Publications

Selected Publications

(After independence:
* denotes corresponding author

1. Peng, R., Chen, X., Xu, F., Hailstone, R., Men, Y., and Du, K*. Pneumatic nano-sieve for CRISPR-based detection of drug-resistant bacteria, Nanoscale Horizons, in press.

2. Liu, L., Xu, Z., Vargas A., Dollery, S., Schrlau, M., Cormier, D., O'Connell, M., Tobin, G., and Du, K*. (2023). Aerosol jet printing enabled dual-function electrochemical and colorimetric biosensor for SARS-CoV-2 detection, Analytical Chemistry, 95, 32, 11997-12005. (Featured as supplementary cover)

3. Lei, Z., Lian, L., Zhang, L., Liu, C., Zhai, S., Yuan, X., Wei, J., Liu, H., Liu, Y., Du, Z., Gul, I., Zhang, H., Qin, Z., Zeng, S., Jia, P., Du, K., Deng, L., Yu, D., He, Q., Qin, P. (2023). Detection of frog virus 3 by integrating RPA-CRISPR/Cas12a-spm with deep learning, ACS Omega, 8, 36, 32555-32564.

4. Scher, K., Chen, X., Pan, L., Du, K., Fabris, L., and Xu, S*. Three-dimensional imaging and reconstruction of porous sub-micron particles and core-shell sub-micron particles with FIB-SEM, in preparation.

5. Kasputis, T., Yeh, P., Liu, L., Du, K., Weger-Lucarelli, J., Lin, L., and Chen, J*. Development of ready-to-use digitalized loop-mediated isothermal amplification microfluidic chip for the detection of Zika virus, in preparation.

6. Yuqing, H., Zhang, S., Ernst, O., Lapizco-Encinas, B., Liu, R., and Du, K*. ZnO covered 3-D printed microstructures for wear-resistant antimicrobial surface, in preparation.

7. Raheem, M., Rahim, M., Gul, I., Zhong, X., Xiao, C., Zhang, H., Wei, J., He, Q., Hassan, M., Zhang, Can., Yu, D., Pandey, V., Du, K., Wang, R., Han, S., Han, Y., and Qin, P*. (2023). Advances in nanoparticle-based approaches in cancer theranostics, OpenNano, 12, 100152.

8. Chen, X., Wang, R., Du, K., and Xu, S*. A novel 3D-printed demo device for the visualization of dental tubules occlusion, in preparation.

9. Chen, Q., Gul, I., Liu, C., Lei, Z., Li, X., Raheem, M., He, Q., Zhang, H., Leeansyah, E., Zhang, C., Pandey, V., Du, K., and Qin, P. (2023). CRISPR-Cas12-based field-deployable system for rapid detection of synthetic DNA sequence of the monkeypox virus genome, Journal of Medical Virology, 95, e28385.

10. Chen, X., Ryan, K., Hines, D., Pan, L., Du, K., and Xu, S*. (2023). Three-dimensional visualization of dentine occlusion based FIB-SEM tomography, Scientific Reports, 13, 2270.

11. J. He., R, Peng., Yuqing, F., Karim, R., Chen, J., Lu, G., and Du, K*. (2023). Superhydrophobic-based Rotation-Chip for multiplexing detection drug-resistant bacteria, ACS Applied Materials and Interfaces, 15, 23, 27732-27741.

12. Dissanayake, W., Hailstone, R., Castillo L., Nafar, F., Bao, M., Wang, R., Gates, C., Yong, X., and Du, K*. (2023). The effect of CdSe/ZnS quantum dots on the photosynthesis rate of the chlorella vulgaris beads, Algal Research, 103095.

13. Yong, X*., and Du, K. (2023). Shape effect on interaction dynamic of tetrahedral nanoplastics and cell membrane, Journal of Physical Chemistry B, 127, 1652. (Featured as supplementary cover)

14. Gul, I., Liu, C., Yuan, X., Du, Z., Zhai, S., Lei, Z., Chen, Q., Raheem, M., He, Q., Hu, Q., Xiao, C., Zhang, H., Wang, R., Han, S., Du, K., Yu, D., Zhang, C., and Qin, P*. (2022). Current and perspective sensing methods for Monkeypox virus, Bioengineering, 9, 571.

