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Description
Charge transport in molecular systems, including DNA (Deoxyribonucleic acid), is involved in many basic chemical and biological processes. Studying their charge transport properties can help developing DNA based electronic devices with many tunable functionalities. This thesis investigates the electric properties of double-stranded DNA, DNA G-quadruplex and dsDNA with modified base.

First,

Charge transport in molecular systems, including DNA (Deoxyribonucleic acid), is involved in many basic chemical and biological processes. Studying their charge transport properties can help developing DNA based electronic devices with many tunable functionalities. This thesis investigates the electric properties of double-stranded DNA, DNA G-quadruplex and dsDNA with modified base.

First, double-stranded DNA with alternating GC sequence and stacked GC sequence were measured with respect to length. The resistance of DNA sequences increases linearly with length, indicating a hopping transport mechanism. However, for DNA sequences with stacked GC, a periodic oscillation is superimposed on the linear length dependence, indicating a partial coherent transport. The result is supported by the finding of delocalization of the highest occupied molecular orbitals of Guanines from theoretical simulation and by fitting based on the Büttiker’s theory.

Then, a DNA G4-duplex structures with a G-quadruplex as the core and DNA duplexes as the arms were studied. Similar conductance values were observed by varying the linker positions, thus a charge splitter is developed. The conductance of the DNA G-tetrads structures was found to be sensitive to the π-stacking at the interface between the G-quadruplex and DNA duplexes by observing a higher conductance value when one duplex was removed and a polyethylene glycol (PEG) linker was added into the interface. This was further supported by molecular dynamic simulations.

Finally, a double-stranded DNA with one of the bases replaced by an anthraquinone group was studied via electrochemical STM break junction technique. Anthraquinone can be reversibly switched into the oxidized state or reduced state, to give a low conductance or high conductance respectively. Furthermore, the thermodynamics and kinetics properties of the switching were systematically studied. Theoretical simulation shows that the difference between the two states is due to a difference in the energy alignment with neighboring Guanine bases.
ContributorsXiang, Liming (Author) / Tao, Nongjian (Thesis advisor) / Lindsay, Stuart (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2016
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Description
Detection of molecular interactions is critical for understanding many biological processes, for detecting disease biomarkers, and for screening drug candidates. Fluorescence-based approach can be problematic, especially when applied to the detection of small molecules. Various label-free techniques, such as surface plasmon resonance technique are sensitive to mass, making it extremely

Detection of molecular interactions is critical for understanding many biological processes, for detecting disease biomarkers, and for screening drug candidates. Fluorescence-based approach can be problematic, especially when applied to the detection of small molecules. Various label-free techniques, such as surface plasmon resonance technique are sensitive to mass, making it extremely challenging to detect small molecules. In this thesis, novel detection methods for molecular interactions are described.

First, a simple detection paradigm based on reflectance interferometry is developed. This method is simple, low cost and can be easily applied for protein array detection.

Second, a label-free charge sensitive optical detection (CSOD) technique is developed for detecting of both large and small molecules. The technique is based on that most molecules relevant to biomedical research and applications are charged or partially charged. An optical fiber is dipped into the well of a microplate. It detects the surface charge of the fiber, which does not decrease with the size (mass) of the molecule, making it particularly attractive for studying small molecules.

Third, a method for mechanically amplification detection of molecular interactions (MADMI) is developed. It provides quantitative analysis of small molecules interaction with membrane proteins in intact cells. The interactions are monitored by detecting a mechanical deformation in the membrane induced by the molecular interactions. With this novel method small molecules and membrane proteins interaction in the intact cells can be detected. This new paradigm provides mechanical amplification of small interaction signals, allowing us to measure the binding kinetics of both large and small molecules with membrane proteins, and to analyze heterogeneous nature of the binding kinetics between different cells, and different regions of a single cell.

Last, by tracking the cell membrane edge deformation, binding caused downstream event – granule secretory has been measured. This method focuses on the plasma membrane change when granules fuse with the cell. The fusion of granules increases the plasma membrane area and thus the cell edge expands. The expansion is localized at the vesicle release location. Granule size was calculated based on measured edge expansion. The membrane deformation due to the granule release is real-time monitored by this method.
ContributorsGuan, Yan (Author) / Tao, Nongjian (Thesis advisor) / LaBaer, Joshua (Committee member) / Goryll, Michael (Committee member) / Wang, Shaopeng (Committee member) / Arizona State University (Publisher)
Created2015
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Description
Software-Defined Networking (SDN) is an emerging network paradigm that decouples the control plane from the data plane, which allows network administrators to consolidate common network services into a centralized module named SDN controller. Applications’ policies are transformed into standardized network rules in the data plane via SDN controller. Even though

Software-Defined Networking (SDN) is an emerging network paradigm that decouples the control plane from the data plane, which allows network administrators to consolidate common network services into a centralized module named SDN controller. Applications’ policies are transformed into standardized network rules in the data plane via SDN controller. Even though this centralization brings a great flexibility and programmability to the network, network rules generated by SDN applications cannot be trusted because there may exist malicious SDN applications, and insecure network flows can be made due to complex relations across network rules. In this dissertation, I investigate how to identify and resolve these security violations in SDN caused by the combination of network rules and applications’ policies. To this end, I propose a systematic policy management framework that better protects SDN itself and hardens existing network defense mechanisms using SDN.

More specifically, I discuss the following four security challenges in this dissertation: (1) In SDN, generating reliable network rules is challenging because SDN applications cannot be trusted and have complicated dependencies each other. To address this problem, I analyze applications’ policies and remove those dependencies by applying grid-based policy decomposition mechanism; (2) One network rule could accidentally affect others (or by malicious users), which lead to creating of indirect security violations. I build systematic and automated tools that analyze network rules in the data plane to detect a wide range of security violations and resolve them in an automated fashion; (3) A fundamental limitation of current SDN protocol (OpenFlow) is a lack of statefulness, which is extremely important to several security applications such as stateful firewall. To bring statelessness to SDN-based environment, I come up with an innovative stateful monitoring scheme by extending existing OpenFlow specifications; (4) Existing honeynet architecture is suffering from its limited functionalities of ’data control’ and ’data capture’. To address this challenge, I design and implement an innovative next generation SDN-based honeynet architecture.
ContributorsHan, Wonkyu (Author) / Ahn, Gail-Joon (Thesis advisor) / Zhao, Ziming (Thesis advisor) / Doupe, Adam (Committee member) / Huang, Dijiang (Committee member) / Zhang, Yanchao (Committee member) / Arizona State University (Publisher)
Created2016
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Description
Data privacy is emerging as one of the most serious concerns of big data analytics, particularly with the growing use of personal data and the ever-improving capability of data analysis. This dissertation first investigates the relation between different privacy notions, and then puts the main focus on developing economic foundations

Data privacy is emerging as one of the most serious concerns of big data analytics, particularly with the growing use of personal data and the ever-improving capability of data analysis. This dissertation first investigates the relation between different privacy notions, and then puts the main focus on developing economic foundations for a market model of trading private data.

The first part characterizes differential privacy, identifiability and mutual-information privacy by their privacy--distortion functions, which is the optimal achievable privacy level as a function of the maximum allowable distortion. The results show that these notions are fundamentally related and exhibit certain consistency: (1) The gap between the privacy--distortion functions of identifiability and differential privacy is upper bounded by a constant determined by the prior. (2) Identifiability and mutual-information privacy share the same optimal mechanism. (3) The mutual-information optimal mechanism satisfies differential privacy with a level at most a constant away from the optimal level.

