Related Experiment Video
Updated: Aug 26, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
Published on: March 1, 2022
Simulation of the kinetics of a sphere attached to a fluctuating polymer: Implications for target search by
1S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Calcutta 700091, India. jaydeb@boson.bose.res.in
Abstract:
We simulate the dynamics of a sphere, bound with a certain probability onto the beads of a harmonic bead-spring polymer in a confined geometry. The sphere hops from ith to the spatially closest i+/-kth bead. There is a crossover between kinetics dominated by different mechanisms with increasing binding probability. We relate these observations to the context of a biologically important problem of target location by DNA-binding proteins within a genome.