15. Ten Pas, C., Du, K., Pan, L., Wang, R*., and Xu, S*. (2022). Understanding the dynamics of fluid-structure interaction with an air deflected microfluidic chip (ADMC). Scientific Reports, 12, 1, 1-9.

16. Bao, M., Zhang, S., Ten Pas, C., Dollery, S., Bushell, R., Yuqing, F., Liu, R., Lu, G., Tobin, G., and Du, K*. (2022). Computer vision enabled funnel adapted sensing tube (FAST) for power-free and pipette-free nucleic acid detection, Lab on a Chip, 22, 4849-4859.

17. Nanaware, A., Kranbuhl, T., Ching, J., Chen, J., Chen, X., Tu, Q*., and Du, K*. (2022). Pneumatic controlled nano-sieve for efficient capture and release of nanoparticles, Journal of Vacuum Science and Technology B, 40, 063002. (Featured as the Front Cover)

18. Waitkus, J., Chang, Y., Liu, L., Puttaswamy, S., Chung, T., Vargas, A., Dollery, S., O'Connell, M., Cai, H., Tobin, G., Bhalla, N*., and Du, K*. (2022). Gold nanoparticle enabled localized surface plasmon resonance on unique gold nanomushroom structures for on-chip CRISPR-Cas13a sensing, Advanced Materials Interfaces, 2201261. (Featured as inside back cover)

19. Chang, Y., Bao, M., Waitkus, J., Cai, H., and Du, K*. (2022). On-demand fully-enclosed superhydrophobic-based optofluidic device enabled by microstereolithography, Langmuir, 38, 34, 10672. (Featured as supplementary cover)

20. Liu, L., Xu, Z., Awayda, K., Dollery, S., Bao, M., Fan, J., Cormier, D., O'Connell, M., Tobin, G., and Du, K*. (2022). Gold nanoparticle labeled CRISPR-Cas13a assay for the sensitive solid-state nanopore molecular counting, Advanced Materials Technologies, 7, 2101550. (Editor's pick)

21. Bao, M., Waitkus, J., Liu, L., Chang, Y., Xu, Z., Qin, P., Chen, J, and Du, K*. (2023). Micro-and nanosystems for the detection of hemorrhagic fever viruses, Lab on a Chip, 23, 4173-4200.

22. Xu, S., Stranick, M., Hines, D., Du, K., and Pan, L. (2022). Super high-quality SEM/FIB imaging of dentine structures without collagen fiber loss through a metal staining process, Scientific Reports, 12, 2369.

23. Kim, J., Bao, M., Bushnell, R., Tobin, G., He, J., Du, K., and Park, M. Sensitive SARS-CoV-2 detection with a miniaturized fluorometer and CRISPR-Cas12a assay, in preparation.

24. Yang, F., Liu, L., Neuenschwander, P., Idell, S., Vankayalapati, R., Jain, K., Du, K., H, J., and Yi, G. (2022). A phage display-derived peptide for the specific binding of SARS-CoV-2, ACS Omega, 7, 4, 3203-3211. (Featured as front cover)

25. He, Q., Chen, Q., Li, F., Yuan, X., Liu, C., Xu, L., Zhong, X., Wei, J., Kumar Pandey, V., Yu, D., Dong, Y., Zhang, Y., Deng, L., Du, K., and Qin, P. Amplification-free detection of viral RNA by super resolution microscopy-based CRISPR/Cas13a system, submitted.

26. Bao, M., Chen, Q., Xu, Z., Jensen, E., Liu, C., Waitkus, J., Yuan, X., He, Q., Qin, P., and Du, K*. (2021). Challenges and opportunities for clustered regularly interspaced short palindromic repeats based molecular biosensing, ACS Sensors, 6, 2497 (Featured as supplement cover)

27. Chen, X., Zhang, S., Gan, Y., Liu, R., Wang, R., and Du, K*. (2022). Understanding microbeads stacking in deformable microfluidics for plasma separation and blood cell retrieval, Journal of Colloid & Interface Science, 606, 1609.

28. Li, L., Dubrovsky M., Gundavarapu, S., Vermeulen, D., and Du, K*. (2021). Viral nucleic acid detection with CRISPR-Cas12a using high contrast cleavage detection on micro-ring resonator biosensors, Proceedings of SPIE, Frontiers in Biological Detection: From Nanosensors to Systems XIII, 1166207. (Invited paper)

29. Layouni, R., Dubrovsky, M., Bao, M., Chung, H., Du, K., Boriskina, S., Weiss, S., and Vermeulen, D. (2021). High contrast probe cleavage detection on porous silicon biosensors via quantum dot labeled DNA probes, Optics Express, 29, 1.

30. Yang, J., He, Y., Zhang, X., Yang, W., Li, Y., Li, X., Chen, Q., Chen, X., Du, K., and Yang, X. (2022). Improvement of electrical conductivity of copper/graphene composite by reducing the interfacial impurities, Journal of Materials Research and Technology, 15, 3005.

31. Yuan, X., Yang, C., He, Q., Chen, J., Yu, D., Li, J., Zhai, S., Qin, Z., Du, K*., Chu, Z., and Qin, P. (2020). Current and perspective diagnostic techniques for COVID-19, ACS Infectious Diseases, 6, 1998. (Featured as supplement cover)

32. Korensky, G., Chen, X., Bao, M., Miller, A., Lapizco-Encinas, B., Park, M., and Du, K*. (2020). Single Chlamydomonas Reinhardi cell separation and auto-fluorescence tracking with a nano-sieve device, Electrophoresis, 00, 1-8. (Featured as front cover)

33. Bao, M., Jensen, E., Chang, Y., Korensky, G., and Du, K*. (2020). Magnetic bead-quantum dot (MB_Qdot) CRISPR assay for simple viral DNA detection, ACS Applied Materials and Interfaces, 12, 43435.

34. Hass, K., Bao, M., He, Q., Liu, L., He, J., Park, M., Qin, P., and Du, K*. (2020). Integrated micro pillar accurate CRISPR detection (IMPACT) chip for one-step and background-free nucleic acid sensing, ACS Omega, 5, 27433-27441. (Featured as supplement cover)

35. Liu, Y†., Du, K†., Wathuthanthri, I., Xu, W., and Choi, C. H. (2020). Free-standing photoresist film: a versatile template for three-dimensional micro-and nanofabrication, Advanced Functional Materials, 30, 2004129. (Featured as front inside cover)
†Equal contribution.

36. He, Q., Yu, D., Bao, M., Korensky, G., Chen, J., Shin, M., Kim, J., Park, M., Qin, P., and Du, K*. (2020). High-throughput and all-solution phase African swine fever virus (ASFV) detection with CRISPR-Cas12a and fluorescence based point-of-care system, Biosensors and Bioelectronics, 154, 112068.

37. Chen, X., Miller, Cao, S., Gan, Y., Zhang, J., He, Q., Wang, R., Yong, X., Qin, P., Lapizco-Encinas, B., and Du, K*. (2020). Rapid Escherichia coli trapping, concentrating, and retrieval via nano-sieve packed magnetic microbeads array, ACS Applied Materials and Interfaces, 12, 7888-7896. (Featured as complementary cover)
*RIT news, *Rutgers Today, *nano werk, *Science Daily, *Eurek Alert!, *Bio-Medicine, *New Medical, *Medical Press

38. He, Q., Bao, M., Hass, K., Lin, W., Qin, P*., and Du, K*. (2019). Perspective of molecular diagnosis in healthcare: From barcode to pattern recognition, Diagnostics, 9, 75.

39. Chen, X., Falzon, L., Zhang, X., Wang, R., and Du, K*. (2020). Experimental and theoretical study on the microparticle trapping and release in a deformable nano-sieve channel, Nanotechnology, 31, 05LT01.

40. Qin, P., Park, M., Alfson, K., Tamhankar, M., Carrion, R., Patterson, J., Griffiths, A., Yildiz, A., Mathies, R., and Du, K*. (2019). Rapid and fully microfluidic Ebola virus detection with CRISPR-Cas13a, ACS Sensors, 4, 1048. (Featured as complementary cover)
*RIT news, *Yahoo Finance, *WHAM, *The Science Times, *Materials Post, *News Medical Life Sciences, *R&D, *ERIE NEWS NOW, *WRCBtv, *Agenparl, *News9, *WFMJ

41. Du, K., Wathuthanthri, I., Ding, J., and Choi, C. H. (2018). Superhydrophobic waveguide: liquid-core air cladding waveguide platform for optofluidics. Applied Physics Letters, 113, 143701.

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Before RIT:

1. Du, K., Jiang, Y., Liu, Y., Wathuthanthri, I., and Choi, C. H. (2018). Manipulation of superhydrophobicity of plasma-etched polymer nanostructures. Micromachines, 9, 304.

2. Du, K., Jiang, Y., Huang, P., Ding, J., Gao, T., and Choi, C. H. (2018). Self-formation of polymer nanostructures in plasma etching: mechanisms and applications. Journal of Micromechanics and Microengineering, 28, 014006.

3. Du, K., Park, M., Griffiths, A., Carrion, R., Patterson, J., Schmidt, H., and Mathies, R. (2017). Microfluidics for the detection of Viral RNA in whole blood samples using digital-coded barcode fluorescence dye and photo-cleavable capture probe. Analytical Chemistry, 89, 12433.

4. Du, K*., Park, M., Ding, J., Hu, H., and Zhang, Z. (2017). Sub-10 nm patterning with DNA nanostructures: a short perspective. Nanotechnology, 28, 442501.

5. Du, K., Ding, J., Wathuthanthri, I., and Choi, C. H. (2017). Selective hierarchical patterning of silicon nanostructures via soft stencil lithography. Nanotechnology, 28, 465303.

6. Du, K., Wathuthanthri, I., and Choi, C. H. (2017). The rise of scalable micro/nanopatterning. Micromachines, 8, 275.

7. Jiang, Y., Xu, J., Lee, J., Du, K., Yang, E. H., Moon, W., and Choi, C. H. (2017). Nanotexturing of conjugated polymers via one-step maskless oxygen plasma etching for enhanced tunable wettability. Langmuir, 33, 6885-6894.

8. Chauvin, A., Stephant, N., Du, K., Ding, J., Wathuthanthri, I., Choi, C. H., Tessier, P. Y., and El Mel, A. A. (2017). Large-scale fabrication of porous gold nanowires via laser interference lithography and dealloying of gold-silver nano-alloys. Micromachines, 8, 168.

9. Du, K., Ding, J., Liu, Y., Wathuthanthri. I., and Choi, C. H. (2017). Stencil lithography for scalable micro- and nanomanufacturing. Micromachines, 8, 131.
*Highlighted by Microfluidic Technology Review

10. Du, K., Cai, H., Park, M., Wall, T., Stott, M., Alfson, K., Griffiths, A., Carrion, R., Patterson, J., Hawkins, A., Schmidt, H., and Mathies, R. (2017). Multiplexed on-chip sample preparation and sensitive detection of Ebola virus. Biosensors and Bioelectronics, 91, 489-496.

11. El Mel, A. A., Chettab, M., Gautron, E., Chauvin, A., Humbert, B., Mevellec, J. Y., Cyril, D., Thiry, D., Stephant, N., Ding, J., Du, K., Choi, C. H., and Tessier, P. Y. (2016). Galvanic Replacement Reaction: A Route to Highly Ordered Bimetallic Nanotubes. The Journal of Physical Chemistry C. 120 (31), 17652-17659.

12. El Mel, A. A. E., Tessier, P. Y., Buffiere, M., Gautron, E., Ding, J., Du, K., Choi, C. H., Konstantinidis, E., Snyders, R., Bittencourt, C., and Molina‐Luna, L. (2016). Controlling the Formation of Nanocavities in Kirkendall Nanoobjects through Sequential Thermal Ex Situ Oxidation and In Situ Reduction Reactions. Small, 12 (21), 2885-2892.

