Publications

1. Pradhan H†, Poudel A, Shrestha D†, Rogers A†, Stewart M†, Jereb A†, Harper J‡, Li M‡, Zhang W, Chen J, and Wang Y#. Concentration-Dependent Responses of C. reinhardtii to Silver Ions: Hormetic Response in Growth and Reduction of Motility. Under Review, 2025.

2. Jereb A†, Sebag C, Sadoon A†, Shrestha D†, Savin M, Zhang W#, Wang Y#. Efficient Separation Methods for Quantifying Antibiotic Resistance Genes: Insights from Synthetic and Environmental Water Samples. Under Review, 2025.

3. Shrestha D†, Mahmud K, Mortenson S‡, Savin M, Zhang W and Wang Y#. Bacterial motility in aqueous micro-environment with natural soil particles. Biointerphases, 2025; 20(4):041001. https://doi.org/10.1116/6.0004380

4. Bullard K‡, Okyere D, Foster SJ‡, Sadoon AA†, Li J, Chen J, and Wang Y#. Understanding the Mechanism of Bent DNA Amplifying Sensors using All-Atom Molecular Dynamics Simulations. Biosensors, 2025; 15(5):272. https://doi.org/10.3390/bios15050272

5. Rogers A†, Niyonshuti II, Ou J, Shrestha D†, Okyere D, Chen J, Wang Y#. The Shape Modulation of Laser-Induced Nanowelded Microstructures Using Two Colors. Colloids and Interfaces, 2023; 7:67. https://doi.org/10.3390/colloids7040067.

6. Rogers A†, He Z†, Wang Y#. Exploring the potential of tesla valve for filtering and sorting microscale active swimmers: A computational study. Applications in Engineering Science, 2023;16:100159. https://doi.org/10.1016/j.apples.2023.100159.

7. Russell B†, Rogers A†, Yoder R‡, Kurilich M‡, Krishnamurthi VR†, Chen J, Wang Y#. Silver Ions Inhibit Bacterial Movement and Stall Flagellar Motor. International Journal of Molecular Sciences, 2023;24:11704. https://doi.org/10.3390/ijms241411704.

8. Nguyen AT, Baucom DR, Wang Y, Heyes CD#. Compact, Fast Blinking Cd-Free Quantum Dots for Super-Resolution Fluorescence Imaging. Chemical & Biomedical Imaging, 2023;1:251–9. https://doi.org/10.1021/cbmi.3c00018.

9. Shrestha D†, Ou J, Rogers A, Jereb A, Okyere D, Chen J, Wang Y#. Bacterial mobility and motility in porous media mimicked by microspheres. Colloids and Surfaces B: Biointerfaces, 2023, 222:113128. https://doi.org/10.1016/j.colsurfb.2023.113128

10. Sadoon AA†, William F Oliver, Wang Y#. Revisiting the temperature dependence of protein diffusion inside bacteria: validity of the Stokes-Einstein equation. Physical Review Letters, 2022, 129(1):018101. https://doi.org/10.1103/PhysRevLett.129.018101

11. Rogers A†, Bullard KB‡, Dod AC‡, Wang Y#. Bacterial Growth Curve Measurements with a Multimode Microplate Reader. Bio-Protocol, 2022; 12, no. 9: e4410-e4410. doi: https://doi.org/10.21769/BioProtoc.4410.

12. Krishnamurthi VR†, Harris N, Rogers A†, Zou M, Wang Y#. Interactions of E. Coli with Cylindrical Micro-Pillars of Different Geometric Modifications.” Colloids and Surfaces B: Biointerfaces, 2022; 209, 112190. doi: https://doi.org/10.1016/j.colsurfb.2021.112190.

