Quantum gate algorithm for reference-guided DNA sequence alignment

Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be re-sequenced. Each human genome has 3.2B base pairs, and each one could be stored with 2 bits of information, so one human genome would take 6.4B bits or ∼760MB of storage (National Institute of General Medical Sciences, n.d.). Today's most powerful tensor processing units cannot handle the volume of DNA data necessitating a major leap in computing power. It is, therefore, important to investigate the usefulness of quantum computers in genomic data analysis, especially in DNA sequence alignment. Quantum computers are expected to be involved in DNA sequencing, initially as parts of classical systems, acting as quantum accelerators. The number of available qubits is increasing annually, and future quantum computers could conduct DNA sequencing, taking the place of classical computing systems. We present a novel quantum algorithm for reference-guided DNA sequence alignment modeled with gate-based quantum computing. The algorithm is scalable, can be integrated into existing classical DNA sequencing systems and is intentionally structured to limit computational errors. The quantum algorithm has been tested using the quantum processing units and simulators provided by IBM Quantum, and its correctness has been confirmed.

Quantum algorithm for de novo DNA sequence assembly based on quantum walks on graphs

De novo DNA sequence assembly is based on finding paths in overlap graphs, which is a NP-hard problem. We developed a quantum algorithm for de novo assembly based on quantum walks in graphs. The overlap graph is partitioned repeatedly to smaller graphs that form a hierarchical structure. We use quantum walks to find paths in low rank graphs and a quantum algorithm that finds Hamiltonian paths in high hierarchical rank. We tested the partitioning quantum algorithm, as well as the quantum algorithm that finds Hamiltonian paths in high hierarchical rank and confirmed its correct operation using Qiskit. We developed a custom simulation for quantum walks to search for paths in low rank graphs. The approach described in this paper may serve as a basis for the development of efficient quantum algorithms that solve the de novo DNA assembly problem.

An investigation of the textural properties of mesostructured silica-based adsorbents for predicting CO2 adsorption capacity

The CO₂ uptake of more than 30 physisorbents was found to correlate with their textural parameters, namely the product of the available surface area (S_BET) and the affinity of the surface toward adsorptives (C parameter).

[An unrecognized oesophageal rupture]

Perforation of the abdominal oesophagus from blunt trauma is an extremely rare injury. We report a case of an initially unrecognized oesophageal injury. The patient underwent an immediate laparotomy for haemorrhagic shock. The diagnosis was made by tomodensitometry and was delayed by modified radiological interpretation secondary to laparotomy. Finally, the outcome was favourable.

Activity and resistance of iron-containing amorphous, zeolitic and mesostructured materials for wet peroxide oxidation of phenol

Iron-containing materials have been prepared following several strategies of synthesis and using different silica supports (amorphous, zeolitic and mesostructured materials). Activity and stability of these materials was evaluated on the wet peroxide oxidation of phenol under mild reaction conditions (100 degrees C, air pressure of 1MPa and stoichiometric amount of hydrogen peroxide for the complete mineralisation of phenol). Their catalytic performance was monitored in terms of phenol and total organic carbon (TOC) conversions, by-products distribution (aromatics compounds and carboxylic acids) and degree of metal leached into the aqueous solution. The nature and local environment of iron species is strongly dependent on the synthetic route, which dramatically influences their catalytic performance. Crystalline iron oxide species supported over mesostructured SBA-15 materials have demonstrated to be the most interesting catalysts for phenol degradation according to its high organic mineralisation, low sensitivity to leaching out and good oxidant efficiency.