Theses and Dissertations
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Item Open Access On designing DNA codes and their applications(Dhirubhai Ambani Institute of Information and Communication Technology, 2019) Limbachiya, Dixita; Gupta, Manish K.Bio-computing uses the complexes of biomolecules such as DNA (Deoxyribonucleic acid), RNA (Ribonucleic acid) and proteins to perform the computational processes for encoding and processing the data. In 1994, L. Adleman introduced the field of DNA computing by solving an instance of the Hamiltonian path problem using the bunch of DNA sequences and biotechnology lab methods. An idea of DNA hybridization was used to perform this experiment. DNA hybridization is a backbone for any computation using the DNA sequences. However, it is also cause of errors. To use the DNA for computing, a specific set of the DNA sequences (DNA codes) which satisfies particular properties (DNA codes constraints) that avoid cross-hybridization are designed to perform a particular task. Contributions of this dissertation can be broadly divided into two parts as 1) Designing the DNA codes by using algebraic coding theory. 2) Codes for DNA data storage systems to encode the data in the DNA. The main research objective in designing the DNA codes over the quaternary alphabets {A, C, G, T}, is to find the largest possible set of M codewords each of length n such that they are at least at the distance d and satisfies the desired constraints which are feasible with respect to practical implementation. In the literature, various computational and theoretical approaches have been used to design a set of DNA codes which are sufficiently dissimilar. Furthermore, DNA codes are constructed using coding theoretic approaches using fields and rings. In this dissertation, one such approach is used to generate the DNA codes from the ring R = Z4 + wZ4, where w2 = 2 + 2w. Some of the algebraic properties of the ring R are explored. In order to define an isometry from the elements of the ring R to DNA, a new distance called Gau distance is defined. The Gau distance motivates the distance preserving map called Gau map f. Linear and closure properties of the Gau map are obtained. General conditions on the generator matrix over the ring R to satisfy reverse and reverse complement constraints on the DNA code are derived. Using this map, several new classes of the DNA codes which satisfies the Hamming distance, reverse and reverse complement constraints are given. The families of the DNA codes via the Simplex type codes, first order and rth order Reed-Muller type codes and Octa type codes are developed. Some of the general results on the generator matrix to satisfy the reverse and reverse complement constraints are given. Some of the constructed DNA codes are optimal with respect to the bounds on M, the size of the code. These DNA codes can be used for a myriad of applications, one of which is data storage. DNA is stable, robust and reliable. Theoretically, it is estimated that one gram of DNA can store 455 EB (1 Exabyte = 1018 bytes). These properties make the DNA a potential candidate for data storage. However, there are various practical constraints for the DNA data storage system. In this work, we construct DNA codes with some of the DNA constraints to design efficient codes to store data in DNA. One of the practical constraints in designing DNA codes for storage is the repeated bases (runlengths) of the same DNA nucleotides. Hence, it is essential that each DNA codeword should avoid long runlengths. In this thesis, codes are proposed for data storage that will dis-allow runlengths of any base to develop DNA data storage error-free codes. A fixed GC-weight u (the occurrence of G and C nucleotides in a DNA codeword) is another requirement for DNA codewords used in DNA storage. DNA codewords with large GC-weight lead to insertion and deletion (indel) errors in DNA reading and amplification process thus, it is crucial to consider a fixed GCweight for DNA code. In this work, we propose methods that generate families of codes for the DNA data storage systems that satisfy no-runlength and fixed GC-weight constraints for the DNA codewords used for data storage. The first is the constrained codes which use the quaternary code and the second is DNA Golay subcodes that use the ternary encoding. The constrained quaternary coding is presented to generate DNA codes for the data storage. We give a construction algorithm for finding families of DNA codes with the no-runlength and fixed GC-weight constraints. The number of DNA codewords of fixed GC-weight with the no-runlength constraint is enumerated. We note that the prior work only gave bounds on the number of such codewords while in this work we count the number of these DNA codewords exactly. We observe that the bound mentioned in the previous work does not take into account the distance of the code which is essential for data reliability. Thus, we consider distance to obtain a lower bound on the number of codewords along with the fixed GC-weight and no-runlength constraints. In the second method, we demonstrate the Golay subcode method to encode the data in a variable chunk architecture of the DNA using ternary encoding. N.Goldman et al. introduced the first proof of concept of the DNA data storage in 2013 by encoding the data without using error correction in the DNA which motivated us to implement this method. While implementing this method, a bottleneck of this approach was identified which limited the amount of data that can be encoded due to fix length chunk architecture used for data encoding. In this work, we propose a modified scheme using a non-linear family of ternary codes based on the Golay subcode that includes