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Dynamic power allocation and routing for satellite and wireless networks with time varying channels

Neely, Michael J. (Michael James), 1975-
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 295 p.; 1502113 bytes; 1500707 bytes; application/pdf; application/pdf
ENG
Relevância na Pesquisa
85.49%
Satellite and wireless networks operate over time varying channels that depend on attenuation conditions, power allocation decisions, and inter-channel interference. In order to reliably integrate these systems into a high speed data network and meet the increasing demand for high throughput and low delay, it is necessary to develop efficient network layer strategies that fully utilize the physical layer capabilities of each network element. In this thesis, we develop the notion of network layer capacity and describe capacity achieving power allocation and routing algorithms for general networks with wireless links and adaptive transmission rates. Fundamental issues of delay, throughput optimality, fairness, implementation complexity, and robustness to time varying channel conditions and changing user demands are discussed. Analysis is performed at the packet level and fully considers the queueing dynamics in systems with arbitrary, potentially bursty, arrival processes. Applications of this research are examined for the specific cases of satellite networks and ad-hoc wireless networks. Indeed, in Chapter 3 we consider a multi-beam satellite downlink and develop a dynamic power allocation algorithm that allocates power to each link in reaction to queue backlog and current channel conditions. The algorithm operates without knowledge of the arriving traffic or channel statistics...

Distributed coordination in network information theory

Schein, Brett E. (Brett Eric)
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 231 p.; 1678843 bytes; 1678596 bytes; application/pdf; application/pdf
ENG
Relevância na Pesquisa
75.51%
Constructing a large-scale wireless data network is spectacularly expensive. It is therefore important to understand how to efficiently utilize the physical infrastructure and available battery power, which are expensive system resources. Unfortunately, we currently understand very little about efficient communication in a distributed environment. In distributed wireless networks, there appears to be an interesting and complex trade-off between trying to take advantage of independent noisy signals at different relays and closely coordinating relay transmissions to a receiver. Designing the right structure for efficient communication, by choice of source transmission codebook and relay terminal processing, is the important and difficult problem on which we focus. We use an information theoretic framework to study several very simple multiple terminal networks, focusing exclusively on single source, single destination networks where communication must take place through intermediate nodes. Our goal is to determine how much data we can get reliably from source to destination, placing no importance on delay or computational complexity. The core problem then involves distributed detection at the intermediate nodes and coordination in relaying information to the destination.; by Brett E. Schein.; Thesis (Ph. D.)--Massachusetts Institute of Technology...

Multiaccess and fading in communication networks

Yeh, Edmund Meng, 1971-
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 163 p.; 771750 bytes; 771450 bytes; application/pdf; application/pdf
ENG
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Two fundamental issues in the design of wireless communication networks are the interference among multiple users and the time-varying nature of the fading wireless channel. We apply fundamental techniques in information theory and queueing theory to gain insights into the structure of these problems. In a terrestrial cellular or space network, multi-user interference arises naturally as different users in the same cell or region attempt to transmit to the base station or satellite at the same time and in the same frequency range. We first examine the impact of this interference on the design of error correction codes for reliable data transmission. At the physical layer of the wireless network, the phenomenon of multi-user interference is captured by the multiaccess (many-to-one) channel model. The set of all data rates at which reliable communication can take place over this channel is characterized via information theory by the so-called multiaccess capacity region. A basic problem is developing coding schemes of relatively low complexity to achieve all rates in this capacity region. By exploiting the underlying geometrical structure of the capacity region, we develop a method of reducing the multi-user coding problem to a set of single-user coding problems using the ideas of time-sharing and successive decoding. Next...

