Fabrication of waveguide spatial light modulators via femtosecond laser micromachining

We have previously introduced an anisotropic leaky-mode modulator as a waveguide-based, acousto-optic solution for spatial light modulation in holographic video display systems. Waveguide fabrication for these and similar surface acoustic wave devices relies on proton exchange of a lithium niobate substrate, which involves the immersion of the substrate in an acid melt. While simple and effective, waveguide depth and index profiles resulting from proton exchange are often non-uniform over the device length or inconsistent between waveguides fabricated at different times using the same melt and annealing parameters. In contrast to proton exchange, direct writing of waveguides has the appeal of simplifying fabrication (as these methods are inherently maskless) and the potential of fine and consistent control over waveguide depth and index profiles. In this paper, we explore femtosecond laser micromachining as an alternative to proton exchange in the fabrication of waveguides for anisotropic leaky-mode modulators

Learning hierarchical motif embeddings for protein engineering

Thesis: S.M., Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2017.Cataloged from PDF version of thesis.Includes bibliographical references (pages 75-79).This thesis lays the foundation for an integrated machine learning framework for the evolutionary analysis, search and design of proteins, based on a hierarchical decomposition of proteins into a set of functional motif embeddings. We introduce, CoMET - Convolutional Motif Embeddings Tool, a machine learning framework that allows the automated extraction of nonlinear motif representations from large sets of protein sequences. At the core of CoMET, lies a Deep Convolutional Neural Network, trained to learn a basis set of motif embeddings by minimizing any desired objective function. CoMET is successfully trained to extract all known motifs across Transcription Factors and CRISPR Associated proteins, without requiring any prior knowledge about the nature of the motifs or their distribution. We demonstrate that motif embeddings can model efficiently inter- and intra- family relationships. Furthermore, we provide novel protein meta-family clusters, formed by taking into account a hierarchical conserved motif phylogeny for each protein instead of a single ultra-conserved region. Lastly, we investigate the generative ability of CoMET and develop computational methods that allow the directed evolution of proteins towards altered or novel functions. We trained a highly accurate predictive model on the DNA recognition code of the Type II restriction enzymes. Based on the promising prediction results, we used the trained models to generate de novo restriction enzymes and paved the way towards the computational design of a restriction enzyme that will cut a given arbitrary DNA sequence with high precision.by Thrasyvoulos Karydis.S.M

Progress in fabrication of anisotropic Bragg gratings fabricated in lithium niobate via femtosecond laser micromachining

© 2018 SPIE. We have previously introduced a femtosecond laser micromachining-based scheme for the fabrication of anisotropic waveguides and isotropic Bragg reflection gratings in lithium niobate for application in future integrated-optic spatial light modulators. In this paper, we depict progress in fabrication and characterization of anisotropic Bragg reflection gratings fabricated in lithium niobate via Type I femtosecond laser-based permittivity modulation. We furthermore depict an electromagnetic analysis of such multilayer grating structures based around coupled-wave theory for thick holographic gratings

Progress in fabrication of waveguide spatial light modulators via femtosecond laser micromachining

We have previously introduced a femtosecond laser micromachining-based scheme for the fabrication of anisotropic waveguides in lithium niobate for use in a guided-wave acousto-optic spatial light modulator. This spatial light modulation scheme is extensible to off-plane waveguide holography via the integration of a Bragg reflection grating. In this paper, we present femtosecond laser-based direct-write approaches for the fabrication of (1) waveguide in-coupling gratings and (2) volume Bragg reflection gratings via permanent refractive index changes within the lithium niobate substrate. In combination with metal surface-acoustic-wave transducers, these direct-write approaches allow for complete fabrication of a functional spatial light modulator via femtosecond laser direct writing. Keywords: guided-wave acousto-optics, femtosecond laser micromachining, laser-written waveguides, laser-written gratings, lithium niobate, volume gratingsUnited States. Air Force. Research Laboratory (Contract FA8650-14-C-6571)MIT Media Lab Consortiu

Evolthon: A community endeavor to evolve lab evolution.

In experimental evolution, scientists evolve organisms in the lab, typically by challenging them to new environmental conditions. How best to evolve a desired trait? Should the challenge be applied abruptly, gradually, periodically, sporadically? Should one apply chemical mutagenesis, and do strains with high innate mutation rate evolve faster? What are ideal population sizes of evolving populations? There are endless strategies, beyond those that can be exposed by individual labs. We therefore arranged a community challenge, Evolthon, in which students and scientists from different labs were asked to evolve Escherichia coli or Saccharomyces cerevisiae for an abiotic stress-low temperature. About 30 participants from around the world explored diverse environmental and genetic regimes of evolution. After a period of evolution in each lab, all strains of each species were competed with one another. In yeast, the most successful strategies were those that used mating, underscoring the importance of sex in evolution. In bacteria, the fittest strain used a strategy based on exploration of different mutation rates. Different strategies displayed variable levels of performance and stability across additional challenges and conditions. This study therefore uncovers principles of effective experimental evolutionary regimens and might prove useful also for biotechnological developments of new strains and for understanding natural strategies in evolutionary arms races between species. Evolthon constitutes a model for community-based scientific exploration that encourages creativity and cooperation