Quantum error correction with biased noise

Quantum computing offers powerful new techniques for speeding up the calculation of many classically intractable problems. Quantum algorithms can allow for the efficient simulation of physical systems, with applications to basic research, chemical modeling, and drug discovery; other algorithms have important implications for cryptography and internet security.

At the same time, building a quantum computer is a daunting task, requiring the coherent manipulation of systems with many quantum degrees of freedom while preventing environmental noise from interacting too strongly with the system. Fortunately, we know that, under reasonable assumptions, we can use the techniques of quantum error correction and fault tolerance to achieve an arbitrary reduction in the noise level.

In this thesis, we look at how additional information about the structure of noise, or "noise bias," can improve or alter the performance of techniques in quantum error correction and fault tolerance. In Chapter 2, we explore the possibility of designing certain quantum gates to be extremely robust with respect to errors in their operation. This naturally leads to structured noise where certain gates can be implemented in a protected manner, allowing the user to focus their protection on the noisier unprotected operations.

In Chapter 3, we examine how to tailor error-correcting codes and fault-tolerant quantum circuits in the presence of dephasing biased noise, where dephasing errors are far more common than bit-flip errors. By using an appropriately asymmetric code, we demonstrate the ability to improve the amount of error reduction and decrease the physical resources required for error correction.

In Chapter 4, we analyze a variety of protocols for distilling magic states, which enable universal quantum computation, in the presence of faulty Clifford operations. Here again there is a hierarchy of noise levels, with a fixed error rate for faulty gates, and a second rate for errors in the distilled states which decreases as the states are distilled to better quality. The interplay of of these different rates sets limits on the achievable distillation and how quickly states converge to that limit.

Lattice quantum codes and exotic topological phases of matter

This thesis addresses whether it is possible to build a robust memory device for quantum information. Many schemes for fault-tolerant quantum information processing have been developed so far, one of which, called topological quantum computation, makes use of degrees of freedom that are inherently insensitive to local errors. However, this scheme is not so reliable against thermal errors. Other fault-tolerant schemes achieve better reliability through active error correction, but incur a substantial overhead cost. Thus, it is of practical importance and theoretical interest to design and assess fault-tolerant schemes that work well at finite temperature without active error correction.

In this thesis, a three-dimensional gapped lattice spin model is found which demonstrates for the first time that a reliable quantum memory at finite temperature is possible, at least to some extent. When quantum information is encoded into a highly entangled ground state of this model and subjected to thermal errors, the errors remain easily correctable for a long time without any active intervention, because a macroscopic energy barrier keeps the errors well localized. As a result, stored quantum information can be retrieved faithfully for a memory time which grows exponentially with the square of the inverse temperature. In contrast, for previously known types of topological quantum storage in three or fewer spatial dimensions the memory time scales exponentially with the inverse temperature, rather than its square.

This spin model exhibits a previously unexpected topological quantum order, in which ground states are locally indistinguishable, pointlike excitations are immobile, and the immobility is not affected by small perturbations of the Hamiltonian. The degeneracy of the ground state, though also insensitive to perturbations, is a complicated number-theoretic function of the system size, and the system bifurcates into multiple noninteracting copies of itself under real-space renormalization group transformations. The degeneracy, the excitations, and the renormalization group flow can be analyzed using a framework that exploits the spin model's symmetry and some associated free resolutions of modules over polynomial algebras.

Rewriting Schemes for Flash Memory

Flash memory is a leading storage media with excellent features such as random access and high storage density. However, it also faces significant reliability and endurance challenges. In flash memory, the charge level in the cells can be easily increased, but removing charge requires an expensive erasure operation. In this thesis we study rewriting schemes that enable the data stored in a set of cells to be rewritten by only increasing the charge level in the cells. We consider two types of modulation scheme; a convectional modulation based on the absolute levels of the cells, and a recently-proposed scheme based on the relative cell levels, called rank modulation. The contributions of this thesis to the study of rewriting schemes for rank modulation include the following: we

•propose a new method of rewriting in rank modulation, beyond the previously proposed method of “push-to-the-top”;

•study the limits of rewriting with the newly proposed method, and derive a tight upper bound of 1 bit per cell;

•extend the rank-modulation scheme to support rankings with repetitions, in order to improve the storage density;

•derive a tight upper bound of 2 bits per cell for rewriting in rank modulation with repetitions;

•construct an efficient rewriting scheme that asymptotically approaches the upper bound of 2 bit per cell.

