Theory of DNA translocation through narrow ion channels and nanopores with charged walls

Translocation of a single stranded DNA through genetically engineered $\alpha$-hemolysin channels with positively charged walls is studied. It is predicted that transport properties of such channels are dramatically different from neutral wild type $\alpha$-hemolysin channel. We assume that the wall charges compensate the fraction $x$ of the bare charge $q_{b}$ of the DNA piece residing in the channel. Our prediction are as follows (i) At small concentration of salt the blocked ion current decreases with $x$. (ii) The effective charge $q$ of DNA piece, which is very small at $x = 0$ (neutral channel) grows with $x$ and at $x=1$ reaches $q_{b}$. (iii) The rate of DNA capture by the channel exponentially grows with $x$. Our theory is also applicable to translocation of a double stranded DNA in narrow solid state nanopores with positively charged walls.Comment: 3 pages, 1 figur

Hopping conductivity of a suspension of nanowires in an insulator

We study the hopping conduction in a composite made of straight metallic nanowires randomly and isotropically suspended in an insulator. Uncontrolled donors and acceptors in the insulator lead to random charging of wires and hence finite bare density of states at the Fermi level. Then the Coulomb interactions between electrons of distant wires result in the soft Coulomb gap. At low temperatures the conductivity is due to variable range hopping of electrons between wires and obeys the Efros-Shklovskii (ES) law $\ln\sigma \propto -(T_{ES}/T)^{1/2}$. We show that $T_{ES} \propto 1/(nL^3)^2$, where $n$ is the concentration of wires and $L$ is the wire length. Due to enhanced screening of Coulomb potentials, at large enough $nL^3$, the ES law is replaced by the Mott law.Comment: 5 pages, 5 figure

How a protein searches for its specific site on DNA: the role of intersegment transfer

Proteins are known to locate their specific targets on DNA up to two orders of magnitude faster than predicted by the Smoluchowski three-dimensional diffusion rate. One of the mechanisms proposed to resolve this discrepancy is termed "intersegment transfer". Many proteins have two DNA binding sites and can transfer from one DNA segment to another without dissociation to water. We calculate the target search rate for such proteins in a dense globular DNA, taking into account intersegment transfer working in conjunction with DNA motion and protein sliding along DNA. We show that intersegment transfer plays a very important role in cases where the protein spends most of its time adsorbed on DNA.Comment: 9 pages, 7 figure

Improved transfer matrix method without numerical instability

A new improved transfer matrix method (TMM) is presented. It is shown that the method not only overcomes the numerical instability found in the original TMM, but also greatly improves the scalability of computation. The new improved TMM has no extra cost of computing time as the length of homogeneous scattering region becomes large. The comparison between the scattering matrix method(SMM) and our new TMM is given. It clearly shows that our new method is much faster than SMM.Comment: 5 pages,3 figure

Approximation in LQG control of a thermoelastic rod

Control and estimator gains are computed for linear-quadratic-Gaussian (LQG) optimal control of the axial vibrations of a thermoelastic rod. The computations are based on a modal approximation of the partial differential equations representing the rod, and convergence of the approximations to control and estimator gains is the main issue

Simple Recurrent Units for Highly Parallelizable Recurrence

Common recurrent neural architectures scale poorly due to the intrinsic difficulty in parallelizing their state computations. In this work, we propose the Simple Recurrent Unit (SRU), a light recurrent unit that balances model capacity and scalability. SRU is designed to provide expressive recurrence, enable highly parallelized implementation, and comes with careful initialization to facilitate training of deep models. We demonstrate the effectiveness of SRU on multiple NLP tasks. SRU achieves 5--9x speed-up over cuDNN-optimized LSTM on classification and question answering datasets, and delivers stronger results than LSTM and convolutional models. We also obtain an average of 0.7 BLEU improvement over the Transformer model on translation by incorporating SRU into the architecture.Comment: EMNL

How does a protein search for the specific site on DNA: the role of disorder

Proteins can locate their specific targets on DNA up to two orders of magnitude faster than the Smoluchowski three-dimensional diffusion rate. This happens due to non-specific adsorption of proteins to DNA and subsequent one-dimensional sliding along DNA. We call such one-dimensional route towards the target "antenna". We studied the role of the dispersion of nonspecific binding energies within the antenna due to quasi random sequence of natural DNA. Random energy profile for sliding proteins slows the searching rate for the target. We show that this slowdown is different for the macroscopic and mesoscopic antennas.Comment: 4 pages, 4 figure