The second part studies a market model of trading private data, where a data collector purchases private data from strategic data subjects (individuals) through an incentive mechanism. The value of epsilon units of privacy is measured by the minimum payment such that an individual's equilibrium strategy is to report data in an epsilon-differentially private manner. For the setting with binary private data that represents individuals' knowledge about a common underlying state, asymptotically tight lower and upper bounds on the value of privacy are established as the number of individuals becomes large, and the payment--accuracy tradeoff for learning the state is obtained. The lower bound assures the impossibility of using lower payment to buy epsilon units of privacy, and the upper bound is given by a designed reward mechanism. When the individuals' valuations of privacy are unknown to the data collector, mechanisms with possible negative payments (aiming to penalize individuals with "unacceptably" high privacy valuations) are designed to fulfill the accuracy goal and drive the total payment to zero. For the setting with binary private data following a general joint probability distribution with some symmetry, asymptotically optimal mechanisms are designed in the high data quality regime.
ContributorsWang, Weina (Author) / Ying, Lei (Thesis advisor) / Zhang, Junshan (Thesis advisor) / Scaglione, Anna (Committee member) / Zhang, Yanchao (Committee member) / Arizona State University (Publisher)
Created2016
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Description
Wireless communication technologies have been playing an important role in modern society. Due to its inherent mobility property, wireless networks are more vulnerable to passive attacks than traditional wired networks. Anonymity, as an important issue in mobile network environment, serves as the first topic that leads to all the research

Wireless communication technologies have been playing an important role in modern society. Due to its inherent mobility property, wireless networks are more vulnerable to passive attacks than traditional wired networks. Anonymity, as an important issue in mobile network environment, serves as the first topic that leads to all the research work presented in this manuscript. Specifically, anonymity issue in Mobile Ad hoc Networks (MANETs) is discussed with details as the first section of research.



To thoroughly study on this topic, the presented work approaches it from an attacker's perspective. Under a perfect scenario, all the traffic in a targeted MANET exhibits the communication relations to a passive attacker. However, localization errors pose a significant influence on the accuracy of the derived communication patterns. To handle such issue, a new scheme is proposed to generate super nodes, which represent the activities of user groups in the target MANET. This scheme also helps reduce the scale of monitoring work by grouping users based on their behaviors.



The first part of work on anonymity in MANET leads to the thought on its major cause. The link-based communication pattern is a key contributor to the success of the traffic analysis attack. A natural way to circumvent such issue is to use link-less approaches. Information Centric Networking (ICN) is a typical instance of such kind. Its communication pattern is able to overcome the anonymity issue with MANET. However, it also comes with its own shortcomings. One of them is access control enforcement. To tackle this issue, a new naming scheme for contents transmitted in ICN networks is presented. This scheme is based on a new Attribute-Based Encryption (ABE) algorithm. It enforces access control in ICN with minimum requirements on additional network components.



Following the research work on ABE, an important function, delegation, exhibits a potential security issue. In traditional ABE schemes, Ciphertext-Policy ABE (CP-ABE), a user is able to generate a subset of authentic attribute key components for other users using delegation function. This capability is not monitored or controlled by the trusted third party (TTP) in the cryptosystem. A direct threat caused from this issue is that any user may intentionally or unintentionally lower the standards for attribute assignments. Unauthorized users/attackers may be able to obtain their desired attributes through a delegation party instead of directly from the TTP. As the third part of work presented in this manuscript, a three-level delegation restriction architecture is proposed. Furthermore, a delegation restriction scheme following this architecture is also presented. This scheme allows the TTP to have full control on the delegation function of all its direct users.
ContributorsLi, Bing (Author) / Huang, Dijiang (Thesis advisor) / Xue, Guoliang (Committee member) / Ahn, Gail-Joon (Committee member) / Zhang, Yanchao (Committee member) / Arizona State University (Publisher)
Created2016
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Description
Smartphones are pervasive nowadays. They are supported by mobile platforms that allow users to download and run feature-rich mobile applications (apps). While mobile apps help users conveniently process personal data on mobile devices, they also pose security and privacy threats and put user's data at risk. Even though modern mobile

