Biomedical subjects

Debaprasad Giri

Publications and source records attributed to Debaprasad Giri.

5 recordsLinked to original sources

PubMed2006

Probability distribution analysis of force induced unzipping of DNA.

We present a semimicroscopic model of dsDNA by incorporating the directional nature of hydrogen bond to describe the force induced unzipping transition. Using exact enumeration technique, we obtain the force-temperature and the force-extension curves and compare our results with the other models of dsDNA. The model proposed by us is rich enough to describe the basic mechanism of dsDNA unzipping and predicts the existence of an "eye phase." We show oscillations in the probability distribution function during unzipping. Effects of stacking energies on the melting profile have also been studied.

Biophysics↗

PubMed2006

Effects of the eye phase in DNA unzipping.

The onset of the "eye phase" (a phase consisting of configurations of eye-type conformations or bubbles in the double-stranded DNA) and its role during the DNA unzipping is studied when a force is applied to the interior of the chain. The directionality of the hydrogen bond introduced here shows oscillations in force-extension curve similar to a "sawtooth" kind of oscillations seen in the protein unfolding experiments. The effects of intermediates (hairpins) and stacking energies on the melting profile have also been discussed.

Computer Simulation↗

PubMed2005

Force-induced conformational transition in a system of interacting stiff polymers: application to unfolding.

We consider a stiff polymer chain in poor solvent and apply a force at one end of the chain. We find that by varying the stiffness parameter, the polymer undergoes a transition from the globule state to the foldedlike state. The conformation of the folded state mimics the beta sheet as seen in the titin molecule. Using the exact enumeration technique, we study the extension-force and force-temperature diagrams of such a system. The force-temperature diagram shows the re-entrance behavior for a flexible chain. However, for a stiff chain this re-entrance behavior is absent and there is an enhancement in theta temperature with the rise of stiffness. We further propose that the internal information about the frozen structure of a polymer can be read from the distribution of end-to-end distance which shows a sawtoothlike behavior.

Biopolymers↗

PubMed2005

Force-induced triple point for interacting polymers.

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 two 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. A general phase diagram with multicritical points in an extended parameter space is also discussed.

Journal Article↗

PubMed2002

Adsorption and collapse transitions in a linear polymer chain near an attractive wall.

We deduce the qualitative phase diagram of a long flexible neutral polymer chain immersed in a poor solvent near an attracting surface using phenomenological arguments. The actual positions of the phase boundaries are estimated numerically from series expansion up to 19 sites of a self-attracting self-avoiding walk in three dimensions. In two dimensions, we calculate phase boundaries analytically in some cases for a partially directed model. Both the numerical and analytical results corroborate the proposed qualitative phase diagram.

Journal Article↗