FRET between pairs of fluorophores is widely used as a biological assay. However, the properties of larger fluorophore networks are poorly understood and their application space has not yet been fully explored. This dissertation introduces DNA self-assembled FÖrster Resonance Energy Transfer (FRET) networks that provide a unique optical output when probed by a series of light pulses. We create a Markov model of the FRET networks and analyze over 1200 time-resolved fluorescence measurements on 300 prototypical networks. Our results show that the optical responses of FRET networks are highly repeatable and minor variations between the FRET networks can be discriminated resulting in a total of 10375 unique responses. These results are used in the following breakthrough applications: 1. Unclonable Cryptographic Key for Secure Authentication and Communication Modern authentication protocols rely on an asymmetry in the effort required by a legitimate user and an adversary to accurately decrypt an encoded message. These protocols ensure that communication between legitimate users is possible in polynomial time using a private key but a user without access to the exact key cannot compute the function using a probabilistic polynomial-time algorithm. Private-key cryptographic techniques currently employ physical keys based on algorithmic one-way functions, which are conjectured mathematical objects that are easy to compute but difficult to invert. Well-known examples of such one-way functions include the RSA and the Rabin functions. Although algorithmic one-way functions are widely used for authentication, their reliance on computational difficulty to provide security implies that they are not protected against future advances in computational capacity or speed. Also, use of a highly parallel network of conventional computers could potentially reverse engineer a key from the challenge-response pairs used in past communications. The key may also be obtained by duplicating the device. Most of the current physical embodiments of algorithmic one-way functions come with a tamper resistant packaging but remain vulnerable to sophisticated attacks. We develop a RET based physical key to overcome the limitations of conventional security keys. The key exploits resonance energy transfer between a network of fluorophores placed on a nanostructure. The fluorophores provide a unique, unpredictable output when probed by a series of light pulses of specific wavelengths and delays. A critical advantage of the RET key over existing keys is that the manufacturing process allows two identical devices to be produced allowing us to exploit the advantages of symmetric key encryption, for the first time, without the need to physically transfer the device between the two communicating parties. It is infeasible to model, characterize or replicate our key using modern cryptographic attacks including unfettered physical access to the device. This is because of the difficulty in characterizing the nanoscale structure and the large number of challenge-response pairs achievable for each key. Atomic force microscopy and time -resolved fluorescence measurements are performed to characterize the nanoscale structures. From over 1200 measurements on 300 prototypical keys, we estimate that a legitimate user would have a computational advantage of 10340 years over an attacker even if the attacker uses all the computational resources available in the world. Thus, the computational advantage of our key ensures perfect theoretical security for the foreseeable future. We provide an authentication protocol for use of the key and demonstrate that legitimate users are successfully authenticated 99.48% of the time with two trials. 2. Multiplexed Fluorescence Sensor for Cancer Detection Fluorescence microscopy is one of the most widely used assays in biological systems. However, the technique suffers from limited multiplexing capability with previous attempts at detecting more than 11 fluorophores simultaneously resulting in barcodes that are too big for in vivo analysis, expensive and involve time-consuming detection schemes. Here, we introduce DNA self-assembled FRET networks that provide a unique, optical output when probed by a series of light pulses. Markov and entropy modeling of the nanoscale FRET sensors show that 125 fluorophores can be observed simultaneously. Furthermore, experimental analyses of over 1200 time-resolved fluorescence signatures show that the optical responses are repeatable 99.48% of the time and that minor variations between FRET networks can be discriminated resulting in a total of 10375 unique responses. This enormous increase in spatial information density enabled by FRET networks allowed us to identify molecular signatures in lung and breast cancer tumors. It is now known that the presence of aberrant DNA/RNA secondary structure in the regulatory regions of genes involved in cell proliferation, cells growth and apoptosis can lead to cancer. The FRET sensor we designed, self-assembles DNA probes labeled with acceptor fluorophores to the target DNA/RNA secondary structure forming an optical network. A DNA strand labeled with a donor fluorophore triplex binds to a unique sequence adjacent to the secondary structure. When the donor fluorophore is excited, the optical network results in a different optical signal based on the presence of the wild-type or the aberrant secondary structure, through which we identified lung and breast cancer cells with high specificity and over 99.9% repeatability. The small size of fluorophores results in molecular scale spatial resolution while the optical sensing mechanism enables in vitro and in vivo characterization of the structure at picosecond resolution.
