Melting behavior and different bound states in three-stranded DNA models

Thermal denaturation of DNA is often studied with coarse-grained models in which native sequential base pairing is mimicked by the existence of attractive interactions only between monomers at the same position along strands (Poland and Scheraga models). Within this framework, the existence of a three strand DNA bound state in conditions where a duplex DNA would be in the denaturated state was recently predicted from a study of three directed polymer models on simplified hierarchical lattices ($d>2$) and in $1+1$ dimensions. Such phenomenon which is similar to the Efimov effect in nuclear physics was named Efimov-DNA. In this paper we study the melting of the three-stranded DNA on a Sierpinski gasket of dimensions $d<2$ by assigning extra weight factors to fork openings and closings, to induce a two-strand DNA melting. In such a context we can find again the existence of the Efimov-DNA-like state but quite surprisingly we discover also the presence of a different phase, to be called a mixed state, where the strands are pair-wise bound but without three chain contacts. Whereas the Efimov DNA turns out to be a crossover near melting, the mixed phase is a thermodynamic phase.Comment: corrected file uploade

Dynamic phase transition in the conversion of B-DNA to Z-DNA

The long time dynamics of the conformational transition from B-DNA to Z-DNA is shown to undergo a dynamic phase transition. We obtained the dynamic phase diagram for the stability of the front separating B and Z. The instability in this front results in two split fronts moving with different velocities. Hence, depending on the system parameters a denatured state may develop dynamically eventhough it is thermodynamically forbidden. This resolves the current controversies on the transition mechanism of the B-DNA to Z-DNA.Comment: 5 pages, 4 figures. New version with correction of typos, new references, minor modifications in Fig 2, 3. To appear in EP

TYPE II DNA: when the interfacial energy becomes negative

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 classification of DNAs into two types, Type-I and Type-II, like superconductors, depending on the sign of the energy of the interface separating the zipped and the unzipped phases. This is determined by the energies of helical ordering and stretching over two independent length scales. The negative interfacial energy in Type II DNA leads to domains of helically ordered state separated by defect regions, or blobs, enclosed by the interfaces. The defect blobs, pinned by non-coding promoter regions, would be physically distinct from all other types of bubbles. We also show that the order of the melting transition under a force is different for Type I and Type II.Comment: 4 pages, 2 figures, Eq.(4) corrected in 4th versio

Nonequilibrium tricriticality in one dimension

We show the existence of a nonequilibrium tricritical point induced by a repulsive interaction in one dimensional asymmetric exclusion process. The tricritical point is associated with the particle-hole symmetry breaking introduced by the repulsion. The phase diagram and the crossover in the neighbourhood of the tricritical point for the shock formation at one of the boundaries are determined.Comment: 6 pages; 4 figure

When a DNA Triple helix melts: An analog of the Efimov state

The base sequences of DNA contain the genetic code and to decode it a double helical DNA has to open its base pairs. Recent studies have shown that one can use a third strand to identify the base sequences without opening the double helix but by forming a triple helix. It is predicted here that such a three chain system exhibits the unusual behaviour of the existence of a three chain bound state in the absence of any two being bound. This phenomenon is analogous to the Efimov state in three particle quantum mechanics. A scaling theory is used to justify the Efimov connection. Real space renormalization group (RG), and exact numerical calculations are used to validate the prediction of a biological Efimov effect.Comment: Replaced by the (almost) published version, except the word "curiouser

Cobalt(II) and Copper(II) based Molecular Catalysts for Hydrogen Production

Hydrogen takes special attention as the most promising fuel for the future use in transportation and energy storing in terms of sustainability, C-Neutrality and energy conversion. Solar-driven water splitting for hydrogen production represents one fascinating pathway for clean energy conversion and energy storage from visible light irradiation into chemical bonds. The transition metal complexes especially first row transition (3d) metals like iron, manganese, cobalt, nickel and copper based molecular complexes are capable to catalyze the reduction of protons into molecular hydrogen at low over potential or using light energy sources. We are interested to develop robust cobalt and copper based catalyst that could preserve their molecular nature under photo and electrocatalytic conditions. This thesis describes the development of different ligands with different substituents which will help to compare the reactivity as well as redox potential of complexes for water reduction. Here, we successfully designed and synthesized four different types of tridentate ligands (L1, L2, L3, L4). We successfully synthesized Co(II) complexes M1 and M2 with ligands L3 and L4 respectively. The binuclear Cu(II) complex M3 synthesized by using L4. All the ligands and metal complexes were characterized by various spectroscopic tools. The molecular structure of the metal complexes confirmed by single crystal X-ray crystallography which would be robust catalysts for hydrogen evolution

Bubble-bound state of triple-stranded DNA: Efimov physics in DNA with repulsion

The presence of a thermodynamic phase of a three-stranded DNA, namely, a mixed phase of bubbles of two bound strands and a single one, is established for large dimensions (d 65 5) by using exact real space renormalization group transformations and exact computations of specific heat for finite length chains. Similar exact computations for the fractal Sierpinski gasket of dimension d < 2 establish the stability of the phase in the presence of a repulsive three chain interaction. Although, for d < 2, cooperativity factors for bubbles or noncrossing conditions are needed for the melting transition, the mixed phase may exist even in absence of those. In contrast to the Efimov DNA, where three strands are bound though no two are bound, the mixed phase appears at temperatures less than the two chain melting temperature.Both the Efimov-DNA and the mixed phase are formed essentially due to the strand exchange mechanism

Efimov-Like Behaviour in Low-Dimensional Polymer Models

In the quantum Efimov effect, identical bosons form infinitely many bound trimer states at the bound dimer dissociation threshold, with their energy spectrum obeying a universal geometrical scaling law. Inspired by the formal correspondence between the possible trajectories of a quantum particle and the possible conformations of a polymer chain, the existence of a triple-stranded DNA bound state when a double-stranded DNA is not stable was recently predicted by modelling three directed polymer chains in low-dimensional lattices, both fractal (d<1) and euclidean (d=1). A finite melting temperature for double-stranded DNA requires in d 642 the introduction of a weighting factor penalizing the formation of denaturation bubbles, that is non-base paired portions of DNA. The details of how bubble weighting is defined for a three-chain system were shown to crucially affect the presence of Efimov-like behaviour on a fractal lattice. Here we assess the same dependence on the euclidean 1+1 lattice, by setting up the transfer matrix method for three infinitely long chains confined in a finite size geometry. This allows us to discriminate unambiguously between the absence of Efimov-like behaviour and its presence in a very narrow temperature range, in close correspondence with what was already found on the fractal lattice. When present, however, no evidence is found for triple-stranded bound states other than the ground state at the two-chain melting temperature