Related papers: Two-Domain DNA Strand Displacement
Because of the limitations of classical silicon based computational technology, several alternatives to traditional method in form of unconventional computing have been proposed. In this paper we will focus on DNA computing which is showing…
We report theoretical studies of charge transport in single-stranded DNA in the direction perpendicular to the backbone axis. We find that, if the electrodes which sandwich the DNA have the appropriate spatial width, each nucleotide carries…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
We study the melting of a double stranded DNA in the presence of stretching forces, via 3D Monte-Carlo simulations, exactly solvable models and heuristic arguments. The resulting force-temperature phase diagram is dramatically different for…
We introduce a model of thermalized conformations in space of RNA -or single stranded DNA- molecules, which includes the possibility of hairpin formation. This model contains the usual secondary structure information, but extends it to the…
We predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible…
Prediction of protein-ligand complexes for flexible proteins remains still a challenging problem in computational structural biology and drug design. Here we present two novel deep neural network approaches with significant improvement in…
Because of several technological limitations of traditional silicon based computing, for past few years a paradigm shift, from silicon to carbon, is occurring in computational world. DNA computing has been considered to be quite promising…
The translocation of double-stranded DNA through a solid-state nanopore may either decrease or increase the ionic current depending on the ionic concentration of the surrounding solution. Below a certain crossover ionic concentration, the…
We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single…
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…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
In weakly coupled, current biased, doped semiconductor superlattices, domain walls may move upstream against the flow of electrons. For appropriate doping values, a domain wall separating two electric field domains moves downstream below a…
We investigate the voltage-driven transport of hybridized DNA through membrane channels. As membrane channels are typically too narrow to accommodate hybridized DNA, the dehybridization of the DNA is the critical rate limiting step in the…
We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…
It is well known that during homology recognition and strand exchange the double stranded DNA (dsDNA) in DNA/RecA filaments is highly extended, but the functional role of the extension has been unclear. We present an analytical model that…
We present a theoretical study of single-stranded DNA under stretching. Within the proposed framework, the effects of basepairing on the mechanical response of the molecule can be studied in combination with an arbitrary underlying model of…
We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal…
We separate double stranded lambda phage DNA by applying a fixed force at a constant temperature ranging from 15C to 50C, and measure the minimum force required to separate the two strands, providing the first experimental determination of…