Related papers: Dynamical modelling of molecular constructions and…
Recent single-molecule pulling experiments have shown how it is possible to manipulate RNA molecules using optical tweezers force microscopy. We investigate a minimal model for the experimental setup which includes a RNA molecule connected…
Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different…
We study the basepairing dynamics of DNA with repetitive sequences where local strand slippage can create, annihilate, and move bulge loops. Using an explicit theoretical model, we find a rich dynamical behavior as a function of an applied…
A unified model is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle $\phi$), bending…
We unzip DNA molecules using optical tweezers and determine the sizes of the cooperatively unzipping and zipping regions separating consecutive metastable intermediates along the unzipping pathway. Sizes are found to be distributed…
We predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible…
This work introduces a methodology for the statistical mechanical analysis of polymeric chains under tension controlled by optical or magnetic tweezers at thermal equilibrium with an embedding fluid medium. The response of single bonds…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
Molecular dynamics simulations are often used to provide feedback in the design workflow of DNA nanostructures. However, even with coarse-grained models, convergence of distributions from unbiased simulation is slow, limiting applications…
Recent experiments on unzipping of RNA helix-loop structures by force have shown that about 40-base molecules can undergo kinetic transitions between two well-defined `open' and `closed' states, on a timescale = 1 sec [Liphardt et al.,…
In this work, we show that by varying the experimental conditions, the driving amplitude, a dynamic force microscope allows DNA properties to be selectively imaged. The substrate on which the DNA is fixed is a silica surface grafted with…
Experimental studies of the thermal denaturation of DNA yield a strong indication that the transition is first order. This transition has been theoretically studied since the early sixties, mostly within an approach in which the microscopic…
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 study by using Monte Carlo simulations the hysteresis in unzipping and rezipping of a double stranded DNA (dsDNA) by pulling its strands in opposite directions in the fixed force ensemble. The force is increased, at a constant rate from…
Recent experiments showed that multiple copies of the molecular machine RNA polymerase (RNAP) can efficiently synthesize mRNA collectively in the active state of the promoter. However, environmentally-induced promoter repression results in…
The cations, in form of salt, present in the solution containing DNA play a crucial role in the opening of two strands of DNA. We use a simple non linear model and investigate the role of these cations on the mechanical unzipping of DNA.…
Many proteins interact with and deform double-stranded DNA in cells. Single-molecule experiments have studied the elasticity of DNA with helix-deforming proteins, including proteins that bend DNA. These experiments increase the need for…
Collective coordinate and direct numerical integration methods are applied to the analysis of a one-dimensional DNA model. A modification of the coupling constant in an extended region is found to be less selective towards the breather it…
We consider an elastic rod model for twisted DNA in the plectonemic regime. The molecule is treated as an impenetrable tube with an effective, adjustable radius. The model is solved analytically and we derive formulas for the contact…