A theoretical study of the role of bulk crowders on target search dynamics of DNA binding proteins

DOI10.1088/1742-5468/ABB019MaRDI QIDQ5856909zbMATH OpenOpenAlexFDO

Authors Kinjal Mondal, Srabanti Chaudhury

Publication date 30 March 2021

Published in Journal of Statistical Mechanics: Theory and Experiment (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1088/1742-5468/abb019

zbMATH Keywords

stochastic processesdiffusionnumerical simulations

Mathematics Subject Classification ID

Applications of continuous-time Markov processes on discrete state spaces (60J28) Protein sequences, DNA sequences (92D20) Signal detection and filtering (aspects of stochastic processes) (60G35)

Recommendations

• Protein diffusion along DNA: on the effect of roadblocks and crowders
• Facilitated diffusion in a crowded environment: from kinetics to stochastics
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Cites work

• How a protein searches for its site on DNA: the mechanism of facilitated diffusion
• Stochastic processes in physics and chemistry.

Cited in

(9)

• Crowding and hopping in a protein's diffusive transport on DNA
• Protein diffusion along DNA: on the effect of roadblocks and crowders
• Exploring the role of heterogeneity in quorum sensing cells: a discrete state stochastic approach
• How a protein searches for its site on DNA: the mechanism of facilitated diffusion
• Facilitated diffusion in a crowded environment: from kinetics to stochastics
• Theoretical study of the role of dynamic bulk crowders in the protein search for targets on DNA
• How conformational dynamics influences the protein search for targets on DNA
• Molecular crowding effects on conformation and stability of G-quadruplex DNA structure: insights from molecular dynamics simulation
• The influence of spatial variation in chromatin density determined by X-ray tomograms on the time to find DNA binding sites

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