Related papers: Reversible B/A Transitions in Single DNA Molecule …
We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are…
The behavior of liquid water under an electric field is a crucial phenomenon in science and engineering. However, its detailed description at a microscopic level is difficult to achieve experimentally. Here we report on the first ab initio…
Water is an associated liquid in which the main intermolecular interaction is the hydrogen bond (HB) which is limited to four per atom, independently of the number of neighbours. We have considered a hydrogen bond net superposed on Bernal's…
Using an activation mechanism reproducing facilitation, a dynamic phase transition triggered by a few active molecules was recently found in a supercooled model liquid. Prompted by this finding we investigate the presence of a similar…
DNA melting and hybridization is a fundamental biological process as well as a crucial step in many modern biotechnology applications. DNA confined on surfaces exhibits different behavior from that in free solutions. The system of…
We study a complex formation between the DNA and cationic amphiphilic molecules. As the amphiphile is added to the solution containing DNA, a cooperative binding of surfactants to the DNA molecules is found. This binding transition occurs…
The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double-helix is made of two interacting bead-spring freely rotating strands, with a…
Biomolecules couple to their aqueous environment through a variety of noncovalent interactions. Local structures at the surface of DNA and RNA are frequently determined by hydrogen bonds with water molecules, complemented by non-specific…
Polymorphism, the phenomenon that a species can exist in many discrete forms, is common in nature, such as hair colors in an animal species, flower colors in a tree species, and blood types in humans, etc. In materials science, it refers to…
RNA's diversity of structures and functions impacts all life forms since primordia. We use calorimetric force spectroscopy to investigate RNA folding landscapes in previously unexplored low-temperature conditions. We find that Watson-Crick…
The existence of water dimers in equilibrium water vapor at room temperature and their anomalous properties revealed by recent studies suggest the benchmark role of water dimer in both experiment and theory. However, there has been a…
Water molecules on lipid membrane surfaces are known to contribute to membrane stability by connecting lipid molecules and acting as a water bridge. Although the number of water molecules near the membrane fluctuates dynamically, the…
Digital information can be encoded in the building-block sequence of macromolecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive. In…
We study the structural transition from `B' form of DNA to 'A' form of DNA using group theoretic methods. The transition is not of the order-disorder type and hence to construct a Landau kind of theory for the transition we define a higher…
Previous studies of the structure of liquid water under pressure performed by neutron diffraction, allowed us to establish two structural limits in liquid water. These two limits are closely connected to the two known forms of amorphous ice…
The experimental conditions by which electromagnetic signals (EMS) of low frequency can be emitted by diluted aqueous solutions of some bacterial and viral DNAs are described. That the recorded EMS and nanostructures induced in water carry…
We investigate the dynamics of DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions (2D) to study how the translocation dynamics depend on the details of the DNA sequences.…
The short-term transient falling dynamics of a dripping water drop in quiescent air has been investigated through both simulation and experiment. The focus is on the short term behavior and the time range considered covers about eight…
DNA nanocompartment is a typical DNA-based machine whose function is dependent of molecular collective effect. Fundamental properties of the device have been addressed via electrochemical analysis, fluorescent microscopy, and atomic force…
We report here a molecular dynamics simulation study on water and aqueous LiCl solutions confined in 1.6 nm cylindrical pores of silica to investigate a dynamical cross-over, observed earlier experimentally, wherein LiCl slows down confined…