13. Rogers A†, Niyoshuti II, Cai A, Wang F, Benamara M, Chen J#, Wang Y#. Real-time imaging of laser-induced nanowelding of silver nanoparticles in solution. Journal of Physical Chemistry C. 2021; 125(19). doi: https://doi.org/10.1021/acs.jpcc.1c00184 

14. Dulal N, Rogers AM, Proko R, Bieger BD, Liyanage R, Krishnamurthi VR†, Wang Y, Egan MJ#. Turgor-dependent and coronin-mediated F-actin dynamics drive septin disc-to-ring remodeling in the blast fungus. Journal of Cell Science. 2021; 134(5). doi: https://doi.org/10.1242/jcs.251298 

15. Krishnamurthi VR†, Niyonshuti II, Chen J, Wang Y#. A new analysis method for evaluating bacterial growth with microplate readers. PLoS One. 2021; 16(1):e0245205. doi: https://doi.org/10.1371/journal.pone.0245205 PubMed PMID: 33434196; PubMed Central PMCID: PMC7802944.

16. Saran R, Wang Y, Li I#. Mechanical flexibility of DNA: A quintessential tool for DNA nanotechnology. Sensors. 2020/12; 20(24):7019. doi: https://doi.org/10.3390/s20247019 

17. Niyonshuti II*, Krishnamurthi VR†*, Okyere D, Song L, Benamara M, Tong X, Wang Y#, Chen J#. Polydopamine Surface Coating Synergizes the Antimicrobial Activity of Silver Nanoparticles. ACS Appl Mater Interfaces. 2020 Sep 9;12(36):40067-40077. doi: https://doi.org/10.1021/acsami.0c10517 Epub 2020 Aug 28. PubMed PMID: 32794690. (*: co-first authors)

18. Krishnamurthi VR†, Rogers A†‡, Peifer J‡, Niyonshuti II, Chen J, Wang Y#. Microampere Electric Current Causes Bacterial Membrane Damage and Two-Way Leakage in a Short Period of Time. Appl Environ Microbiol. 2020 Aug 3;86(16). doi: https://doi.org/10.1128/AEM.01015-20 Print 2020 Aug 3. PubMed PMID: 32561580; PubMed Central PMCID: PMC7414946. (In the News)

19. Freeland J‡, Zhang L, Wang ST, Ruiz M‡, Wang Y#. Bent DNA bows as sensing amplifiers for detecting DNA-interacting salts and molecules. Sensors. 2020 May; 20(11):3112. doi: https://doi.org/10.3390/s20113112 (In the News)

20. Freeland J‡, Krishnamurthi VR†, Wang Y#. Learning the lens equation using water and smartphones/tablets. The Physics Teacher. 2020 May; 58(5):360-361. doi: https://doi.org/10.1119/1.5145539 

21. Dulal N, Rogers A, Wang Y, Egan M#. Dynamic assembly of a higher-order septin structure during appressorium morphogenesis by the rice blast fungus. Fungal Genet Biol. 2020 Apr 16;:103385. doi: https://doi.org/10.1016/j.fgb.2020.103385 PubMed PMID: 32305452.

22. Wang Y#, Fei J#. Continuous active development of super-resolution fluorescence microscopy. Phys Biol. 2020 Apr 7;17(3):030401. doi: https://doi.org/10.1088/1478-3975/ab7731  PubMed PMID: 32066124.

23. Sadoon AA†, Khadka P§, Freeland J‡, Gundampati RK, Manso R, Ruiz M‡, Krishnamurthi VR†, Thallapuranam SK, Chen J#, Wang Y#. Silver Ions Caused Faster Diffusive Dynamics of Histone-Like Nucleoid-Structuring Proteins in Live Bacteria. Appl Environ Microbiol. 2020 Jan 17;. doi: https://doi.org/10.1128/AEM.02479-19 PubMed PMID: 31953329. (In the News)

24. Krishnamurthi VR†, Chen J, Wang Y#. Silver ions cause oscillation of bacterial length of Escherichia coli. Sci Rep. 2019 Aug 13;9(1):11745. doi: https://doi.org/10.1038/s41598-019-48113-4 PubMed PMID: 31409877; PubMed Central PMCID: PMC6692348.

