Related papers: DNA Barcodes using a Double Nanopore System
We analyze the structure of DNA molecules of different organisms by using the additive Markov chain approach. Transforming nucleotide sequences into binary strings, we perform statistical analysis of the corresponding "texts". We develop…
Nanoscale molecular systems such as DNA require an atomistic quantum treatment to accurately capture their electrical properties, owing to their small dimensions. A central challenge in modeling transport through these systems is the…
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages,…
DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve…
In order to understand the physical processes of nanopore experiments at the molecular level, microscopic information from molecular dynamics is greatly needed. Coarse-grained models are a good alternative to classical all-atom models since…
Phage display is a powerful laboratory technique used to study the interactions between proteins and other molecules, whether other proteins, peptides, DNA or RNA. The under-utilisation of this data in conjunction with deep learning models…
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…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
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…
We study plane trees as a model for RNA secondary structure, assigning energy to each tree based on the Nearest Neighbor Thermodynamic Model, and defining a corresponding Gibbs distribution on the trees. Through a bijection between plane…
We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localisation lengths, crudely speaking the length over which…
Extracting the intrinsic kinetic information of biological molecule from its single-molecule kinetic data is of considerable biophysical interest. In this work, we theoretically investigate the feasibility of inferring single RNA's…
We investigate the ionic current modulation in DNA nanopore translocation setups by numerically solving the electrokinetic mean-field equations for an idealized model. Specifically, we study the dependence of the ionic current on the…
Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…
Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
Recent experiments of translocation of double stranded DNA through nanopores [M. Wanunu \textit{et al.} Nature Nanotech. {\bf 5}, 160 (2010)] reveal that the DNA capture rate can be significantly influenced by a salt gradient across the…
We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems,…
We investigate the translocation of a stiff polymer consisting of M monomers through a nanopore in a membrane, in the presence of binding particles (chaperones) that bind onto the polymer, and partially prevent backsliding of the polymer…
The local mechanical properties of DNA are believed to play an important role in their biological functions and DNA-based nanomechanical devices. Using a simple sphere-tip compression system, the local radial mechanical properties of DNA…
Transport measurements allow sensitive detection of nanomechanical motion of suspended carbon nanotubes. It has been predicted that when the electro-mechanical coupling is sufficiently large a bistability with a current blockade appears.…