Related papers: Discontinuities at the DNA supercoiling transition
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…
Cells often exhibit different and stable phenotypes from the same DNA sequence. Robustness and plasticity of such cellular states are controlled by diverse transcriptional and epigenetic mechanisms, among them the modification of…
DNA nanotubes are tubular structures composed of DNA crossover molecules. We present a bottom up approach for construction and characterization of these structures. Various possible topologies of nanotubes are constructed such as 6-helix,…
We use Monte-Carlo simulations to study the effect of variable rigidity on plectoneme formation and localization in supercoiled dsDNA. We show that the presence of soft sequences increases the number of plectoneme branches and that the…
Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an…
In recent years, significant progress in understanding the properties of supercoiled DNA has been obtained due to nanotechniques that made stretching and twisting of single molecules possible. Quantitative interpretation of such experiments…
The emergence of biochemical activities in a protein seem to commence with the onset of atomic mean-square displacements along the protein lattice. The ensuing protein dynamical transition has been discussed extensively in the literature,…
A theory is presented of the longitudinal dispersion of DNA under equilibrium confined in a nanochannel. Orientational fluctuations of the DNA chain build up to give rise to substantial fluctuations of the coil in the longitudinal direction…
We here examine the nonlinear dynamics of artificial homogeneous DNA chain relying on the plain-base rotator model. It is shown that such dynamics can exhibit kink and antikink solitons of sine-Gordon type. In that respect we propose…
Because of the double-helical structure of DNA, in which two strands of complementary nucleotides intertwine around each other, a covalently closed DNA molecule with no interruptions in either strand can be viewed as two interlocked…
The complex mechanisms governing charge migration in DNA oligomers reflect the rich structural and electronic properties of the molecule of life. Controlling the mechanical stability of DNA nanowires in charge transport experiments is a…
Two significant consequences of quantum fluctuations are entanglement and criticality. Entangled states may not be critical but a critical state shows signatures of universality in entanglement. A surprising result found here is that the…
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…
We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…
The nature of the quantum valence transition is studied in the one-dimensional periodic Anderson model with Coulomb repulsion between f and conduction electrons by the density-matrix renormalization group method. It is found that the…
We study the nonlinear dynamics of a deformed Deoxyribonucleic acid (DNA) molecular chain which is governed by a perturbed sine-Gordon equation coupled with a linear wave equation representing the lattice deformation. The DNA chain…
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…
We investigate the melting transition of non-supercoiled circular DNA of different lengths, employing Brownian dynamics simulation. In the absence of supercoiling, we find that melting of circular DNA is driven by a large bubble, which…
Quasi-one-dimensional superconductors or nanowires exhibit a transition into a nonsuperconducting regime, as their diameter shrinks. We present measurements on ultrashort nanowires (~40-190 nm long) in the vicinity of this quantum…
The relaxation of twist in elastic filaments often drives conformational changes. We explore this paradigm using all-atom computations and report the formation of novel supercoiled shapes in individual carbon nanotubes (CNTs). Decreasing…