Bio


Colin Ophus is an Associate Professor in the Department of Materials Science and Engineering and a Center Fellow at the Precourt Institute for Energy, Stanford University. He previously worked as a Staff Scientist at the National Center for Electron Microscopy (NCEM), part of the Molecular Foundry, at Lawrence Berkeley Lab. He was awarded a US Department of Energy (DOE) Early Career award in 2018, and the Burton medal from the Microscopy Society of America (MSA) in 2018. His research focuses on experimental methods, reconstruction algorithms, and software codes for simulation, analysis, and instrument design of transmission electron microscopy (TEM) and scanning TEM (STEM).

Colin advocates for open science and his group has developed open-source scientific software including as the Prismatic STEM simulation code and py4DSTEM analysis toolkit. He has taught many workshops around the world on topics ranging from scientific visualization to large scale data analysis. He also is the founder and editor-in-chief for a new journal based on interactive science communication named Elemental Microscopy.

Academic Appointments


Honors & Awards


  • Burton Medal in Physical Sciences, Microscopy Society of America (2022)
  • Early Career Research Award, US Department of Energy (2018)

2024-25 Courses


Stanford Advisees


All Publications


  • Integrated rocksalt-polyanion cathodes with excess lithium and stabilized cycling NATURE ENERGY Huang, Y., Dong, Y., Yang, Y., Liu, T., Yoon, M., Li, S., Wang, B., Zheng, E., Lee, J., Sun, Y., Han, Y., Ciston, J., Ophus, C., Song, C., Penn, A., Liao, Y., Ji, H., Shi, T., Liao, M., Cheng, Z., Xiang, J., Peng, Y., Ma, L., Xiao, X., Kan, W., Chen, H., Yin, W., Guo, L., Liu, W., Muruganantham, R., Yang, C., Zhu, Y., Li, Q., Li, J. 2024
  • Considerations for extracting moiré-level strain from dark field intensities in transmission electron microscopy JOURNAL OF APPLIED PHYSICS Craig, I. M., Van Winkle, M., Ophus, C., Bediako, D. 2024; 136 (7)

    View details for DOI 10.1063/5.0222102

    View details for Web of Science ID 001293864000008

  • Electronic structure along Sm2Co3Ge5 twin boundaries ACTA MATERIALIA Kennedy, E., Kyrk, T. M., Ophus, C., McCandless, G. T., Chan, J. Y., Scott, M. C. 2024; 270
  • Structural Study of Hydrated Organic Mixed Ionic Electronic Conductors Using Cryogenic 4D-STEM. Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada Tsarfati, Y., Bustillo, K. C., Savitzky, B. H., Ophus, C., McCulloch, I., Salleo, A., Minor, A. M. 2023; 29 (Supplement_1): 264-265

    View details for DOI 10.1093/micmic/ozad067.119

    View details for PubMedID 37613608

  • Multimodal Characterization of Crystal Structure and Formation in Rubrene Thin Films Reveals Erasure of Orientational Discontinuities ADVANCED FUNCTIONAL MATERIALS Tan, J. A., Dull, J. T., Zeltmann, S. E., Tulyagankhodjaev, J. A., Johnson, H. M., Liebman-Pelaez, A., Folie, B. D., Donges, S. A., Khatib, O., Raybin, J. G., Roberts, T. D., Hamerlynck, L. M., Tanner, C. N., Lee, J., Ophus, C., Bustillo, K. C., Raschke, M. B., Ohldag, H., Minor, A. M., Rand, B. P., Ginsberg, N. S. 2023
  • Spatially resolved structural order in low-temperature liquid electrolyte. Science advances Xie, Y., Wang, J., Savitzky, B. H., Chen, Z., Wang, Y., Betzler, S., Bustillo, K., Persson, K., Cui, Y., Wang, L. W., Ophus, C., Ercius, P., Zheng, H. 2023; 9 (2): eadc9721

    Abstract

    Determining the degree and the spatial extent of structural order in liquids is a grand challenge. Here, we are able to resolve the structural order in a model organic electrolyte of 1 M lithium hexafluorophosphate (LiPF6) dissolved in 1:1 (v/v) ethylene carbonate:diethylcarbonate by developing an integrated method of liquid-phase transmission electron microscopy (TEM), cryo-TEM operated at -30°C, four-dimensional scanning TEM, and data analysis based on deep learning. This study reveals the presence of short-range order (SRO) in the high-salt concentration domains of the liquid electrolyte from liquid phase separation at the low temperature. Molecular dynamics simulations suggest the SRO originates from the Li+-(PF6-)n (n > 2) local structural order induced by high LiPF6 salt concentration.

