Software and Data
A directory of public repository links containing code and relevant raw data for publications that acknowledge support by Brandeis NSF MRSEC, Bioinspired Soft Materials, DMR-2011846.
2025
Videbaek, T. E., Hayakawa, D., Hagan, M. F., Grason, G. M., Fraden, S. and Rogers, W. B., "Measuring multisubunit mechanics of geometrically programmed colloidal assemblies via cryo-EM multi-body refinement," Proc Natl Acad Sci U S A 122, e2500716122 (2025).
Code: https://zenodo.org/records/15596047
Rados, Theopi, Leland, Olivia S, Escudeiro, Pedro, Mallon, John, Andre, Katherine, Caspy, Ido, von Kügelgen, Andriko, Stolovicki, Elad, Nguyen, Sinead, Patop, Inés Lucía, Rangel, L Thiberio, Kadener, Sebastian, Renner, Lars D, Thiel, Vera, Soen, Yoav, Bharat, Tanmay A M , Alva, Vikram and Bisson, Alex, "Tissue-like multicellular development triggered by mechanical compression in archaea," Science 388, 109-115 (2025).
Paper: https://doi.org/10.1126/science.adu0047
Code: https://doi.org/10.5281/zenodo.14568734
Seyforth, Hunter, Chatterjee, Sambarta, Videbæk, Thomas E, Mondal, Manodeep, Jacobs, William and Rogers, W Benjamin, "The underappreciated role of nonspecific interactions in the crystallization of DNA-coated colloids," Soft Matter 21, 2654-2663 (2025).
Paper: https://doi.org/10.1039/d5sm00001g
Code: https://github.com/wmjac/dnacc-binary-crystal-pub
Wang, Michael, Roy, Sourav, Santangelo, Christian and Grason, Gregory, "Geometrically frustrated, mechanical metamaterial membranes: Large-scale stress accumulation and size-selective assembly," Physical Review Letters 134, 078201 (2025).
Paper: https://doi.org/10.1103/PhysRevLett.134.078201
Code: https://doi.org/10.7275/yh0f-er06
Zia, Ayisha, Yi, Meihui, Liu, Zhiyu, Wang, Fengbin and Xu, Bing, "Fragment‐Based Approach for Hierarchical Nanotube Assembly of Small Molecules in Aqueous Phase," Chemistry–A European Journal 31, e202404630 (2025).
Paper: https://doi.org/10.1002/chem.202404630
Code: https://chemistry-europe.onlinelibrary.wiley.com
2024
Luo, W., Baskaran, A., Pelcovits, R. A. and Powers, T. R., "Flow states of two dimensional active gels driven by external shear," Soft Matter 20, 738-753 (2024).
Paper: https://doi.org/10.1039/d3sm00919j
Code: https://github.com/wluo2/2D_Active_Gel
Wang, M. and Grason, G., "Thermal stability and secondary aggregation of self-limiting, geometrically frustrated assemblies: Chain assembly of incommensurate polybricks," Physical Review E 109, 014608 (2024).
Paper: https://doi.org/10.1103/PhysRevE.109.014608
Code: https://doi.org/10.7275/410
Hayakawa, Daichi, Videbæk, Thomas E, Grason, Gregory M and Rogers, W Benjamin, "Symmetry-guided inverse design of self-assembling multiscale DNA origami tilings," ACS nano 18, 19169-19178 (2024).
Paper: https://doi.org/10.1021/acsnano.4c04515
Code: https://pubs.acs.org/doi/suppl/10.1021/acsnano.4c04515/suppl_file/nn4c04515_si_001.pdf
Guo, Jiaqi, Tan, Weiyi and Xu, Bing, "Enzymatic self-assembly of short peptides for cell spheroid formation," Journal of Materials Chemistry B, (2024).
Paper: https://doi.org/10.1039/d4tb01154f
Code: https://www.rsc.org/suppdata/d4/tb/d4tb01154f/d4tb01154f1.pdf
Guo, Jiaqi, Chang, Annabelle and Xu, Bing, "Autocleaving Bonds for Better Drugs," ChemMedChem 19, e202400130 (2024).
Paper: https://doi.org/10.1002/cmdc.202400130
Code: https://pmc.ncbi.nlm.nih.gov/articles/PMC11219257/
Duque, Carlos M, Hall, Douglas M, Tyukodi, Botond, Hagan, Michael F, Santangelo, Christian D and Grason, Gregory M, "Limits of economy and fidelity for programmable assembly of size-controlled triply periodic polyhedra," Proceedings of the National Academy of Sciences 121, e2315648121 (2024).
