D. Sebastian Arias Roldan

I graduated from the University of California, Santa Barbara (UCSB) with a Bachelors of Science in physics. While at UCSB, I interned in Deborah Fygenson's NanoBio Physics Lab, where I acquired a passion for DNA nanotechnology research. After graduating, I completed research at the University of South Florida's Physics department as part of the American Physical Society (APS) Bridge Program, at UCSB as a Jr. Specialist, and finally at Los Alamos National Laboratory's Center for Integrated Nanotechnologies as a GEM Fellow.

Current Project

My current project is focused on the design and development of a nano-scale DNA strain sensor capable of measuring sub-nanometer displacements through mechanical amplification and the application of Förster Resonance Energy Transfer (FRET). Currently, we plan to use these sensors to verify conformation change of twisting DNA nanotubes. Thanks to DNA's versatility we expect that such a device will have wide-ranging applications beyond this, including as a lipid bilayer strain sensor.

Previous projects

  • Characterizing Amphiphilic Copolymers Bilayer Fluidity- Using Fluorescence recovery after photobleaching (FRAP), I characterized the fluidity of polybutadiene-block-poly(acrylic acid) (PBD_PAA) supported bilayers across buffer conditions, including pH and ionic strength, with the ultimate aim to engineer these into biomimetic systems.

  • NunchuckNet- I carried out all the initial implementations, performance characterization and development of a neural network capable of analyzing fluorescence microscopy images. I also developed a synthetic data generator used to create training data sets. NunchuckNet vastly reduced the time of analysis and increased accuracy.

  • Amyloid Fibrils Growth Kinetics Characterization- I focused on identifying and characterizing amyloid dyes with aggregate-specific binding in order to examine amyloid fibrils growth inhibition due to the curvilinear fibrils concentration in solution.

  • Advancement of DNA Nunchucks- These are DNA nanostructures formed with fluorescently labeled DNA nanotubes whose nucleation is controlled by DNA origami "seeds". Two of these seeded nanotubes (2-5um long) are connected by a double stranded "linker" of varying length and sequence giving it the characteristic nunchuck look. The purpose of these nunchucks are to mechanically amplify the angle formed by the linker strand between them. Fluorescence microscopy then allows the visualization of DNA bending and bending dynamics.

Publications

  • Babatunde, Bolutito, D. Sebastian Arias, Jonathan Cagan, and Rebecca E. Taylor. “Generating DNA Origami Nanostructures through Shape Annealing.” Applied Sciences 11, no. 7 (January 2021): 2950. https://doi.org/10.3390/app11072950.

  • Wang, Weitao*, D. Sebastian Arias*, Markus Deserno, Xi Ren, and Rebecca E. Taylor. “Emerging Applications at the Interface of DNA Nanotechnology and Cellular Membranes: Perspectives from Biology, Engineering, and Physics.” APL Bioengineering 4, no. 4 (December 1, 2020): 041507. https://doi.org/10.1063/5.0027022. * denotes equal contribution to the work

  • Cai, Xinyue, D. Sebastian Arias, Lourdes R. Velazquez, Shelby Vexler, Alexander L. Bevier, and D. Kuchnir Fygenson. “DNA Nunchucks: Nanoinstrumentation for Single-Molecule Measurement of Stiffness and Bending.” Nano Letters, December 24, 2019. https://doi.org/10.1021/acs.nanolett.9b04980.

  • Barton, Jeremy, D. Sebastian Arias, Chamani Niyangoda, Gustavo Borjas, Nathan Le, Saefallah Mohamed, and Martin Muschol. “Kinetic Transition in Amyloid Assembly as a Screening Assay for Oligomer-Selective Dyes.” Biomolecules 9, no. 10 (October 2019): 539. https://doi.org/10.3390/biom9100539.

  • Brashears, Travis, Philip Lubin, Gary B. Hughes, Kyle McDonough, Sebastian Arias, Alex Lang, Caio Motta, et al. “Directed Energy Interstellar Propulsion of Wafersats.” In Nanophotonics and Macrophotonics for Space Environments IX, 9616:961609. International Society for Optics and Photonics, 2015. https://doi.org/10.1117/12.2189005.

Scholarships and Awards

  • HSF (Hispanic Scholarship Fund) Scholar, 2021
  • Milton Shaw PhD Research Award, 2021
  • Los Alamos National Laboratory Spot Award, 2019
  • GEM Fellow with Los Alamos National Laboratory Sponsorship, 2019
  • USF/APS Bridge-to-Doctorate Fellowship, 2017
  • UCSB Department of Physics Research Honors Award, 2017
  • California Alliance for Minority Participation (CAMP) Statewide Symposium Honorable Mention, 2016

Presentations

  • Optimization ofDNA Nunchuck Seed Design for the Accurate Measurement ofDNA Bend Angle- California Alliance for Minority Participation (CAMP) Statewide Symposium , Winter 2017; Society for Advancement of Chicanos/Hispanics and Native Americans in Science (SACNAS) Conference, Fall 2016; UCSB Undergraduate Research Poster Symposium, Summer 2016.
  • DNA Origami Aggregation as a Function of Staple Strand Concentration in Solution- UCSB Physics Undergraduate Summer Research Symposium, Summer 2016.
  • Quantification ofDNA Origami Purity and Concentration Within Solution- California Alliance for Minority Participation (CAMP) Statewide Symposium , Winter 2016; UCSB Undergraduate Research Poster Symposium, Summer 2015.

Contact Information

Email: dariasro@andrew.cmu.edu