    View details for DOI 10.1126/sciadv.adc9721

    View details for PubMedID 36638171

  • Correlative image learning of chemo-mechanics in phase-transforming solids. Nature materials Deng, H. D., Zhao, H., Jin, N., Hughes, L., Savitzky, B. H., Ophus, C., Fraggedakis, D., Borbely, A., Yu, Y., Lomeli, E. G., Yan, R., Liu, J., Shapiro, D. A., Cai, W., Bazant, M. Z., Minor, A. M., Chueh, W. C. 2022

    Abstract

    Constitutive laws underlie most physical processes in nature. However, learning such equations in heterogeneous solids (for example, due to phase separation) is challenging. One such relationship is between composition and eigenstrain, which governs the chemo-mechanical expansion in solids. Here we developed a generalizable, physically constrained image-learning framework to algorithmically learn the chemo-mechanical constitutive law at the nanoscale from correlative four-dimensional scanning transmission electron microscopy and X-ray spectro-ptychography images. We demonstrated this approach on LiXFePO4, a technologically relevant battery positive electrode material. We uncovered the functional form of the composition-eigenstrain relation in this two-phase binary solid across the entire composition range (0≤X≤1), including inside the thermodynamically unstable miscibility gap. The learned relation directly validates Vegard's law of linear response at the nanoscale. Our physics-constrained data-driven approach directly visualizes the residual strain field (by removing the compositional and coherency strain), which is otherwise impossible to quantify. Heterogeneities in the residual strain arise from misfit dislocations and were independently verified by X-ray diffraction line profile analysis. Our work provides the means to simultaneously quantify chemical expansion, coherency strain and dislocations in battery electrodes, which has implications on rate capabilities and lifetime. Broadly, this work also highlights the potential of integrating correlative microscopy and image learning for extracting material properties and physics.

    View details for DOI 10.1038/s41563-021-01191-0

    View details for PubMedID 35177785

  • Correlative analysis of structure and chemistry of LixFePO(4) platelets using 4D-STEM and X-ray ptychography MATERIALS TODAY Hughes, L. A., Savitzky, B. H., Deng, H. D., Jin, N. L., Lomeli, E. G., Yu, Y., Shapiro, D. A., Herring, P., Anapolsky, A., Chueh, W. C., Ophus, C., Minor, A. M. 2022; 52: 102-111
  • Design and synthesis of multigrain nanocrystals via geometric misfit strain. Nature Oh, M. H., Cho, M. G., Chung, D. Y., Park, I. n., Kwon, Y. P., Ophus, C. n., Kim, D. n., Kim, M. G., Jeong, B. n., Gu, X. W., Jo, J. n., Yoo, J. M., Hong, J. n., McMains, S. n., Kang, K. n., Sung, Y. E., Alivisatos, A. P., Hyeon, T. n. 2020; 577 (7790): 359–63

    Abstract

    The impact of topological defects associated with grain boundaries (GB defects) on the electrical, optical, magnetic, mechanical and chemical properties of nanocrystalline materials1,2 is well known. However, elucidating this influence experimentally is difficult because grains typically exhibit a large range of sizes, shapes and random relative orientations3-5. Here we demonstrate that precise control of the heteroepitaxy of colloidal polyhedral nanocrystals enables ordered grain growth and can thereby produce material samples with uniform GB defects. We illustrate our approach with a multigrain nanocrystal comprising a Co3O4 nanocube core that carries a Mn3O4 shell on each facet. The individual shells are symmetry-related interconnected grains6, and the large geometric misfit between adjacent tetragonal Mn3O4 grains results in tilt boundaries at the sharp edges of the Co3O4 nanocube core that join via disclinations. We identify four design principles that govern the production of these highly ordered multigrain nanostructures. First, the shape of the substrate nanocrystal must guide the crystallographic orientation of the overgrowth phase7. Second, the size of the substrate must be smaller than the characteristic distance between the dislocations. Third, the incompatible symmetry between the overgrowth phase and the substrate increases the geometric misfit strain between the grains. Fourth, for GB formation under near-equilibrium conditions, the surface energy of the shell needs to be balanced by the increasing elastic energy through ligand passivation8-10. With these principles, we can produce a range of multigrain nanocrystals containing distinct GB defects.

