Related papers: Conformational impact on deformation of DNA TATA-b…
We study the effects of higher-order deformations $\beta_\lambda$ ($\lambda=4,6,8,$ and $10$) on the ground state properties of superheavy nuclei (SHN) near the doubly magic deformed nucleus $^{270}$Hs by using the…
Many bacteria use rotating helical flagellar filaments to swim. The filaments undergo polymorphic transformations in which the helical pitch and radius change abruptly. These transformations arise in response to mechanical loading, changes…
Crystals form regular and robust structures that under extreme conditions can melt and recrystallize into different arrangements in a process that is called crystal metamorphism. While crystals exist due to the breaking of a continuous…
SAXS studies of four 60 base-pair DNA duplexes with sequences closely related to part of the GAGE6 (G-antigen 6) promoter have been performed to study the role of DNA conformations in solution and their potential relationship to DNA-protein…
Confined thin structures are ubiquitous in nature. Spatial and length constraints have led to a number of novel packing strategies at both the micro-scale, as when DNA packages inside a capsid, and the macro-scale, seen in plant root…
The single-particle spectrum of deformed shell-model states in nuclei, is shown to exhibit a supersymmetric pattern. The latter involves deformed pseudospin doublets and intruder levels. The underlying supersymmetry is associated with the…
We investigate quantum transport characteristics of a ladder model, which effectively mimics the topology of a double-stranded DNA molecule. We consider the interaction of tunneling charges with a selected internal vibrational degree of…
Double-stranded DNA may contain mismatched base pairs beyond the Watson-Crick pairs guanine-cytosine and adenine-thymine. Such mismatches bear adverse consequences for human health. We utilize molecular dynamics and metadynamics computer…
Soft colloids allow to explore high density states well beyond random close packing. An important open question is whether softness controls the dynamics under these dense conditions. While experimental works reported conflicting results,…
The phase diagram of a water solution of DNA and oppositely charged spherical macroions is studied. DNA winds around spheres to form beads-on-a-string complexes resembling the chromatin 10 nm fiber. At small enough concentration of spheres…
A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers…
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…
Recent experiments [J. van Mameren et al. PNAS 106, 18231 (2009)] provide a detailed spatial picture of overstretched DNA, showing that under certain conditions the two strands of the double helix separate at about 65 pN. It was proposed…
Molecular topology of polymers plays a key role in determining their physical properties. We studied herein the topological effects on the static and dynamic properties of a 2D catenated network of DNA rings called a kinetoplast.…
We study equilibrium shapes and shape transformations of a confined semiflexible chain inside a soft lipid tubule using simulations and continuum theories. The deformed tubular shapes and chain conformations depend on the relative magnitude…
Inspired by a recently proposed Duality and Conformal invariant modification of Maxwell theory (ModMax), we construct a one-parameter family of two-dimensional dynamical system in classical mechanics that share many features with the ModMax…
Long length-scale structural deformations of DNA play a central role in many biological processes including gene expression. The elastic rod model, which uses a continuum approximation, has emerged as a viable tool to model deformations of…
The mechanical properties of DNA are typically described by elastic theories with purely local couplings (on-site models). We discuss and analyze coarse-grained (oxDNA) and all-atom simulations, which indicate that in DNA distal sites are…
The combination of self-assembly and electronic properties as well as its true nanoscale dimensions make DNA a promising candidate for a building block of single molecule electronics. We argue that the intrinsic double helix conformation of…
Using Langevin Dynamic simulations, we study effects of the shear force on the rupture of a double stranded DNA molecule. The model studied here contains two single diblock copolymers interacting with each other. The elastic constants of…