flexible length chunk architecture for data encoding in DNA. By using the Golay ternary subcode, two substitution errors can be corrected. In a nutshell, the significant contributions of this thesis are designing DNA codes with specific constraints. First, DNA codes from the ring using algebraic coding by defining a new type of distance (Gau distance) and map (Gau map) are proposed. These DNA codes satisfy reverse, reverse complement and complement with the minimum Hamming distance constraints. Several families of these DNA codes and their properties are studied. Second, DNA codes using constrained coding and Golay subcode method are developed that satisfy norunlength and GC-weight constraints for a DNA data storage system.Item Open Access Traffic profile measurement and traffic driven network reconfiguration(Dhirubhai Ambani Institute of Information and Communication Technology, 2011) Monga, Jasneet Kaur; Srivastava, SanjayIn multi hop ad hoc network, nodes are constrained by the power or the energy sources that are available. Efficient algorithms for saving the energy are required to manage the network in such a manner that the resources available, get properly utilized and nodes in the network do not drain out. Switching and working over idle and busy periods of a node, one can achieve this dual goal and it comes under the category of sleep scheduling. In this approach, the basic emphasis is on the traffic profiles of the network nodes which is estimated based on the network traffic flows. The traffic estimated becomes the weight of the path between the different source destination pairs available in the network and this value averaged either at the local level or the global level is needed to be reduced, hence saving the overall energy of the network. The traffic weighted paths which consume energy above the average or the threshold value become the prime candidates for the consideration. The aim is to go for shorter and lighter paths in the network which require the sleeping nodes in the proximity of heavy and longer paths to be awaken to be a part of network topology and saving the extra energy wasted on longer paths. This makes the nodes in longer paths go through a sleep state so that they can be utilized when they are required, hence making topology changes by reconfiguring the paths.Item Open Access Bidirectional service composition(Dhirubhai Ambani Institute of Information and Communication Technology, 2010) Khakhkhar, Sandip; Chaudhary, SanjayService is a network addressable software component to perform a specific task. A service consumes given input parameters, performs specific task based on input parameters and returns the result in terms of output parameters. A service request specifies required task in terms of input parameters that can be provided and output parameters that are required. A service discovery mechanism can be used to find services that can be executed to satisfy service request. Service and service request is match by comparing their input/output parameters. A service request may be complex enough that it can not be satisfied by an individual service. It might be possible to execute a chain of services in a particular order to satisfy service request. This chain of services is referred as composition plan and service offered by executing this composition plan is referred as composite service. The aim of service composition algorithm is to generate a composition plan and generate composite service to satisfy service request. Services involved in composition plan are selected manually while designing composite service in static composition process. This process consumes considerable amount of time and effort. It is also vulnerable to changes in input/output of services. A dynamic composition algorithm is required that can automatically select services involved in composite plan and generate a composite service on-the-fly. Main issue with dynamic composition algorithms is composition time taken by algorithm to generate a composite service. Composition time indicates duration of the time at which the service request was submitted to the algorithm till the algorithm generate a composite service that can satisfy service request. Composition time depends upon the number of services required to explore in order to find services that can take part in composite plan. Dynamic composition algorithms presented in previous work mainly follows either forward chaining approach or backward chaining approach to find a composite service. Performance of algorithms based on forward chaining approach or backward chaining approach suffers for certain cases to generate a composite service where number of services explored increases exponentially as number of iterations increases. This work proposes a dynamic composition algorithm that gives consistent performance across all the cases. Proposed algorithm approaches from two directions alternatively, one follows forward chaining approach and other follows backward chaining approach. Composition algorithm following only forward chaining approach or backward chaining approach performs all the iterations in one direction only where as proposed algorithm requires only half number of iterations in both directions. Algorithm uses two types of matching strategy to compare input/output parameters. First one is based on keyword matching and second one based on semantic matching strategy. Performance of proposed algorithm is evaluated by performing relevant experiments and results are compared with algorithms based on only forward chaining approach or backward chaining approach. Proposed algorithm explores less number of services and takes less composition time compared to algorithms based on only forward chaining approach