether the COD can achieve transceiver signal linearization, a property that facilitates practical implementation by, for example, significantly simplifying the receiver structure for iterative decoding. It has been shown that a COD can achieve this transceiver signal linearization if the nonzero entries in any given row of the matrix are either all conjugated or all nonconjugated. This paper determines the conditions under which maximum rate CODs can achieve this desirable property. For an odd number of transmit antennas, it is shown that maximum rate CODs that achieve the lower bound on decoding delay can also achieve transceiver signal linearization. In contrast, for an even number of transmit antennas, maximum rate CODs that achieve the lower bound on delay cannot achieve this linearization. In this latter case, linearization is possible only if the COD achieves at least twice the lower bound on delay. This work highlights the tradeoffs among these three important properties.

Nanoparticle-based drug delivery systems provide a feasible method of efficiently delivering drugs in-vivo. These drug delivery systems could greatly benefit from a robust method of nano-scale communication. Additionally, there are numerous naturally occurring nano-scale communication systems and the opportunity to develop a system based on these principles is highly promising. A layered communication protocol provides a simple, succinct method of understanding macro to nano-scale communication systems. This protocol may be used to expand and eventually apply commonly used telecommunications techniques to nanoparticle signalling. Such a protocol may begin to pave the way for future communication systems at a nano-scale.

This paper presents a physical and MAC layer analysis of the recently introduced IEEE 802.15.3c standard for multi Gbps communication at 60 GHz. We find the optimal beamwidth of the transmitting antenna, achieving a trade-off between the Piconet Coordinator discovery and the duration of the contention access period (CAP) of the IEEE 802.15.3c MAC superframe. To find the optimal beamwidth, we first analyze the link budget of 60 GHz based directional communication, to identify the transmitting and receiving antenna gain, and hence the minimum beamwidth required to achieve a specific bit error probability (BEP) for a given distance between transmitter and receiver. We introduce a more efficient method for analytically modeling the binary exponential backoff (BEB) process during the CSMA/CA based CAP of the superframe, using a 1-dimentional Markov chain. Numerical results for the required antenna gain and optimal beamwidth, demonstrate the usefulness of our analysis technique.

Guaranteeing Quality of Service (QoS) in Cognitive Radio (CR) networks is a challenging task due to the random nature of radio channel conditions and primary user traffic. In this paper we analyze the recently proposed mean-variance based QoS and resource management methods, and introduce the concept of mean-variance evaluation of QoS and resource management techniques. Inspired by financial Portfolio Selection theory, mean-variance based resource management techniques for CR networks are statistical approaches and do not require instantaneous knowledge of channel state and Primary User (PU) activity, and enable the option to tradeoff between risk (QoS variance) and reward (QoS mean). Using throughput as a measure of QoS, we present a derivation of the theoretical throughput mean-variance characteristics of a CR-OFDM system employing a mean-variance based QoS management strategy. We conduct an analysis of existing Portfolio Selection based strategies in the mean-variance domain and compare them to the theoretical performance. Finally, we present a further enhancement of the approach by explicitly considering constraints on individual channel power allocation in the mean-variance optimization problem. Simulation results illustrate the effect of our enhancements in improving the risk-reward profile of the mean-variance based QoS management strategy, by moving it closer to the theoretical characteristic.

This paper presents a customizable framework for employing Cognitive Radio in Intermittently Connected Wireless Networks, which aims to maximize transmission opportunities that arise when fully connected network partitions are formed. Various layer 3 routing and information dissemination protocols would benefit from increased opportunity utility. We propose to use Cognitive Radio to permit multiple flows to occur in close proximity while minimizing spectrum wastage. We provide an example implementation of the proposed MAC framework which could increase the MAC throughput of networks exhibiting intermittent connectivity and network partition.

This paper present a new routing protocol for Ad hoc networks, called On-demand Tree-based Routing Protocol (OTRP). This protocol combines the idea of hop-by-hop routing such as AODV with an efficient route discovery algorithm called Tree-based Optimized Flooding (TOF) to improve scalability of Ad hoc networks when there is no previous knowledge about the destination. To achieve this in OTRP, route discovery overheads are minimized by selectively flooding the network through a limited set of nodes, referred to as branching-nodes. The theoretical analysis and simulation results showed that OTRP outperforms AODV, DYMO, and OLSR and it reduces overheads as number of nodes and traffic increase.

Constructions of square, maximum rate complex orthogonal space–time block codes (CO STBCs) are well known, however codes constructed via the known methods include numerous zeros, which impede their practical implementation. By modifying the Williamson and Wallis-Whiteman arrays to apply to complex matrices, we propose two methods of construction ofsquare, order-$4n$CO STBCs fromsquare, order-$n$codes which satisfy certain properties. Applying the proposed methods, we constructsquare,maximum rate, order-8 CO STBCs with no zeros, such that the transmitted symbols are equally dispersed through transmit antennas. Those codes, referred to as theimproved square CO STBCs, have the advantages that the power is equally transmitted via each transmit antenna during every symbol time slot and that a lower peak-to-average power ratio (PAPR) is required to achieve the same bit error rates as the conventional CO STBCs with zeros.

