Xin Shi

Delft University of Technology

Department of Bionanoscience, Faculty of Applied Sciences
Email: x.shi#tudelft.nl, dan.shixin#outlook.com
Date of birth: January 1991

Research Interest

• DNA nanomachinery
• Solid-state nanopores
• Plasmonic single-molecule sensing
• Surface-enhanced Raman spectroscopy
• Dark-field microscopy and spectroscopy

Work Experience

Delft University of Technology, Netherlands
Supervisor: Prof. Cees Dekker
Postdoc
2018.10-present

Education

Delft University of Technology, Netherlands
Supervisor: Prof. Cees Dekker
Visiting PhD student
2016.08-2018.07

East China University of Science and Technology, China
Supervisor: Prof. Yi-Tao Long
PhD
2013.06-2018.09

East China University of Science and Technology, China
B. Sc.
2009.09-2013.06

Professional Skills

• Single-molecule biophysics experiments
  • solid-state nanopores
  • single molecular fluorescence imaging
• Dark-field microscopy
  • single nanoparticle scattering
• Molecular and single-particle spectroscopy
  • surface-enhanced Raman spectroscopy
  • single particle dark-field scattering spectroscopy)
• Nanodevice fabrication
  • electron-beam lithography
  • optical lithography, film evaporation/sputtering, scanning-electron microscopy etc.
• Optical/microscopy system design and construction
  • plasmonic nanopore setups & dark-field nanopore setups
• LabVIEW programing
• Matlab
• 3D CAD

Publications

1. X. Shi, A-K Pumm, C M Maffeo, W Zhao, D. Verschueren, A. Aksimentiev, H. Dietz, C. Dekker. A nanopore-powered DNA turbine. Submitted. arXiv:2206.06612. (2022)
2. X. Shi, A-K Pumm, J. Isensee, W. Zhao, D. Verschueren, A. Martin-Gonzalez, R. Golestanian, H. Dietz, C. Dekker, Sustained unidirectional rotation of a self-organized DNA rotor on a nanopore. Nature Physics, doi: 10.1038/s41567-022-01683-z. arXiv:2206.06613. (2022)
3. D. V. Verschueren, X. Shi, C. Dekker. Nano-Optical Tweezing of Single Proteins in Plasmonic Nanopores. Small Methods (2019)
4. D. V. Verschueren, S. Pud , X. Shi, L. D. Angelis, L. Kuipers , and C. Dekke. Label-Free Optical Detection of DNA Translocations through Plasmonic Nanopores. ACS Nano DOI: 10.1021/acsnano.8b06758 (2019)
5. X. Shi, D. Verschueren, and C. Dekker, Active delivery of single DNA molecules into a plasmonic nanopore for label-free optical sensing. Nano Letters. 18 (12), 8003–8010 (2018)
6. X. Shi, Q. Li, R. Gao, W. Si, SC. Liu, A. Aksimentiev and YT. Long, Dynamics of a Molecular Plug Docked onto a Solid-State Nanopore. Journal of Physical Chemistry Letters, 9, 4686–4694 (2018)
7. X. Shi, D. Verschueren, S. Pud, and Cees Dekker, 2017. Integrating sub-3nm plasmonic gaps into solid-state nanopores. Small, 14. 18: 1703307. (2017)
8. Y. Lin., Y. L. Ying, X. Shi, SC. Liu, YT. Long, (2017). Direct sensing of cancer biomarkers in clinical samples with a designed nanopore. Chemical Communications, 53(84), 11564-11567 (2017).
9. R. Gao, Y. Lin, YL. Ying, XY. Liu, X. Shi, YX Hu, Long YT, Tian H. Dynamic self‐assembly of homogenous microcyclic structures controlled by a silver‐coated nanopore. Small. 13, 1700234. (2017)
10. Y. Lin, X. Shi (equal contribution), S.C. Liu, Y.L. Ying, Q. Li, R. Gao, F. Fathi, Y.T. Long, and H. Tian. Characterization of DNA duplex unzipping through a sub-2 nm solid-state nanopore. Chemical Communications, 53(25), 3539-3542 (2017).
11. X. Shi, R. Gao, YL. Ying, ,W. Si, YF Chen, and YT. Long, A Scattering Nanopore for Single Nanoentity Sensing. ACS Sensors, 1(9), 1086-1090. (2016)
12. X. Shi, HW. Li, C. Liu, L. Zhang, YT. Long. In situ monitoring of catalytic process variations in a single nanowire by dark-field-assisted surface-enhanced Raman spectroscopy. Chemical Communications, 52, 1044-1047 (2016)
13. X. Shi, R. Gao, YL. Ying, W. Si, YF. Chen, YT. Long. Single Molecule Microscopy: An integrated system for optical and electrical detection of single molecules/particles inside a solid-state nanopore. Faraday Discussions, 184, 85–99 (2015)
14. C. Jing, F. J. Rawson, H. Zhou, X. Shi, WH. Li, DW. Li, and YT. Long. New Insights into Electrocatalysis Based on Plasmon Resonance for the Real-Time Monitoring of Catalytic Events on Single Gold Nanorods. Analytical Chemistry 86, 5513-5518 (2014).
15. Z. Liu, L. Cheng, L. Zhang, C. Jing, X. Shi, Z. Yang, YT. Long and J. Fang. Large-area fabrication of highly reproducible surface enhanced Raman substrate via a facile double sided tape-assisted transfer approach using hollow Au-Ag alloy nanourchins. Nanoscale 6, 2567-2572 (2014).

