Debaprasad Giri

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.

Stretching of a single-stranded DNA: evidence for structural transition.

Recent experiments have shown that the force-extension (F-x) curve for single-stranded DNA (ssDNA) consisting only of adenine [poly(dA)] is significantly different from thymine [poly(dT)]. Here, we show that the base stacking interaction is not sufficient to describe the F-x curves as seen in the experiments. A reduction in the reaction coordinate arising from the formation of helix at low forces and an increase in the distance between consecutive phosphates of unstacked bases in the stretched state at high force in the proposed model qualitatively reproduce the experimentally observed features. The multistep plateau in the F-x curve is a signature of structural change in ssDNA.

Crossover of a polymer chain from bulk to surface states

Using exact enumeration, conformational properties of a surface-interacting long flexible polymer chain are determined in a two-dimensional poor solvent where the possibility of collapse in bulk exists. A model of a self-attracting self-avoiding walk (SASAW) on a square lattice is considered and up to 28 steps in series were evaluated. A new state having the conformation of a surface attached globule in between the adsorbed and desorbed collapsed phases is found. The fact that this state may not represent a new thermodynamic phase is emphasised. The phase diagram is drawn showing the region of existence of the four phases: (i) desorbed expanded, (ii) desorbed collapsed, (iii) adsorbed expanded, and (iv) surface attached globule. The uncertainities in locating the phase boundaries particularly in the vicinity of multicritical point is mentioned.

Does changing the pulling direction give better insight into biomolecules

Single-molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different phase diagrams. The simple model proposed here indicates that in one case the system undergoes a transition akin to the unzipping of a beta sheet, while in the other case the transition is of a shearing (slippage) nature. Our results are qualitatively similar to experimental results. This demonstrates the importance of varying the pulling direction since this may yield enhanced insights into the molecular interactions responsible for the stability of biomolecules.

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.

Effects of molecular crowding on stretching of polymers in poor solvent

We consider a linear polymer chain in a disordered environment modeled by percolation clusters on a square lattice. The disordered environment is meant to roughly represent molecular crowding as seen in cells. The model may be viewed as the simplest representation of biopolymers in a cell. We show the existence of intermediate states during stretching arising as a consequence of molecular crowding. In the constant distance ensemble the force-extension curves exhibit oscillations. We observe the emergence of two or more peaks in the probability distribution curves signaling the coexistence of different states and indicating that the transition is discontinuous unlike what is observed in the absence of molecular crowding.

Force induced melting of the constrained DNA

We develop a simple model to study the effects of the applied force on the melting of a double stranded DNA (dsDNA). Using this model, we could study the stretching, unzipping, rupture and slippagelike transition in a dsDNA. We show that in absence of an applied force, the melting temperature and the melting profile of dsDNA strongly depend on the constrained imposed on the ends of dsDNA. The nature of the phase boundary of the force-temperature diagram, which separates the zipped and the open state for the shearinglike transition is remarkably different than the DNA unzipping.

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.

Surface adsorption and collapse transition of a linear polymer chain in three dimensions

A phase diagram for a surface-interacting long flexible polymer chain in a poor solvent where the possibility of collapse exists is calculated using an exact enumeration method. A model of a self-attracting self-avoiding walk on a simple cubic lattice was considered and up to 16 steps in series were evaluated. The phase diagram indicates that while the boundary between the expanded and collapsed phases is straight in the bulk, it exhibits a bend in the surface resulting in two adsorbed collapsed phases separated by an adsorbed expanded phase. This is attributed to competition between the entropic fluctuations and effects due to monomer-monomer attraction.

Role of loop entropy in the force induced melting of DNA hairpin

Dynamics of a single stranded DNA, which can form a hairpin have been studied in the constant force ensemble. Using Langevin dynamics simulations, we obtained the force-temperature diagram, which differs from the theoretical prediction based on the lattice model. Probability analysis of the extreme bases of the stem revealed that at high temperature, the hairpin to coil transition is entropy dominated and the loop contributes significantly in its opening. However, at low temperature, the transition is force driven and the hairpin opens from the stem side. It is shown that the elastic energy plays a crucial role at high force. As a result, the force-temperature diagram differs significantly with the theoretical prediction.