Signal processing in biological cells : proteins, networks, and models

Said, Maya Rida, 1976-
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 210 p.; 11825455 bytes; 11825355 bytes; application/pdf; application/pdf
ENG
Relevância na Pesquisa
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This thesis introduces systematic engineering principles to model, at different levels of abstraction the information processing in biological cells in order to understand the algorithms implemented by the signaling pathways that perform the processing. An example of how to emulate one of these algorithms in other signal processing contexts is also presented. At a high modeling level, the focus is on the network topology rather than the dynamical properties of the components of the signaling network. In this regime, we examine and analyze the distribution and properties of the network graph. Specifically, we present a global network investigation of the genotype/phenotype data-set recently developed for the yeast Saccharomyces cerevisiae from exposure to DNA damaging agents, enabling explicit study of how protein-protein interaction network characteristics may be associated with phenotypic functional effects. The properties of several functional yeast networks are also compared and a simple method to combine gene expression data with network information is proposed to better predict pathophysiological behavior. At a low level of modeling, the thesis introduces a new framework for modeling cellular signal processing based on interacting Markov chains. This framework provides a unified way to simultaneously capture the stochasticity of signaling networks in individual cells while computing a deterministic solution which provides average behavior. The use of this framework is demonstrated on two classical signaling networks: the mitogen activated protein kinase cascade and the bacterial chemotaxis pathway. The prospects of using cell biology as a metaphor for signal processing are also considered in a preliminary way by presenting a surface mapping algorithm based on bacterial chemotaxis.; by Maya Rida Said.; Thesis (Sc. D.)--Massachusetts Institute of Technology...

Inference in sensor networks : graphical models and particle methods

Ihler, Alexander T. (Alexander Thomas), 1976-
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 183 p.; 2754333 bytes; 2849375 bytes; application/pdf; application/pdf
ENG
Relevância na Pesquisa
75.5%
Sensor networks have quickly risen in importance over the last several years to become an active field of research, full of difficult problems and applications. At the same time, graphical models have shown themselves to be an extremely useful formalism for describing the underlying statistical structure of problems for sensor networks. In part, this is due to a number of efficient methods for solving inference problems defined on graphical models, but even more important is the fact that many of these methods (such as belief propagation) can be interpreted as a set of message passing operations, for which it is not difficult to describe a simple, distributed architecture in which each sensor performs local processing and fusion of information, and passes messages locally among neighboring sensors. At the same time, many of the tasks which are most important in sensor networks are characterized by such features as complex uncertainty and nonlinear observation processes. Particle filtering is one common technique for dealing with inference under these conditions in certain types of sequential problems, such as tracking of mobile objects.; (cont.) However, many sensor network applications do not have the necessary structure to apply particle filtering...

Communication between layers in biological transcriptional networks

Tsankov, Alex
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 89 leaves; 2107488 bytes; 2120757 bytes; application/pdf; application/pdf
ENG
Relevância na Pesquisa
75.5%
Chromatin-immunoprecipitation experiments in combination with microarrays (known as ChIP-chip) have recently allowed biologists to map where proteins bind in the yeast genome. The combinatorial binding of different proteins at or near a gene controls the transcription (copying) of a gene and the production of the functional RNA or protein that the gene encodes. Therefore, ChIP-chip data provides powerful insight on how genes and gene products (i.e., proteins, RNA) interact and regulate one another in the underlying network of the cell. Much of the current work in modeling yeast transcriptional networks focuses on the regulatory effect of a class of proteins known as transcription factors (TF). However, other sets of factors also influence transcription, including histone modifications and states (HS), histone modifiers (HM) and remodelers, nuclear processing (NP), and nuclear transport (NT) proteins. In order to gain a holistic understanding of the non-linear process of transcription, our work examines the communication between all five forementioned classes (or layers) of regulators. We use vastly available rich-media ChIP-chip data for various proteins within the five classes to model a multi-layered transcriptional network of the yeast species Saccharomyces cerevisiae.; (cont.) Following the introduction in Chapter 1...

