Related papers: Current enhancement in solid-state nanopores depen…
Fast, reliable and inexpensive DNA sequencing is an important pursuit in healthcare, especially in personalized medicine with possible deep societal impacts. Despite significant progress of various nanopore-based sequencing configurations,…
Metropolis Monte Carlo simulation is used to investigate the elasticity of torsionally stressed double-stranded DNA, in which twist and supercoiling are incorporated as a natural result of base-stacking interaction and backbone bending…
In nanopore sequencing, electrical signal is measured as DNA molecules pass through the sequencing pores. Translating these signals into DNA bases (base calling) is a highly non-trivial task, and its quality has a large impact on the…
We measure the rheology of transient hydrogels comprised of a single type of DNA nanostar that makes both strong and weak bonds. These gels exhibit power-law frequency-dependence of their storage and loss moduli, with scaling exponents that…
The capture and translocation of biomolecules through nanometer-scale pores are processes with a potential large number of applications, and hence they have been intensively studied in the recent years. The aim of this paper is to review…
DNA molecules spin-coated on amorphous quartz substrates are shown to form stable films. Electron density profiles (EDPs) along the film depth show that film prepared from aqueous solution of DNA exhibits layering of the molecules in three…
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…
A tandem cell is proposed for DNA sequencing in which an exonuclease enzyme cleaves bases (mononucleotides) from a strand of DNA for identification inside a nanopore. It has two nanopores and three compartments with the structure [cis1,…
The transport of polymers with folded configurations across membrane pores is investigated theoretically by analyzing simple discrete stochastic models. The translocation dynamics is viewed as a sequence of two events: motion of the folded…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
We propose a model that can account for the experimentally observed phase behavior of DNA-nanoparticle assemblies (R. Jin et al., JACS 125, 1643 (2003); T. A. Taton et al., Science 289, 1757 (2000)). The binding of DNA-coated nano-particles…
The formation of complexes between like-charged polyelectrolytes challenges conventional electrostatic intuition and highlights the central role of ions in mediating macromolecular organization. Here, we investigate the salt-dependent…
This paper devotes to formulating several multiscale models to study the effect of pH-dependent ionic inhomogeneity on the electrical potential distributions and the graded elastic properties of a nanoscale DNA film and the related bending…
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 present a simplified model of the dynamics of translocation of RNA through a nanopore which only allows the passage of unbound nucleotides. In particular, we consider the disorder averaged translocation dynamics of random, two-component,…
Flow-driven rotary motors drive functional processes in human society such as windmills and water wheels. Although examples of such rotary motors also feature prominently in cell biology, their synthetic construction at the nanoscale has…
Digital information can be encoded in the building-block sequence of macro-molecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive.…
There has been tremendous experimental progress in the last decade in identifying the structure and function of biological pores (ion channels) and fabricating synthetic pores. Despite this progress, many questions still remain about the…
We investigate the charge transport in synthetic DNA polymers built up from single types of base pairs. In the context of a polaron-like model, for which an electronic tight-binding system and bond vibrations of the double helix are…
The phase diagram of a water solution of DNA and oppositely charged spherical macroions is studied. DNA winds around spheres to form beads-on-a-string complexes resembling the chromatin 10 nm fiber. At small enough concentration of spheres…