Smartphones are pervasive nowadays. They are supported by mobile platforms that allow users to download and run feature-rich mobile applications (apps). While mobile apps help users conveniently process personal data on mobile devices, they also pose security and privacy threats and put user's data at risk. Even though modern mobile platforms such as Android have integrated security mechanisms to protect users, most mechanisms do not easily adapt to user's security requirements and rapidly evolving threats. They either fail to provide sufficient intelligence for a user to make informed security decisions, or require great sophistication to configure the mechanisms for enforcing security decisions. These limitations lead to a situation where users are disadvantageous against emerging malware on modern mobile platforms. To remedy this situation, I propose automated and systematic approaches to address three security management tasks: monitoring, assessment, and confinement of mobile apps. In particular, monitoring apps helps a user observe and record apps' runtime behaviors as controlled under security mechanisms. Automated assessment distills intelligence from the observed behaviors and the security configurations of security mechanisms. The distilled intelligence further fuels enhanced confinement mechanisms that flexibly and accurately shape apps' behaviors. To demonstrate the feasibility of my approaches, I design and implement a suite of proof-of-concept prototypes that support the three tasks respectively.
ContributorsJing, Yiming (Author) / Ahn, Gail-Joon (Thesis advisor) / Doupe, Adam (Committee member) / Huang, Dijiang (Committee member) / Zhang, Yanchao (Committee member) / Arizona State University (Publisher)
Created2015
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Description
Monitoring of air pollutants is critical for many applications and studies. In

order to access air pollutants with high spatial and temporal resolutions, it is

necessary

Monitoring of air pollutants is critical for many applications and studies. In

order to access air pollutants with high spatial and temporal resolutions, it is

necessary to develop an affordable, small size and weight, low power, high

sensitivity and selectivity, and wireless enable device that can provide real time

monitoring of air pollutants. Three different kind of such devices are presented, they

are targeting environmental pollutants such as volatile organic components (VOCs),

nitrogen dioxide (NO2) and ozone. These devices employ innovative detection

methods, such as quartz crystal tuning fork coated with molecularly imprinted

polymer and chemical reaction induced color change colorimetric sensing. These

portable devices are validated using the gold standards in the laboratory, and their

functionality and capability are proved during the field tests, make them great tools

for various air quality monitoring applications.
ContributorsChen, Cheng, Ph.D (Author) / Tao, Nongjian (Thesis advisor) / Kiaei, Sayfe (Committee member) / Zhang, Yanchao (Committee member) / Tsow, Tsing (Committee member) / Arizona State University (Publisher)
Created2014
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Description
Wide spread adoption of photovoltaic technology is limited by cost. Developing photovoltaics based on low-cost materials and processing techniques is one strategy for reducing the cost of electricity generated by photovoltaics. With this in mind, novel porphyrin and porphyrin-fullerene electropolymers have been developed here at Arizona State University. Porphyrins are

Wide spread adoption of photovoltaic technology is limited by cost. Developing photovoltaics based on low-cost materials and processing techniques is one strategy for reducing the cost of electricity generated by photovoltaics. With this in mind, novel porphyrin and porphyrin-fullerene electropolymers have been developed here at Arizona State University. Porphyrins are attractive for inclusion in the light absorbing layer of photovoltaics due to their high absorption coefficients (on the order of 105 cm-1) and porphyrin-fullerene dyads are attractive for use in photovoltaics due to their ability to produce ultrafast photoinduced charge separation (on the order of 10-15 s). The focus of this thesis is the characterization of the photovoltaic properties of these electropolymer films. Films formed on transparent conductive oxide (TCO) substrates were contacted using a mercury drop electrode in order to measure photocurrent spectra and current-voltage curves. Surface treatment of both the TCO substrate and the mercury drop is shown to have a dramatic effect on the photovoltaic performance of the electropolymer films. Treating the TCO substrates with chlorotrimethylsilane and the mercury drop with hexanethiol was found to produce an optimal tradeoff between photocurrent and photovoltage. Incident photon to current efficiency spectra of the films show that the dominant photocurrent generation mechanism in this system is located at the polymer-mercury interface. The optical field intensity at this interface approaches zero due to interference from the light reflected by the mercury surface. Reliance upon photocurrent generation at this interface limits the performance of this system and suggests that these polymers may be useful in solar cells which have structures optimized to take advantage of their internal optical field distributions.
ContributorsBridgewater, James W (Author) / Gust, Devens (Thesis advisor) / Tao, Nongjian (Thesis advisor) / Gould, Ian (Committee member) / Diaz, Rodolfo (Committee member) / Arizona State University (Publisher)
Created2014
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Description
LTE-Advanced networks employ random access based on preambles

