[{"acknowledgement":"We thank B. Isaac and A. Tiano for their technical support with the electron microscopy and S. Waitukaitis for helpful comments on the manuscript. The TEM images were prepared and imaged at the Brandeis Electron Microscopy facility. This work was supported by the Gesellschaft für Forschungsförderung Niederösterreich under project FTI23-G-011 (M.C.H. and C.P.G.), the Brandeis University Materials Research Science and Engineering Center (MRSEC) under grant number NSF DMR-2011846 (T.E.V., D.H. and W.B.R.) and the Smith Family Foundation (W.B.R.). Open access funding provided by Institute of Science and Technology (IST Austria).","doi":"10.1038/s41567-025-03120-3","oa":1,"author":[{"last_name":"Hübl","full_name":"Hübl, Maximilian","first_name":"Maximilian","id":"5eb8629e-15b2-11ec-abd3-e6f3e5e01f32"},{"first_name":"Thomas E.","last_name":"Videbæk","full_name":"Videbæk, Thomas E."},{"last_name":"Hayakawa","full_name":"Hayakawa, Daichi","first_name":"Daichi"},{"last_name":"Rogers","full_name":"Rogers, W. Benjamin","first_name":"W. Benjamin"},{"orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter"}],"project":[{"grant_number":"FTI23-G-011","_id":"8dd93da8-16d5-11f0-9cad-d2c70200d9a5","name":"Dynamically reconfigurable self-assembly with triangular DNA-origami bricks"}],"article_type":"original","month":"01","department":[{"_id":"CaGo"},{"_id":"GradSch"}],"corr_author":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes (via OA deal)","publisher":"Springer Nature","publication_status":"epub_ahead","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"date_created":"2026-01-20T10:02:19Z","title":"A polyhedral structure controls programmable self-assembly","oa_version":"Published Version","OA_type":"hybrid","publication":"Nature Physics","date_updated":"2026-01-21T10:26:32Z","PlanS_conform":"1","status":"public","license":"https://creativecommons.org/licenses/by/4.0/","scopus_import":"1","_id":"21006","language":[{"iso":"eng"}],"abstract":[{"text":"Modern experimental methods in programmable self-assembly make it possible to precisely design particle concentrations, shapes and interactions. However, more physical insight is needed before we can take full advantage of this vast design space to assemble nanostructures with complex form and function. Here we show how a substantial part of this design space can be quickly and comprehensively understood by identifying a class of thermodynamic constraints that act on it. These thermodynamic constraints form a high-dimensional convex polyhedron that determines which nanostructures can be assembled at high equilibrium yield and reveals limitations that govern the coexistence of structures. We validate our predictions through detailed, quantitative assembly experiments of nanoscale particles synthesized using DNA origami. Our results uncover physical relationships underpinning many-component programmable self-assembly in equilibrium and form the basis for robust inverse design, applicable to various systems from biological protein complexes to synthetic nanomachines.","lang":"eng"}],"type":"journal_article","quality_controlled":"1","has_accepted_license":"1","citation":{"chicago":"Hübl, Maximilian, Thomas E. Videbæk, Daichi Hayakawa, W. Benjamin Rogers, and Carl Peter Goodrich. “A Polyhedral Structure Controls Programmable Self-Assembly.” <i>Nature Physics</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41567-025-03120-3\">https://doi.org/10.1038/s41567-025-03120-3</a>.","ama":"Hübl M, Videbæk TE, Hayakawa D, Rogers WB, Goodrich CP. A polyhedral structure controls programmable self-assembly. <i>Nature Physics</i>. 2026. doi:<a href=\"https://doi.org/10.1038/s41567-025-03120-3\">10.1038/s41567-025-03120-3</a>","ista":"Hübl M, Videbæk TE, Hayakawa D, Rogers WB, Goodrich CP. 2026. A polyhedral structure controls programmable self-assembly. Nature Physics.","apa":"Hübl, M., Videbæk, T. E., Hayakawa, D., Rogers, W. B., &#38; Goodrich, C. P. (2026). A polyhedral structure controls programmable self-assembly. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-025-03120-3\">https://doi.org/10.1038/s41567-025-03120-3</a>","mla":"Hübl, Maximilian, et al. “A Polyhedral Structure Controls Programmable Self-Assembly.” <i>Nature Physics</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41567-025-03120-3\">10.1038/s41567-025-03120-3</a>.","short":"M. Hübl, T.E. Videbæk, D. Hayakawa, W.B. Rogers, C.P. Goodrich, Nature Physics (2026).","ieee":"M. Hübl, T. E. Videbæk, D. Hayakawa, W. B. Rogers, and C. P. Goodrich, “A polyhedral structure controls programmable self-assembly,” <i>Nature Physics</i>. Springer Nature, 2026."},"day":"08","year":"2026","ddc":["570","540"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2026-01-08T00:00:00Z","OA_place":"publisher","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41567-025-03120-3"}]},{"OA_type":"hybrid","oa_version":"Published Version","title":"Simultaneous optimization of assembly time and yield in programmable self-assembly","date_created":"2026-03-08T23:01:45Z","arxiv":1,"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"file":[{"content_type":"application/pdf","success":1,"file_size":6903766,"date_created":"2026-03-09T10:38:55Z","access_level":"open_access","relation":"main_file","file_id":"21415","date_updated":"2026-03-09T10:38:55Z","creator":"dernst","checksum":"9bdb8870930e83edb973408da3038559","file_name":"2026_JourChemPhysics_Huebl.pdf"}],"publication_status":"published","publisher":"AIP Publishing","article_processing_charge":"Yes (via OA deal)","corr_author":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"month":"02","department":[{"_id":"CaGo"},{"_id":"GradSch"}],"project":[{"_id":"8dd93da8-16d5-11f0-9cad-d2c70200d9a5","grant_number":"FTI23-G-011","name":"Dynamically reconfigurable self-assembly with triangular DNA-origami bricks"}],"article_type":"original","volume":164,"author":[{"first_name":"Maximilian","id":"5eb8629e-15b2-11ec-abd3-e6f3e5e01f32","last_name":"Hübl","full_name":"Hübl, Maximilian"},{"last_name":"Goodrich","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"}],"doi":"10.1063/5.0304731","oa":1,"acknowledgement":"The research was supported by the Gesellschaft für Forschungsförderung Niederösterreich under Project No. FTI23-G-011.","OA_place":"publisher","date_published":"2026-02-28T00:00:00Z","ddc":["540"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2026","article_number":"084904","intvolume":"       164","citation":{"ama":"Hübl M, Goodrich CP. Simultaneous optimization of assembly time and yield in programmable self-assembly. <i>Journal of Chemical Physics</i>. 2026;164(8). doi:<a href=\"https://doi.org/10.1063/5.0304731\">10.1063/5.0304731</a>","ista":"Hübl M, Goodrich CP. 2026. Simultaneous optimization of assembly time and yield in programmable self-assembly. Journal of Chemical Physics. 164(8), 084904.","chicago":"Hübl, Maximilian, and Carl Peter Goodrich. “Simultaneous Optimization of Assembly Time and Yield in Programmable Self-Assembly.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2026. <a href=\"https://doi.org/10.1063/5.0304731\">https://doi.org/10.1063/5.0304731</a>.","mla":"Hübl, Maximilian, and Carl Peter Goodrich. “Simultaneous Optimization of Assembly Time and Yield in Programmable Self-Assembly.” <i>Journal of Chemical Physics</i>, vol. 164, no. 8, 084904, AIP Publishing, 2026, doi:<a href=\"https://doi.org/10.1063/5.0304731\">10.1063/5.0304731</a>.","ieee":"M. Hübl and C. P. Goodrich, “Simultaneous optimization of assembly time and yield in programmable self-assembly,” <i>Journal of Chemical Physics</i>, vol. 164, no. 8. AIP Publishing, 2026.","short":"M. Hübl, C.P. Goodrich, Journal of Chemical Physics 164 (2026).","apa":"Hübl, M., &#38; Goodrich, C. P. (2026). Simultaneous optimization of assembly time and yield in programmable self-assembly. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0304731\">https://doi.org/10.1063/5.0304731</a>"},"day":"28","has_accepted_license":"1","quality_controlled":"1","type":"journal_article","external_id":{"arxiv":["2510.07876"]},"abstract":[{"text":"Rational design strategies for self-assembly require a detailed understanding of both the equilibrium state and the assembly kinetics. While the former is starting to be well understood, the latter remains a major theoretical challenge, especially in programmable systems and the so-called semi-addressable regime, where binding is often nondeterministic and the formation of off-target structures negatively influences the assembly. Here, we show that it is possible to simultaneously sculpt the assembly outcome and the assembly kinetics through the underexplored design space of binding energies and particle concentrations. By formulating the assembly process as a complex reaction network, we calculate and optimize the tradeoff between assembly speed and quality and show that parameter optimization can speed up assembly by many orders of magnitude without lowering the yield of the target structure. Although the exact speedup varies from design to design, we find the largest speedups for nondeterministic systems where unoptimized assembly is the slowest, sometimes even making them assemble faster than optimized, fully addressable designs. Therefore, these results not only solve a key challenge in semi-addressable self-assembly but further emphasize the utility of semi-addressability, where designs have the potential to be faster as well as cheaper (fewer particle species) and better (higher yield). More broadly, our results highlight the importance of parameter optimization in programmable self-assembly and provide practical tools for simultaneous optimization of kinetics and yield in a wide range of systems.","lang":"eng"}],"_id":"21408","language":[{"iso":"eng"}],"scopus_import":"1","issue":"8","status":"public","date_updated":"2026-03-09T10:40:41Z","publication":"Journal of Chemical Physics","file_date_updated":"2026-03-09T10:38:55Z"},{"article_processing_charge":"Yes","corr_author":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"American Physical Society","volume":8,"author":[{"first_name":"Maximilian","id":"5eb8629e-15b2-11ec-abd3-e6f3e5e01f32","full_name":"Hübl, Maximilian","last_name":"Hübl"},{"orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter"}],"month":"03","department":[{"_id":"CaGo"},{"_id":"GradSch"}],"article_type":"original","project":[{"name":"Dynamically reconfigurable self-assembly with triangular DNA-origami bricks","_id":"8dd93da8-16d5-11f0-9cad-d2c70200d9a5","grant_number":"FTI23-G-011"}],"doi":"10.1103/68rs-3qgn","oa":1,"acknowledgement":"We thank Maitane Muñoz-Basagoiti for helpful discussions. The research was supported by the Gesellschaft für Forschungsförderung Niederösterreich under Project No. FTI23-G-011.","date_created":"2026-03-23T14:58:31Z","title":"Entropic size control of self-assembled filaments","OA_type":"gold","oa_version":"Published Version","publication_identifier":{"eissn":["2643-1564"]},"file":[{"date_updated":"2026-03-23T15:53:29Z","file_id":"21493","creator":"dernst","relation":"main_file","checksum":"6d8a68e4a19f8dad5abdf75f72316f3d","file_name":"2026_PhysicalReviewResearch_Huebl.pdf","success":1,"content_type":"application/pdf","date_created":"2026-03-23T15:53:29Z","file_size":2680924,"access_level":"open_access"}],"publication_status":"published","DOAJ_listed":"1","status":"public","publication":"Physical Review Research","date_updated":"2026-03-23T15:59:11Z","file_date_updated":"2026-03-23T15:53:29Z","OA_place":"publisher","date_published":"2026-03-05T00:00:00Z","article_number":"L012054","intvolume":"         8","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2026","day":"05","citation":{"short":"M. Hübl, C.P. Goodrich, Physical Review Research 8 (2026).","ieee":"M. Hübl and C. P. Goodrich, “Entropic size control of self-assembled filaments,” <i>Physical Review Research</i>, vol. 8. American Physical Society, 2026.","mla":"Hübl, Maximilian, and Carl Peter Goodrich. “Entropic Size Control of Self-Assembled Filaments.” <i>Physical Review Research</i>, vol. 8, L012054, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/68rs-3qgn\">10.1103/68rs-3qgn</a>.","apa":"Hübl, M., &#38; Goodrich, C. P. (2026). Entropic size control of self-assembled filaments. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/68rs-3qgn\">https://doi.org/10.1103/68rs-3qgn</a>","ista":"Hübl M, Goodrich CP. 2026. Entropic size control of self-assembled filaments. Physical Review Research. 