The next part of this thesis studies rewriting schemes for a conventional absolute-levels modulation. The considered model is called “write-once memory” (WOM). We focus on WOM schemes that achieve the capacity of the model. In recent years several capacity-achieving WOM schemes were proposed, based on polar codes and randomness extractors. The contributions of this thesis to the study of WOM scheme include the following: we

•propose a new capacity-achievingWOM scheme based on sparse-graph codes, and show its attractive properties for practical implementation;

•improve the design of polarWOMschemes to remove the reliance on shared randomness and include an error-correction capability.

The last part of the thesis studies the local rank-modulation (LRM) scheme, in which a sliding window going over a sequence of real-valued variables induces a sequence of permutations. The LRM scheme is used to simulate a single conventional multi-level flash cell. The simulated cell is realized by a Gray code traversing all the relative-value states where, physically, the transition between two adjacent states in the Gray code is achieved by using a single “push-to-the-top” operation. The main results of the last part of the thesis are two constructions of Gray codes with asymptotically-optimal rate.

Accelerogram processing using reliability bounds and optimal correction methods

This study addresses the problem of obtaining reliable velocities and displacements from accelerograms, a concern which often arises in earthquake engineering. A closed-form acceleration expression with random parameters is developed to test any strong-motion accelerogram processing method. Integration of this analytical time history yields the exact velocities, displacements and Fourier spectra. Noise and truncation can also be added. A two-step testing procedure is proposed and the original Volume II routine is used as an illustration. The main sources of error are identified and discussed. Although these errors may be reduced, it is impossible to extract the true time histories from an analog or digital accelerogram because of the uncertain noise level and missing data. Based on these uncertainties, a probabilistic approach is proposed as a new accelerogram processing method. A most probable record is presented as well as a reliability interval which reflects the level of error-uncertainty introduced by the recording and digitization process. The data is processed in the frequency domain, under assumptions governing either the initial value or the temporal mean of the time histories. This new processing approach is tested on synthetic records. It induces little error and the digitization noise is adequately bounded. Filtering is intended to be kept to a minimum and two optimal error-reduction methods are proposed. The "noise filters" reduce the noise level at each harmonic of the spectrum as a function of the signal-to-noise ratio. However, the correction at low frequencies is not sufficient to significantly reduce the drifts in the integrated time histories. The "spectral substitution method" uses optimization techniques to fit spectral models of near-field, far-field or structural motions to the amplitude spectrum of the measured data. The extremes of the spectrum of the recorded data where noise and error prevail are then partly altered, but not removed, and statistical criteria provide the choice of the appropriate cutoff frequencies. This correction method has been applied to existing strong-motion far-field, near-field and structural data with promising results. Since this correction method maintains the whole frequency range of the record, it should prove to be very useful in studying the long-period dynamics of local geology and structures.

Crystals that count! Physical principles and experimental investigations of DNA tile self-assembly

Algorithmic DNA tiles systems are fascinating. From a theoretical perspective, they can result in simple systems that assemble themselves into beautiful, complex structures through fundamental interactions and logical rules. As an experimental technique, they provide a promising method for programmably assembling complex, precise crystals that can grow to considerable size while retaining nanoscale resolution. In the journey from theoretical abstractions to experimental demonstrations, however, lie numerous challenges and complications.

In this thesis, to examine these challenges, we consider the physical principles behind DNA tile self-assembly. We survey recent progress in experimental algorithmic self-assembly, and explain the simple physical models behind this progress. Using direct observation of individual tile attachments and detachments with an atomic force microscope, we test some of the fundamental assumptions of the widely-used kinetic Tile Assembly Model, obtaining results that fit the model to within error. We then depart from the simplest form of that model, examining the effects of DNA sticky end sequence energetics on tile system behavior. We develop theoretical models, sequence assignment algorithms, and a software package, StickyDesign, for sticky end sequence design.

As a demonstration of a specific tile system, we design a binary counting ribbon that can accurately count from a programmable starting value and stop growing after overflowing, resulting in a single system that can construct ribbons of precise and programmable length. In the process of designing the system, we explain numerous considerations that provide insight into more general tile system design, particularly with regards to tile concentrations, facet nucleation, the construction of finite assemblies, and design beyond the abstract Tile Assembly Model.

Finally, we present our crystals that count: experimental results with our binary counting system that represent a significant improvement in the accuracy of experimental algorithmic self-assembly, including crystals that count perfectly with 5 bits from 0 to 31. We show some preliminary experimental results on the construction of our capping system to stop growth after counters overflow, and offer some speculation on potential future directions of the field.

Studies on T-even bacteriophage DNA

Part I. The regions of sequence homology and non-homology between the DNA molecules of T2, T4, and T6 have been mapped by the electron microscopic heteroduplex method. The heteroduplex maps have been oriented with respect to the T4 genetic map. They show characteristic, reproducible patterns of substitution and deletion loops. All heteroduplex molecules show more than 85% homology. Some of the loop patterns in T2/T4 heteroduplexes are similar to those in T4/T6.

We find that the rII, the lysozyme and ac genes, the D region, and gene 52 are homologous in T2, T4, and T6. Genes 43 and 47 are probably homologous between T2 and T4. The region of greatest homology is that bearing the late genes. The host range region, which comprises a part of gene 37 and all of gene 38, is heterologous in T2, T4, and T6. The remainder of gene 37 is partially homologous in the T2/T4 heteroduplex (Beckendorf, Kim and Lielausis, 1972) but it is heterologous in T4/T6 and in T2/T6. Some of the tRNA genes are homologous and some are not. The internal protein genes in general seem to be non-homologous.

The molecular lengths of the T-even DNAs are the same within the limit of experimental error; their calculated molecular weights are correspondingly different due to unequal glucosylation. The size of the T2 genome is smaller than that of T4 or T6, but the terminally repetitious region in T2 is larger. There is a length distribution of the terminal repetition for any one phage DNA, indicating a variability in length of the DNA molecules packaged within the phage.

Part II. E. coli cells infected with phage strains carrying extensive deletions encompassing the gene for the phage ser-tRNA are missing the phage tRNAs normally present in wild type infected cells. By DNA-RNA hybridization we have demonstrated that the DNA complementary to the missing tRNAs is also absent in such deletion mutants. Thus the genes for these tRNAs must be clustered in the same region of the genome as the ser-tRNA gene. Physical mapping of several deletions of the ser-tRNA and lysozyme genes, by examination of heteroduplex DNA in the electron microscope, has enabled us to locate the cluster, to define its maximum size, and to order a few of the tRNA genes within it. That such deletions can be isolated indicates that the phage-specific tRNAs from this cluster are dispensable.

Part III. Genes 37 and 38 between closely related phages T2 and T4 have been compared by genetic, biochemical, and hetero-duplex studies. Homologous, partially homologous and non-homologous regions of the gene 37 have been mapped. The host range determinant which interacts with the gene 38 product is identified.

Part IV. A population of double-stranded ØX-RF DNA molecules carrying a deletion of about 9% of the wild-type DNA has been discovered in a sample cultivated under conditions where the phage lysozyme gene is nonessential. The structures of deleted monomers, dimers, and trimers have been studied by the electron microscope heteroduplex method. The dimers and trimers are shown to be head-to-tail repeats of the deleted monomers. Some interesting examples of the dynamical phenomenon of branch migration in vitro have been observed in heteroduplexes of deleted dimer and trimer strands with undeleted wild-type monomer viral strands.