25. Alqahtany M†*, Khadka P§*, Niyonshuti II*, Krishnamurthi VR†, Sadoon AA†, Challapalli SD†, Chen J, Wang Y#. Nanoscale reorganizations of histone-like nucleoid structuring proteins in Escherichia coli are caused by silver nanoparticles. Nanotechnology. 2019 Sep 20;30(38):385101. doi: https://doi.org/10.1088/1361-6528/ab2a9f PubMed PMID: 31212266. (*: co-first authors)

26. Freeland J‡, Khadka P§, Wang Y#. Mechanical-energy-based amplifiers for probing interactions of DNA with metal ions. Physical Review E. 2018 December; 98(6):062403. doi: https://doi.org/10.1103/PhysRevE.98.062403 (In the News)

27. Sadoon AA†, Wang Y#. Anomalous, non-Gaussian, viscoelastic, and age-dependent dynamics of histonelike nucleoid-structuring proteins in live Escherichia coli. Physical Review E. 2018 October; 98(4):042411. doi: https://doi.org/10.1103/PhysRevE.98.042411 (Editor’s suggestion, In the News)

28. Haque MA†, Imamura R, Brown GA‡, Krishnamurthi VR†, Niyonshuti II, Marcelle T‡, Mathurin LE, Chen J#, Wang Y#. An experiment-based model quantifying antimicrobial activity of silver nanoparticles on Escherichia coli. RSC Advances. 2017 December; 8(89):56173-56182. doi: https://doi.org/10.1039/C7RA10495B 

29. Jiang S‡, Park S, Challapalli SD†, Fei J, Wang Y#. Robust nonparametric quantification of clustering density of molecules in single-molecule localization microscopy. PLoS One. 2017;12(6):e0179975. doi: https://doi.org/10.1371/journal.pone.0179975 eCollection 2017. PubMed PMID: 28636661; PubMed Central PMCID: PMC5479598. (‡: high-school student from my group)

30. Nino D, Rafiei N, Wang Y, Zilman A, Milstein JN#. Molecular Counting with Localization Microscopy: A Bayesian Estimate Based on Fluorophore Statistics. Biophys J. 2017 May 9;112(9):1777-1785. doi: https://doi.org/10.1016/j.bpj.2017.03.020 PubMed PMID: 28494949; PubMed Central PMCID: PMC5425379.

31. Wang Y#. Spatial distribution of high copy number plasmids in bacteria. Plasmid. 2017 May;91:2-8. doi: https://doi.org/10.1016/j.plasmid.2017.02.005  PubMed PMID: 28263761.

32. Wang Y#, Penkul P, Milstein JN# (2016). Quantitative localization microscopy in combination with DNA smFISH reveals new features of the organization of high-copy number plasmids in bacteria, Biophysical Journal, 111:467–79. doi: https://doi.org/10.1016/j.bpj.2016.06.033 

33. Wang Y, Cai E, Rosenkranz T, Ge P, Teng KW, Lim SJ, Smith AM, Chung HJ, Sachs F, Green WN, Gottlieb P, Selvin PR#. Small quantum dots conjugated to nanobodies as immunofluorescence probes for nanometric microscopy. Bioconjug Chem. 2014 Dec 17;25(12):2205-11. doi: https://doi.org/10.1021/bc5004179 Epub 2014 Nov 25. PubMed PMID: 25397889; PubMed Central PMCID: PMC4275168.

34. Cai E, Ge P, Lee SH, Jeyifous O, Wang Y, Liu Y, Wilson KM, Lim SJ, Baird MA, Stone JE, Lee KY, Davidson MW, Chung HJ, Schulten K, Smith AM, Green WN, Selvin PR#. Stable small quantum dots for synaptic receptor tracking on live neurons. Angew Chem Int Ed Engl. 2014 Nov 10;53(46):12484-8. doi: https://doi.org/10.1002/anie.201405735 Epub 2014 Sep 26. PubMed PMID: 25255882; PubMed Central PMCID: PMC4240739.