FRET between pairs of fluorophores is widely used as a biological assay. However, the properties of larger fluorophore networks are poorly understood and their application space has not yet been fully explored. This dissertation introduces DNA self-assembled FÖrster Resonance Energy Transfer (FRET) networks that provide a unique optical output when probed by a series of light pulses. We create a Markov model of the FRET networks and analyze over 1200 time-resolved fluorescence measurements on 300 prototypical networks. Our results show that the optical responses of FRET networks are highly repeatable and minor variations between the FRET networks can be discriminated resulting in a total of 10375 unique responses. These results are used in the following breakthrough applications: 1. Unclonable Cryptographic Key for Secure Authentication and Communication Modern authentication protocols rely on an asymmetry in the effort required by a legitimate user and an adversary to accurately decrypt an encoded message. These protocols ensure that communication between legitimate users is possible in polynomial time using a private key but a user without access to the exact key cannot compute the function using a probabilistic polynomial-time algorithm. Private-key cryptographic techniques currently employ physical keys based on algorithmic one-way functions, which are conjectured mathematical objects that are easy to compute but difficult to invert. Well-known examples of such one-way functions include the RSA and the Rabin functions. Although algorithmic one-way functions are widely used for authentication, their reliance on computational difficulty to provide security implies that they are not protected against future advances in computational capacity or speed. Also, use of a highly parallel network of conventional computers could potentially reverse engineer a key from the challenge-response pairs used in past communications. The key may also be obtained by duplicating the device. Most of the current physical embodiments of algorithmic one-way functions come with a tamper resistant packaging but remain vulnerable to sophisticated attacks. We develop a RET based physical key to overcome the limitations of conventional security keys. The key exploits resonance energy transfer between a network of fluorophores placed on a nanostructure. The fluorophores provide a unique, unpredictable output when probed by a series of light pulses of specific wavelengths and delays. A critical advantage of the RET key over existing keys is that the manufacturing process allows two identical devices to be produced allowing us to exploit the advantages of symmetric key encryption, for the first time, without the need to physically transfer the device between the two communicating parties. It is infeasible to model, characterize or replicate our key using modern cryptographic attacks including unfettered physical access to the device. This is because of the difficulty in characterizing the nanoscale structure and the large number of challenge-response pairs achievable for each key. Atomic force microscopy and time -resolved fluorescence measurements are performed to characterize the nanoscale structures. From over 1200 measurements on 300 prototypical keys, we estimate that a legitimate user would have a computational advantage of 10340 years over an attacker even if the attacker uses all the computational resources available in the world. Thus, the computational advantage of our key ensures perfect theoretical security for the foreseeable future. We provide an authentication protocol for use of the key and demonstrate that legitimate users are successfully authenticated 99.48% of the time with two trials. 2. Multiplexed Fluorescence Sensor for Cancer Detection Fluorescence microscopy is one of the most widely used assays in biological systems. However, the technique suffers from limited multiplexing capability with previous attempts at detecting more than 11 fluorophores simultaneously resulting in barcodes that are too big for in vivo analysis, expensive and involve time-consuming detection schemes. Here, we introduce DNA self-assembled FRET networks that provide a unique, optical output when probed by a series of light pulses. Markov and entropy modeling of the nanoscale FRET sensors show that 125 fluorophores can be observed simultaneously. Furthermore, experimental analyses of over 1200 time-resolved fluorescence signatures show that the optical responses are repeatable 99.48% of the time and that minor variations between FRET networks can be discriminated resulting in a total of 10375 unique responses. This enormous increase in spatial information density enabled by FRET networks allowed us to identify molecular signatures in lung and breast cancer tumors. It is now known that the presence of aberrant DNA/RNA secondary structure in the regulatory regions of genes involved in cell proliferation, cells growth and apoptosis can lead to cancer. The FRET sensor we designed, self-assembles DNA probes labeled with acceptor fluorophores to the target DNA/RNA secondary structure forming an optical network. A DNA strand labeled with a donor fluorophore triplex binds to a unique sequence adjacent to the secondary structure. When the donor fluorophore is excited, the optical network results in a different optical signal based on the presence of the wild-type or the aberrant secondary structure, through which we identified lung and breast cancer cells with high specificity and over 99.9% repeatability. The small size of fluorophores results in molecular scale spatial resolution while the optical sensing mechanism enables in vitro and in vivo characterization of the structure at picosecond resolution.