transmitted according to multi-channel slotted Aloha principles. The

random access is controlled through a limit W on the number of

transmission attempts and a timeout period for uniform backoff after a

collision. We model the LTE-Advanced random access system by formulating

the equilibrium condition for the ratio

LTE-Advanced networks employ random access based on preambles

transmitted according to multi-channel slotted Aloha principles. The

random access is controlled through a limit W on the number of

transmission attempts and a timeout period for uniform backoff after a

collision. We model the LTE-Advanced random access system by formulating

the equilibrium condition for the ratio of the number of requests

successful within the permitted number of transmission attempts to those

successful in one attempt. We prove that for W≤8 there is only one

equilibrium operating point and for W≥9 there are three operating

points if the request load ρ is between load boundaries ρ1

and ρ2. We analytically identify these load boundaries as well as

the corresponding system operating points. We analyze the throughput and

delay of successful requests at the operating points and validate the

analytical results through simulations. Further, we generalize the

results using a steady-state equilibrium based approach and develop

models for single-channel and multi-channel systems, incorporating the

barring probability PB. Ultimately, we identify the de-correlating

effect of parameters O, PB, and Tomax and introduce the

Poissonization effect due to the backlogged requests in a slot. We

investigate the impact of Poissonization on different traffic and

conclude this thesis.
ContributorsTyagi, Revak (Author) / Reisslein, Martin (Thesis advisor) / Tepedelenlioğlu, Cihan (Committee member) / McGarry, Michael (Committee member) / Zhang, Yanchao (Committee member) / Arizona State University (Publisher)
Created2014
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Description
The widespread adoption of mobile devices gives rise to new opportunities and challenges for authentication mechanisms. Many traditional authentication mechanisms become unsuitable for smart devices. For example, while password is widely used on computers as user identity authentication, inputting password on small smartphone screen is error-prone and not convenient. In

The widespread adoption of mobile devices gives rise to new opportunities and challenges for authentication mechanisms. Many traditional authentication mechanisms become unsuitable for smart devices. For example, while password is widely used on computers as user identity authentication, inputting password on small smartphone screen is error-prone and not convenient. In the meantime, there are emerging demands for new types of authentication. Proximity authentication is an example, which is not needed for computers but quite necessary for smart devices. These challenges motivate me to study and develop novel authentication mechanisms specific for smart devices.

In this dissertation, I am interested in the special authentication demands of smart devices and about to satisfy the demands. First, I study how the features of smart devices affect user identity authentications. For identity authentication domain, I aim to design a continuous, forge-resistant authentication mechanism that does not interrupt user-device interactions. I propose a mechanism that authenticates user identity based on the user's finger movement patterns. Next, I study a smart-device-specific authentication, proximity authentication, which authenticates whether two devices are in close proximity. For prox- imity authentication domain, I aim to design a user-friendly authentication mechanism that can defend against relay attacks. In addition, I restrict the authenticated distance to the scale of near field, i.e., a few centimeters. My first design utilizes a user's coherent two-finger movement on smart device screen to restrict the distance. To achieve a fully-automated system, I explore acoustic communications and propose a novel near field authentication system.
ContributorsLi, Lingjun (Author) / Xue, Guoliang (Thesis advisor) / Ahn, Gail-Joon (Committee member) / Ye, Jieping (Committee member) / Zhang, Yanchao (Committee member) / Arizona State University (Publisher)
Created2014