35. Wang Y, Cai E, Sheung J, Lee SH, Teng KW, Selvin PR#. Fluorescence imaging with one-nanometer accuracy (FIONA). J Vis Exp. 2014 Sep 26;(91):51774. doi: https://doi.org/10.3791/51774 PubMed PMID: 25286081; PubMed Central PMCID: PMC4828134.

36. Wang Y, Liu Y, Deberg HA, Nomura T, Hoffman MT, Rohde PR, Schulten K, Martinac B, Selvin PR#. Single molecule FRET reveals pore size and opening mechanism of a mechano-sensitive ion channel. Elife. 2014 Feb 18;3:e01834. doi: https://doi.org/10.7554/eLife.01834 PubMed PMID: 24550255; PubMed Central PMCID: PMC3925968. (In the News)

37. Wang Y, Fruhwirth G, Cai E, Ng T, Selvin PR#. 3D super-resolution imaging with blinking quantum dots. Nano Lett. 2013 Nov 13;13(11):5233-41. doi: https://doi.org/10.1021/nl4026665  Epub 2013 Oct 10. PubMed PMID: 24093439; PubMed Central PMCID: PMC3874875.

38. Wang Y, Zocchi G#. Viscoelastic transition and yield strain of the folded protein. PLoS One. 2011;6(12):e28097. doi: https://doi.org/10.1371/journal.pone.0028097  Epub 2011 Dec 8. PubMed PMID: 22174767; PubMed Central PMCID: PMC3234265. (In the News)

39. Qu H, Wang Y, Tseng C, Zocchi G#. Critical torque for kink formation in double-stranded DNA. Physical Review X. 2011 November; 1(2):021008. doi: https://doi.org/10.1103/PhysRevX.1.021008 

40. Wang Y, Zocchi G#. The folded protein as a viscoelastic solid. EPL (Europhysics Letters). 2011 September; 96(1):18003. doi: https://doi.org/10.1209/0295-5075/96/18003 

41. Wang Y, Zocchi G#. Elasticity of globular proteins measured from the ac susceptibility. Phys Rev Lett. 2010 Dec 3;105(23):238104. doi: https://doi.org/10.1103/PhysRevLett.105.238104  Epub 2010 Dec 3. PubMed PMID: 21231509. (Editor’s Suggestion; highlighted by the Physics Spotlighting Exceptional Research and Materials 360)

42. Qu H, Tseng C, Wang Y, Levine AJ, Zocchi G#. The elastic energy of sharply bent nicked DNA. EPL (Europhysics Letters). 2010 April; 90(1):18003. doi: https://doi.org/10.1209/0295-5075/90/18003  (In the News)

43. Wang Y, Zocchi G#. Shape of fair weather clouds. Phys Rev Lett. 2010 Mar 19;104(11):118502. doi: https://doi.org/10.1103/PhysRevLett.104.118502  Epub 2010 Mar 18. PubMed PMID: 20366506. (Invited to APS Press Conference)

44. Wang Y, Wang A, Qu H, Zocchi G#. Protein-DNA chimeras: synthesis of two-arm chimeras and non-mechanical effects of the DNA spring. J Phys Condens Matter. 2009 Aug 19;21(33):335103. doi: https://doi.org/10.1088/0953-8984/21/33/335103  Epub 2009 Jul 8. PubMed PMID: 21828597.

45. Lai F#, Wang Y, Li M, Wang H, Song Y, Jiang Y. Determination of optical constants and inhomogeneity of optical films by two-step film envelope method. Thin Solid Films. 2007 April; 515(11):4763-4767. doi: https://doi.org/10.1016/j.tsf.2006.11.035 

46. Fan H#, Wang Y. Study Hankel Transforms and Properties of Bessel Function via Entangled State Representation Transformation in Quantum Mechanics. Communications in theoretical physics. 2006 May; 45(5):819. doi: https://doi.org/10.1088/0253-6102/45/5/012 

47. Fan H#, Wang Y. Generating Generalized Bessel Equations by Virtue of Bose Operator Algebra and Entangled State Representations. Communications in theoretical physics. 2006 January; 45(1):71. doi: https://doi.org/10.1088/0253-6102/45/1/013