Paper: https://doi.org/10.1073/pnas.2315648121
Code: https://doi.org/10.7275/kx17-b561
Curtis, Zachary, Escudeiro, Pedro, Mallon, John, Leland, Olivia, Rados, Theopi, Dodge, Ashley, Andre, Katherine, Kwak, Jasmin, Yun, Kun and Isaac, Berith, "Halofilins as emerging bactofilin families of archaeal cell shape plasticity orchestrators," Proceedings of the National Academy of Sciences 121, e2401583121 (2024).
Paper: https://doi.org/10.1073/pnas.2401583121
Code: https://doi.org/10.5281/zenodo.17259028
Videbæk, Thomas E, Hayakawa, Daichi, Grason, Gregory M, Hagan, Michael F, Fraden, Seth and Rogers, W Benjamin, "Economical routes to size-specific assembly of self-closing structures," Science advances 10, eado5979 (2024).
Paper: https://doi.org/10.1126/sciadv.ado5979
Code: https://zenodo.org/records/10933968
Prabhune, Ameya G, García-Gordillo, Andy S, Aranson, Igor S, Powers, Thomas R and Figueroa-Morales, Nuris, "Bacteria Navigate Anisotropic Media using a Flagellar Tug-of-Oars," PRX Life 2, 033004 (2024).
Paper: https://doi.org/10.1103/PRXLife.2.033004
Code: https://github.com/prabhuneameya-dot/Flagella-Tug-of-Oars
2023
Guo, J., Rich-New, S. T., Liu, C., Huang, Y., Tan, W., He, H., Yi, M., Zhang, X., Egelman, E. H., Wang, F. and Xu, B., "Hierarchical Assembly of Intrinsically Disordered Short Peptides," Chem 9, 2530-2546 (2023).
Code: https://ars.els-cdn.com/content/image/1-s2.0-S2451929423002048-mmc1.pdf
Guo, J., Wang, F., Huang, Y., He, H., Tan, W., Yi, M., Egelman, E. H. and Xu, B., "Cell spheroid creation by transcytotic intercellular gelation," Nature nanotechnology 18, 1-11 (2023).
Zheng, J., Mallon, J., Lammers, A., Rados, T., Litschel, T., Moody, E. R. R., Ramirez-Diaz, D. A., Schmid, A., Williams, T. A., Bisson-Filho, A. W. and Garner, E., "Salactin, a dynamically unstable actin homolog in Haloarchaea," mBio 14, e02272-02223 (2023).
Code: https://doi.org/10.5281/zenodo.17259152
Malakar, K., Rubenstein, R. I., Bi, D. and Chakraborty, B., "A mechanistic model of the organization of cell shapes in epithelial tissues," Frontiers in Soft Matter 3, (2023).
Paper: https://doi.org/10.3389/frsfm.2023.1214159
Code: https://github.com/kanaya-m/A-Mechanistic-Model-of-the-Organization-of-Cell-Shapes-in-Epithelial-Tissues.git
Liu, Z., Guo, J., Qiao, Y. and Xu, B., "Enzyme-Instructed Intracellular Peptide Assemblies," Accounts of chemical research 56, 3076-3088 (2023).
Code: https://pmc.ncbi.nlm.nih.gov/articles/PMC10842413
Wang, D., Moreno, S., Gao, M., Guo, J., Xu, B., Voigt, D., Voit, B. and Appelhans, D., "Protocells Capable of Generating a Cytoskeleton‐Like Structure from Intracellular Membrane‐Active Artificial Organelles," Advanced Functional Materials, (2023).
Del Signore, S. J., Mitzner, M. G., Silveira, A. M., Fai, T. G. and Rodal, A. A., "An approach for quantitative mapping of synaptic periactive zone architecture and organization," Molecular biology of the cell 34, ar51 (2023).
Paper: https://doi.org/10.1091/mbc.E22-08-0372Code: https://github.com/rodallab/paz-analysis
2022
Liu, S., Zhang, Q., He, H., Yi, M., Tan, W., Guo, J. and Xu, B., "Intranuclear Nanoribbons for Selective Killing of Osteosarcoma Cells," Angew Chem Int Ed Engl 61, e202210568 (2022).
Paper: https://doi.org/10.1002/anie.202210568
Code: https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fanie.202210568&file=anie202210568-sup-0001-misc_information.pdf;
Tan, W., Zhang, Q., Quinones-Frias, M. C., Hsu, A. Y., Zhang, Y., Rodal, A., Hong, P., Luo, H. R. and Xu, B., "Enzyme-Responsive Peptide Thioesters for Targeting Golgi Apparatus," Journal of the American Chemical Society 144, 6709-6713 (2022).
Paper: https://doi.org/10.1021/jacs.2c02238
Code: https://pubs.acs.org/doi/suppl/10.1021/jacs.2c02238/suppl_file/ja2c02238_si_001.pdf
Tan, W., Zhang, Q., Hong, P. and Xu, B., "A Self-Assembling Probe for Imaging the States of Golgi Apparatus in Live Single Cells," Bioconjug Chem 33, 1983-1988 (2022).