or backward chaining approach.Item Open Access Game theory based strategies for cooperation in ad hoc wireless networks(Dhirubhai Ambani Institute of Information and Communication Technology, 2010) Rajput, Nitin Singh; Srivastava, Sanjay; Divakaran, SrikrishnanIn self-organized ad-hoc wireless networks, nodes belong to different authorities, pursue different goals, have constrains like energy; therefore, cooperation among them cannot be taken for granted. Non cooperation of nodes causes increase in probability of packet drop and increase in probability of route or network failure, which leads to poor network performance. On other hand if nodes always cooperate, network does not last for a long as nodes are energy constrained. Several schemes are proposed in literature based on incentive and reputation mechanism. All of them outperforms in their own set of assumptions and have certain issues.Researchers started looking at game theory as a probable solution and proposed some schemes, but yet to come up with better solutions. We focus on optimization of service received by a node from network and delivered to network considering energy as constraint. We first derive the probability by which a node accept the relay request of other nodes based on energy constraint. Then apply game theory based schemes Generous Tit For Tat (GTFT), Neighboring GTFT (N-GTFT) and contrite Tit For Tat (C-TFT) for acceptance of relay requests; well known in economics, behavioral science and biology for cooperation. We find that all above mention scheme converges towards parato optimal values of service received and deliver to network in presence and absentia of noise in network. We find that when network has pair wise mixed strategies (any two from GTFT, N-GTFT and C-TFT) then also convergences remain same as it is for single strategy. But when there are 50% non cooperative nodes (Always Drops strategy), C-TFT is the dominating strategy. Also C-TFT copes up with 10% or more noise in the network as other strategy fail to do so, however they cope well with lesser amount of noise. At the end CTFT evolve as the dominating strategy when all strategies including Always Drops simulated under evolutionary method of comparison in noisy and noise free network. C-TFT out performs because it switches to mutual Tit For Tat after cooperating against fixed unilateral non cooperation from other nodes and also cope up with own unintentional defection caused by noise.
Item Open Access Testbed based experimental analysis of transport protocols over wireless ad hoc networks(Dhirubhai Ambani Institute of Information and Communication Technology, 2009) Shah, Harshil Anilkumar; Srivastava, SanjayAd hoc networks are networks with no infrastructure and self-organized in nature. ad hoc networks allow nodes to form network when they come into range of each other provided nodes are configured in ad hoc mode. But these types of network are challenges like high bit error rates, route failures due to mobility, high noise, signal fading and low speed etc. to deal with. Due to this, protocols which are widely used in traditional wired networks may not perform well in MANETs. lower layers like MAC and network layer are either completely changed like 802.11 instead of 802.3 at MAC layer and introducing reactive routing protocols instead of only proactive routing at network layer or significant improvement schemes have been proposed for wireless networks in the existing legacy wired network protocols. But transport layer in MANET is mostly similar to wired networks except some improvements like TCP-ELFN and TCP-Feedback and new transport protocols like Ad hoc-TCP (ATCP), Transport Protocol for Ad hoc networks (TPA) and Ad-hoc Transport Pro- tool (ATP).performance degradation of TCP over wireless links is mainly due to wireless characteristics, TCP features like self-clocking, loss based congestion control, coupling of congestion and reliability, slow start. Several studies have been carried out to evaluate performance of TCP over MANETs but most of them are simulation based studies. But as simulation scenarios can not model exactly the unpredictable nature of wireless environment, we have decided to analyze performance of trans- port protocols over experimental test bed which can be more accurate evaluation of protocols in real-life situation. Performance of 2 transport protocols is analyzed.Item Open Access Cache performance evaluation in DSR protocol through cross-layering for mobile ad hoc networks(Dhirubhai Ambani Institute of Information and Communication Technology, 2009) Sharma, Kapil; Sunitha, V.Wireless mobile ad-hoc networks are being actively studied by many researchers these days. These networks are suitable to be used in various situations because of (i) their infrastructure-less property and (ii) the mobility of the nodes of the network. However, it is these features which give rice to problems in study of such networks. Further, routing is one of the basic issues in any network design. Inclusion of moving capability to the nodes, make the routing problem more complicated. One is always interested in increasing the throughput and reducing overhead while at the same time solving the issues related to routing. DSR is a protocol that is extensively used for routing in such networks. Cache management and route caching play a significant role in using DSR successively to attain the best behavior for these networks. This thesis looks at and suggests some methods for route caching in DSR.Item Open Access Cooperation enforcement mechanisms in wireless adhoc networks(Dhirubhai Ambani Institute of Information and Communication Technology, 2009) Chaturvedi, Manish Shivshankar; Srivastava, SanjayWireless adhoc networks are