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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
About me
About me
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Posts
Future Blog Post
Published:
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Blog Post number 4
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 3
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 2
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 1
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
portfolio
Portfolio item number 1
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Portfolio item number 2
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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
My Research Journey – Machine learning, automation, and renewable energy
Published:
Invited by the Duke Campus Club – an organization of women affiliated with Duke – to do a presentation on my research followed by a panel discussion and Q&A. Joined by two fellow Duke Faculty Scholars for the Class of 2021.
Machine-learning-accelerated simulations for heuristic-free surface reconstruction
Published:
Invited by Prof. Volker Blum of Duke University to give a talk on my recent preprint.
teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
Teaching experience 2
Workshop, University 1, Department, 2015
This is a description of a teaching experience. You can use markdown like any other post.