Related papers: Excluded Volume Effect in Unzipping DNA with a For…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
Mechanical properties of DNA, in particular their stretch dependent extension and their loop formation characteristics, have been recognized as an effective probe for understanding the possible biochemical role played by them in a living…
Optical tweezers are employed to measure the forces of interaction within a single pair of DNA-grafted colloids in dependence of the molecular weight of the DNA-chains, and the concentration and valence of the surrounding ionic medium. The…
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…
Near the melting transition the bending elastic constant, $\kappa$, an emergent property of double-stranded DNA (dsDNA), is shown not to follow the rod-like scaling for small length $N$. The reduction in $\kappa$ with temperature is…
We propose a formalism for deriving force-elongation and elongation-force relations for flexible chain molecules from analytical expressions for their radial distribution function, which provides insight into the factors controlling the…
We construct a theoretical model for the dynamics of a microscale colloidal particle, modeled as an interval, moving horizontally on a DNA-coated surface, modelled as a line coated with springs that can stick to the interval. Averaging over…
We investigate the thermodynamics and kinetics of DNA hairpins that fold/unfold under the action of applied mechanical force. We introduce the concept of the molecular free energy landscape and derive simplified expressions for the force…
The stability of DNA molecule during the encapsulation process is a topic of intense research. We study the thermal stability of the double-stranded DNA molecule of different lengths in a confined space. Using a statistical model we…
We used the Transfer-Integral method to compute, with an uncertainty smaller than 5%, the six fundamental characteristic exponents of two dynamical models for DNA thermal denaturation and investigate the validity of the scaling laws. Doubts…
The conjunction of insights from structural biology, solution biochemistry, genetics and single molecule biophysics has provided a renewed impetus for the construction of quantitative models of biological processes. One area that has been a…
We study the role of cations on the stability of double stranded DNA (dsDNA) molecules.It is known that the two strands of double stranded DNA(dsDNA) have negative charge due to phosphate group. Cations in the form of salt in the solution,…
We discuss possible mechanisms that may impact the order of the transition between denaturated and bound DNA states and lead to changes in the scaling laws that govern conformational properties of DNA strands. To this end, we re-consider…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
We investigate the excluded volume effects in good solvents for the isolated comb polymers having $\nu_{0}=1/4$. In particular, we investigate the change of the size exponent, $\nu$, defined by $\langle s_{N}^{2}\rangle\propto N^{2\nu}$,…
We consider the unbinding of a directed polymer in a random media from a wall in $d=1+1$ dimensions and a simple one-dimensional model for DNA unzipping. Using the replica trick we show that the restricted partition functions of these…
The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general physical principle. As…
We analyze the effects of a distortion of the nuclear potential of a molecular quantum dot (QD), as well as a shift of its equilibrium position, on nonequilibrium-vibration-assisted tunneling through the QD with a single level…
We use a recently developed coarse-grained model to simulate the overstretching of duplex DNA. Overstretching at 23C occurs at 74 pN in the model, about 6-7 pN higher than the experimental value at equivalent salt conditions. Furthermore,…
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…