Modern authentication and communication protocols increasingly use physical keys in lieu of conventional software-based keys for security. This shift is primarily driven by the ability to derive a unique, unforgeable signature from a physical key. The sole demonstration of an unforgeable key, thus far, has been through quantum key distribution, which suffers from limited communication distances and expensive infrastructure requirements. Here, we show a method for creating unclonable keys by molecular self-assembly of resonance energy transfer (RET) devices. It is infeasible to clone the RET-key due to the inability to characterize the key using current technology, the large number of input-output combinations per key, and the variation of the key's response with time. However, the manufacturer can produce multiple identical devices, which enables inexpensive, secure authentication and communication over classical channels, and thus any distance. Through a detailed experimental survey of the nanoscale keys, we demonstrate that legitimate users are successfully authenticated 99.48% of the time and the false-positives are only 0.39%, over two attempts. We estimate that a legitimate user would have a computational advantage of more than 10(340) years over an attacker. Our method enables the discovery of physical key based multiparty authentication and communication schemes that are both practical and possess unprecedented security.
The rapid development of technology has provided a wealth of resources enabling the trust of everyday interactions to be undermined. Authentication schemes aim to address this challenge by providing proof of identity. This can be achieved by using devices that, when challenged, give unique but reproducible responses. At present, these distinct signatures are commonly generated by physically unclonable functions, or PUFs. These devices provide a straightforward measurement of a physical characteristic of their structure that has inherent randomness, due to imperfections in the manufacturing process. These hard-to-predict physical responses can generate a unique identity that can be used for authentication without relying on the secrecy of stored data. However, the classical design of these devices limits both their size and security. Here we show that the extensively studied problematic fluctuations in the current-voltage measurements of resonant tunnelling diodes (RTDs) provide an uncomplicated, robust measurement that can function as a PUF without conventional resource limitations. This is possible due to quantum tunnelling within the RTD, and on account of these room temperature quantum effects, we term such devices QUFs - quantum unclonable functions. As a result of the current-voltage spectra being dependent on the atomic structure and composition of the nanostructure within the RTD, each device provides a high degree of uniqueness, whilst being impossible to clone or simulate, even with state-of-the-art technology. We have thus created PUF-like devices requiring the fewest resources which make use of quantum phenomena in a highly manufacturable electronic device operating at room temperature. Conventional spectral analysis techniques, when applied to our QUFs, will enable reliable generation of unpredictable unique identities which can be employed in advanced authentication systems.
Physical unclonable functions (PUFs), physical objects that are practically unclonable because of their andom and uncontrollable manufacturing variations, are becoming increasingly popular as security primitives and unique identifiers in a fully digitized world. One of the central PUF premises states that both friends and foes, both legitimate manufacturers and external attackers alike, cannot clone a PUF, producing two instances that are the same. Using the latest nanofabrication techniques, we show that this premise is not always met: We demonstrate the possibility of effective PUF duplication through sophisticated manufacturers by producing 63 copies of a non-trivial optical scattering structure which exhibit essentially the same scattering behavior. The remaining minuscule differences are close to or below noise levels, whence the duplicates have to be considered fully equivalent from a PUF perspective. The possibility for manufacturer-based optical PUF duplication has positive and negative consequences at the same time: While fully breaking the security of certain schemes, it enables new applications, too. For example, it facilitates unforgeable labels for valuable items; the first key-free group identification schemes over digital networks; or new types of encryption/decryption devices that do not contain secret keys.