autonomous, infrastrutureless networks where there are no dedicated routers or base stations and nodes are expected to cooperate in Wireless performing routing duties to keep network connected. Cooperation can be assumed if all nodes belong to single authority (e.g. military service or disaster management). But in applications where nodes do not belong to single authority and have limited resources (energy of battery driven devices), like pervasive computing or ubiquitous computing environment, one can not deny possibility of node selfishness. Also as there is no central authority to control node behavior, one can not deny possibility of node maliciousness. Many cooperation enforcement schemes are proposed in literature, and every scheme is shown to perform better under its own set of assumptions. These assumptions are different for different schemes. So, we aim at defining common set of assumptions and comparing selected schemes on this common ground with respect to packet delivery ratio, energy consumption, routing and other control overhead. We find that with the traffic scenario where nodes do not need services of one another at the same time, the cooperation schemes are not effective in dealing with node selfish ness. We also find that, while dealing with malicious nodes, all cooperation schemes perform better than Dynamic Source Routing(DSR) protocol in improving packet de- livery ratio(PDR), but this improvement comes at the cost of significant increase in routing control packets overhead and energy consumption of cooperation enforcement schemes is higher than that of DSR. Also they fail in punishing misbehaving nodes and the PDR of malicious nodes is comparable to that of good nodes.Item Open Access Identifying small world network properties in ad-hoc networks(Dhirubhai Ambani Institute of Information and Communication Technology, 2009) Garg, Neha; Sunitha, V.Small World Network is a densely connected network with low degree of separation. These types of networks have high clustering property like regular network as well as have low average path length like random network. Thus, Small World Networks are both Locally and Globally ecient as compared to other networks. The above prop- erties can be described using parameters like characteristic path length (L), clustering coefficient (C), local efficiency (Eloc) and global efficiency (Eglob). Through experiments, done in the past, it has been found that many real world networks exihibit the properties of small world network. This has given rise To finding models for real world networks so that the models reflect small world ness of the real world network. This thesis uses the model of converting a square grid into a small world model by introducing some special nodes. The equations to compute the small world parameters for this model with one and or two special nodes derived in this thesis.Item Open Access Comparative study between exponential back off and dynamic waiting strategies for medium access in wireless ad hoc networks(Dhirubhai Ambani Institute of Information and Communication Technology, 2009) Shah, Rahul; Srivastava, SanjayIEEE 802.11 DCF (IEEE 802.11 Distributed Coordination Function) is widely used MAC protocol for wireless channel access. Although it is developed for single hop networks where all nodes are in the same radio range, it can be directly used for wireless multiphop hoc networks. But performance of IEEE 802.11 DCF in wireless ad hoc networks suers as it has been developed considering single hop networks only. Many amendments has been proposed to enhance its performance in multihop ad hoc networks. One such scheme is DWMAC (Dynamic Waiting Medium Access Control). In this work, performance of IEEE 802.11 DCF and DWMAC are compared for different network scenarios and traffic patterns. It has been observed that the performance of DWMAC can be further improved if we alter the restricted mode operation of the nodes. We have proposed a new modified protocol DWMAC-Modied and have shown by simulations that DWMAC-Modied offers singnificant improvements.
Item Open Access Queueing-theoretic framework for perfermance analysis of mobile ad hoc networks with finite buffer nodes(Dhirubhai Ambani Institute of Information and Communication Technology, 2008) Shah, Sapan; Lenin, R. B.; Srivastava, SanjayWireless Ad Hoc network is a decentralized wireless network which allows nodes to join and create networks without any infrastructure. These kinds of networks are advantageous because they can be readily deployed anywhere, anytime. Mobile Ad Hoc Network (MANET) is a special type of ad hoc network where nodes are mobile. Due to mobility of the nodes, network topology may change rapidly and unpredictably. MANETs are expected to plat a vital role in a variety of applications and are therefore studied extensively. It is imperative to analyze these networks, to assess the suitability of their use in different scenarios and to identify the techniques to improve their performance. In last few years, many models have been proposed to analyze MANETs. Many of then have an unrealistic assumption of an infinite buffer in each node. Moreover, in MANETs, as nodes are mobile, a packet may revisit the same node which creates feedback loops of a packet. These loops make modeling and analysis of MANETs difficult as the network becomes cyclic. This work analyzes MANET with finite buffer nodes. Open finite queuing network with gated queue, intermittent links and servers is used. The expansion method technique has been used to study the open finite queuing network with stable links and servers. We modify the method for intermittency. Numerical results are derived and compared with simulation results to show effectiveness of the method.