Related papers: How the surrounding water changes the electronic a…
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…
As the dimensions of a conductor approach the nano-scale, quantum effects will begin to dominate its behavior. This entails the exciting possibility of controlling the conductance of a device by direct manipulation of the electron wave…
Quantun spin transport through a short DNA chain connected to ferromagnetic electrodes has been investigated by the transfer matrix method. We describe the system by a tight-binding model where the parameters are extracted from the…
We have investigated the diffusion and structure of TIP4P/2005 water confined in carbon nanotubes subjected to external electric fields. A wide range of diameters has been used to show a highly size-dependent behavior of the water…
We investigate quantum transport characteristics of a ladder model, which effectively mimics the topology of a double-stranded DNA molecule. We consider the interaction of tunneling charges with a selected internal vibrational degree of…
There are two approaches to describing DNA-ions interactions. The physical approach is an analysis of electrostatic interactions between ions and charges on the DNA molecule. The coordination chemistry approach is a search for modes of…
Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that…
The absorption of ultraviolet light creates excitations in DNA, which subsequently start moving in the helix. Their fate is important for an understanding of photo damage, and is determined by the interplay of electronic couplings between…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
Electrostatic interaction is the driving force for the encapsulation by virus coat proteins of nanoparticles such as quantum dots, gold particles and magnetic beads for, e.g., imaging and therapeutic purposes. In recent experimental work,…
Nanoscale confinement of molecules in a fluid can result in enhanced viscosity, local fluidic order, or collective motion. Confinement also affects ion transport and/or the rate and equilibrium concentration in a chemical reaction, all of…
Magnetic resonance spectroscopy of single biomolecules under near-physiological conditions may substantially advance understanding of biological function, yet remains very challenging. Here we use nitrogen-vacancy centers in diamonds to…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
We study migration of DNA molecules through a microchannel with a series of electric traps controlled by an ac electric field. We describe the motion of DNA based on Brownian dynamics simulations of a beads-spring chain. Our simulation…
We present a first-principle study of the electronic and conduction properties of a few classes of nanowires constituted of guanine (G) molecules, self-assembled in different geometries. We first analyze the effect of the vertical…
Previous theoretical studies have shown that measuring the transverse current across DNA strands while they translocate through a nanopore or channel may provide a statistically distinguishable signature of the DNA bases, and may thus allow…
By confining water in nanopores, so narrow that the liquid cannot freeze, it is possible to explore its properties well below its homogeneous nucleation temperature TH ~ 235 K. In particular, the dynamical parameters of water can be…
The classical electrostatic interaction between DNA molecules in water in the presence of counterions is reconsidered and we propose it is governed by a modified Poisson-Boltzmann equation. Quantum fluctuations are then studied and shown to…
The zero-temperature magnetic field-dependent conductance of electrons through a one-dimensional non-interacting tight-binding chain with an interacting {\it side} dot is reviewed and analized further. When the number of electrons in the…
Recent years have seen a surge of interest in nanopores because such structures show a strong potential for characterizing nanoparticles, proteins, DNA, and even single molecules. These systems have been extensively studied in experiment as…