Related papers: Nanoscopic Characterization of DNA within Hydropho…

Although carbon nanotubes are potential candidates for DNA encapsulation and subsequent delivery of biological payloads to living cells, the thermodynamical spontaneity of DNA encapsulation under physiological conditions is still a matter…

It is well known that water inside hydrophobic nano-channels diffuses faster than bulk water. Recent theoretical studies have shown that this enhancement depends on the size of the hydrophobic nanochannels. However, experimental evidence of…

We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…

When water molecules are confined to nanoscale spacings, such as in the nanometer size pores of activated carbon fiber (ACF), their freezing point gets suppressed down to very low temperatures ($\sim$ 150 K), leading to a metastable liquid…

We use molecular dynamics simulations to study the diffusion of water inside deformed carbon nanotubes, with different degrees of eccentricity at 300K. We found a water structural transition between tubular-like to single-file for the (7,7)…

Water, when confined at the nanoscale acquires extraordinary transport properties. And yet there is no direct experimental evidence of these properties at nanoscale resolution. Here, by using 2D NMR diffusion-relaxation (D-T2) and…

Experiments and computer simulations demonstrate that water spontaneously fills the hydrophobic cavity of a carbon nanotube. To gain a quantitative thermody- namic understanding of this phenomenon, we use the recently developed Two Phase…

Bacteriophages, phages for short, are viruses of bacteria. The majority of phages contain a double-stranded DNA genome packaged in a capsid at a density of ~500 mg/ml. This high density requires substantial compression of the normal B form…

We report a study of the effects of pressure on the diffusivity of water molecules confined in single- wall carbon nanotubes (SWNT) with average mean pore diameter of 16 Angstroms. The measurements were carried out using high-resolution…

We have used atomistic molecular dynamics (MD) simulations to study the structure and dynamics of water molecules inside an open ended carbon nanotube placed in a bath of water molecules. The size of the nanotube allows only a single file…

We report translocation experiments on double-strand DNA through a silicon oxide nanopore. Samples containing DNA fragments with seven different lengths between 2000 to 96000 basepairs have been electrophoretically driven through a 10 nm…

We propose two-terminal devices for DNA sequencing which consist of a metallic graphene nanoribbon with zigzag edges (ZGNR) and a nanopore in its interior through which the DNA molecule is translocated. Using the nonequilibrium Green…

We consider voltage-driving DNA translocation through a nanopore in the present study. By assuming the DNA is coaxial with the cylindrical nanopore, a hydrodynamic model for determining effective force on a single DNA molecule in a nanopore…

A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…

We report spontaneous translocation of small interfering RNA (siRNA) inside carbon nanotubes (CNTs) of various diameters and chirality using all atom molecular dynamics (MD) simulations with explicit solvent. We use Umbrella sampling method…

A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm…

Encapsulation of dsDNA fragments (contour length 54 nm) by the cationic diblock copolymer poly(butadiene-b-N-methyl 4-vinyl pyridinium) [PBd-b-P4VPQ] has been studied with phase contrast, polarized light, and fluorescence microscopy, as…

Using theory and simulations, we carried out a first systematic characterization of DNA unzipping via nanopore translocation. Starting from partially unzipped states, we found three dynamical regimes depending on the applied force, f: (i)…

We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…

We compared the diffusion of water confined in armchair and zigzag carbon nanotubes for rigid and flexible water models. Using one rigid model, TIP4P/2005, and two flexible models, SPC/Fw and SPC/FH, we found that the number of the number…