8, L012054.","ama":"Hübl M, Goodrich CP. Entropic size control of self-assembled filaments. <i>Physical Review Research</i>. 2026;8. doi:<a href=\"https://doi.org/10.1103/68rs-3qgn\">10.1103/68rs-3qgn</a>","chicago":"Hübl, Maximilian, and Carl Peter Goodrich. “Entropic Size Control of Self-Assembled Filaments.” <i>Physical Review Research</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/68rs-3qgn\">https://doi.org/10.1103/68rs-3qgn</a>."},"has_accepted_license":"1","_id":"21482","abstract":[{"lang":"eng","text":"Controlling the size and shape of assembled structures is a fundamental challenge in self-assembly and is highly relevant in material design and biology. Here, we show that specific but promiscuous short-range binding interactions make it possible to economically assemble linear filaments of user-defined length. Our approach leads to independent control over the mean and width of the filament size distribution and allows us to smoothly explore design trade-offs between assembly quality (spread in size) and cost (number of particle species). We employ a simple hierarchical assembly protocol to minimize assembly times and show that multiple stages of hierarchy make it possible to extend our approach to the assembly of higher-dimensional structures. Our work provides a conceptually simple solution to size control that is applicable to a broad range of systems, from DNA nanoparticles to supramolecular polymers and beyond."}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article"},{"OA_place":"publisher","date_published":"2025-06-13T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["530"],"year":"2025","article_number":"238201","intvolume":"       134","day":"13","citation":{"apa":"Zu, M., Desai, A. A., &#38; Goodrich, C. P. (2025). Fully independent response in disordered solids. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.134.238201\">https://doi.org/10.1103/PhysRevLett.134.238201</a>","mla":"Zu, Mengjie, et al. “Fully Independent Response in Disordered Solids.” <i>Physical Review Letters</i>, vol. 134, no. 23, 238201, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.134.238201\">10.1103/PhysRevLett.134.238201</a>.","short":"M. Zu, A.A. Desai, C.P. Goodrich, Physical Review Letters 134 (2025).","ieee":"M. Zu, A. A. Desai, and C. P. Goodrich, “Fully independent response in disordered solids,” <i>Physical Review Letters</i>, vol. 134, no. 23. American Physical Society, 2025.","chicago":"Zu, Mengjie, Aayush A Desai, and Carl Peter Goodrich. “Fully Independent Response in Disordered Solids.” <i>Physical Review Letters</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/PhysRevLett.134.238201\">https://doi.org/10.1103/PhysRevLett.134.238201</a>.","ama":"Zu M, Desai AA, Goodrich CP. Fully independent response in disordered solids. <i>Physical Review Letters</i>. 2025;134(23). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.134.238201\">10.1103/PhysRevLett.134.238201</a>","ista":"Zu M, Desai AA, Goodrich CP. 2025. Fully independent response in disordered solids. Physical Review Letters. 134(23), 238201."},"has_accepted_license":"1","quality_controlled":"1","type":"journal_article","external_id":{"isi":["001509005900006"],"arxiv":["2412.05031"]},"abstract":[{"lang":"eng","text":"Unlike in crystals, it is difficult to trace emergent material properties of amorphous solids to their underlying structure. Nevertheless, one can tune features of a disordered spring network, ranging from bulk elastic constants to specific allosteric responses, through highly precise alterations of the structure. This has been understood through the notion of independent bond-level response—the observation that, in many cases, different springs have different effects on different properties. While this idea has motivated inverse design in numerous contexts, it has not been formalized and quantified in a general context that not just informs but enables and predicts inverse design. Here, we show how to quantify independent response by linearizing the simultaneous change in multiple emergent features, and introduce the much stronger notion of fully independent response. Remarkably, we find that the mechanical properties of disordered solids are always fully independent across a wide array of scenarios, regardless of the target features, tunable parameters, system size, dimensionality, and class of interactions. Furthermore, our formulation quantifies the susceptibility of features to parameter changes, which is correlated with the maximum linear tunability. We also demonstrate the implications for multifeature inverse design beyond the linear regime. These results formalize our understanding of a key fundamental difference between ordered and disordered solids while also creating a practical tool to both understand and perform inverse design."