Related papers: Rigidity of Melting DNA
Stability is an important and fruitful avenue of research for liquid crystal elastomers. At constant temperature, upon stretching, the homogeneous state of a nematic body becomes unstable, and alternating shear stripes develop at very low…
We study the unexpected high flexibility of short dsDNA which recently has been reported by a number of experiments. Via the Langevin dynamics simulation of our Breathing DNA model, first we observe the formation of bubbles within the…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…
DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and…
The shapes of epithelial tissues result from a complex interplay of contractile forces in the cytoskeleta of the cells in the tissue, and adhesion forces between them. A host of discrete, cell-based models describe these forces by assigning…
A simple model of DNA based on two interacting polymers has been used to study the unzipping of a double stranded DNA subjected to a periodic force. We propose a dynamical transition, where without changing the physiological condition, it…
A dynamical mean-field theory is developed to analyze stochastic single-cell dynamics of gene expression. By explicitly taking account of nonequilibrium and nonadiabatic features of the DNA state fluctuation, two-time correlation functions…
The elastocapillary instability of a flexible plate plunged in a liquid bath is analysed theoretically. We show that the plate can bend due to two separate destabilizing mechanisms, when the liquid is partially wetting the solid. For…
The elastic response is studied of a single flexible chain grafted on a rigid plane and an ensemble of non-interacting tethered chains. It is demonstrated that the entropic theory of rubber elasticity leads to conclusions that disagree with…
Using Monte Carlo simulations, we study the hysteresis in unzipping of a double stranded block copolymer DNA with $-A_n B_n-$ repeat units. Here $A$ and $B$ represent two different types of base pairs having two- and three-bonds,…
DNA inside the cellular environment works under a confined space. An intense research of the transcription and replication of DNA in the confined state is structurally significant to command the self assembly of DNA in a chamber or channel.…
The mechanics of complex soft matter often cannot be understood in the classical physical frame of flexible polymers or rigid rods. The underlying constituents are semiflexible polymers, whose finite bending stiffness ($\kappa$) leads to…
Based on the relativistic mean field (RMF) model with Thomas-Fermi approximation, we investigate the elastic properties of neutron star matter. The elastic constants are estimated by introducing deformations on the nuclear pasta structures…
Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorportated nucleotide. The replication fidelity is shown to increase…
The complementary strands of DNA molecules can be separated when stretched apart by a force; the unzipping signal is correlated to the base content of the sequence but is affected by thermal and instrumental noise. We consider here the…
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…
What characterises a solid is its way to respond to external stresses. Ordered solids, such crystals, display an elastic regime followed by a plastic one, both well understood microscopically in terms of lattice distortion and dislocations.…
We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder…
Solid-state nanopore DNA sequencers present mechanical and chemical stability, reusability, and large-scale integrability. However, their development is hindered by the absence of a protein-free mechanism for controlling DNA translocation,…
Unlike most synthetic materials, biological materials often stiffen as they are deformed. This nonlinear elastic response, critical for the physiological function of some tissues, has been documented since at least the 19th century, but the…