Dimitris Ntalaperas

A novel quantum algorithm for biological sequence alignment is presented and analyzed. The large volumes of data generated through genome sequencing, de novo assembly, resequencing, and transcriptome sequencing at the DNA and RNA levels foreshadow the growing demand for higher computational power and more sophisticated alignment methodologies. The rapid advancement of modern sequencing technologies in genomics has motivated the reconsideration of existing approaches for the design and implementation of alignment protocols. Emerging quantum computing accelerators may provide transformative solutions in this domain as quantum hardware progressively reaches higher levels of gate-operation maturity. This work proposes a computer-vision-based approach that exploits the unique properties of quantum entanglement within a dot-matrix representation to address the increasing demand for efficient processing of biological data. A quantum-accelerated protocol is developed and evaluated using the Qiskit software framework of IBM. Runtime experiments support the potential of the proposed methodology to provide advantageous sequence-alignment performance in terms of accuracy, completeness, and computational complexity. The system is evaluated under multiple operational conditions and demonstrates promising performance advantages.

Vast amounts of genomic, proteomic, transcriptomics and other forms, commonly referred to as -omics data, are generated daily in an unprecedented way thanks to high-throughput Next Generation Sequencing technologies. One of the main processes to generate value and insights from this data in bioinformatics is “sequence alignment”, an algorithmic routine that matches a “reference” sequence to a larger sequence. Despite the plethora of approaches, pairwise and multiple sequence alignment remain a complex problem that requires high computational power. In this article, the most prominent sequence alignment approaches of the past three decades are reviewed and categorized, examining different aspects, such as their overall algorithmic synthesis, alignment quality and performance benchmarking tests in a uniform way. The latest trends reveal an increased specialization on biology-based directions, the need for alternative heuristic approaches and a promise in optics-enabled approaches and the quantum computing paradigm shift.

Qudits allow the encoding and manipulation of additional quantum information compared to that stored to a two-level qubit system. Although manipulations of qudit states are generally more complex and can introduce extra sources of noise, qudits can still be used in a number of applications when this error can be kept sufficiently low. One such application is the case of the Bucket Brigade Algorithm for realizing a Quantum RAM (QRAM), which inherently uses qutrits for encoding the state of address switches. In this paper, we study a methodology for qutrit manipulation that leverages efficient encoding techniques and pulse calibration methods for the case of transmon systems. The methodology employs an encoding scheme that allows the execution of controlled operations, using the subspace spanned by the two lowest levels of the transmon; we show how this scheme can be used for generating one- and two-qutrit gates by leveraging the Qiskit and Boulder Opal frameworks to compute the parameters of pulses that implement the quantum gates that are used by the BBA. For this type of gate, simulations show that the pulses perform the required operations with a low infidelity when errors introduced by the qutrit Hamiltonian dynamics are considered.

The quantum phase estimation algorithm has been utilized by a variety of quantum algorithms, most notably Shor’s algorithm, to obtain information regarding the period of a function that is appropriately encoded into a unitary operator. In many cases, it is desired to estimate whether a specific state exhibits a certain pattern quickly. In this paper, we exhibit a methodology based on the QPE algorithm to identify certain patterns. In particular, starting from a properly encoded state, we demonstrate how to construct unitary operators whose eigenvectors correspond to states with proper diagonals. QPE will then output an eigenphase equal to zero with certainty for these states, thereby identifying this class of matrices. For partial matches, our algorithm, based on the tolerance threshold used, will show areas of high similarity, and it will outperform classical ones when the number of mismatches defined by the tolerance is significantly low when compared to the size of the diagonal.

Contemporary wastewater reclamation units entail several diverse treatment and extraction processes, with a multitude of monitored quality characteristics, controlled by a variety of key operational parameters directly affecting the efficiency of treatment. The conventional optimization of this highly complex system is time- and energy- consuming, frequently relying on intuitive decision making by operators, and does not predict or forecast efficiency changes and system maintenance. In this paper, we introduce intelligent solutions to enhance the operational control of the unit with minimal human intervention and to develop an AI-powered DSS that is installed atop the sensors of a water treatment module. The DSS uses an expert model, both to assess the quality of water and to offer suggestions based on current values and future trends. More specifically, the quality of the produced water was successfully visualized, assessed and rated, based on a set of input operational variables (pH, TOC for this case), while future values of monitored sensors were forecasted. Additionally, monitoring services of the DSS were able to identify unexpected events and to generate alerts in the case of observed violation of operational limits, as well as to implement changes (automatic responses) to operational parameters so as to reestablish normal operating conditions and to avoid such events in the future. Up to now, the DSS suggestion and forecasting services have proven to be adequately accurate. Though data are still being collected from early adopters, the solution is expected to provide a complete water treatment solution that can be adopted by a vast range of parties.

In this paper, we introduce a novel coding scheme, which allows single quantum systems to encode multi-qubit registers. This allows for more efficient use of resources and the economy in designing quantum systems. The scheme is based on the notion of encoding logical quantum states using the charge degree of freedom of the discrete energy spectrum that is formed by introducing impurities in a semiconductor material. We propose a mechanism of performing single qubit operations and controlled two-qubit operations, providing a mechanism for achieving these operations using appropriate pulses generated by Rabi oscillations. The above architecture is simulated using the Armonk single qubit quantum computer of IBM to encode two logical quantum states into the energy states of Armonk’s qubit and using custom pulses to perform one and two-qubit quantum operations.

We propose an architecture based on Quantum Cellular Automata which allows the use of only one type of quantum gate per computational step, using nearest neighbor interactions. The model is built in partial steps, each one of them analyzed using nearest neighbor interactions, starting with single-qubit operations and continuing with two-qubit ones. A demonstration of the model is given, by analyzing how the techniques can be used to design a circuit implementing the Quantum Fourier Transform. Since the model uses only one type of quantum gate at each phase of the computation, physical implementation can be easier since at each step only one kind of input pulse needs to be applied to the apparatus.