}],"_id":"19856","language":[{"iso":"eng"}],"scopus_import":"1","issue":"23","status":"public","isi":1,"publication":"Physical Review Letters","date_updated":"2025-09-30T13:38:43Z","file_date_updated":"2025-06-23T11:41:08Z","OA_type":"hybrid","oa_version":"Published Version","date_created":"2025-06-22T22:02:06Z","title":"Fully independent response in disordered solids","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"arxiv":1,"file":[{"checksum":"040b6779c91aac62c15a9b2cc417b360","file_name":"2025_PhysReviewLetters_Zu.pdf","date_updated":"2025-06-23T11:41:08Z","file_id":"19874","creator":"dernst","relation":"main_file","access_level":"open_access","success":1,"content_type":"application/pdf","file_size":1132625,"date_created":"2025-06-23T11:41:08Z"}],"publication_status":"published","publisher":"American Physical Society","article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"corr_author":"1","department":[{"_id":"CaGo"},{"_id":"IlCa"}],"month":"06","article_type":"original","volume":134,"author":[{"full_name":"Zu, Mengjie","last_name":"Zu","id":"26dd9e7c-e86a-11eb-a854-82ac731c9ae2","first_name":"Mengjie"},{"id":"502cfd30-32c1-11ee-a9a4-d8dad5c6739e","first_name":"Aayush A","full_name":"Desai, Aayush A","last_name":"Desai"},{"orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter","last_name":"Goodrich"}],"doi":"10.1103/PhysRevLett.134.238201","oa":1,"acknowledgement":"We gratefully acknowledge Edouard Hannezo for helpful comments on the manuscript. The work was funded by the Institute of Science and Technology Austria."},{"arxiv":1,"publication_identifier":{"eissn":["1091-6490"]},"OA_type":"hybrid","oa_version":"Published Version","title":"Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter","date_created":"2025-12-07T23:02:00Z","publication_status":"published","file":[{"checksum":"c40dc4c909724b9d1146636612e8821a","file_name":"2025_PNAS_Shi.pdf","file_id":"20744","relation":"main_file","date_updated":"2025-12-09T12:45:53Z","creator":"dernst","access_level":"open_access","content_type":"application/pdf","success":1,"file_size":10621381,"date_created":"2025-12-09T12:45:53Z"}],"publisher":"National Academy of Sciences","article_processing_charge":"Yes (in subscription journal)","corr_author":"1","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"related_material":{"record":[{"status":"public","id":"20749","relation":"research_data"}]},"doi":"10.1073/pnas.2516865122","oa":1,"acknowledgement":"We thank Dustin Kleckner, Jack-William Barotta, and Daniel M. Harris for insightful discussions. We acknowledge the Miba machine shop at the Institute of Science and Technology Austria for instrumentation support. M.C.H. and C.P.G. acknowledge funding by the Gesellschaft für Forschungsförderung Niederösterreich under project FTI23-G-011.","department":[{"_id":"ScWa"},{"_id":"CaGo"}],"month":"12","project":[{"name":"Dynamically reconfigurable self-assembly with triangular DNA-origami bricks","grant_number":"FTI23-G-011","_id":"8dd93da8-16d5-11f0-9cad-d2c70200d9a5"}],"article_type":"original","author":[{"id":"5c5b9247-15b2-11ec-abd3-fd958715639c","first_name":"Sue","full_name":"Shi, Sue","last_name":"Shi"},{"last_name":"Hübl","full_name":"Hübl, Maximilian","first_name":"Maximilian","id":"5eb8629e-15b2-11ec-abd3-e6f3e5e01f32"},{"last_name":"Grosjean","full_name":"Grosjean, Galien M","orcid":"0000-0001-5154-417X","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","first_name":"Galien M"},{"full_name":"Goodrich, Carl