BHU Institutional Repository :: Browsing by Author "Chauhan, Keerti"

Browsing by Author "Chauhan, Keerti"

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Appearance of de Gennes length in force-induced transitions
(American Physical Society, 2023) Chauhan, Keerti; Mishra, Garima; Kishore, Vimal; Kumar, Sanjay
Using Langevin dynamic simulations, a simple coarse-grained model of a DNA protein construct is used to study the DNA rupture and the protein unfolding. We identify three distinct states: (i) zipped DNA and collapsed protein, (ii) unzipped DNA and stretched protein, and (iii) unzipped DNA and collapsed protein. Here, we find a phase diagram that shows these states depending on the size of the DNA handle and the protein. For a less stable protein, unfolding is solely governed by the size of the linker DNA, whereas if the protein's stability increases, complete unfolding becomes impossible because the rupture force for DNA has reached a saturation regime influenced by the de Gennes length. We show that unfolding occurs via a few intermediate states by monitoring the force-extension curve of the entire protein. We extend our study to a heterogeneous protein system, where similar intermediate states in two systems can lead to different protein unfolding paths. � 2023 American Physical Society.
Can one detect intermediate denaturation states of DNA sequences by following the equilibrium open-close dynamic fluctuations of a single base pair?
(American Institute of Physics Inc., 2022) Chauhan, Keerti; Singh, Amit Raj; Kumar, Sanjay; Granek, Rony
Melting of DNA sequences may occur through a few major intermediate states, whose influence on the melting curve has been discussed previously, while their effect on the kinetics has not been explored thoroughly. Here, we chose a simple DNA sequence, forming a hairpin in its native (zipped) state, and study it using molecular dynamic (MD) simulations and a model integrating the Gaussian network model with bond-binding energies - the Gaussian binding energy (GBE) model. We find two major partial denaturation states, a bubble state and a partial unzipping state. We demonstrate the influence of these two states on the closing-opening base pair dynamics, as probed by a tagged bond auto-correlation function (ACF). We argue that the latter is measured by fluorescence correlation spectroscopy experiments, in which one base of the pair is linked to a fluorescent dye, while the complementary base is linked to a quencher, similar to the experiment reported by Altan-Bonnet et al. [Phys. Rev. Lett. 90, 138101 (2003)]. We find that tagging certain base pairs at temperatures around the melting temperature results in a multi-step relaxation of the ACF, while tagging other base pairs leads to an effectively single-step relaxation, albeit non-exponential. Only the latter type of relaxation has been observed experimentally, and we suggest which of the other base pairs should be tagged in order to observe multi-step relaxation. We demonstrate that this behavior can be observed with other sequences and argue that the GBE can reliably predict these dynamics for very long sequences, where MD simulations might be limited. � 2022 Author(s).
Delayed collapse transitions in a pinned polymer system
(American Physical Society, 2022) Chauhan, Keerti; Singh, Ankit
Employing Langevin dynamics simulations, we investigated the kinetics of the collapse transition for a polymer of length N when a particular monomer at a position 1=X=N is pinned. The results are compared with the kinetics of a free polymer. The equilibrium ?-point separating the coil from the globule phase is located by a crossover in (Rg2)/N plots of different chain lengths. Our simulation supports a three-stage mechanism for free and pinned polymer collapse: the formation of pearls, the coarsening of pearls, and the formation of a compact globule. Pinning the central monomer has negligible effects on the kinetics as it does not break the symmetry. However, pinning a monomer elsewhere causes the process to be delayed by a constant factor fX depending linearly upon X. The total collapse time scales with N as tc~fXN1.60�0.03, which implies tc is maximum when an end monomer is pinned (X=1 or N), while when pinning the central monomer (X=N/2) it is minimum and identical to that of a free polymer. The average cluster size Nc(t) grows in time as tz, where z=1.00�0.04 for a free particle, whereas we identify two time regimes separated by a plateau for pinned polymers. At longer times, z=1.00�0.04, while it deviates in early time regimes significantly, depending on the value of X. � 2022 American Physical Society.
Dynamics of a polymer chain translocating through varying cone-shaped channels
(American Physical Society, 2021) Chauhan, Keerti; Kumar, Sanjay
By employing the exact enumeration technique, we study consequences of different apex angles of a wedge-shaped channel on the mean first passage time and free-energy profile of a linear polymer chain translocating from the cis- to the trans-side through an interacting pore. We investigate effects of asymmetry arising in the free-energy profile due to the change in apex angles and its dependence on the first passage time. We report the combined effect of entropy (arising due to apex angles) and pore interaction on the nonmonotonic behavior of the translocation time. The effect of different solvent quality across the channel has also been explored. We show that the increase in monomer-monomer interaction leads to the formation of globules near the pore, which drives the process faster. � 2021 American Physical Society.
Force-induced melting of DNA hairpin: Unfolding pathways and phase diagrams
(American Physical Society, 2023) Rudra, Sumitra; Chauhan, Keerti; Singh, Amit Raj; Kumar, Sanjay
Using the exact enumeration technique, we have studied the force-induced melting of a DNA hairpin on the face centered cubic lattice for two different sequences which differ in terms of loop closing base pairs. The melting profiles obtained from the exact enumeration technique is consistent with the Gaussian network model and Langevin dynamics simulations. Probability distribution analysis based on the exact density of states revealed the microscopic details of the opening of the hairpin. We showed the existence of intermediate states near the melting temperature. We further showed that different ensembles used to model single-molecule force spectroscopy setups may give different force-temperature diagrams. We delineate the possible reasons for the observed discrepancies. � 2023 American Physical Society.
Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges
(Multidisciplinary Digital Publishing Institute (MDPI), 2023) Singh, Swarn Lata; Chauhan, Keerti; Bharadwaj, Atul S.; Kishore, Vimal; Laux, Peter; Luch, Andreas; Singh, Ajay Vikram
Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores. � 2023 by the authors.
Role of Hoogsteen interaction in the stability of different phases of triplex DNA
(American Physical Society, 2022) Pal, Tanmoy; Chauhan, Keerti; Kumar, Sanjay
A simple coarse-grained model of DNA which includes both Watson-Crick and Hoogsteen base pairing has been used to study the melting and unzipping of triplex DNA. Using Langevin dynamics simulations, we reproduce the qualitative features of one-step and two-step thermal melting of triplex as seen in experiments. The thermal melting phase diagram shows the existence of a stable interchain three-strand complex (bubble-bound state). Our studies based on the mechanical unzipping of a triplex revealed that it is mechanically more stable compared to an isolated duplex-DNA. � 2022 American Physical Society.

Browsing by Author "Chauhan, Keerti"

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