Search for: All records

Abstract Combinatorial optimization problems on graphs have broad applications in science and engineering. The quantum approximate optimization algorithm (QAOA) is a method to solve these problems on a quantum computer by applying multiple rounds of variational circuits. However, there exist several challenges limiting the application of QAOA to real-world problems. In this paper, we demonstrate on a trapped-ion quantum computer that QAOA results improve with the number of rounds for multiple problems on several arbitrary graphs. We also demonstrate an advanced mixing Hamiltonian that allows sampling of all optimal solutions with predetermined weights. Our results are a step toward applying quantum algorithms to real-world problems. 

We propose a set of Bell-type nonlocal games that can be used to prove an unconditional quantum advantage in an objective and hardware-agnostic manner. In these games, the circuit depth needed to prepare a cyclic cluster state and measure a subset of its Pauli stabilizers on a quantum computer is compared to that of classical Boolean circuits with the same, nearest-neighboring gate connectivity. Using a circuit-based trapped-ion quantum computer, we prepare and measure a six-qubit cyclic cluster state with an overall fidelity of 60.6% and 66.4%, before and after correcting for measurement-readout errors, respectively. Our experimental results indicate that while this fidelity readily passes conventional (or depth-0) Bell bounds for local hidden-variable models, it is on the cusp of demonstrating a higher probability of success than what is possible by depth-1 classical circuits. Our games offer a practical and scalable set of quantitative benchmarks for quantum computers in the pre-fault-tolerant regime as the number of qubits available increases. 

Abstract Symbiosis with protists is common among cnidarians such as corals and sea anemones and is associated with homeostatic and phenotypic changes in the host that could have epigenetic underpinnings, such as methylation of CpG dinucleotides. We leveraged the sensitivity to base modifications of nanopore sequencing to probe the effect of symbiosis with the chlorophyte Elliptochloris marina on methylation in the sea anemone Anthopleura elegantissima. We first validated the approach by comparison of nanopore-derived methylation levels with CpG depletion analysis of a published transcriptome, finding that high methylation levels are associated with CpG depletion as expected. Next, using reads generated exclusively from aposymbiotic anemones, a largely complete draft genome comprising 243 Mb was assembled. Reads from aposymbiotic and symbiotic sea anemones were then mapped to this genome and assessed for methylation using the program Nanopolish, which detects signal disruptions from base modifications as they pass through the nanopore. Based on assessment of 452,841 CpGs for which there was adequate read coverage (approximately 8% of the CpGs in the genome), symbiosis with E. marina was, surprisingly, associated with only subtle changes in the host methylome. However, we did identify one extended genomic region with consistently higher methylation among symbiotic individuals. The region was associated with a DNA polymerase zeta that is noted for its role in translesion synthesis, which opens interesting questions about the biology of this symbiosis. Our study highlights the power and relative simplicity of nanopore sequencing for studies of nucleic acid base modifications in non-model species. 

Wrinkling is a ubiquitous surface phenomenon in many biological tissues and is believed to play an important role in arterial health. As arteries are highly nonlinear, anisotropic, multilayered composite systems, it is necessary to investigate wrinkling incorporating these material characteristics. Several studies have examined surface wrinkling mechanisms with nonlinear isotropic material relationships. Nevertheless, wrinkling associated with anisotropic constitutive models such as Ogden–Gasser–Holzapfel (OGH), which is suitable for soft biological tissues, and in particular arteries, still requires investigation. Here, the effects of OGH parameters such as fibers’ orientation, stiffness, and dispersion on the onset of wrinkling, wrinkle wavelength and amplitude are elucidated through analysis of a bilayer system composed of a thin, stiff neo-Hookean membrane and a soft OGH substrate subjected to compression. Critical contractile strain at which wrinkles occur is predicted using both finite element analysis and analytical linear perturbation approach. Results suggest that besides stiffness mismatch, anisotropic features associated with fiber stiffness and distribution might be used in natural layered systems to adjust wrinkling and subsequent folding behaviors. Further analysis of a bilayer system with fibers in the (x–y) plane subjected to compression in the x direction shows a complex dependence of wrinkling strain and wavelength on fiber angle, stiffness, and dispersion. This behavior is captured by an approximation utilizing the linearized anisotropic properties derived from OGH model. Such understanding of wrinkling in this artery wall-like system will help identify the role of wrinkling mechanisms in biological artery in addition to the design of its synthetic counterparts.