Peter","last_name":"Goodrich","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176"}],"volume":122,"ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","intvolume":"       122","OA_place":"publisher","date_published":"2025-12-16T00:00:00Z","quality_controlled":"1","type":"journal_article","external_id":{"arxiv":["2507.01739"]},"_id":"20727","language":[{"iso":"eng"}],"abstract":[{"text":"Acoustic levitation provides a unique method for manipulating small particles as it completely evades effects from gravity, container walls, or physical handling. These advantages make it a tantalizing platform for studying complex phenomena in many-particle systems. In most standing-wave traps, however, particles interact via acoustic scattering forces that cause them to merge into a single dense object. Here, we introduce a complementary approach that combines acoustic levitation with electrostatic charging to assemble, adapt, and activate complex, separated many-particle systems. The key idea is to superimpose electrostatic repulsion on the intrinsic acoustic attraction, rendering a so-called “mermaid” potential where interactions are attractive at short range and repulsive at long range. By controlling the attraction–repulsion balance, we can levitate expanded structures where all particles are separated, collapsed structures where they are in contact, and hybrid ones consisting of both expanded and collapsed components. We find that collapsed and expanded structures are inherently stable, whereas hybrid ones exhibit transient stability governed by acoustically unstable dimers. Furthermore, we show how electrostatics allow us to adapt between configurations on the fly, either by quasistatic discharge or discrete up/down charge steps. Finally, we demonstrate how large structures experience selective energy pumping from the acoustic field—thrusting some particles into motion while others remain stationary—leading to complex dynamics including coupled rotations and oscillations. Our approach establishes a design space beyond acoustic collapse, offering possibilities to study many-particle systems with complex interactions, while suggesting pathways toward scalable integration into materials processing and other applications.","lang":"eng"}],"citation":{"apa":"Shi, S., Hübl, M., Grosjean, G. M., Goodrich, C. P., &#38; Waitukaitis, S. R. (2025). Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2516865122\">https://doi.org/10.1073/pnas.2516865122</a>","short":"S. Shi, M. Hübl, G.M. Grosjean, C.P. Goodrich, S.R. Waitukaitis, Proceedings of the National Academy of Sciences 122 (2025) e2516865122.","ieee":"S. Shi, M. Hübl, G. M. Grosjean, C. P. Goodrich, and S. R. Waitukaitis, “Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 50. National Academy of Sciences, p. e2516865122, 2025.","mla":"Shi, Sue, et al. “Electrostatics Overcome Acoustic Collapse to Assemble, Adapt, and Activate Levitated Matter.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 50, National Academy of Sciences, 2025, p. e2516865122, doi:<a href=\"https://doi.org/10.1073/pnas.2516865122\">10.1073/pnas.2516865122</a>.","chicago":"Shi, Sue, Maximilian Hübl, Galien M Grosjean, Carl Peter Goodrich, and Scott R Waitukaitis. “Electrostatics Overcome Acoustic Collapse to Assemble, Adapt, and Activate Levitated Matter.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2516865122\">https://doi.org/10.1073/pnas.2516865122</a>.","ista":"Shi S, Hübl M, Grosjean GM, Goodrich CP, Waitukaitis SR. 2025. Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter. Proceedings of the National Academy of Sciences. 122(50), e2516865122.","ama":"Shi S, Hübl M, Grosjean GM, Goodrich CP, Waitukaitis SR. Electrostatics overcome acoustic collapse to assemble, adapt, and activate levitated matter. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(50):e2516865122. doi:<a href=\"https://doi.org/10.1073/pnas.2516865122\">10.1073/pnas.2516865122</a>"},"day":"16","has_accepted_license":"1","page":"e2516865122","status":"public","scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","issue":"50","file_date_updated":"2025-12-09T12:45:53Z","acknowledged_ssus":[{"_id":"M-Shop"}],"date_updated":"2026-02-16T12:33:43Z","publication":"Proceedings of the National Academy of Sciences"},{"article_processing_charge":"No","corr_author":"1","publisher":"American Physical Society","related_material":{"link":[{"url":"https://github.com/mxhbl/Roly.jl","relation":"software"}]},"pmid":1,"oa":1,"doi":"10.1103/PhysRevLett.134.058204","acknowledgement":"We thank Daichi Hayakawa, Thomas E. Videbæk, and W. Benjamin Rogers for important discussions and Jérémie Palacci, Anđela Šarić, and Scott Waitukaitis for helpful comments on the manuscript. The research was supported by the Gesellschaft für Forschungsförderung Niederösterreich under Project No. FTI23-G-011.","author":[{"id":"5eb8629e-15b2-11ec-abd3-e6f3e5e01f32","first_name":"Maximilian","full_name":"Hübl, Maximilian","last_name":"Hübl"},{"orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter","last_name":"Goodrich"}],"volume":134,"department":[{"_id":"CaGo"},{"_id":"GradSch"}],"month":"02","article_type":"original","project":[{"_id":"8dd93da8-16d5-11f0-9cad-d2c70200d9a5","grant_number":"FTI23-G-011","name":"Dynamically reconfigurable self-assembly with triangular DNA-origami bricks"}],"arxiv":1,"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"date_created":"2025-02-23T23:01:55Z","title":"Accessing semiaddressable self-assembly with efficient structure enumeration","OA_type":"green","oa_version":"Preprint","publication_status":"published","status":"public","issue":"5","scopus_import":"1","publication":"Physical Review Letters","date_updated":"2025-09-30T10:35:47Z","isi":1,"intvolume":"       134","article_number":"058204","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2025","OA_place":"repository","date_published":"2025-02-07T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2405.13567","open_access":"1"}],"external_id":{"pmid":["39983190"],"isi":["001454696800003"],"arxiv":["2405.13567"]},"_id":"19067","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Modern experimental methods enable the creation of self-assembly building blocks with tunable interactions, but optimally exploiting this tunability for the self-assembly of desired structures remains an important challenge. Many studies of this inverse problem start with the so-called fully addressable limit, where every particle in a target structure is different. This leads to clear design principles that often result in high assembly yield, but it is not a scalable approach—at some point, one must grapple with “reusing” building blocks, which lowers the degree of addressability and may cause a multitude of off-target structures to form, complicating the design process. Here, we solve a key obstacle preventing robust inverse design in the “semiaddressable regime” by developing a highly efficient algorithm that enumerates all structures that can be formed from a given set of building blocks. By combining this with established partition-function-based yield calculations, we show that it is almost always possible to find economical semiaddressable designs where the entropic gain from reusing building blocks outweighs the presence of off-target structures and even increases the yield of the target. Thus, not only does our enumeration algorithm enable robust and scalable inverse design in the semiaddressable regime, our results demonstrate that it is possible to operate in this regime while maintaining the level of control often associated with full addressability."}],"quality_controlled":"1","type":"journal_article","day":"07","citation":{"chicago":"Hübl, Maximilian, and Carl Peter Goodrich. “Accessing Semiaddressable Self-Assembly with Efficient Structure Enumeration.” <i>Physical Review Letters</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/PhysRevLett.134.058204\">https://doi.org/10.1103/PhysRevLett.134.058204</a>.","ama":"Hübl M, Goodrich CP. Accessing semiaddressable self-assembly with efficient structure enumeration. <i>Physical Review Letters</i>. 2025;134(5). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.134.058204\">10.1103/PhysRevLett.134.058204</a>","ista":"Hübl M, Goodrich CP. 2025. Accessing semiaddressable self-assembly with efficient structure enumeration. Physical Review Letters. 