Related papers: Conformational impact on deformation of DNA TATA-b…
The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One solely relies on base…
The equilibrium structure of a Dinucleosome is studied using an elastic model that takes into account the force and torque balance conditions. Using the proper boundary conditions, it is found that the conformational energy of the problem…
Several recent experiments suggest that sharply bent DNA has a surprisingly high bending flexibility, but the cause of this flexibility is poorly understood. Although excitation of flexible defects can explain these results, whether such…
Blends of polymers of different topologies, such as ring and supercoiled, naturally occur in biology and often exhibit emergent viscoelastic properties coveted in industry. However, due to their complexity, along with the difficulty of…
Fabrication of DNA nanostructures primarily follows two fundamental rules. First, DNA oligonucleotides mutually combine by Watson-Crick base pairing rules between complementary base sequences. Second, the geometrical compatibility of the…
The rotating nuclei represent one of most interesting subjects for theoretical and experimental studies. They open a new dimension of nuclear landscape, namely, spin direction. Contrary to the majority of nuclear systems, their properties…
Soft matter systems are common in nature and make up nearly all the essential components necessary for life, from cells to the organelles within those cells. The ability of these soft materials to deform is crucial for the proper…
We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
Clarification of the detailed mechanisms involved in the DNA polymorphism is an important challenge for computational molecular biophysics. This paper reports about reversible A/B transitions in DNA observed in silico in a simulated…
The Kirchhoff elastic theory of thin filaments with spontaneous curvature is employed in the understanding of the onset of the kink transitions observed in short DNA rings. Dynamical analysis shows that when its actual curvature is less…
While relativistic heavy-ion collisions become an alternative way of studying nucleus structure, the accurate extraction of nucleus structure could be hampered by the uncertainty of nucleon size, and the latter has attracted people's…
Precision tests of the Standard Model and searches for beyond the Standard Model physics often require nuclear structure input. There has been a tremendous progress in the development of nuclear ab initio techniques capable of providing…
Single-molecule experiments in which force is applied to DNA or RNA molecules have enabled important discoveries of nucleic acid properties and nucleic acid-enzyme interactions. These experiments rely on a model of the polymer…
We have employed molecular dynamics simulations based on the TIP4P/2005 water model to investigate the local structural, dynamical, and dielectric properties of the two recently reported body-centered-cubic and face-centered-cubic plastic…
Very special $T\bar{J}$ deformations of a conformal field theory are irrelevant deformations that break the Lorentz symmetry but preserve the twisted Lorentz symmetry. We construct a holographic description of very special $T\bar{J}$…
DNA looping is important in DNA condensation and regulation. One method for forming a DNA loop, thought to be used by the condensing agent protamine, is bind-and-bend. In bind-and-bend, molecules bind all along the DNA, each creating a bend…
We discern hydration geometries around the sugar-phosphate-backbone of an RNA double helix at the molecular level. RNA disordering upon melting is connected with a transition from ordered water structures towards local phosphate group…
A single semiflexible polymer chain folds into a toroidal object under poor solvent conditions. In this study, we examined the morphological change in such a toroidal state as a function of the width and stiffness of the chain together with…