Patents

1. YT. Long, X. Shi, R. Gao, YL. Ying, C. Jing, HW. Li. Synchronous optical and electrical nanopore sensing based on dark-field microscopy, Appl. No(s): CN201510225193.5 Granted (Chinese patent for invention)
2. YT. Long, X. Shi, R. Gao, SC. Liu, YL. Ying. A detection system for optical and electrical readout of metal-coated nanopore, Appl. No(s): CN201520285880.1 Granted (Chinese patent for utility model)

Conference Experience

1. (scheduled) Building DNA nanoturbines on nanopores. NWO Biophysics 2022. Oral presentation. October 10th to 11th 2022, Veldhoven, the Netherlands.
2. (scheduled) Building DNA nanoturbines on nanopores. Wageningen University & Research, 2022. Invited Seminar talk. September 30th 2022, Wageningen, the Netherlands.
3. Nanopore-powered DNA turbines. ArtBio 2022. Contributing talk. August 15th to 17th 2022, Aarhus, Denmark.
4. Building DNA nanoturbines on nanopores. Max Planck Institute for Dynamics and Self-Organization 2022. Invited Seminar talk. August 9th 2022, Göttingen, Germany.
5. Building DNA nanoturbines on nanopores. From Solid State to Biophysics X 2022. Oral presentation. June 11th to 18th 2022, Dubrovnik, Croatia.
6. X. Shi, D. Verschueren, and C. Dekker. Label-free optical sensing using Plasmonic nanopores. Single-Molecule Sensors and NanoSystems International Conference – S3IC 2019. invited talk. April 3-5, 2019 Munich, Germany
7. X. Shi, D. Verschueren, and C. Dekker. Fast label-free optical detection of DNA translocations through plasmonic nanopores. Nanofluidics in physics and biology. Poster. July 9-12th 2018 Lyon, France
8. X. Shi, D. Verschueren, J. van der Torre, S. Pud, C. Dekker. Single molecule Raman spectroscopy using plasmonic nanopores. WE-Heraeus-Seminar: Transport Mechanisms in Biological and Synthetic Nanopores and –channels. Poster. July 16-21 2017 Bremen, Germany
9. X. Shi, D. Verschueren, S. Pud, C. Dekker. Single molecule raman Spectroscopy using plasmonic nanopores. NanoFront Winter Retreat. Poster Award. Mar 27-31 2017 Courchevel, France
10. X. Shi, R. Gao, SC Liu, Q. Li, YT Long. Direct observation of single biopolymer folding and unfolding process by solid-state nanopore. Biophysical society 61th annual meeting. Poster, Travel Award. Feb 11-15. 2017 New Orleans, US
11. X. Shi, R. Gao, YL. Ying, W. Si, YF. Chen, YT. Long. Single molecule microscopy: an integrated system for optical and electrical detection of single molecules/particles inside a solid-state nanopore. Faraday Discuss. Oral presentation. Sept 13-15. 2015 London, UK