A machine learning approach for accurate and real-time DNA sequence identification

BackgroundThe all-electronic Single Molecule Break Junction (SMBJ) method is an emerging alternative to traditional polymerase chain reaction (PCR) techniques for genetic sequencing and identification. Existing work indicates that the current spectra recorded from SMBJ experimentations contain unique signatures to identify known sequences from a dataset. However, the spectra are typically extremely noisy due to the stochastic and complex interactions between the substrate, sample, environment, and the measuring system, necessitating hundreds or thousands of experimentations to obtain reliable and accurate results.ResultsThis article presents a DNA sequence identification system based on the current spectra of ten short strand sequences, including a pair that differs by a single mismatch. By employing a gradient boosted tree classifier model trained on conductance histograms, we demonstrate that extremely high accuracy, ranging from approximately 96 % for molecules differing by a single mismatch to 99.5 % otherwise, is possible. Further, such accuracy metrics are achievable in near real-time with just twenty or thirty SMBJ measurements instead of hundreds or thousands. We also demonstrate that a tandem classifier architecture, where the first stage is a multiclass classifier and the second stage is a binary classifier, can be employed to boost the single mismatched pair's identification accuracy to 99.5 %.ConclusionsA monolithic classifier, or more generally, a multistage classifier with model specific parameters that depend on experimental current spectra can be used to successfully identify DNA strands

Shot Noise in Mesoscopic Diffusive Andreev Wires

We study shot noise in mesoscopic diffusive wires between a normal and a superconducting terminal. We particularly focus on the regime, in which the proximity-induced reentrance effect is important. We will examine the difference between a simple Boltzmann-Langevin description, which neglects induced correlations beyond the simple conductivity correction, and a full quantum calculation. In the latter approach, it turns out that two Andreev pairs propagating coherently into the normal metal are anti-correlated for E<E_c, where E_c=D/L^2 is the Thouless energy. In a fork geometry the flux-sensitive suppression of the effective charge was confirmed experimentally.Comment: 12 pages, proceedings of the NATO ARW MQO, Bled, Sloveni

Shot noise in mesoscopic systems

This is a review of shot noise, the time-dependent fluctuations in the electrical current due to the discreteness of the electron charge, in small conductors. The shot-noise power can be smaller than that of a Poisson process as a result of correlations in the electron transmission imposed by the Pauli principle. This suppression takes on simple universal values in a symmetric double-barrier junction (suppression factor 1/2), a disordered metal (factor 1/3), and a chaotic cavity (factor 1/4). Loss of phase coherence has no effect on this shot-noise suppression, while thermalization of the electrons due to electron-electron scattering increases the shot noise slightly. Sub-Poissonian shot noise has been observed experimentally. So far unobserved phenomena involve the interplay of shot noise with the Aharonov-Bohm effect, Andreev reflection, and the fractional quantum Hall effect.Comment: 37 pages, Latex, 10 figures (eps). To be published in "Mesoscopic Electron Transport," edited by L. P. Kouwenhoven, G. Schoen, and L. L. Sohn, NATO ASI Series E (Kluwer Academic Publishing, Dordrecht

Tuning the conductance of single-walled carbon nanotubes by ion irradiation in the Anderson localization regime

Carbon nanotubes are a good realization of one-dimensional crystals where basic science and potential nanodevice applications merge. Defects are known to modify the electrical resistance of carbon nanotubes. They can be present in as-grown carbon nanotubes, but controlling externally their density opens a path towards the tuning of the nanotube electronic characteristics. In this work consecutive Ar+ irradiation doses are applied to single-walled nanotubes (SWNTs) producing a uniform density of defects. After each dose, the room temperature resistance versus SWNT-length [R(L)] along the nanotube is measured. Our data show an exponential dependence of R(L) indicating that the system is within the strong Anderson localization regime. Theoretical simulations demonstrate that mainly di-vacancies contribute to the resistance increase induced by irradiation and that just a 0.03% of di-vacancies produces an increase of three orders of magnitude in the resistance of a 400 nm SWNT length.Comment: 16 pages, 4 figure

Hall Measurements on Carbon Nanotube Paper Modified With Electroless Deposited Platinum

Carbon nanotube paper, sometimes referred to as bucky paper, is a random arrangement of carbon nanotubes meshed into a single robust structure, which can be manipulated with relative ease. Multi-walled carbon nanotubes were used to make the nanotube paper, and were subsequently modified with platinum using an electroless deposition method based on substrate enhanced electroless deposition. This involves the use of a sacrificial metal substrate that undergoes electro-dissolution while the platinum metal deposits out of solution onto the nanotube paper via a galvanic displacement reaction. The samples were characterized using SEM/EDS, and Hall-effect measurements. The SEM/EDS analysis clearly revealed deposits of platinum (Pt) distributed over the nanotube paper surface, and the qualitative elemental analysis revealed co-deposition of other elements from the metal substrates used. When stainless steel was used as sacrificial metal a large degree of Pt contamination with various other metals was observed. Whereas when pure sacrificial metals were used bimetallic Pt clusters resulted. The co-deposition of a bimetallic system upon carbon nanotubes was a function of the metal type and the time of exposure. Hall-effect measurements revealed some interesting fluctuations in sheet carrier density and the dominant carrier switched from N- to P-type when Pt was deposited onto the nanotube paper. Perspectives on the use of the nanotube paper as a replacement to traditional carbon cloth in water electrolysis systems are also discussed