Stanford Advisors

All Publications

  • Amplification of mid-IR continuum for broadband 2D IR spectroscopy OPTICS LETTERS Hack, J. H., Lewis, N. C., Carpenter, W. B., Tokmakoff, A. 2023; 48 (4): 960-963


    We report the generation and characterization of microjoule level, broad bandwidth femtosecond pulses in the mid-infrared (MIR) using optical parametric amplification of continuum MIR seed pulses in GaSe. The signal (3 μm) and idler (6 μm) pulses have energies of 6 μJ and 3 μJ with bandwidths of ∼950 cm-1 and 650 cm-1 FWHM and pulse lengths of 34 fs and 80 fs. Broadband 2D IR spectra of O-H and N-H transitions are acquired with the signal beam demonstrating the capabilities of this source for cross peak and line shape measurements.

    View details for DOI 10.1364/OL.481088

    View details for Web of Science ID 000943013200002

    View details for PubMedID 36790985

  • Ratiometric sensing of redox environments inside individual carboxysomes trapped in solution. Biophysical journal Carpenter, W. B., Lavania, A. A., Turnsek, J. B., Perez, D., Oltrogge, L. M., Dahlberg, P. D., Savage, D. F., Moerner, W. E. 2023; 122 (3S1): 304a

    View details for DOI 10.1016/j.bpj.2022.11.1712

    View details for PubMedID 36783520

  • Exploring Masses and Internal Mass Distributions of Single Carboxysomes in Free Solution Using Fluorescence and Interferometric Scattering in an Anti-Brownian Trap. The journal of physical chemistry. B Lavania, A. A., Carpenter, W. B., Oltrogge, L. M., Perez, D., Turnsek, J. B., Savage, D. F., Moerner, W. E. 2022


    Carboxysomes are self-assembled bacterial microcompartments that facilitate carbon assimilation by colocalizing the enzymes of CO2 fixation within a protein shell. These microcompartments can be highly heterogeneous in their composition and filling, so measuring the mass and loading of an individual carboxysome would allow for better characterization of its assembly and function. To enable detailed and extended characterizations of single nanoparticles in solution, we recently demonstrated an improved interferometric scattering anti-Brownian electrokinetic (ISABEL) trap, which tracks the position of a single nanoparticle via its scattering of a near-infrared beam and applies feedback to counteract its Brownian motion. Importantly, the scattering signal can be related to the mass of nanoscale proteinaceous objects, whose refractive indices are well-characterized. We calibrate single-particle scattering cross-section measurements in the ISABEL trap and determine individual carboxysome masses in the 50-400 MDa range by analyzing their scattering cross sections with a core-shell model. We further investigate carboxysome loading by combining mass measurements with simultaneous fluorescence reporting from labeled internal components. This method may be extended to other biological objects, such as viruses or extracellular vesicles, and can be combined with orthogonal fluorescence reporters to achieve precise physical and chemical characterization of individual nanoscale biological objects.

    View details for DOI 10.1021/acs.jpcb.2c05939

    View details for PubMedID 36282790

  • Ratiometric Sensing of Redox Environments Inside Individual Carboxysomes Trapped in Solution. The journal of physical chemistry letters Carpenter, W. B., Lavania, A. A., Borden, J. S., Oltrogge, L. M., Perez, D., Dahlberg, P. D., Savage, D. F., Moerner, W. E. 2022: 4455-4462


    Diffusion of biological nanoparticles in solution impedes our ability to continuously monitor individual particles and measure their physical and chemical properties. To overcome this, we previously developed the interferometric scattering anti-Brownian electrokinetic (ISABEL) trap, which uses scattering to localize a particle and applies electrokinetic forces that counteract Brownian motion, thus enabling extended observation. Here we present an improved ISABEL trap that incorporates a near-infrared scatter illumination beam and rapidly interleaves 405 and 488 nm fluorescence excitation reporter beams. With the ISABEL trap, we monitored the internal redox environment of individual carboxysomes labeled with the ratiometric redox reporter roGFP2. Carboxysomes widely vary in scattering contrast (reporting on size) and redox-dependent ratiometric fluorescence. Furthermore, we used redox sensing to explore the chemical kinetics within intact carboxysomes, where bulk measurements may contain unwanted contributions from aggregates or interfering fluorescent proteins. Overall, we demonstrate the ISABEL trap's ability to sensitively monitor nanoscale biological objects, enabling new experiments on these systems.

    View details for DOI 10.1021/acs.jpclett.2c00782

    View details for PubMedID 35549289

  • Characterizing physical properties of single carboxysomes in the Interferometric Scattering Anti-Brownian ELectrokinetic trap Lavania, A. A., Carpenter, W. B., Oltrogge, L. M., Borden, J., Perez, D. D., Squires, A. H., Dahlberg, P. D., Savage, D. F., Moerner, W. E. CELL PRESS. 2022: 431A
  • Redox sensing inside individual carboxysomes in the ISABEL trap Carpenter, W. B., Borden, J., Oltrogge, L. M., Lavania, A., Perez, D., Dahlberg, P. D., Savage, D., Moerner, W. E. CELL PRESS. 2022: 104