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Identification of non-amplified DNA sequences and single-base mutations is essential for molecular biology and genetic diagnostics. This paper reports a novel sensor consisting of electrochemically-gated graphene coplanar waveguides coupled…
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…
Nanopore sensing is a key technology for single-molecule detection and analysis. Solid-state nanopores have emerged as a versatile platform, since their fabrication allows to engineer their properties by controlling size, shape, and…
Nanopore resistive pulse techniques are based on analysis of current or voltage spikes in the recorded signal. These spikes result from translocation of nanometer sized analytes through a nanopore. The most important information that needs…
Surface-enhanced Raman spectroscopy (SERS) sensing of DNA sequences by plasmonic nanopores could pave a way to new generation single-molecule sequencing platforms. The SERS discrimination of single DNA bases depends critically on the time…
Throughout our history, we, humans, have sought to better control and understand our environment. To this end, we have extended our natural senses with a host of sensors-tools that enable us to detect both the very large, such as the…
Plasmonic nanopores combine nanofluidic confinement with electromagnetic field enhancement, enabling optical interrogation of single molecules in sub-wavelength volumes. Yet, direct optical readout within these metallic geometries has…
We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are…
Nanopore sequencing is an emerging DNA sequencing technology that has been proposed for use in DNA storage systems. We propose the noisy nanopore channel model for nanopore sequencing. This model captures duplications, inter-symbol…
The emerging field of DNA storage employs strands of DNA bases (A/T/C/G) as a storage medium for digital information to enable massive density and durability. The DNA storage pipeline includes: (1) encoding the raw data into sequences of…
In this thesis various plasmonic materials, such as hyperbolic metamaterial nanohole arrays and Au-coated free standing nanoassembly supporting nanopores, are investigated with the aim to perform optical sensing of DNA molecules with…
Nanopore sequencing accuracy is inherently limited by the quality of data from individual molecular translocation events, requiring advances beyond traditional sequencing-by-synthesis methods. We introduce an oxidized pyramidal sub-nm pore…
Efficient capture and detection of minute amount of deoxyribonucleic acid (DNA) molecules are pivotal for an array of modern gene technologies which are widely utilized in medical, forensic and defense applications, including DNA…
Double-stranded DNA translocates through sufficiently large nanopores either in a linear, single-file fashion or in a folded hairpin conformation when captured somewhere along its length. We show that the folding state of DNA can be…
Recent advances in top-down mass spectrometry enabled identification of intact proteins, but this technology still faces challenges. For example, top-down mass spectrometry suffers from a lack of sensitivity since the ion counts for a…
A hypercomplex representation of DNA is proposed to facilitate comparison of DNA sequences with fuzzy composition. Using hypercomplex number representation, conventional sequence analysis method, such as, dot matrix analysis, dynamic…
The requirement to boost the resolution of nanopore-based biosequencing devices necessitates the integration of novel biosensing techniques with reduced sensitivity to background noise. In this article, we probe the signatures of…
We propose a water-immersed nucleobase-functionalized suspended graphene nanoribbon as an intrinsically selective device for nucleotide detection. The proposed sensing method combines Watson-Crick selective base pairing with graphene's…
In nanopore technology, the development of multiplexed detection and release platforms with high spatial and temporal resolution remains a significant challenge due to the difficulty in distinguishing signals originating from different…
Nanopore sequencers generate raw electrical signals representing the contents of a biological sequence molecule passing through the nanopore. These signals can be analyzed directly, avoiding basecalling entirely. We observe that while…