Interfacial instability and DNA fork reversal by repair proteins

A repair protein like RecG moves the stalled replication fork in the direction from the zipped to the unzipped state of DNA. It is proposed here that a softening of the zipped-unzipped interface at the fork results in the front propagating towards the unzipped side. In this scenario, an ordinary helicase destabilizes the zipped state locally near the interface and the fork propagates towards the zipped side. The softening of the interface can be produced by the aromatic interaction, predicted from crystal structure, between RecG and the nascent broken base pairs at the Y-fork. A numerical analysis of the model also reveals the possibility of a stop and go type motion.Comment: 7 pages, revtex, 5 eps figures; v2:shorter title, 2 additional schematic figures in introductio

Critical Phenomena: An Introduction from a modern perspective

Our aim in this set of lectures is to give an introduction to critical phenomena that emphasizes the emergence of and the role played by diverging length-scales. It is now accepted that renormalization group gives the basic understanding of these phenomena and so, instead of following the traditional historical trail, we try to develop the subject in a way that emphasizes the length-scale based approach.Comment: Revtex, 26 pages, 2 figures. Lectures given at the SERC School on "Field theoretic methods in Condensed matter physics", held at MRI, Allahabad, Indi

Entropy and perpetual computers

A definition of entropy via the Kolmogorov algorithmic complexity is discussed. As examples, we show how the meanfield theory for the Ising model, and the entropy of a perfect gas can be recovered. The connection with computations are pointed out, by paraphrasing the laws of thermodynamics for computers. Also discussed is an approach that may be adopted to develop statistical mechanics using the algorithmic point of view.Comment: Based on Chanchal Majumdar memorial lectures given in Kolkata. 9 pages, 3 eps figures. For publication in "Physics Teacher"; v2. Sec 3 fragmented into smaller subsection

Unzipping DNA - towards the first step of replication

The opening of the Y-fork - the first step of DNA replication - is shown to be a critical phenomenon under an external force at one of its ends. From the results of an equivalent delocalization in a non-hermitian quantum-mechanics problem we show the different scaling behavior of unzipping and melting. The resultant long-range critical features within the unzipped part of Y might play a role in the highly correlated biochemical functions during replication.Comment: 4 pages, revtex, 2 eps figure

Nonequilibrium Growth problems

We discuss the features of nonequilibrium growth problems, their scaling description and their differences from equilibrium problems. The emphasis is on the Kardar-Parisi-Zhang equation and the renormalization group point of view. Some of the recent developments along these lines are mentioned.Comment: 9 pages, revtex, A brief overview as published in Current Science 77, 394 (1999

Incommensuration in quantum antiferromagnetic chain

A dimerized quantum Heisenberg or XY antiferromagnetic chain has a gap in the spectrum. We show that a weak incommensurate modulation around a dimerized chain produces a zero temperature quantum critical point. As the incommensuration wavelength is varied, there is a transition to a modulated gapless state. The critical behaviour is in the universality class of the classical commensurate-incommensurate (Pokrovsky-Talapov) transition. An analogous metal-insulator transition can also take place for an incommensurate chain.Comment: 5 pages, revtex, no figures, to appear in J. Phys A Letter