Related papers: Loop Dynamics in DNA Denaturation
Cells operate in part by compartmentalizing chemical reactions. For example, recent work has shown that chromatin, the material that contains the cell's genome, can auto-regulate its structure by utilizing reaction products (proteins, RNA)…
DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA "breathing") play a central role in such…
Within the framework of master equation, we study decay dynamics of an atom-molecule system strongly coupled by two photoassociation lasers. Summing over the infinite number of electromagnetic vacuum modes that are coupled to the…
The pair interaction between two stiff parallel linear DNA molecules depends not only on the distance between their axes but on their azimuthal orientation. The positional and orientational order in columnar B-DNA assemblies in solution is…
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…
The self-alignment concentrations, $c(x)$, as functions of the length, $x$, of the identically matching maximal segments in the genomes of a variety of species, typically present power-law tails extending to the largest scales, i.e., $c(x)…
A systematic study of electron or hole transfer along DNA dimers, trimers and polymers is presented with a tight-binding approach at the base-pair level, using the relevant on-site energies of the base-pairs and the hopping parameters…
We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…
X-ray photon correlation is used to probe the slow dynamics of the glass-former B2O3 across the glass transition. In the undercooled liquid phase the decay times of the measured correlation functions are consistent with visible light…
We examine the elastic model of short circular DNA. We obtain analytic expressions for configurations, elastic energy, twist and linking number of our solutions. We find the onset of the plectonemic transition. We suggest ways to use our…
The entropy loss due to the formation of one or multiple loops in circular and linear DNA chains is calculated from a scaling approach in the limit of long chain segments. The analytical results allow to obtain a fast estimate for the…
Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to…
Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups…
Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy c ln m for a…
DNA amplification is the process of replication of a specified DNA sequence \emph{in vitro} through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating…
The spin state of two magnetically inequivalent protons in contiguous atoms of a molecule becomes entangeled by the indirect spin-spin interaction (j-coupling). The degree of entanglement oscillates at the beat frequency resulting from the…
The macromolecules that encode and translate information in living systems, DNA and RNA, exhibit distinctive structural asymmetries, including homochirality or mirror image asymmetry and $3' - 5'$ directionality, that are invariant across…
Effect of bending anisotropy on a planar DNA loop, using energy minimization and neglecting entropic effects, is studied. We show that the anisotropy results in polygonal shape of the loop and increasing the anisotropy makes the edges…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe…