M. A. Shahzad

Periodically driven force protein translocation through a α-hemolysin biological nano-pore

The paper uses Langevin molecular dynamics to study protein translocation through an α-hemolysin pore under periodic external forces, finding that time-dependent forces enhance translocation efficiency.

Computer simulation of knotted proteins unfold and translocation through nano-pores

This study simulates the unfolding and translocation of knotted proteins YibK and YbeA through a nano-pore, finding that knots unfold before translocation and that YibK takes longer to translocate under low pulling force.

Polymer translocation through nano-pores: influence of pore and polymer deformation

This study simulates polymer translocation through a nano-pore, showing that pore deformation can significantly affect translocation time and polymer-pore interactions.

Free energy calculations of protein-water complexes with Gromacs

The paper performs molecular dynamics simulations of GFP in water using Gromacs to analyze its structure and stability.

Time-Periodically Driven Brownian Motion of Rigid Rod in one dimensional space

The paper uses a theoretical model to study protein translocation through a fluctuating pore by analyzing the dynamics of a Brownian particle under periodic driving forces.

Translocation of structured biomolecule through a vibrating nanopore

This study examines how a vibrating nanopore affects protein translocation dynamics, finding that oscillations can accelerate the process and reveal resonant activation.

Mechanical unfold and transport of Green Florescent Protein through a nanopore

The paper studies how GFP and MBP unfold and translocate through a nanopore under constant force, showing structural differences in their unfolding behavior based on their native topology.