Assembling regions for efficacious aggregate query processing in wireless sensor networks

Fertis, Apostolos
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 125 p.; 6573564 bytes; 6579912 bytes; application/pdf; application/pdf
ENG
Relevância na Pesquisa
75.52%
The field of sensor networks is rapidly developing enabling us to deploy them to an unpredictable environment and draw diverse and interesting information from it. Their capabilities are improving. They can sense complicated phenomena, they take measurements for several attributes, they make numerous computations and they communicate large amounts of information. Most sensors are battery operated and in most cases they are not easily rechargeable, as the environment in which they are located is not easily accessible. Thus, they have limited energy, which should be used to draw out as much useful information as possible. Moreover, quite often we need to receive data from a sensor network at a high rate. In order to be able to manage energy and time efficiently in sensor networks, we have to develop protocols that synchronize the cooperation among sensors and send information to the targets as quickly as possible and with low energy consumption. In many cases, the whole set of values that are measured is not required by the query which is submitted to the network. The query asks for an aggregate over the measurements. The propagation of all measured values to a central computation point is resource consuming. Tiny AGgregation (TAG) provides an algorithm to compute aggregates by merging and forwarding partial results. The merging is done in the internal nodes of the routing tree that is formed. Sometimes...

Consensus and collision detectors in wireless ad hoc networks

Newport, Calvin (Calvin Charles)
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 80 leaves
ENG
Relevância na Pesquisa
75.49%
In this study, we consider the fault-tolerant consensus problem in wireless ad hoc networks with crashprone nodes. Specifically, we develop lower bounds and matching upper bounds for this problem in single-hop wireless networks, where all nodes are located within broadcast range of each other. In a novel break from existing work, we introduce a highly unpredictable communication model in which each node may lose an arbitrary subset of the messages sent by its neighbors during each round. We argue that this model better matches behavior observed in empirical studies of these networks. To cope with this communication unreliability we augment nodes with receiver-side collision detectors and present a new classification of these detectors in terms of accuracy and completeness. This classification is motivated by practical realities and allows us to determine, roughly speaking, how much collision detection capability is enough to solve the consensus problem efficiently in this setting. We consider ten different combinations of completeness and accuracy properties in total, determining for each whether consensus is solvable, and, if it is, a lower bound on the number of rounds required.; (cont.) Furthermore, we distinguish anonymous and non-anonymous protocols-where "anonymous" implies that devices do not have unique identifiers-determining what effect (if any) this extra information has on the complexity of the problem. In all relevant cases...

Distributed detection and coding in information networks

Ho, Shan-Yuan
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 136 p.
ENG
Relevância na Pesquisa
85.46%
This thesis investigates the distributed information and detection of a binary source through a parallel system of relays. Each relay observes the source output through a noisy channel, and the channel outputs are independent conditional on the source input. The relays forward limited information through a noiseless link to the final destination which makes an optimal decision. The essence of the problem lies in the loss of information at the relays. To solve this problem, the characteristics of the error curve are established and developed as a tool to build a fundamental framework for analysis. For understanding, the simplest non-trivial case of two relays, each forwarding only a single binary digit to the final destination is first studied. If the binary output constraint is removed and the output alphabet size for one relay is M, then no more than M + 1 alphabet symbols are required from the other relay for optimal operation. For arbitrary channels, a number of insights are developed about the structure of the optimal strategies for the relay and final destination. These lead to a characterization of the optimal solution. Furthermore, the complete solution to the Additive Gaussian Noise channel is also provided.; by Shan-Yuan Ho.; Thesis (Ph. D.)--Massachusetts Institute of Technology...

Proactive mobile wireless networks : an infrastructureless wireless network architecture for delay-sensitive applications; Infrastructureless wireless network architecture for delay-sensitive applications

Dai, Lillian Lei, 1978-
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 213 p.
ENG
Relevância na Pesquisa
75.53%
Infrastructureless wireless networks are an important class of wireless networks that is best suited for scenarios where there is temporary and localized telecommunication demand. Such networks consist of wireless devices that can form a network autonomously without the need for pre-deployed telecommunication infrastructures such as base-stations and access points. Over the past several decades, significant research and development efforts have been devoted to a particular type of infrastructureless wireless networks called mobile ad hoc wireless networks (MANETs). In addition to autonomous network formation, wireless devices in MANETs have routing capabilities and help one another to forward information in a multihop fashion. The applications envisioned for MANETs include communication during disaster relief, search and rescue, and small tactical unit operations where the existing telecommunication infrastructures may be destroyed or are unavailable. While significant strides have been made in all aspects of MANET networking, adoption of such technology has been limited to date despite its potential. We believe that this lack of adoption is due to a fundamental mismatch between application demands and the MANET network architecture. While the flexibility of anytime and anywhere communication offered by MANETs is appealing...

