Amanda Holt Jones

Amanda Holt Jones's picture
Associate Research Scientist (Sweeney)
University of California
Research Areas: 
Biographical Sketch: 

Amanda Holt is a research scientist in Professor Alison Sweeney’s lab at Yale University. Amanda recieved her B.A. in both physics and music at Bard College and her Ph.D. from the University of California at Santa Cruz on organic electronic devices such as polyer-based photovoltaics, light-emitting diodes and electrochromics. Before joining Alison Sweeney’s group at the University of Pennsylvania, Amanda was a postdoctorate at the University of California at Santa Barbara where she researched bioinspired technologies.

Research : 

Amanda studies the interaction of light with optically purposed cells or systems of cells in marine animals. She uses both modeling and experimental techniques to understand the functionalities of these intricate systems. Amanda has developed sophisticated and creative models based on the transfer matrix method for analyzing the reflectance from complex biological micro-structures in the Loligo squid eye and models based on finite-difference time-domain method to model the light guides for bioluminescence in the mid-water squid Galiteuthis. Of particular interest is the colorful “Giant” clam which harbors symbiotic algae that helps them grow large in nutrient poor tropical waters. Giant clams also have iridescent cells which scatter intense tropical sun into the tissue. Amanda designed micro-probes for measuring irradiance and photochemical efficiencies at near-single cell resolution inside the tissue of the giant clam. She also developed a unique Monte Carlo model which verified measurements made with the radiometric probes. This model allows exploration of light scattering within an explicitly defined set of cells coordinates in three dimensions matching the real clam tissue. Amanda is currently working on detailed aspects of their monte carlo model and on designing other models to further understand the system of cellular scatterers in the giant clam as well as experimental techniques for quantifying optical properties such as spectroscopy and photography.

Ph.D. University of California, Santa Cruz, 2007
Honors & Awards: 

GAANN (Graduate Assistance in Areas of National Need), 2005-2007
UCSC Teaching Assistant Sabbatical Fellowship, 2004
Excellence at Equal Cost Scholarship (1997-2001), Bard College

Public education/outreach/service: 

Amanda is the lead science fair coordinator at Brook Knoll elementary school in Northern California. As the science fair is not a required part of the curriculum, Amanda focuses on making the science fair  accessable for all students especially those underrepresented at the regional and state fairs. She also shares her research and love of science with several 1st-5th grade classes every year as a guest speaker.

Selected Publications: 
  • “A highly-distributed Bragg stack with unique geometry provides effective camouflage for Loliiginid squid eyes,” A. L. Holt, A. M. Sweeney, S. Johnsen and D. E. Morse, J Roy. Soc. Int. 8, 1385 (2011).
  • “Photosymbiotic Giant Clams are Transformers of Solar Flux,” A. L. Holt, S. Vahidinia, Y. Gagnon, D. E. Morse and A. M. Sweeney J. Roy. Soc. Int. 11, 1 (2014).
  • “Open water camouflage via ‘leaky’ light guides in the midwater squid Galiteuthis,” A. L. Holt and A. M. Sweeney J. Roy. Soc. Int. 13, 1 (2016).
  • “Three-dimensional midwater camouflage from a novel two-component photonic structure in hatchetfish skin,” E. I. Rosenthal, A. L. Holt, A. M. Sweeney J. Roy. Soc. Int. 11, 1 (2017).
  • “Adaptive Thermogenesis in Mice Is Enhanced by Opsin 3-Dependent Adipocyte Light Sensing,” G. Nayak, K. X. Zhang, S.Vemaraju, Y. Odaka, E. D. Buhr, A. Holt-Jones, et al. CellReports, 30, 672 (2020).