ﻻ يوجد ملخص باللغة العربية
In this work, we model the zero-bias conductance for the four different DNA strands that were used in conductance measurement experiment [A. K. Mahapatro, K. J. Jeong, G. U. Lee, and D. B. Janes, Nanotechnology 18, 195202 (2007)]. Our approach consists of three elements: (i) ab initio calculations of DNA, (ii) Greens function approach for transport calculations, and (iii) the use of two parameters to determine the decoherence rates. We first study the role of the backbone. We find that the backbone can alter the coherent transmission significantly at some energy points by interacting with the bases, though the overall shape of the transmission stays similar for the two cases. More importantly, we find that the coherent electrical conductance is tremendously smaller than what the experiments measure. We consider DNA strands under a variety of different experimental conditions and show that even in the most ideal cases, the calculated coherent conductance is much smaller than the experimental conductance. To understand the reasons for this, we carefully look at the effect of decoherence. By including decoherence, we show that our model can rationalize the measured conductance of the four strands, both qualitatively and quantitatively. We find that the effect of decoherence on G:C base pairs is crucial in getting agreement with the experiments. However, the decoherence on G:C base pairs alone does not explain the experimental conductance in strands containing a number of A:T base pairs. Including decoherence on A:T base pairs is also essential. By fitting the experimental trends and magnitudes in the conductance of the four different DNA molecules, we estimate for the first time that the deocherence rate is 6 meV for G:C and 1.5 meV for A:T base pairs.
We perform a spatially resolved simulation study of an AND gate based on DNA strand displacement using several lengths of the toehold and the adjacent domains. DNA strands are modelled using a coarse-grained dynamic bonding model {[}C. Svaneborg, Com
In the independent electron approximation, the average (energy/charge/entropy) current flowing through a finite sample S connected to two electronic reservoirs can be computed by scattering theoretic arguments which lead to the famous Landauer-Buttik
When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this melting transition have been intensively investigated. Recently t
Solid-state nanopores are single molecule sensors that measure changes in ionic current as charged polymers such as DNA pass through. Here, we present comprehensive experiments on the length, voltage and salt dependence of the frequency of double-str
Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the possibility o