arXiv subjects
Publications and source records attributed to Somendra M. Bhattacharjee.
We study the unzipping of double stranded DNA (dsDNA) by applying a pulling force at a fraction $s$ $(0 \le s \le 1)$ from the anchored end. From exact analytical and numerical results, the complete phase diagram is presented. The phase diagram shows a strong ensemble dependence for various values of $s$. In addition, we show the existence of an ``eye'' phase and a triple point.
We show the existence of a force induced triple point in an interacting polymer problem that allows two zero-force thermal phase transitions. The phase diagrams for three different models of mutually attracting but self avoiding polymers are presented. One of these models has an intermediate phase and it shows a triple point but not the others. A general phase diagram with multicritical points in an extended parameter space is also discussed.
We develop a propagating front analysis, in terms of a local probability of zipping, for the helicase activity of opening up a double stranded DNA (dsDNA). In a fixed-distance ensemble (conjugate to the fixed-force ensemble) the front separates the zipped and unzipped phases of a dsDNA and a drive acts locally around the front. Bounds from variational analysis and numerical estimates for the speed of a helicase are obtained. Different types of helicase behaviours can be distinguished by the nature of the drive.
This is a set of introductory lectures on the behaviour of a directed polymer in a random medium. Both the intuitive picture that helps in developing an understanding and systematic approaches for quantitative studies are discussed.
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.
We propose a phase coexistence based mechanism for activity of helicases, ubiquitous enzymes that unwind double stranded DNA. The helicase-DNA complex constitutes a fixed-stretch ensemble that entails a coexistence of domains of zipped and unzipped phases of DNA, separated by a domain wall. The motor action of the helicase leads to a change in the position of the fixed constraint thereby shifting the domain wall on dsDNA. We associate this off-equilibrium domain wall motion with the unzipping activity of helicase. We show that this proposal gives a clear and consistent explanation of the main observed features of helicases.
The possibility of detecting mutations in a DNA from force measurements (as a first step towards sequence analysis) is discussed theoretically based on exact calculations. The force signal is associated with the domain wall separating the zipped from the unzipped regions. We propose a comparison method (``differential force microscope'') to detect mutations. Two lattice models are treated as specific examples.
The replacment of mutual avoidance of polymers by a long-range interaction of the type proposed by Garel etal (Europhys. Lett. 55, 132 (2001), cond-mat/0101058) is inconsistent with the prevalent renormalization group arguments.
We show that non-locality in the conservation of both the order parameter and a noncritical density (model D dynamics) leads to new fixed points for critical dynamics. Depending upon the parameters characterizing the non-locality in the two fields, we find four regions: (i) model-A like where both the conservations are irrelevant (ii) model B-like with the conservation in the order parameter field relevant and the conservation in the coupling field irrelevant (iii) model C like where the conservation in the order parameter field is irrelevant but the conservation in the coupling field is relevant, and (iv) model D-like where both the conservations are relevant. While the first three behaviours are already known in dynamical critical phenomena, the last one is a novel phenomena due entirely to the non-locality in the two fields.
We use renormalization group to calculate the reunion and survival exponents of a set of random walkers interacting with a long range $1/r^2$ and a short range interaction. These exponents are used to study the binding-unbinding transition of polymers and the behavior of several quantum problems.
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs of self avoiding walks (SAW) which are pulled apart by a force applied at the two extremities. The whole phase diagram is spanned by extensive Monte Carlo (MC) simulations and the existence of a low temperature denaturation is confirmed. The basic features of the phase diagram and the re-entrant phase boundary are also obtained with a simple heuristic argument based on an energy-entropy estimate.
Data-collapse is a way of establishing scaling and extracting associated exponents in problems showing self-similar or self-affine characteristics as e.g. in equilibrium or non-equilibrium phase transitions, in critical phases, in dynamics of complex systems and many others. We propose a measure to quantify the nature of data collapse. Via a minimization of this measure, the exponents and their error-bars can be obtained. The procedure is illustrated by considering finite-size-scaling near phase transitions and quite strikingly recovering the exact exponents.
Based on the result of an unzipping phase transition by a force in a model of DNA, we hypothesize that the DnaA-type proteins act as a pulling agent with a force slightly less than the critical force for unzipping. The dynamic (space-time) correlation of unzipping then drives the subsequent events of replication. In such a correlation driven scenario, there is no need of a replisome as a structural unit and this elusive replisome may not exist at all.
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.
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.
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.
We propose that the phases of all vicinal surfaces can be characterized by four fixed lines, in the renormalization group sense, in a three-dimensional space of coupling constants. The observed configurations of several Si surfaces are consistent with this picture. One of these fixed lines also describes one-dimensional quantum particles with fractional exclusion statistics. The featureless steps of a vicinal surface can therefore be thought of as a realization of fractional-statistics particles, possibly with additional short-range interactions.
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.