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Homopolymer and heteropolymer translocation through patterned pores under fluctuating forces

  • Regular Article - Soft Matter
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Abstract

We investigate the translocation of a semiflexible polymer through extended patterned pores using Langevin dynamics simulations, specifically focusing on the influence of a time-dependent driving force. Our findings reveal that, akin to its flexible counterpart, a rigid chain-like molecule translocates faster when subjected to an oscillating force than a constant force of equivalent average magnitude. The enhanced translocation is strongly correlated with the stiffness of the polymer and the stickiness of the pores. The arrangement of the pores plays a pivotal role in translocation dynamics, deeply influenced by the interplay between polymer stiffness and pore-polymer interactions. For heterogeneous polymers with periodically varying stiffness, the oscillating force introduces significant variations in the translocation time distributions based on segment sizes and orientations. On the basis of these insights, we propose a sequencing approach that harnesses distinct pore surface properties that are capable of accurately predicting sequences in heteropolymers with diverse bending rigidities.

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Data availability

Data sets generated during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

The authors acknowledge the use of high performance computing facility at IISER Mohali and PARAM Smriti.

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Authors and Affiliations

  1. Department of Physical Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, Knowledge City, S. A. S. Nagar, Manauli, 140306, India

    Gokul Upadhyay, Rajeev Kapri & Abhishek Chaudhuri

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  1. Gokul Upadhyay
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  2. Rajeev Kapri
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  3. Abhishek Chaudhuri
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Contributions

AC designed the project. GU and RK developed the numerical code. Data collection and analysis were performed by GU. The first draft of the manuscript was written by AC and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Abhishek Chaudhuri.

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Upadhyay, G., Kapri, R. & Chaudhuri, A. Homopolymer and heteropolymer translocation through patterned pores under fluctuating forces. Eur. Phys. J. E 47, 23 (2024). https://doi.org/10.1140/epje/s10189-024-00417-8

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