The combination of user multiplexing and data encoding within Ultra Wideband systems has been proposed to improve bit error performance. Relative to conventional binary coding, this technique has shown to reduce error rates in scarcely populated systems. Where non-binary turbo coding modulates data to form an integer sequence, a random mapping is generally applied to develop a time hopping sequence. This paper explores the possibility of mapping through the application of truncated hyperbolic congruence codes. Comparative results against a random mapping indicate an improvement in system performance for higher turbo iteration levels in the receiver. Transceiver architecture is based upon the transmitter side equalization approach of time reversed communications.

Though cooperative communication has been intensively examined for general wireless systems, such as mobile and ad-hoc networks, it has been almost unexplored in the case of space-time-frequency coded multi-band OFDM ultra-wideband (STFC MB-OFDM UWB). This paper proposes a framework of cooperative communication in such systems where nodes are equipped with only one antenna. Simulation results show that cooperative communication might, in some cases, provide better error performance than non-cooperative communication without any additional transmission power.

With significant research being conducted in Ultra Wideband communications to increase error performance, this paper proposes a combination of user multiplexing and data encoding to achieve a BER improvement. Through the use of non-binary turbo coding, data is modulated to form a time hopping code which is applied to a time-reversed UWB system. Comparative results with conventional binary coding are given, showing the possibility for BER improvements in systems with a low number of users. Slight performance degradations for a large number of users exist. The effects of a user applying turbo coding on other users not applying forward error correction is also studied.

Because of the wide deployment of 802.11 equipments in the past decade, current applications are not limited anymore to only single Access Points (AP) deployments for indoor usage, but have been extended to multi-hop networks to fulfill the need of high speed connectivity in mobile environments, where the analysis of multi-hop networks is extremely complicated. The behavior of an AP is dependent not only on its neighbors’ behavior, but also on the behavior of other hidden nodes. In this paper, we provide an accurate and verified multi-hop wireless backhaul analysis for performance of IEEE 802.11 DCF in terms of the channel throughput using a static channel error rate. The model is based on analysis of a single hop communications for evaluating the multi-hop wireless backhaul networks. We utilized our existing 3.5-mile Federal Railroad Administration (FRA) test bed on the BNSF railroad track in Nebraska to validate the model. Our field measurements and simulation results show that our proposed model is accurate.

This letter proposes a simple but highly efficient technique to jointly utilize space, time, and polarization diversities. The technique is based on extending orthogonal space-time block codes into the quaternion domain and utilizing a description of the dual-polarized signal by means of quaternions, which are a generalization of complex numbers. In the given example, the achievable performance gain for two transmit and one receive antennas is approximately 6 dB at a bit error rate of 10-4when compared with the Alamouti code.

A simple algorithm for the weight calculation of turbo codes with convolutional interleavers is presented. For codes with short interleaver lengths, the weight distributions are computed using conventionally proposed methods and then utilised together with the interleaver properties to determine the weight specifications for the code with a longer desired length. Based on the calculated weights, a new upper bound for the code is computed. It agrees with simulation results of the code performance in the error-floor region.

Ultra wideband is a short-range wireless communication technique which has seen increased interest over the past decade. Having several methods of implementation, a key issue will always be the avoidance of multi-user interference. For time-hopped ultra wideband, this is achieved through the use of different codes assigned to each user, performing time-hopped code division multiple access. This paper presents a performance comparison of several time hopping sequence construction methods. It presents correlation results between sequences, and simulation results in a Gaussian noise degraded, scattering rich multi-user environment. Simulations are based on the IEEE channel model for UWB communications

Constructions of square, maximum rate complex orthogonal space-time block codes (CO STBCs) are well known, however codes constructed via the known methods include numerous zeros, which impede their practical implementation. By modifying the Williamson and Wallis-Whiteman arrays to apply to complex matrices, we propose two methods of construction or square, order-4n CO STBCs from square, order-n codes, which satisfy certain properties. Applying the proposed methods, we construct square, maximum rate, order-8 CO STBCs with no zeros, such that the transmitted symbols equally disperse through transmit antennas. Those codes, referred to as the improved square CO STBCs, have the advantages that the power is equally transmitted via each transmit antenna during every symbol time slot and that a lower peak-to-mean power ratio per each antenna is required to achieve the same bit error rates as for the conventional CO STBCs with zeros

Although the generation of correlated Rayleigh fading envelopes has been intensively considered in the literature, all conventional methods have their own particular shortcomings, which seriously impedes their applicability. A very general, straightforward algorithm is proposed for the generation of an arbitrary number of Rayleigh envelopes with any desired, equal or unequal power in wireless channels, either with or without Doppler frequency shifts. The proposed algorithm can be applied in the case of spatial correlation, such as with antenna arrays in multiple input multiple output (MIMO) systems, or spectral correlation between random processes, as in orthogonal frequency division multiplexing (OFDM) systems. It can also be used for generating correlated Rayleigh fading envelopes in either discrete-time instants or a real-time scenario. Besides being more generalized, our proposed algorithm is more precise, while overcoming all the shortcomings of conventional methods.

