Related papers: Twist-diameter coupling drives DNA twist changes b…
Strongly correlated electrostatics of DNA systems has drawn the interest of many groups, especially the condensation and overcharging of DNA by multivalent counterions. By adding counterions of different valencies and shapes, one can…
The interplay between global constraints and local material properties of chain molecules is a subject of emerging interest. Studies of molecules that are intrinsically chiral, such as double-stranded DNA, is one example. Their properties…
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…
Na-ion conduction, and correlations between Na-ion conduction pathways and crystal structure have been investigated as a function of temperature in the layered battery material Na2Ni2TeO6 by impedance spectroscopy and neutron diffraction,…
Secondary structure formation of nucleic acids strongly depends on salt concentration and temperature. We develop a theory for RNA folding that correctly accounts for sequence effects, the entropic contributions associated with loop…
We propose a new strategy to improve the self-assembly properties of DNA-functionalised colloids. The problem that we address is that DNA-functionalised colloids typically crystallize in a narrow temperature window, if at all. The…
The electronic orders appearing in condensed matter systems are originating from the precise arrangement of atoms constituting the crystal as well as their nature. This teneous relationship can lead to highly different phases in condensed…
We use optical tweezers to perform stretching experiments on DNA molecules when interacting with the drugs daunomycin and ethidium bromide, which intercalate the DNA molecule. These experiments are performed in the low-force regime from…
We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are delocalized. Above a threshold torque, the bubbles of…
In living systems, DNA undergoes continuous and rhythmic mechanical remodeling through condensation, looping, and disentangling to regulate gene expression, segregate chromosomes, and guide morphogenesis. Here, we demonstrate a purely…
Friction and wear of metals are critically influenced by the microstructures of the bodies constituting the tribological contact. Understanding the microstructural evolution taking place over the lifetime of a tribological system therefore…
Graphene nanoslit pore is used for nanofluidic devices like water desalination, ion-selective channels, ionic transistors, sensing, molecular sieving, blue energy harvesting, and protein sequencing. It is a strenuous task to prepare…
Recent advances in operating and manipulating DNA have provided unique experimental possibilities in many fields of DNA research, especially in gene therapy. Researchers have deployed many techniques, experimental and theoretical, to study…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
Conformational change of a DNA molecule is frequently observed in multiple biological processes and has been modelled using a chain of strongly coupled oscillators with a nonlinear bistable potential. While the mechanism and properties of…
The local mechanical properties of DNA are believed to play an important role in their biological functions and DNA-based nanomechanical devices. Using a simple sphere-tip compression system, the local radial mechanical properties of DNA…
This paper introduces the use of cable dynamics models as a means to explore the mechanics of DNA on long-length scales. It is on these length scales that DNA forms twisted and curved three-dimensional shapes known as supercoils and loops.…
The recently proposed compressed backbone theory suggested that the intrinsic curvature in DNA can result from a geometric mismatch between the specific backbone length and optimal base stacking orientations. It predicted that the curvature…
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…
Here we present a systematic study of supercoil formation in DNA minicircles under varying linking number by using molecular dynamics simulations of a two-bead coarse-grained model. Our model is designed with the purpose of simulating long…