Xiaochen Du

Xiaochen Du

PhD student @ MIT

Posts by Collection

portfolio

publications

MatD3: A Database and Online Presentation Package for Research Data Supporting Materials Discovery, Design, and Dissemination

Published in The Journal of Open Source Software, 2020

MatD3 is an open-source, dedicated database and web application framework designed to store, curate and disseminate experimental and theoretical materials data generated by indi- vidual research groups or research consortia.

Recommended citation: Laasner, R., Du, X., Tanikanti, A., Clayton, C., Govoni, M., Galli, G., Ropo, M. & Blum, V. (2020). "MatD3: A Database and Online Presentation Package for Research Data Supporting Materials Discovery, Design, and Dissemination." Journal of Open Source Software, 5(45), 1945. https://doi.org/10.21105/joss.01945

Correlation Between Charge Transport and Base Excision Repair in the MutY DNA Glycosylase

Published in The Journal of Physical Chemistry B, 2021

We analyzed the dominant charge transfer (CT) pathways in the base excision repair glycosylase MutY using molecular dynamics simulations and hole hopping pathway analysis.

Recommended citation: Teo, R., Du, X., Vera, H., Migliore, A. & Beratan, D. (2021). "Correlation Between Charge Transport and Base Excision Repair in the MutY DNA Glycosylase." J. Phys. Chem. B, 125(1), 17. https://doi.org/10.1021/acs.jpcb.0c08598

Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography

Published in Nature Communications, 2021

Tomographic reconstructions of cryopreserved specimens enable in-situ structural studies. Here, the authors present the beam image-shift electron cryo-tomography (BISECT) approach that accelerates data collection speed and improves the map resolution compared to earlier approaches and present the in vitro structure of a 300 kDa protein complex that was solved at 3.6 Å resolution as a test case.

Recommended citation: Bouvette, J.*, Liu, H.*, Du, X., Zhou, Y., Sikkema, A.P., Mello, J.F.R., Klemm, B.P., Huang, R., Schaaper, R.M., Borgnia, M.J. & Bartesaghi, A. (2021). "Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography." Nat. Commun., 12(1957). https://doi.org/10.1038/s41467-021-22251-8

nextPYP: a comprehensive and scalable platform for characterizing protein variability in situ using single-particle cryo-electron tomography

Published in Nature Methods, 2023

nextPYP is a turn-key framework for single-particle cryo-ET that streamlines complex data analysis pipelines, from pre-processing of tilt series to high-resolution refinement, for efficient analysis of large datasets.

Recommended citation: Liu, HF.*, Zhou, Y.*, Huang, Q., Piland, J., Jin, W., Mandel, J., Du, X., Martin, J. & Bartesaghi, A. (2023). "nextPYP: a comprehensive and scalable platform for characterizing protein variability in situ using single-particle cryo-electron tomography." Nat. Methods., 20, 1909. https://doi.org/10.1038/s41592-023-02045-0

Machine-learning-accelerated simulations to enable automatic surface reconstruction

Published in Nature Computational Science, 2023

VSSR-MC is a Markov chain method based on virtual adsorption sites that interfaces with a neural network force field to provide fast, accurate and comprehensive sampling of material surfaces.

Recommended citation: Du, X., Damewood, J.K., Lunger, J.R., Millan, R., Yildiz, B., Li, L. & Gómez-Bombarelli, R. (2023). "Machine-learning-accelerated simulations to enable automatic surface reconstruction." Nat. Comput. Sci., 3, 1044. https://doi.org/10.1038/s43588-023-00571-7

talks

teaching

Teaching experience 1

Undergraduate course, University 1, Department, 2014

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Teaching experience 2

Workshop, University 1, Department, 2015

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