Scalable fault management architecture for dynamic optical networks : an information-theoretic approach

Wen, Yonggang
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 262 leaves
ENG
Relevância na Pesquisa
75.56%
All-optical switching, in place of electronic switching, of high data-rate lightpaths at intermediate nodes is one of the key enabling technologies for economically scalable future data networks. This replacement of electronic switching with optical switching at intermediate nodes, however, presents new challenges for fault detection and localization in reconfigurable all-optical networks. Presently, fault detection and localization techniques, as implemented in SONET/G.709 networks, rely on electronic processing of parity checks at intermediate nodes. If similar techniques are adapted to all-optical reconfigurable networks, optical signals need to be tapped out at intermediate nodes for parity checks. This additional electronic processing would break the all-optical transparency paradigm and thus significantly diminish the cost advantages of all-optical networks. In this thesis, we propose new fault-diagnosis approaches specifically tailored to all-optical networks, with an objective of keeping the diagnostic capital expenditure and the diagnostic operation effort low. Instead of the aforementioned passive monitoring paradigm based on parity checks, we propose a proactive lightpath probing paradigm: optical probing signals are sent along a set of lightpaths in the network...

Infection processes on networks with structural uncertainty

Zager, Laura (Laura A.)
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 175 p.
ENG
Relevância na Pesquisa
75.5%
Over the last ten years, the interest in network phenomena and the potential for a global pandemic have produced a tremendous volume of research exploring the consequences of human interaction patterns for disease propagation. The research often focuses on a single question: will an emerging infection become an epidemic? This thesis clarifies the relationships among different epidemic threshold criteria in deterministic disease models, and discusses the role and meaning of the basic reproductive ratio, R0. We quantify the incorporation of population structure into this general framework, and identify conditions under which interaction topology and infection characteristics can be decoupled in the computation of threshold functions, which generalizes many existing results in the literature. This decoupling allows us to focus on the impact of network topology via the spectral radius of the adjacency matrix of the network. It is rare, however, that one has complete information about every potential disease-transmitting interaction; this uncertainty in the network structure is often ignored in deterministic models. Neglecting this uncertainty can lead to an underestimate of R0, an unacceptable outcome for public health planning. Is it possible to make guarantees and approximations regarding disease spread when only partial information about the routes of transmission is known? We present methods for making predictions about disease spread over uncertain networks...

Bayesian networks for cardiovascular monitoring

Roberts, Jennifer M. (Jennifer Marie)
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 85 p.
ENG
Relevância na Pesquisa
75.5%
In the Intensive Care Unit, physicians have access to many types of information when treating patients. Physicians attempt to consider as much of the relevant information as possible, but the astronomically large amounts of data collected make it impossible to consider all available information within a reasonable amount of time. In this thesis, I explore Bayesian Networks as a way to integrate patient data into a probabilistic model. I present a small Bayesian Network model of the cardiovascular system and analyze the network's ability to estimate unknown patient parameters using available patient information. I test the network's estimation capabilities using both simulated and real patient data, and I discuss ways to exploit the network's ability to adapt to patient data and learn relationships between patient variables.; by Jennifer Roberts.; Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2006.; Includes bibliographical references (p. 83-85).

