Related papers: Characterizing the Interaction Between DNA and Gel…
We present Monte-Carlo (MC) simulations of the stretching of a single 30 nm chromatin fiber. The model approximates the DNA by a flexible polymer chain with Debye-H\"uckel electrostatics and uses a two-angle zig-zag model for the geometry…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
The stoichiometric binding constants of Nickel(II), Cobalt(II), Manganese(II), Silver(I), Zinc(II) ions with DNA, from Spirulina platensis were determined from their binding isotherms by equilibrium dialysis and atomic absorption…
Metropolis Monte Carlo simulation is used to investigate the elasticity of torsionally stressed double-stranded DNA, in which twist and supercoiling are incorporated as a natural result of base-stacking interaction and backbone bending…
The quite recent technological rise in molecular biology allowed single molecule manipulation experiments, where molecule stretching plays a primary role. In order to understand the experimental data, it is felt the urge of some physical…
The results obtained using my computing program are consistent with the values obtained twenty years ago. It also makes me believe that how to obtain particle size information using the Light Scattering technique needs to be reconsidered.…
The dynamics of a loop in DNA molecules at the denaturation transition is studied by scaling arguments and numerical simulations. The autocorrelation function of the state of complementary bases (either closed or open) is calculated. The…
We present a detailed study of the gain length in an active medium obtained by doping of DNA strands with DCM dye molecules. The superior thermal stability of the composite and its low quenching, permits to obtain optical gain coefficient…
Glasses behave as solids on experimental time scales due to their slow relaxation. Growing dynamic length scales due to cooperative motion of particles are believed to be central to this slow response. For quiescent glasses, however, the…
Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity.…
In this letter, we study the structure-transport property relationships of small ligand intercalated DNA molecules using a multiscale modelling approach where extensive ab-initio calculations are performed on numerous MD-simulated…
We present micro-rheological measurments of the drag force on colloids pulled through a solution of lambda-DNA (used here as a monodisperse model polymer) with an optical tweezer. The experiments show a violation of the Stokes-Einstein…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
Lipid structures exhibit complex and highly dynamic lateral structure; and changes in lipid density and fluidity are believed to play an essential role in membrane targeting and function. The dynamic structure of liquids on the molecular…
The microscopic deformation mechanism of charged colloidal glasses with extended-range interactions under shear is investigated by in-situ small-angle neutron scattering, and a dynamically correlated region (DCR) is identified. This…
Using Langevin dynamics simulations, we study elastic response of single semiflexible polyelectrolytes to an external force pulling on the chain ends, to mimic the stretching of DNA molecules by optical tweezers. The linear chains are…
Recent studies have shown that bacterial nucleoid-associated proteins (NAPs) can bind to DNA and result in altered structural organization and bridging interactions. Under spontaneous self-assembly, NAPs may form anisotropic amyloid fibers,…
We present a new scheme for performing optical spectroscopy on single molecules. A glass capillary with a diameter of 600 nm filled with an organic crystal tightly guides the excitation light and provides a maximum spontaneous emission…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which find a sharp conductance jump for a very short (4.5 %) stretching length, we carried out…