X-Ray Data Analysis

Sineth G Kodikara

********@****.*** 330-***-****) Kent, OH

https://www.linkedin.com/in/sineth-kodikara-191a81131/ SUMMARY

With over six years of experience in advanced scientific research, I specialize in DNA-based liquid crystals and single-molecule biophysics. My expertise spans a range of techniques, including small/wide-angle X-ray scattering (SAXS/WAXS), PAGE purification, cell culture, cell viability assays, RT-qPCR, western blotting, and single-molecule Förster resonance energy transfer (smFRET). I am also skilled in cryogenic sample preparation and cryo-electron microscopy. My work has resulted in fourteen peer-reviewed scientific publications, reflecting my proficiency in using and maintaining scientific equipment, sample characterization, and data analysis. I have successfully collaborated with diverse teams, both internally and externally. Additionally, I bring over two years of experience in semiconductor physics, focusing on the design, processing, and characterization of Organic Electrochemical Transistors, cleanroom- based semiconductor fabrication, and a deep understanding of semiconductor manufacturing. PROFESSIONAL EXPERIENCE

Guest User: Brookhaven National Laboratory(CMS Beamline, NSLS II), Upton, New York. (January 2021-Present)

Design and conduct small-angle and wide-angle x-ray scattering (SAXS/WAXS) experiments on DNA-based liquid crystals.

Characterize liquid crystalline phases of DNA liquid crystals. Graduate Research Assistant: Department of Physics, Kent State University, Kent, Ohio. (August 2019- Present)

Organic Electrochemical Transistors:

Study and explain the equilibrium state and transient response of organic electrochemical transistors (OECTs).

Develop a substrate-free OECT based on liquid crystal elastomers and use it as a strain sensor.

Develop a bending sensor using ionic liquid crystal elastomers as the solid electrolyte of OECTs.

Single Molecule Biophysics, Biochemistry and DNA-based Liquid Crystals:

Gain experience in nucleic acids (DNA/RNA) characterization and purification techniques such as agarose gel electrophoresis, PAGE purification, UV spectroscopy, Circular Dichroism, Nanodrop, and fluorometry.

Utilize the prism-type total internal reflection fluorescence microscope (TIRF) to study the DNA and protein interactions using the single-molecule Fӧrster resonance energy transfer (smFRET) method.

Develop a novel method to purify and concentrate DNA into liquid crystal phases and characterize those phases using SAXS/WAXS and polarized optical microscope (POM).

Conduct systematic studies on the interaction of CRISPR-dCas9 and CRISPR-dCas13d with G-quadruplex structures, revealing their impact on target recognition and DNA cleavage efficiency.

Gain experience in DNA labeling, cell culture, RT-qPCR, western blotting, and cell viability assay.

Perform troubleshooting and maintenance of lab instruments. Research Collaboration, Cleveland Center for Membrane and Structural Biology-Case Western Reserve University, Cleveland, Ohio. (April 2023-present)

Cryo-electron microscopy Sample preparation and imaging of DNA G-Quadruplexes and proteins. Teaching Experience:

Teaching assistant, Kent State University, Kent, Ohio (August 2019-Present).

Teaching assistant, University of Peradeniya, Sri Lanka (January 2018- July 2019). TRAINING

Cryo-EM training: New York Structural Biology Center, New York. (December 2023 and April 2025)

Completed on-site trainings in cryogenic sample preparation (Vitrobots), imaging, and data analysis (CryoSPARC) at the National Center for cryoEM Access and Training in New York Structural Biology Center. 2024 Pathways to a Semiconductor Career Summer Program, funded by Intel Corporation. (May 2024- June 2024)

Followed an in-person semiconductor manufacturing and processing (Lecture) and cleanroom-based semiconductor fabrication

(Lab) summer program.

EDUCATION

Ph.D. Candidate, Physics, (2019-Present) (GPA 3.76/4.00) Kent State University, Kent, Ohio, USA

M.A. Physics, (2019-2021) (GPA 3.76/4.00)

Kent State University, Kent, Ohio, USA

B.Sc. Major in Physics, (2014-2017) (GPA 3.57/4.00) University of Peradeniya, Sri Lanka

AWARDS

Domestic Travel Award (DTA) by Graduate Student Senate (GSS), Kent State University for the Spring 2022 semester.

