61 citations · 422 across the 23 of their papers we have counts for
13 papers · 1 filter
Effect of polydispersity on the dynamics of active Brownian particles
Sameer Kumar, Jay Prakash Singh, Debaprasad Giri +1
We numerically study the dynamics and the phases of self-propelled disk-shaped particles of different sizes with soft repulsive potential in two dimensions. Size diversity is intro…
Statistical mechanics of a polymer chain attached to the interface of a cone-shaped channel
Sanjay Kumar, Sanjiv Kumar, Debaprasad Giri +1
A polymer chain confined in nano-scale geometry has been used to investigate the underlying mechanism of Nuclear Pore Complex (NPC), where transport of cargoes is directional. It w…
On the rupture of DNA molecule
R. K. Mishra, T. Modi, D. Giri +1
Using Langevin Dynamic simulations, we study effects of the shear force on the rupture of a double stranded DNA molecule. The model studied here contains two single diblock copolym…
Single polymer gating of channels under a solvent gradient
S Nath, D P Foster, D Giri +1
We study the effect of a gradient of solvent quality on the coil-globule transition for a polymer in a narrow pore. A simple self-attracting self-avoiding walk model of a polymer i…
Statistical Mechanics of DNA Rupture: Theory and Simulations
S. Nath, T. Modi, R. K. Mishra +3
We study the effects of the shear force on the rupture mechanism on a double stranded DNA. Motivated by recent experiments, we perform the atomistic simulations with explicit solve…
Scaling of hysteresis loop of interacting polymers under a periodic force
Rakesh Kumar Mishra, Garima Mishra, Debaprasad Giri +1
Using Langevin Dynamics simulations, we study a simple model of interacting-polymer under a periodic force. The force-extension curve strongly depends on the magnitude of the ampli…
Role of loop entropy in the force induced melting of DNA hairpin
Garima Mishra, D. Giri, M. S. Li +1
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…
Force induced melting of the constrained DNA
Amit Raj Singh, D. Giri, S. Kumar
We develop a simple model to study the effects of an applied force on the melting of a double stranded DNA (dsDNA). Using this model, we could study the stretching, unzipping, rupt…
Force induced unfolding of bio-polymers in a cellular environment: A model study
Amit Raj Singh, Debaprasad Giri, Sanjay Kumar
Effect of molecular crowding and confinement experienced by protein in the cell during unfolding has been studied by modeling a linear polymer chain on a percolation cluster. It is…
Stretching of a single-stranded DNA: Evidence for structural transition
Garima Mishra, Debaprasad Giri, Sanjay Kumar
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 [po…
Effects of Eye-phase in DNA unzipping
Debaprasad Giri, Sanjay Kumar
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 introduce…
Force induced conformational transition in a system of interacting stiff polymer: Application to unfolding
Sanjay Kumar, Debaprasad Giri
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, polymer undergoes a transition from th…
A simple model for the relative stabilities of DNA hairpin structure
Debaprasad Giri, Sanjay Kumar, Yashwant Singh
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behaviour of a single stranded short DNA molecule that form h…