Related papers: Crowding Effects during DNA Translocation in Nanop…
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. In this work, we study the fundamental limits and trade-offs of DNA-based storage systems by introducing a new channel model, which we…
Nanoparticle (NP)-based applications are becoming increasingly important in the biomedical field. However, understanding the interactions of NPs with biofluids and cells is a major issue in order to develop novel approaches aimed at…
We study the transient phenomena appearing in a subgap region of the double quantum dot coupled in series between the superconducting and normal metallic leads, focusing on the development of the superconducting proximity effect. For the…
I present a Hamiltonian model and a computational method suitable to evaluate structural and thermodynamic properties of helical molecules embedded in crowded environments which may confine the space available to the base pair fluctuations.…
Hybrid nanocomposites can offer a wide range of opportunities to control the light-matter interac- tion and electromagnetic energy flow at the nanoscale, leading to exotic optoelectronic devices. We study theoretically the dipole-dipole…
Molecular carriers represent an increasingly common strategy in the field of nanopore sensing to use secondary molecules to selectively report on the presence of target analytes in solution, allowing for sensitive assays of otherwise…
We demonstrate simultaneous measurements of DNA translocation into glass nanopores using ionic current detection and fluorescent imaging. We verify the correspondence between the passage of a single DNA molecule through the nanopore and the…
Technologies for sequencing (reading) and synthesizing (writing) DNA have progressed on a Moore's law-like trajectory over the last three decades. This has motivated the idea of using DNA for data storage. Theoretically, DNA-based storage…
Charge transfer can take place along double helical DNA over distances as long as 30 nanometers. However, given the active role of the thermal environment surrounding charge carriers in DNA, physical mechanisms driving the transfer process…
We present a tight-binding model study of a two-terminal graphene nanopore device for sequential determination of DNA bases. Using Green's function technique we investigate the changes in electronic transport properties of the device due to…
We study the effect of the crowded nature of the cellular cytoplasm on the translocation of a polymer through a pore in a membrane. By systematically treating the entropic penalty due to crowding, we show that the translocation dynamics are…
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…
We investigate the transport properties of particles driven by colored noise in a flashing ratchet potential, focusing on both non-interacting and single-file interacting regimes. The model incorporates memory effects via a non-Markovian…
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…
In the field of DNA nanotechnology, it is common wisdom that charge transport occurs through the {\pi} stacked bases of double-stranded DNA. However, recent experimental findings by Zhuravel et. al. [Nat. Nanotech. 15, 836 (2020)] suggest…
We study the impact of DNA coiling on the search rate of proteins moving along the DNA contour interspersed by three-dimensional (3D) bulk excursions. When the DNA is coiled proteins performing short 3D hops along a DNA segment can be…
Quantum sensing with nitrogen-vacancy (NV) centers in diamond promises to revolutionize biological research and medical diagnostics. Thanks to their high sensitivity, NV sensors could, in principle, detect specific binding events with…
DNA unzipping by nanopore translocation has implications in diverse contexts, from polymer physics to single-molecule manipulation to DNA-enzyme interactions in biological systems. Here we use molecular dynamics simulations and a…
We present an unique way to detect basepair mismatches in DNA leading to different epigenetic disorder by the method of nanopore sequencing. Based on a tight-binding formulation of graphene nanopore based device, using Greens function…
Based on our formulation of the DNA electrophoresis near a pore [P. Rowghanian and A. Y. Grosberg, Phys. Rev. E 87, 042723 (2013)], we address the electrophoretic DNA capture into a nanopore as a steady-state process of particle absorption…