Related papers: An intermediate phase in DNA melting
Upon the addition of multivalent cations, a giant DNA chain exhibits a large discrete transition from an elongated coil into a folded compact state. We performed single-chain observation of long DNAs in the presence of a tetravalent cation…
An important step in transcription of a DNA base sequence to a protein is the initiation from the exact starting point, called promoter region. We propose a physical mechanism for identification of the promoter region, which relies on a new…
This contribution will survey recent progress toward an understanding of diverse pairing phenomena in dilute nuclear matter at small and moderate isospin asymmetry, with results of potential relevance to supernova envelopes and…
The phase transition near 40~$^{\circ }$C of both as-grown thin epitaxial MnAs films prepared by molecular beam epitaxy on GaAs(001) and nanometer-scale disks fabricated from the same films is studied. The disks are found to exhibit a…
The recombination of two split Bose-Einstein condensates on an atom chip is shown to result in heating which depends on the relative phase of the two condensates. This heating reduces the number of condensate atoms between 10 and 40% and…
Kinetic energy driven phase transitions in Bose superfluids occur at low values of the repulsion when the values of the next-to-nearest and next-to-next-to-nearest hopping term attain certain critical values, resulting in alterations in the…
Understanding the motion of particles with ligand-receptors is important for biomedical applications and material design. Yet, even among a single design, the prototypical DNA-coated colloids, seemingly similar micrometric particles hop or…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
The Poland-Scheraga model for DNA denaturation, besides playing a central role in applications, has been widely studied in the physical and mathematical literature over the past decades. More recently a natural generalization has been…
We propose that supercoiling energizes double-stranded DNA (dsDNA) so as to facilitate thermal fluctuations to an unzipped state. We support this with a model of two elastic rods coupled via forces that represent base pair interactions.…
A unifying theory of the denaturation transition of DNA, driven by temperature T or induced by an external mechanical torque Gamma is presented. Our model couples the hydrogen-bond opening and the untwisting of the helicoidal molecular…
We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the…
Folding of RNA is subject to a competition between entropy, relevant at high temperatures, and the random, or random looking, sequence, determining the low- temperature phase. It is known from numerical simulations that for random as well…
An 1d model with time-dependent random hopping is proposed to describe charge transport in DNA. It admits to investigate both diffusion of electrons and their tunneling between different sites in DNA. The tunneling appears to be strongly…
The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second…
The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of the unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that…
The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA…
Test experiments of hybridization in DNA microarrays show systematic deviations from the equilibrium isotherms. We argue that these deviations are due to the presence of a partially hybridized long-lived state, which we include in a kinetic…