The demands for secure communication systems have been growing rapidly as technologies in computer networks advance. However, classical cryptography employed in network systems is only secure when malicious users do not have enough computational power to break the security in a practical amount of time. Quantum cryptography provides theoretically unbreakable security since its security relies on quantum mechanical properties. This dissertation resolves the weakness of classical cryptography in computer networks by developing novel cryptographic schemes. First, a new encryption scheme, quantum commutative encryption (QCE), has been developed by utilizing quantum superposition states. The analysis of possible attacks to the developed encryption scheme, the advantages of the developed scheme, and the requirements to utilize the developed scheme in a communication system are presented. Also, an example of realization with current technologies is shown.
Considering all the characteristics of the developed encryption scheme, a key distribution protocol, two authentication protocols, secret sharing scheme, and the possible practical application of the secret sharing scheme are designed by making use of the developed encryption scheme. This dissertation also discusses the security analysis for each developed scheme. All developed quantum cryptographic schemes are theoretically unbreakable and can be realized with current technologies.
The main contributions of this dissertation are not only the proposal of novel schemes, but also a demonstration of how quantum mechanical properties can be utilized in computer engineering/science.
Information security becomes an inseparable part of our everyday life. An encryption \nmethod widely used today is public-key encryption. The security of this method is based on \na hard to solve mathematical problems against an adversary with limited computational \npower. Such an assumption could be broken as our understanding of the mathematics \nbeing improved or new computation tools being developed. One such tool that poses a \nthreat to the public key encryption is a quantum computer. As a result, a new encryption \nmethod with a new security assumption is required. \nQuantum key distribution is a point-to-point symmetric key distribution method with \nsecurity based on the law of physics. In theory, the key generated by QKD is informationtheoretic secured. However, in practice, physical devices could have flaws or possess some \nbehaviors deviated from the theoretical model. These imperfections could open security \nloopholes for an adversary to exploit, compromising the security. Thus the security verification and system characterization of practical implementation of QKD are necessary. \nThe necessity of this verification is further emphasized as several QKD systems are being \ncommercialized and used in several discrete communication links today. \nTo extend this new encryption system’s practical implementation on a wider network \nscale requires a set of standards or common practices for developers and service providers \nto follow. This set of rules is set to ensure the compatibility of different device models in \nthe network and ensure the security of each component in the system, which would affect \nthe security of the system as a whole. \nTo fulfill standardization and certification criteria, a record of best practice on security \nanalysis, system design, device characterization, and security verification of QKD implementation is required. The research projects throughout my Ph.D. study contribute toward \nthis practice. These studies also address some issues and provide possible solutions to the \ndevelopment of a standard for QKD. This thesis is a collection of six experimental studies \non performance evaluation and security verification of different components of practical \nquantum key distribution systems. \nThe first study is a comparison between the performance of the QKD system with \nquantum dot (QD) as a single-photon source and the performance of QKD with weakcoherent pulsed (WCP) source. The result shows that the QKD with QD could generate \nthe key at higher channel loss than WCP QKD using the same laser source. This result \nshows the potential of QKD with a single-photon source as a candidate for secret key \ndistribution over high channel loss, such as up-link satellite-based QKD. \nThe second study is a theoretical study on the method to characterize the QKD system \nagainst the Trojan-horse attack being considered as a standard for the QKD system. The \nresult shows a possible loophole of this method against a more powerful adversary than \nassumed in the previously proposed model. An improved version of characterization against \na more general form of Trojan-horse attack has been proposed. \nThe third experiment is on the information leakage from a free-space QKD receiver due \nto detector backflash, a photon produced by the detector upon detection. The result shows \nthat the backflash photons carry the information of the ’clicked’ detector that could be \ntransmitted back to the channel and discriminated by Eve. An experimental demonstration \nof this attack has been performed. Countermeasure both in theory and practical setup has \nbeen proposed. \nThe next experiment is on the effect of atmospheric turbulence on Eve’s spatial-mode \ndetection efficiency mismatch attack on the free-space QKD system. We show that, by \nusing a phase-only spatial light modulator (SLM) and hologram created by Zernike polynomials, atmospheric turbulence with various strength covered from sea level to upper \natmosphere can be experimentally emulated in the lab environment. We then use that \nsetup to show the limit of the distance that Eve’s attack is successful. The theoretical \nlimit of the attack distance also shown. \nIn the fifth study, we use the SLM and Zernike polynomial holograms to characterize a \nfree-space QKD system against spatial mode attack. The result shows that, with higherorder spatial modes and finer control of wavefront intensity distribution, Eve could bypass \nthe countermeasure proposed in our previous study. We proposed a more robust version \nof countermeasure against spatial mode attack. The new countermeasure is verified by the \nSLM setup. \nThe last study is on the fake-state attack on the transition edge sensor (TES). The \nresult shows that TES’s voltage response can be deterministically controlled by Eve using \nbright laser through the input channel. It also shows that the photon number result from \nTES can be controlled by Eve. An attack model exploiting this imperfection has been \nshown. \nIn addition to the contribution to the standardization of the QKD system, I hope that \nthe result of this thesis would emphasize the necessity of security verification of the QKD \nsystem and the verification of countermeasure and characterization method against more \ngeneral attack model. Although the unconditional security, promised in theory, could not \nyet be achieved, this loop of hacking and patching should provide us information and insight \non which security level could be claimed from the practical QKD devices implementing \ntoday.
Quantum Key Distribution (QKD), based on the laws of physics rather than the computational \ncomplexity of mathematical problems, provides a secure way of establishing symmetrical binary \nkeys between two geographically distant users. The keys are secure from eavesdropping during \ntransmission and QKD ensures that any third party’s knowledge of the key is reduced to a \nminimum. In recent years, a noticeable progress in the development of quantum equipment has \nbeen reflected through a number of successful demonstrations of QKD technology. While they \nshow the great achievements of QKD, many practical difficulties still need to be resolved, such as \nto provide better service differentiation. These networks are characterized as being multihop in \nnature where the consumption key rate is often higher than the charging key rate, which means that \nthe links are available for a limited period of time only. Such features impose several challenges \non the effective modeling and evaluation of reliability as well as finding appropriate Quality \nof Service (QoS) solution. This thesis focuses on research in the field of QKD for securing \nreal-time communication by supporting QoS in QKD networks including a novel QoS model \nand novel distributed reactive routing protocol to achieve high-level scalability and minimize the \nconsumption of key material used for securing routing data. \nAs research in QKD networks grows larger and more complex, the need for highly accurate and \nscalable simulation technologies becomes important to assess the practical feasibility and foresee \ndifficulties in the practical implementation of theoretical achievements. Due to the specificity of \nQKD link which requires optical/quantum and Internet connection between the network nodes, it \nis very costly to deploy a complete testbed containing multiple network hosts and links to validate \nand verify a certain network algorithm or protocol. The network simulators in these circumstances \nsave a lot of money and time in accomplishing such task. A simulation environment offers the \ncreation of complex network topologies, a high degree of control and repeatable experiments, \nwhich in turn allows researchers to conduct exactly the same experiments and confirm their results. \nThis thesis describes the design and implementation of QKD network simulation module which \nwas developed in the network simulator of version 3 (NS-3). The module supports simulation \nof QKD network in overlay mode or in a single TCP/IP mode. Therefore, it can be used for \nsimulation of other network technologies regardless of QKD. \nImplemented simulation model was used for verification of proposed QoS solution. A number \nof simulations were performed. The obtained data have confirmed the primary thesis of this study, \nthat it is possible to use real-time applications in QKD networks.