Related papers: Base-pair mismatch can destabilize small DNA loops…
Understanding of the precise mechanisms of high-temperature superconductivity is elusive. In particular, in order to solve the puzzle of the pairing mechanism, it is important to understand the detailed nature of the excitations at energies…
We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…
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…
One of the major functions of RecA protein in the cell is to bind single-stranded DNA exposed upon damage, thereby triggering the SOS repair response.We present fluorescence anisotropy measurements at the binding onset, showing enhanced DNA…
Gel electrophoresis allows to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots being more compact, drift faster than simpler knots. Recent experiments have shown that…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can…
The complex mechanisms governing charge migration in DNA oligomers reflect the rich structural and electronic properties of the molecule of life. Controlling the mechanical stability of DNA nanowires in charge transport experiments is a…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
While Kramers' rates have been studied for almost a century, the transition path time between states has only recently received attention. Transition paths between different energy levels are expected to be indistinguishable in shape and…
DNA strand displacement, where a single-stranded nucleic acid invades a DNA duplex, is pervasive in genomic processes and DNA engineering applications. The kinetics of strand displacement have been studied in bulk; however, the kinetics of…
The purpose of this work is to extend the Geant4-DNA Monte Carlo toolkit to include electron interactions with the four DNA bases using a set of cross sections recently implemented in Geant-DNA CPA100 models and available for liquid water.…
Polymer composites are ideal candidates for next generation biomimetic soft materials because of their exquisite bottom-up designability. However, the richness of behaviours comes at a price: the need for precise and extensive…
When pulled along its axis, double-stranded DNA elongates abruptly at a force of about 65 pN. Two physical pictures have been developed to describe this overstretched state. The first proposes that strong forces induce a phase transition to…
In the demanding biosensing environment, improving selection efficiency strategies has become an issue of great significance. DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, are representative of the…
Histone octamers show a heat-induced mobility along DNA. Recent theoretical studies have established two mechanisms that are qualitatively and quantitatively compatible with in vitro experiments on nucleosome sliding: Octamer repositiong…
We study nuclear spin dynamics in a quantum dot close to the conditions of electron spin resonance. We show that at small frequency mismatch the nuclear field detunes the resonance. Remarkably, at larger frequency mismatch its effect is…
Experiments have evidenced proton pairing in Y-doped BaZrO3. However, the nature of proton pairing and its impact on conduction remain insufficiently understood theoretically. Here, through quantitative computational analysis of…
We present a systematic Density Functional Theory (DFT) study of geometries and energies of the nucleic acid DNA bases (guanine, adenine, cytosine and thymine) and 30 different DNA base-pairs. We use a recently developed linear-scaling DFT…
Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…