    View details for DOI 10.1038/s41586-019-1899-3

    View details for PubMedID 31942056

  • Short-range order and its impact on the CrCoNi medium-entropy alloy. Nature Zhang, R. n., Zhao, S. n., Ding, J. n., Chong, Y. n., Jia, T. n., Ophus, C. n., Asta, M. n., Ritchie, R. O., Minor, A. M. 2020; 581 (7808): 283–87

    Abstract

    Traditional metallic alloys are mixtures of elements in which the atoms of minority species tend to be distributed randomly if they are below their solubility limit, or to form secondary phases if they are above it. The concept of multiple-principal-element alloys has recently expanded this view, as these materials are single-phase solid solutions of generally equiatomic mixtures of metallic elements. This group of materials has received much interest owing to their enhanced mechanical properties1-5. They are usually called medium-entropy alloys in ternary systems and high-entropy alloys in quaternary or quinary systems, alluding to their high degree of configurational entropy. However, the question has remained as to how random these solid solutions actually are, with the influence of short-range order being suggested in computational simulations but not seen experimentally6,7. Here we report the observation, using energy-filtered transmission electron microscopy, of structural features attributable to short-range order in the CrCoNi medium-entropy alloy. Increasing amounts of such order give rise to both higher stacking-fault energy and hardness. These findings suggest that the degree of local ordering at the nanometre scale can be tailored through thermomechanical processing, providing a new avenue for tuning the mechanical properties of medium- and high-entropy alloys.

    View details for DOI 10.1038/s41586-020-2275-z

    View details for PubMedID 32433617

  • The Materials Research Platform: Defining the Requirements from User Stories MATTER Aykol, M., Hummelshoj, J. S., Anapolsky, A., Aoyagi, K., Bazant, M. Z., Bligaard, T., Braatz, R. D., Broderick, S., Cogswell, D., Dagdelen, J., Drisdell, W., Garcia, E., Garikipati, K., Gavini, V., Gent, W. E., Giordano, L., Gomes, C. P., Gomez-Bombarelli, R., Gopal, C., Gregoire, J. M., Grossman, J. C., Herring, P., Hung, L., Jaramillo, T. F., King, L., Kwon, H., Maekawa, R., Minor, A. M., Montoya, J. H., Mueller, T., Ophus, C., Rajan, K., Ramprasad, R., Rohr, B., Schweigert, D., Shao-Horn, Y., Suga, Y., Suram, S. K., Viswanathan, V., Whitacre, J. F., Willard, A. P., Wodo, O., Wolverton, C., Storey, B. D. 2019; 1 (6): 1433–38
  • Diffraction imaging of nanocrystalline structures in organic semiconductor molecular thin films. Nature materials Panova, O. n., Ophus, C. n., Takacs, C. J., Bustillo, K. C., Balhorn, L. n., Salleo, A. n., Balsara, N. n., Minor, A. M. 2019

    Abstract

    The properties of organic solids depend on their structure and morphology, yet direct imaging using conventional electron microscopy methods is hampered by the complex internal structure of these materials and their sensitivity to electron beams. Here, we manage to observe the nanocrystalline structure of two organic molecular thin-film systems using transmission electron microscopy by employing a scanning nanodiffraction method that allows for full access to reciprocal space over the size of a spatially localized probe (~2 nm). The morphologies revealed by this technique vary from grains with pronounced segmentation of the structure-characterized by sharp grain boundaries and overlapping domains-to liquid-crystal structures with crystalline orientations varying smoothly over all possible rotations that contain disclinations representing singularities in the director field. The results show how structure-property relationships can be visualized in organic systems using techniques previously only available for hard materials such as metals and ceramics.

    View details for DOI 10.1038/s41563-019-0387-3

    View details for PubMedID 31160799

  • Multi-pass transmission electron microscopy SCIENTIFIC REPORTS Juffmann, T., Koppell, S. A., Klopfer, B. B., Ophus, C., Glaeser, R. M., Kasevich, M. A. 2017; 7

    Abstract

    Feynman once asked physicists to build better electron microscopes to be able to watch biology at work. While electron microscopes can now provide atomic resolution, electron beam induced specimen damage precludes high resolution imaging of sensitive materials, such as single proteins or polymers. Here, we use simulations to show that an electron microscope based on a multi-pass measurement protocol enables imaging of single proteins, without averaging structures over multiple images. While we demonstrate the method for particular imaging targets, the approach is broadly applicable and is expected to improve resolution and sensitivity for a range of electron microscopy imaging modalities, including, for example, scanning and spectroscopic techniques. The approach implements a quantum mechanically optimal strategy which under idealized conditions can be considered interaction-free.

    View details for DOI 10.1038/s41598-017-01841-x

    View details for Web of Science ID 000400886100039

    View details for PubMedID 28490730