Related papers: Helicase on DNA: A Phase coexistence based mechani…
Surfaces and structures capable of multiple stable configurations have attracted growing interest for on-demand shape morphing. In this work, we consider an elastic compliant plate coupled to a two-dimensional foundation comprising an array…
Evidence of a special chiral nematic phase is provided using numerical simulation and Onsager theory for systems of hard helical particles. This phase appears at the high density end of the nematic phase, when helices are well aligned, and…
The hydrogen peroxide is present in the living cell at small concentrations that increase under the action of the heavy ion beams in the process of anticancer therapy. The interactions of hydrogen peroxide with DNA, proteins and other…
Most of the anticancer drugs bind to double-stranded DNA (dsDNA) by intercalative-binding mode. Although experimental studies have become available recently, a molecular-level understanding of the interactions between the drug and dsDNA…
DNA nanotechnology allows for the realization of complex nanoarchitectures in which the spatial arrangements of different constituents and most functions can be enabled by DNA. When optically active components are integrated in such…
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…
Molecular recognition between two double stranded (ds) DNA with homologous sequences may not seem compatible with the B-DNA structure because the sequence information is hidden when it is used for joining the two strands. Nevertheless, it…
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…
The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic…
It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with…
Under constant applied force, the separation of double-stranded DNA into two single strands is known to proceed through a series of pauses and jumps. Given experimental traces of constant-force unzipping, we present a method whereby the…
The geometrical coupling between strain and twist in double helices is investigated. Overwinding, where strain leads to further winding, is shown to be a universal property for helices, which are stretched along their longitudinal axis when…
The chromatin fiber is a complex of DNA and specific proteins called histones forming the first structural level of organization of eukaryotic chromosomes. In tightly organized chromatin fibers, the short segments of naked DNA linking the…
DEAD-box RNA helicases (DDXs) are essential RNA metabolism regulators that typically unwind dsRNA in an ATP-dependent manner. However, recent studies show some DDXs can also unwind dsRNA without ATP, a phenomenon that remains poorly…
The structure of DNA double helix is stabilized by metal counterions condensed to a diffuse layer around the macromolecule. The dynamics of counterions in real conditions is governed by the electric fields from DNA and other biological…
Switchable elements are key components of dynamic technological and biological systems, enabling reversible transitions between well-defined states. Here, we present a DNA origami-based, mechanically bistable snap-through mechanism that can…
We introduce a simple model for DNA-cationic-lipid complexes in which galleries between planar bilayer lipid lamellae contain DNA 2D smectic lattices that couple orientationally and positionally to lattices in neighboring galleries. We…
We analyze the formation of localized structures in cavity-enhanced second-harmonic generation. We focus on the phase-matched limit, and consider that fundamental and generated waves have opposite sign of group velocity dispersion. We show…
Self-assembly is traditionally described as the process through which an initially disordered system relaxes towards an equilibrium ordered phase only driven by local interactions between its building blocks. However, This definition is too…
The force induced unzipping transition of a double stranded DNA is considered from a purely thermodynamic point of view. This analysis provides us with a set of relations that can be used to test microscopic theories and experiments. The…