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Effect of noise on DNA sequencing via transverse electronic transport.

ABSTRACT: Previous theoretical studies have shown that measuring the transverse current across DNA strands while they translocate through a nanopore or channel may provide a statistically distinguishable signature of the DNA bases, and may thus allow for rapid DNA sequencing. However, fluctuations of the environment, such as ionic and DNA motion, introduce important scattering processes that may affect the viability of this approach to sequencing. To understand this issue, we have analyzed a simple model that captures the role of this complex environment in electronic dephasing and its ability to remove charge carriers from current-carrying states. We find that these effects do not strongly influence the current distributions due to the off-resonant nature of tunneling through the nucleotides--a result we expect to be a common feature of transport in molecular junctions. In particular, only large scattering strengths, as compared to the energetic gap between the molecular states and the Fermi level, significantly alter the form of the current distributions. Since this gap itself is quite large, the current distributions remain protected from this type of noise, further supporting the possibility of using transverse electronic transport measurements for DNA sequencing.

SUBMITTER: Krems M

PROVIDER: S-EPMC2756358 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature

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Effect of noise on DNA sequencing via transverse electronic transport.

Krems Matt M Zwolak Michael M Pershin Yuriy V YV Di Ventra Massimiliano M

Biophysical journal 20091001 7

Previous theoretical studies have shown that measuring the transverse current across DNA strands while they translocate through a nanopore or channel may provide a statistically distinguishable signature of the DNA bases, and may thus allow for rapid DNA sequencing. However, fluctuations of the environment, such as ionic and DNA motion, introduce important scattering processes that may affect the viability of this approach to sequencing. To understand this issue, we have analyzed a simple model ...[more]

PMID: 19804730

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Project description:Near-term quantum computers have been built as intermediate-scale quantum devices and are fragile against quantum noise effects, namely, NISQ devices. Traditional quantum-error-correcting codes are not implemented on such devices and to perform quantum computation in good accuracy with these machines we need to develop alternative approaches for mitigating quantum computational errors. In this work, we propose quantum error mitigation (QEM) scheme for quantum computational errors which occur due to couplings with environments during gate operations, i.e., decoherence. To establish our QEM scheme, first we estimate the quantum noise effects on single-qubit states and represent them as groups of quantum circuits, namely, quantum-noise-effect circuit groups. Then our QEM scheme is conducted by subtracting expectation values generated by the quantum-noise-effect circuit groups from those obtained by the quantum circuits for the quantum algorithms under consideration. As a result, the quantum noise effects are reduced, and we obtain approximately the ideal expectation values via the quantum-noise-effect circuit groups and the numbers of elementary quantum circuits composing them scale polynomial with respect to the products of the depths of quantum algorithms and the numbers of register bits. To numerically demonstrate the validity of our QEM scheme, we run noisy quantum simulations of qubits under amplitude damping effects for four types of quantum algorithms. Furthermore, we implement our QEM scheme on IBM Q Experience processors and examine its efficacy. Consequently, the validity of our scheme is verified via both the quantum simulations and the quantum computations on the real quantum devices. Our QEM scheme is solely composed of quantum-computational operations (quantum gates and measurements), and thus, it can be conducted by any type of quantum device. In addition, it can be applied to error mitigation for many other types of quantum noise effects as well as noisy quantum computing of long-depth quantum algorithms.

Project description:Background Management of recalcitrant diabetic foot ulcer (DFU) remains difficult. Distraction osteogenesis mediates new bone formation and angiogenesis in the bone itself and the surrounding tissues. Recently it was reported that tibial cortex transverse transport (TTT) was associated with neovascularization and increased perfusion at the foot in patients with recalcitrant DFUs and facilitated healing and limb salvage. However, the findings were from several single-center studies with relatively small populations, which need to be confirmed in multicenter cohort studies with relatively large populations. Furthermore, the effect of this technique on patient's health-related quality of life is still unclear. Methods We treated patients with recalcitrant (University of Texas wound grading system 2-C to 3-D and not responding to prior routine conservative and surgical treatments for at least 8 weeks) DFUs from seven centers using TTT (a 5 cm × 1.5 cm corticotomy followed by 4 weeks of medial and lateral distraction) between July 2016 and June 2019. We analyzed ulcer healing, major amputation, recurrence, health-related quality of life (physical and mental component summary scores), and complications in the 2-year follow-up. Foot arterial and perfusion changes were evaluated using computed tomography angiography and perfusion imaging 12 weeks postoperatively. Results A total of 1175 patients were enrolled. Patients who died (85, 7.2%) or lost to follow-up (18, 1.7%) were excluded, leaving 1072 patients for evaluation. Most of the patients were male (752, 70.1%) and with a mean age of 60.4 ± 9.1 years. The mean ulcer size was 41.0 ± 8.5 cm2 and 187 (16.6%) ulcers extended above the ankle. During the follow-up, 1019 (94.9%) patients healed in a mean time of 12.4 ± 5.6 weeks, 53 (4.9%) had major amputations, and 33 (3.1%) experienced recurrences. Compared to preoperatively, the patients had higher physical (26.2 ± 8.3 versus 41.3 ± 10.6, p = 0.008) and mental (33.6 ± 10.7 versus 45.4 ± 11.3, p = 0.031) component summary scores at the 2-year follow-up. Closed tibial fracture at the corticotomy site was found in 8 (0.7%) patients and was treated using external fixation and healed uneventfully. There were 23 (2.1%) patients who had pin site infections and were treated successfully with dressing changes. Compared to preoperatively, the patients had more small arteries and higher foot blood flow (8.1 ± 2.2 versus 28.3 ± 3.9 ml/100 g/min, p = 0.003) and volume (1.5 ± 0.3 versus 2.7 ± 0.4 ml/100 g, p = 0.037) 12 weeks postoperatively. Conclusion TTT promotes healing, limb salvage, and health-related quality of life in patients with recalcitrant DFUs as demonstrated in this multicenter cohort study. The surgical procedure was simple and straightforward and the complications were few and minor. The effect of this technique was associated with neovascularization and improved perfusion at the foot mediated by the cortex distraction. The findings are required to confirm in randomized controlled trials. The Translational Potential of this Article: TTT can be used as an effective treatment in patients with recalcitrant DFUs. The mechanism is associated with neovascularization and consequently increased perfusion in the foot after operation.

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Effect of noise on DNA sequencing via transverse electronic transport.

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Effect of noise on DNA sequencing via transverse electronic transport.

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