Successive structuring of source coding algorithms for data fusion, buffering, and distribution in networks

Draper, Stark Christiaan
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 165 p.; 6835571 bytes; 6835377 bytes; application/pdf; application/pdf
ENG
Relevância na Pesquisa
75.52%
Numerous opportunities to improve network performance present themselves when we make communication networks aware of the characteristics of the data content they are handling. In this thesis, we design such content-aware algorithms that span traditional network layers and are successively structured, focusing on problems of data fusion, buffering, and distribution. The successive structuring of these algorithms provides the flexibility needed to deal with the distributed processing, the heterogeneous sources of information, and the uncertain operating conditions that typify many networks. We investigate the broad interactions between estimation and communication in the context of data fusion in tree-structured sensor networks. We show how to decompose any general tree into serial (pipeline) and parallel (hub-and-spoke) networks. We develop successive coding strategies for these prototype sensor networks based on generalized Wyner-Ziv coding. We extend Wyner-Ziv source coding with side information to "noisy" encoder observations and develop the associated rate-distortion function. We show how to approach the serial and parallel network configurations as cascades of noisy Wyner-Ziv stages. This approach leads to convenient iterative (achievable) distortion-rate expressions for quadratic-Gaussian scenarios. Under a sum-rate constraint...

Proactive techniques for correct and predictable Internet routing

Feamster, Nicholas G. (Nicholas Greer), 1979-
Fonte: Massachusetts Institute of Technology Publicador: Massachusetts Institute of Technology
Tipo: Tese de Doutorado Formato: 193 p.; 2205480 bytes; 2242457 bytes; application/pdf; application/pdf
ENG
Relevância na Pesquisa
75.52%
The Internet is composed of thousands of autonomous, competing networks that exchange reachability information using an interdomain routing protocol. Network operators must continually reconfigure the routing protocols to realize various economic and performance goals. Unfortunately, there is no systematic way to predict how the configuration will affect the behavior of the routing protocol or to determine whether the routing protocol will operate correctly at all. This dissertation develops techniques to reason about the dynamic behavior of Internet routing, based on static analysis of the router configurations, before the protocol ever runs on a live network. Interdomain routing offers each independent network tremendous flexibility in configuring the routing protocols to accomplish various economic and performance tasks. Routing configurations are complex, and writing them is similar to writing a distributed program; the (unavoidable) consequence of configuration complexity is the potential for incorrect and unpredictable behavior. These mistakes and unintended interactions lead to routing faults, which disrupt end-to-end connectivity. Network operators writing configurations make mistakes; they may also specify policies that interact in unexpected ways with policies in other networks.; (cont.) To avoid disrupting network connectivity and degrading performance...

Ranking relations using analogies in biological and information networks

Silva, Ricardo; Heller, Katherine; Ghahramani, Zoubin; Airoldi, Edoardo M.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
85.4%
Analogical reasoning depends fundamentally on the ability to learn and generalize about relations between objects. We develop an approach to relational learning which, given a set of pairs of objects $\mathbf{S}=\{A^{(1)}:B^{(1)},A^{(2)}:B^{(2)},\ldots,A^{(N)}:B ^{(N)}\}$, measures how well other pairs A:B fit in with the set $\mathbf{S}$. Our work addresses the following question: is the relation between objects A and B analogous to those relations found in $\mathbf{S}$? Such questions are particularly relevant in information retrieval, where an investigator might want to search for analogous pairs of objects that match the query set of interest. There are many ways in which objects can be related, making the task of measuring analogies very challenging. Our approach combines a similarity measure on function spaces with Bayesian analysis to produce a ranking. It requires data containing features of the objects of interest and a link matrix specifying which relationships exist; no further attributes of such relationships are necessary. We illustrate the potential of our method on text analysis and information networks. An application on discovering functional interactions between pairs of proteins is discussed in detail, where we show that our approach can work in practice even if a small set of protein pairs is provided.; Comment: Published in at http://dx.doi.org/10.1214/09-AOAS321 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org)

Design and Implementation of Multistage Interconnection Networks for SoC Networks

