Related papers: DNA melting structures in the generalized Poland-S…
We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…
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…
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…
The translocation of double-stranded DNA through a solid-state nanopore may either decrease or increase the ionic current depending on the ionic concentration of the surrounding solution. Below a certain crossover ionic concentration, the…
DNA plays a special role in polymer science not just because of the highly selective recognition of complementary single DNA strands but also because bacteria can express DNA chains that are very long yet perfectly monodisperse. The latter…
Renaturation of complementary single strands of DNA is one of the important processes that requires better understanding in the view of molecular biology and biological physics. Here we develop a stochastic dynamical model on the DNA…
We study the thermal and mechanical behavior of DNA denaturation in the frame of the mesoscopic Peyrard- Bishop-Dauxois model with the inclusion of solvent interaction. By analyzing the melting transition of a homogeneous A-T sequence, we…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system…
We present a theoretical study of single-stranded DNA under stretching. Within the proposed framework, the effects of basepairing on the mechanical response of the molecule can be studied in combination with an arbitrary underlying model of…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
We consider general disordered models of pinning of directed polymers on a defect line. This class contains in particular the $(1+1)$--dimensional interface wetting model, the disordered Poland--Scheraga model of DNA denaturation and other…
Analysis of single-molecule micromanipulation experiments of DNA unzipping process shows some features of the force-distance curve, namely two consequent plateaus in the area of ${\sim}12-14pN$ dependent on nucleotide sequence structure, as…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective…
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…
DNA double-strand breaks (DSBs) represent a serious source of damage for all living things and thus there have been many quantitative studies of DSBs both in vivo and in vitro. Despite this fact, the processes that lead to their production…
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural…
The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double-helix is made of two interacting bead-spring freely rotating strands, with a…
Dynamics of the polymorphic A<->B transitions in DNA is compared for two polypurine sequences, poly(dA).poly(dT) and poly(dG).poly(dC), long known to exhibit contrasting properties in experiments. In free molecular dynamics simulations…