21 research outputs found
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
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.Comment: RevTeX v4, 10 pages with 6 eps figure
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 co-ordinate 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 reproduces the experimentally observed
features. The multi-step plateau in the F-x curve is a signature of structural
change in ssDNA.Comment: 10 pages, 4 figure
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 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.Comment: 4 pages, 8 figures, revtex
Effects of Eye-phase in DNA unzipping
The onset of an "eye-phase" 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 "saw-tooth" 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.Comment: RevTeX v4, 9 pages with 7 eps figure
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.Comment: 14 pages, 6 figure
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 phase diagram differs
significantly with the theoretical prediction.Comment: 9 pages, 8 figures; J. Chem. Phys (2011