This work presents an algorithm for computation of the free distance parameter of turbo codes with a convolutional interleaver implemented to act as a block interleaver. Based on the properties of the interleaver and the algorithm applied, we can also determine the other low weights of turbo codes and this is useful in determining the performance of the error floor of turbo codes. For different turbo code structures, the relevant parameters have been computed. The error rate simulations confirm the algorithm results.

The paper deals with antenna selection techniques for wireless channels utilizing differential space-time modulation. We propose here the restricted N-out-of-M antenna selection technique providing relatively good bit error performance, while using only one feedback bit for transmit diversity purpose. In addition, we also present an improved N-out-of-(N+1) antenna selection technique, which shortens the time required for processing feedback information. These techniques remarkably improve performance of wireless channels using differential detection.

Abstract Orthogonal bipolar spreading sequences are used in direct sequence code division multiple access (DS‐CDMA) systems for both spectrum spreading and channel separation. The most commonly used sequences are Walsh–Hadamard sequences of lengths being an integer power of 2. A construction based on Williamson's arrays leading to sequences of lengths N≡4 (mod 8) is presented in the paper. Aperiodic correlation characteristics, for example sequence sets of lengths 12–252 are presented. The correlation properties of the sequence sets are later improved using a diagonal modification technique. Copyright © 2003 John Wiley & Sons, Ltd.

This paper presents a new routing strategy for mobile ad hoc networks, called dynamic zone-based topology routing protocol (DZTR). We introduce new strategies to maintain up-to-date intrazone and interzone topology information at each node. We also propose a GPS-based location tracking mechanism, which reduces route discovery area and the number of nodes queried to find the required destination. Our routing strategy has been designed to work with a dynamic zone, which contains a set of member nodes. Every node outside a zone is called a single-state node. We perform theoretical performance analysis, which shows that our network topology creation process has significantly fewer overheads than flooding approaches.

This paper addresses experimental measurements from an IEEE 802.11 ad hoc network testbed, which indicate a strong signal strength dependence in the ability of a hidden terminal to gain access to the radio channel. We present analytical results investigating the 'hidden terminal jamming' ability of the IEEE 802.11 DSSS physical layer. Results indicate that in a hidden terminal topology, the presence of an interfering transmission with a signal strength marginally greater than the transmission currently being received will result in an intolerable increase in BER, effectively jamming the ongoing transmission. These results confirm previous experimental measurements which show that after a number of MAC layer timeout/retransmission periods, the original (weaker) connection is effectively prevented from gaining access to the channel.

We investigate the performance of common capture models in terms of the fairness properties they reflect across contenting hidden connections. We propose a new capture model, message retraining, as a means of providing an accurate description of experimental data. Using two fairness indices we undertake a quantitative study of the accuracy with which each capture model is able to reflect experimental data. Standard capture models are shown to be unable to accurately reflect the fairness properties of empirical data. The message retraining capture model is shown to provide a good estimate of actual system performance in varying signal strength conditions.

We propose a simple but efficient method for optimizing correlation properties of polyphase spreading sequences for asynchronous DS CDMA applications. The proposed method can be used to minimize the mean square value of aperiodic crosscorrelation or the mean square value of aperiodic autocorrelation, the maximum value of aperiodic crosscorrelation functions, merit factor or other properties of the sequence set. The important feature of the method is that when applied to orthogonal sequences, it modifies correlation properties of the sequence set, while it preserves their orthogonality for perfect synchronization.

We present simulation results for the 13 channel DS CDMA WATM LAN utilising optimized complex spreading signatures based on Walsh functions. The method to obtain those optimized spreading signatures, as well as the full set of the coefficients giving the minimum level of cross-correlation between any pair of the channels is shown. The resultant system BER as well as the distribution of errors within WATM cells is given. The obtained results indicate that with the application of a hybrid ARQ scheme with errors and erasures decoding, the number of WATM cells which would require retransmission is in the order of 0.46%.

A major challenge in the design of wireless ATM LANs is to overcome the severe degradation of channel bit error rate resulting from channel impairments such as multi-path propagations. In this paper, we propose a WATM LAN which incorporates the CDMA spread spectrum technique together with hybrid ARQ error control schemes to effectively combat multi-path effects. We present a TDMA based multiple access protocol to arbitrate access of ATM cells from mobile terminals into time-slots on multiple CDMA channels. The multiple access protocol can efficiently support a mixture of real-time, delay-sensitive services and loss-sensitive, data services.

We propose a method to partially suppress ISI and MAI for DS SS CDMA schemes in wireless LANs. The method can be regarded as an alternative approach to combat ISI and in particular MAI by the use of advanced multiuser detection. Instead of using very sophisticated detectors, we propose introduction of a simple modification to the carrier waveform which results in very substantial reduction in cross-correlation between users and an off-peak auto-correlation. The method can be applied to any DS SS CDMA scheme, but should be particularly useful in the case of short spreading signatures, as is the case of WLANs.