Related papers: Melting behavior and different bound states in thr…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
When double stranded DNA is turned in experiments it undergoes a transition. We use an interacting self-avoiding walk on a three-dimensional fcc lattice weighted by writhe to relate to these experiments and treat this problem via…
The paper deals with the two-state (opening-closing of base pairs) model used to describe the fluctuation dynamics of a single bubble formation. We present an exact solution for the discrete and finite size version of the model that…
Heat-induced mobility of nucleosomes along DNA is an experimentally well-studied phenomenon. A recent experiment shows that the repositioning is modified in the presence of minor-groove binding DNA ligands. We present here a stochastic…
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…
The Poland-Scheraga model is a celebrated model for the denaturation transition of DNA, which has been widely used in the bio-physical literature to study, and investigated by mathematicians. In the original model, only opposite bases of…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
We separate double stranded lambda phage DNA by applying a fixed force at a constant temperature ranging from 15C to 50C, and measure the minimum force required to separate the two strands, providing the first experimental determination of…
The field of few-body physics has originally been motivated by understanding nuclear matter. New model systems to experimentally explore few-body quantum systems can now be realized in ultracold gases with tunable interactions. Albeit the…
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with…
The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for…
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…
We study the recombination process of three atoms scattering into an atom and diatomic molecule in heteronuclear mixtures of ultracold atomic gases with large and positive interspecies scattering length at finite temperature. We calculate…
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,…
Efimov trimers are exotic three-body quantum states that emerge from the different types of three-body continua in the vicinity of two-atom Feshbach resonances. In particular, as the strength of the interaction is decreased to a critical…
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…
We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…
This paper presents a numerical study of the dynamics of DNA double helix breakage under the influence of external forces using the Peyrard-Bishop-Dauxois (PBD) model. The PBD model represents DNA as a chain of nonlinearly coupled…
We investigate the kinetics of the DNA melting transition using modified versions of the Peyrard-Dauxois-Bishop and Poland-Scheraga models that include long and short range interactions. Using Brownian dynamics and Monte Carlo simulations,…
The stabilization of Cooper pairs of bound electrons in the background of a Fermi sea is the origin of superconductivity and the paradigmatic example of the striking influence of many-body physics on few-body properties. In the…