13. Chauvin, A., Delacôte, C., Molina-Luna, L., Duerrschnabel, M., Boujtita, M., Thiry, Du, K., Ding, J., Choi, C. H., Tessier, P. Y., and El Mel, A. A. (2016). Planar arrays of nanoporous gold nanowires: when electrochemical dealloying meets nanopatterning. ACS Applied Materials & Interfaces, 8 (10), 6611-6620.

14.  Thiry, D., Molina-Luna, L., Gautron, E., Stephant, N., Chauvin, A., Du, K., Ding, J., Choi, C. H., Tessier, P.Y., and El Mel, A. A. (2015). The Kirkendall Effect in Binary Alloys: Trapping Gold in Copper Oxide Nanoshells. Chemistry of Materials, 27 (18), 6374-6384.

15. Du, K., Wathuthanthri, I., Liu, Y., Kang, Y. T., and Choi, C. H. (2014). Fabrication of polymer nanowires via maskless O2 plasma etching. Nanotechnology, 25 (16), 165301.
(Featured cover article)
*Stevens Institute of Technology news:  www.stevens.edu/news/paper-published-cover-nanotechnology

16. Ding, J., Du, K., Wathuthanthri, I., Choi, C. H., Fisher, F. T., and Yang, E. H. (2014). Transfer patterning of large-area graphene nanomesh via holographic lithography and plasma etching. Journal of Vacuum Science & Technology B, 32 (6), 06FF01.
*Most read JVST article
*Editor’s pick

17. El Mel, A. A., Molina-Luna, L., Buffiere, M., Tessier, P. Y., Du, K., Choi, C. H., Kleebe, H. J., Konstantinidis, S., Bittencourt, C., and Snyders, R. (2014). Electron Beam Nanosculpting of Kirkendall Oxide Nanochannels. ACS Nano, 8 (2), 1854-1861.

18. Du, K., Liu, Y., Wathuthanthri, I., and Choi, C. H. (2013). Fabrication of hierarchical nanostructures using free-standing trilayer membrane. Journal of Vacuum Science & Technology B, 31 (6), 06FF04.

19. Wathuthanthri, I., Liu, Y., Du, K., Xu, W., and Choi, C. H. (2013). Simple Holographic Patterning for High‐Aspect‐Ratio Three‐Dimensional Nanostructures with Large Coverage Area. Advanced Functional Materials, 23 (5), 608-618.

20. Lu, Y., Sarshar, M. A., Du, K., Chou, T., Choi, C. H., and Sukhishvili, S. A. (2013). Large- amplitude, reversible, pH-triggered wetting transitions enabled by layer-by-layer films. ACS Applied Materials & Interfaces, 5 (23), 12617-12623.

21. Du, K., Wathuthanthri, I., Liu, Y., Xu, W., and Choi, C. H. (2012). Wafer-Scale pattern transfer of metal nanostructures on polydimethylsiloxane (PDMS) substrates via holographic nanopatterns. ACS Applied Materials & Interfaces, 4 (10), 5505-5514.

22. Liu, Y., Du, K., Wathuthanthri, I., and Choi, C. H. (2012). From nanocone to nanodisc: Structural transformation of gold nanoarrays via simple mechanical stresses. Journal of Vacuum Science & Technology B, 30 (6), 06FF10.

23. El Mel. A. A., Buffière, M., Tessier, P. Y., Konstantinidis, S., Xu, W., Du, K., Wathuthanthri, I., Choi, C. H., Bittencourt, C., and Snyders, R. (2013). Highly ordered hollow oxide nanostructures: the kirkendall effect at the nanoscale. Small, 9 (17), 2838-2843. (Featured frontispiece)

24. Du, K., Liu, Y., Wathuthanthri, I., and Choi, C. H. (2012). Dual applications of free- standing holographic nanopatterns for lift-off and stencil lithography. Journal of Vacuum Science & Technology B, 30 (6), 06FF04.

25. Du, K., Wathuthanthri, I., Mao, W., Xu, W., and Choi, C. H. (2011). Large-area pattern transfer of metallic nanostructures on glass substrates via interference lithography. Nanotechnology, 22 (28), 285306.