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
- 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)
- 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)
- D. V. Verschueren, X. Shi, C. Dekker. Nano-Optical Tweezing of Single Proteins in Plasmonic Nanopores. Small Methods (2019)
- 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)
- 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)
- 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)
- X. Shi, D. Verschueren, S. Pud, and Cees Dekker, 2017. Integrating sub-3nm plasmonic gaps into solid-state nanopores. Small, 14. 18: 1703307. (2017)
- 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).
- 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)
- 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).
- 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)
- 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)
- 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)
- 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).
- 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
- 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)
- 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
- (scheduled) Building DNA nanoturbines on nanopores. NWO Biophysics 2022. Oral presentation. October 10th to 11th 2022, Veldhoven, the Netherlands.
- (scheduled) Building DNA nanoturbines on nanopores. Wageningen University & Research, 2022. Invited Seminar talk. September 30th 2022, Wageningen, the Netherlands.
- Nanopore-powered DNA turbines. ArtBio 2022. Contributing talk. August 15th to 17th 2022, Aarhus, Denmark.
- Building DNA nanoturbines on nanopores. Max Planck Institute for Dynamics and Self-Organization 2022. Invited Seminar talk. August 9th 2022, Göttingen, Germany.
- Building DNA nanoturbines on nanopores. From Solid State to Biophysics X 2022. Oral presentation. June 11th to 18th 2022, Dubrovnik, Croatia.
- 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
- 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
- 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
- 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
- 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
- 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