Paper: https://doi.org/10.1021/acs.bioconjchem.2c00084
Code: https://pubs.acs.org/doi/suppl/10.1021/acs.bioconjchem.2c00084/suppl_file/bc2c00084_si_001.pdf
Khanra, A., Jia, L. L., Mitchell, N. P., Balchunas, A., Pelcovits, R. A., Powers, T. R., Dogic, Z. and Sharma, P., "Controlling the shape and topology of two-component colloidal membranes," Proceedings of the National Academy of Sciences 119, e2204453119 (2022).
Paper: https://doi.org/10.1073/pnas.2204453119
Code: https://github.com/royjia117/enneper-membranes
Yi, M., Wang, F., Tan, W., Hsieh, J.-T., Egelman, E. H. and Xu, B., "Enzyme Responsive Rigid-Rod Aromatics Target “Undruggable” Phosphatases to Kill Cancer Cells in a Mimetic Bone Microenvironment," Journal of the American Chemical Society 144, 13055-13059 (2022).
Paper: https://doi.org/10.1021/jacs.2c05491Code: https://pubs.acs.org/doi/suppl/10.1021/jacs.2c05491/suppl_file/ja2c05491_si_001.pdf
2021
He, H., Guo, J. and Xu, B., "Enzymatic Delivery of Magnetic Nanoparticles into Mitochondria of Live Cells," Chemnanomat, (2021).
Paper: https://doi.org/10.1002/cnma.202100249
Code: https://aces.onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fcnma.202100249&file=cnma202100249-sup-0001-misc_information.pdf
He, H., Guo, J., Xu, J., Wang, J., Liu, S. and Xu, B., "Dynamic Continuum of Nanoscale Peptide Assemblies Facilitates Endocytosis and Endosomal Escape," Nano Letters 21, 4078-4085 (2021).
Paper: https://doi.org/10.1021/acs.nanolett.1c01029
Code: https://pubs.acs.org/doi/suppl/10.1021/acs.nanolett.1c01029/suppl_file/nl1c01029_si_001.pdf
Liu, S., Zhang, Q., Shy, A. N., Yi, M., He, H., Lu, S. and Xu, B., "Enzymatically Forming Intranuclear Peptide Assemblies for Selectively Killing Human Induced Pluripotent Stem Cells," Journal of the American Chemical Society 143, 15852-15862 (2021).
Paper: https://doi.org/10.1021/jacs.1c07923
Code: https://pubs.acs.org/doi/suppl/10.1021/jacs.1c07923/suppl_file/ja1c07923_si_001.pdf
Tan, W., Zhang, Q., Wang, J., Yi, M., He, H. and Xu, B., "Enzymatic Assemblies of Thiophosphopeptides Instantly Target Golgi Apparatus and Selectively Kill Cancer Cells," Angewandte Chemie International Edition, (2021).
Paper: https://doi.org/10.1002/anie.202102601
Code: https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fanie.202102601&file=anie202102601-sup-0001-misc_information.pdf
Yang, D., He, H., Kim, B. J. and Xu, B., "Peptide Assemblies Mimicking Chaperones for Protein Trafficking," Bioconjugate Chemistry 32, 502-506 (2021).
Paper: https://doi.org/10.1021/acs.bioconjchem.1c00032
Code: https://pubs.acs.org/doi/suppl/10.1021/acs.bioconjchem.1c00032/suppl_file/bc1c00032_si_001.pdf
Yi, M., Guo, J., He, H., Tan, W., Harmon, N., Ghebreyessus, K. and Xu, B., "Phosphobisaromatic motifs enable rapid enzymatic self-assembly and hydrogelation of short peptides," Soft Matter 17, 8590-8594 (2021).
Paper: https://doi.org/10.1039/d1sm01221e
Code: https://www.rsc.org/suppdata/d1/sm/d1sm01221e/d1sm01221e1.pdf
Yi, M., Tan, W., Guo, J. and Xu, B., "Enzymatic noncovalent synthesis of peptide assemblies generates multimolecular crowding in cells for biomedical applications," Chemical communications, (2021).
Paper: https://doi.org/10.1039/d1cc05565h
Code: https://www.rsc.org/suppdata/d1/cc/d1cc05565h/d1cc05565h1.pdf
2020
He, H., Lin, X., Wu, D., Wang, J., Guo, J., Green, D. R., Zhang, H. and Xu, B., "Enzymatic Noncovalent Synthesis for Mitochondrial Genetic Engineering of Cancer Cells," Cell Reports Physical Science 1, 100270 (2020).
Paper: https://doi.org/10.1016/j.xcrp.2020.100270
Code: https://ars.els-cdn.com/content/image/1-s2.0-S2666386420302927-mmc1.pdf
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