Moazez, Mahsa; Safaei, Farshad; Rezazadeh, Majid
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 03/12/2012
Relevância na Pesquisa
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In this paper the focus is on a family of Interconnection Networks (INs) known as Multistage Interconnection Networks (MINs). When it is exploited in Network-on-Chip (NoC) architecture designs, smaller circuit area, lower power consumption, less junctions and broader bandwidth can be achieved. Each MIN can be considered as an alternative for an NoC architecture design for its simple topology and easy scalability with low degree. This paper includes two major contributions. First, it compares the performance of seven prominent MINs (i.e. Omega, Butterfly, Flattened Butterfly, Flattened Baseline, Generalized Cube, Bene\v{s} and Clos networks) based on 45nm-CMOS technology and under different types of Synthetic and Trace-driven workloads. Second, a network called Meta-Flattened Network (MFN), was introduced that can decrease the blocking probability by means of reduction the number of hops and increase the intermediate paths between stages. This is also led into significant decrease in power consumption.; Comment: 11 Pages, 14 Figures; International Journal of Computer Science, Engineering and Information Technology (IJCSEIT), Vol.2, No.5, October 2012

A New Efficient Key Management Protocol for Wireless Sensor and Actor Networks

Lee, Yunho; Lee, Soojin
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 03/12/2009
Relevância na Pesquisa
75.51%
Research on sensor networks has become much more active and is currently being applied to many different fields. However since sensor networks are limited to only collecting and reporting information regarding a certain event, and requires human intervention with that given information, it is often difficult to react to an event or situation immediately and proactively. To overcome this kind of limitation, Wireless Sensor and Actor Networks (WSANs) with immediate-response actor nodes have been proposed which adds greater mobility and activity to the existing sensor networks. Although WSANs share many common grounds with sensor networks, it is difficult to apply existing security technologies due to the fact that WSANs contain actor nodes that are resource-independent and mobile. Therefore, this research seeks to demonstrate ways to provide security, integrity, and authentication services for WSANs secure operation, by separating networks into hierarchical structure by each node's abilities and provides different encryption key based secure protocols for each level of hierarchy, Pairwise key, node key, and region key for sensor levels, and public key for actor; Comment: 8 pages IEEE format, International Journal of Computer Science and Information Security...

A Framework for Providing E-Services to the Rural Areas using Wireless Ad Hoc and Sensor Networks

Pathan, Al-Sakib Khan; Islam, Humayun Kadir; Sayeed, Sabit Anjum; Ahmed, Farruk; Hong, Choong Seon
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 26/12/2007
Relevância na Pesquisa
75.49%
In recent years, the proliferation of mobile computing devices has driven a revolutionary change in the computing world. The nature of ubiquitous devices makes wireless networks the easiest solution for their interconnection. This has led to the rapid growth of several wireless systems like wireless ad hoc networks, wireless sensor networks etc. In this paper we have proposed a framework for rural development by providing various e-services to the rural areas with the help of wireless ad hoc and sensor networks. We have discussed how timely and accurate information could be collected from the rural areas using wireless technologies. In addition to this, we have also mentioned the technical and operational challenges that could hinder the implementation of such a framework in the rural areas in the developing countries.; Comment: 5 pages

Computational methods for multi-omic models of cell metabolism and their importance for theoretical computer science

Angione, Claudio
Fonte: University of Cambridge; Faculty of Computer Science and Technology; Computer Laboratory Publicador: University of Cambridge; Faculty of Computer Science and Technology; Computer Laboratory
Tipo: Thesis; doctoral; PhD
EN
Relevância na Pesquisa
85.54%
To paraphrase Stan Ulam, a Polish mathematician who became a leading figure in the Manhattan Project, in this dissertation I focus not only on how computer science can help biologists, but also on how biology can inspire computer scientists. On one hand, computer science provides powerful abstraction tools for metabolic networks. Cell metabolism is the set of chemical reactions taking place in a cell, with the aim of maintaining the living state of the cell. Due to the intrinsic complexity of metabolic networks, predicting the phenotypic traits resulting from a given genotype and metabolic structure is a challenging task. To this end, mathematical models of metabolic networks, called genome-scale metabolic models, contain all known metabolic reactions in an organism and can be analyzed with computational methods. In this dissertation, I propose a set of methods to investigate models of metabolic networks. These include multi-objective optimization, sensitivity, robustness and identifiability analysis, and are applied to a set of genome-scale models. Then, I augment the framework to predict metabolic adaptation to a changing environment. The adaptation of a microorganism to new environmental conditions involves shifts in its biochemical network and in the gene expression level. However...