Stipend award by the Institute for Complex Adaptive Matter (ICAM)-2023.

University Fellowship Award, Kent State University for the 2024-2025 academic year.

“Pathways to a Semiconductor Career Program” full scholarship by Intel Corporation. SKILLS

Instruments: Semiconductor Analyzer (Keithley 4200), Polarizing Optical Microscopy (POM), Total Internal Reflection Fluorescence Microscopy (TIRF), UV/VIS spectrometer, Plate Reader (BioTeK Synergy Neo2), Nanodrop

(Onec), Fluorometer, Cryogenic electron microscopy (TFS Glacious, TFS-Titan Krios), Vitrobot, ChemiDoc Imaging System (ItTS2), Biomolecular Iager (TiphoonTM FLA 9500), PCR Thermocycler (Eppendorf Mastercycler RealPlex2), Circular Dichroism Spectrometer Spectroscopy, Mass photometry (Refeyn twoMP). Clean Room: Photolithography, Dry Etching, Atomic Layer Deposition in 100/1000 cleanroom facilities. Data Analysis: Origin, Excel, MATLAB, SigmaPlot, CryoSPARC. Designing: Adobe Illustrator, Chimera, Adobe Premiere Pro, Adobe Photoshop, ChemDraw. Leadership: President of Physics Graduate Student Association, Kent State University, Kent, Ohio,

(August 2022 – September 2023).

Vice President of Physics Graduate Student Association, Kent State University, Kent, Ohio (August 2020 – August 2022).

Representative of the Department of Physics to the Kent State University graduate student senate, Kent State University, Kent, Ohio ( April 2023- October 2023). Secretary of the Physical Society, University of Peradeniya, Sri Lanka, (January 2016-January 2018). SELECTED PUBLICATIONS (https://scholar.google.com/citations?user=fZ_VqRoAAAAJ&hl=en&oi=ao) 1. Sineth G Kodikara et al., Sequence-Dependent Liquid Crystalline Ordering of Gapped DNA., ACS Macro Letters (2025). 2. Mohammad Kabir, Sineth G. Kodikara et al., Combining the CRISPR Activation and Interference Capabilities Using dCas9 and G-Quadruplex Structures., NAR Molecular Medicine (2025). 3. Sineth G Kodikara et al., Impact of Divalent Cations on In-Layer Positional Order of DNA-Based Liquid Crystals: Implications for DNA Condensation., Biomacromolecules (2024).

4. Sajad Shiekh, Sineth G. Kodikara et al., Protection of the Telomeric Junction by the Shelterin Complex., J. Am. Chem. Soc.

(2024).

5. Sineth G Kodikara et al., Stability of End-to-End Base Stacking Interactions in Highly Concentrated DNA Solutions., Langmuir (2023).

6. Sineth G Kodikara et al., Detecting Secondary Structure Formation with FRET-PAINT, Analyst (2023). 7. Arwa Alyami, Sineth G. Kodikara et al., Bending Sensors Using Ionic Liquid Crystal Elastomers as Solid Electrolyte of Organic Electrochemical Transistors., Liq. Cryst. 00, 1-8 (2023). 8. Sajad Shiekh, Sineth G. Kodikara et al., Emerging Accessibility Patterns in Long Telomeric Overhangs., Proc. Natl. Acad. Sci. U. S. A. 119, 1 (2022).

9. C. P. Hemantha Rajapaksha, P. M. Sineth. G. Kodikara et al., Ionic Liquid Crystal Elastomers-Based Flexible Organic Electrochemical Transistors: Effect of Director Alignment of the Solid Electrolyte., Appl. Phys. Rev. 9, (2022). 10. Prabesh Gyawali, Sineth G. Kodikara et al., Smectic-B Phase and Temperature-Driven Smectic-B to-A Transition in Concentrated Solutions of “gapped” DNA., Phys. Rev. Res. 4, 033046 (2022). 11. Sajad Shiekh, Sineth G. Kodikara et al., Shelterin reduces the Accessibility of Telomeric Overhangs., Nucleic Acids Res. 50, 12885 (2022).

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