Related papers: Reparametrizing loop entropy weights: Effect on DN…
We present a computational method to evaluate the end-to-end and the contour length distribution functions of short DNA molecules described by a mesoscopic Hamiltonian. The method generates a large statistical ensemble of possible…
Despite numerous attempts, the understanding of the thermal denaturation of DNA is still a challenge due to the lack of structural data at the transition since standard experimental approaches to DNA melting are made in solution and do not…
Zero mode waveguide technology of next generation sequencing demonstrated sequence-dependence of the enzymatic reaction, incorporating a base into the genomic DNA. We show that these experimental results indicate existence of a previously…
The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they…
The free energy of looping DNA by proteins and protein complexes determines to what extent distal DNA sites can affect each other. We inferred its in vivo value through a combined computational-experimental approach for different lengths of…
The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in…
In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regulatory proteins depends on such DNA looping interactions. We…
Protein-DNA complexes with loops play a fundamental role in a wide variety of cellular processes, ranging from the regulation of DNA transcription to telomere maintenance. As ubiquitous as they are, their precise in vivo properties and…
We derive the single molecule equation of state (force-extension relation) for DNA molecules bearing sliding loops and deflection defects. Analytical results are obtained in the large force limit by employing an analogy with instantons in…
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…
We study the melting of a domain wall in free-fermion chains, where the periodic variation of the hopping amplitudes gives rise to a band structure. It is shown that the entanglement grows logarithmically in time, and the prefactor is…
A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time dependent paths contributing to the partition function. The…
The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this…
Grafting linkers with open ends of complementary single-stranded DNA makes a flexible tool to tune interactions between colloids,which facilitates the design of complex self-assembly structures. Recently, it has been proposed to coat…
DNA inside the cellular environment works under a confined space. An intense research of the transcription and replication of DNA in the confined state is structurally significant to command the self assembly of DNA in a chamber or channel.…
By extending the classical Peyrard-Bishop model, we are able to obtain a fully analytical description for the mechanical resistance of DNA under stretching at variable values of temperature, number of base pairs and intrachains and…
We show the existence of a high interrelation between the different loops that may appear in a DNA segment. Conformational changes in a chain segment caused by the formation of a particular loop may either promote or prevent the appearance…
In this work, building on state-of-the-art quantum Monte Carlo simulations, we perform systematic finite-size scaling of both entanglement and participation entropies for long-range Heisenberg chain with unfrustrated power-law decaying…
Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of…
The distance distribution between complementary base pairs of the two strands of a DNA molecule is studied near the melting transition. Scaling arguments are presented for a generalized Poland-Scheraga type model which includes…