134(5), 058204.","apa":"Hübl, M., &#38; Goodrich, C. P. (2025). Accessing semiaddressable self-assembly with efficient structure enumeration. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.134.058204\">https://doi.org/10.1103/PhysRevLett.134.058204</a>","mla":"Hübl, Maximilian, and Carl Peter Goodrich. “Accessing Semiaddressable Self-Assembly with Efficient Structure Enumeration.” <i>Physical Review Letters</i>, vol. 134, no. 5, 058204, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.134.058204\">10.1103/PhysRevLett.134.058204</a>.","ieee":"M. Hübl and C. P. Goodrich, “Accessing semiaddressable self-assembly with efficient structure enumeration,” <i>Physical Review Letters</i>, vol. 134, no. 5. American Physical Society, 2025.","short":"M. Hübl, C.P. Goodrich, Physical Review Letters 134 (2025)."}},{"publisher":"Springer Nature","article_processing_charge":"Yes","corr_author":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"month":"08","department":[{"_id":"CaGo"}],"article_type":"original","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"author":[{"last_name":"Zu","full_name":"Zu, Mengjie","id":"26dd9e7c-e86a-11eb-a854-82ac731c9ae2","first_name":"Mengjie"},{"last_name":"Goodrich","full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074"}],"volume":5,"doi":"10.1038/s43246-024-00583-4","oa":1,"acknowledgement":"We thank M. Lechner for helpful discussions.","OA_type":"gold","oa_version":"Published Version","date_created":"2024-08-11T22:01:11Z","title":"Designing athermal disordered solids with automatic differentiation","publication_identifier":{"eissn":["2662-4443"]},"arxiv":1,"file":[{"checksum":"d6f74e242db5f46bb0e380ee23a268af","file_name":"2024_CommMaterials_Zu.pdf","date_updated":"2024-08-12T07:56:38Z","file_id":"17416","relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2024-08-12T07:56:38Z","file_size":9824134}],"publication_status":"published","scopus_import":"1","status":"public","publication":"Communications Materials","date_updated":"2025-05-08T09:45:35Z","file_date_updated":"2024-08-12T07:56:38Z","OA_place":"publisher","date_published":"2024-08-01T00:00:00Z","APC_amount":"3534 EUR","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","article_number":"141","intvolume":"         5","citation":{"ista":"Zu M, Goodrich CP. 2024. Designing athermal disordered solids with automatic differentiation. Communications Materials. 5, 141.","ama":"Zu M, Goodrich CP. Designing athermal disordered solids with automatic differentiation. <i>Communications Materials</i>. 2024;5. doi:<a href=\"https://doi.org/10.1038/s43246-024-00583-4\">10.1038/s43246-024-00583-4</a>","chicago":"Zu, Mengjie, and Carl Peter Goodrich. “Designing Athermal Disordered Solids with Automatic Differentiation.” <i>Communications Materials</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s43246-024-00583-4\">https://doi.org/10.1038/s43246-024-00583-4</a>.","short":"M. Zu, C.P. Goodrich, Communications Materials 5 (2024).","ieee":"M. Zu and C. P. Goodrich, “Designing athermal disordered solids with automatic differentiation,” <i>Communications Materials</i>, vol. 5. Springer Nature, 2024.","mla":"Zu, Mengjie, and Carl Peter Goodrich. “Designing Athermal Disordered Solids with Automatic Differentiation.” <i>Communications Materials</i>, vol. 5, 141, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s43246-024-00583-4\">10.1038/s43246-024-00583-4</a>.","apa":"Zu, M., &#38; Goodrich, C. P. (2024). Designing athermal disordered solids with automatic differentiation. <i>Communications Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s43246-024-00583-4\">https://doi.org/10.1038/s43246-024-00583-4</a>"},"day":"01","has_accepted_license":"1","quality_controlled":"1","type":"journal_article","external_id":{"arxiv":["2404.15101"]},"abstract":[{"text":"The ability to control forces between sub-micron-scale building blocks offers significant potential for designing new materials through self-assembly. Traditionally, this involves identifying a crystal structure with a desired property and then designing building-block interactions so that it assembles spontaneously. However, this paradigm fails for structurally disordered solids, which lack a well-defined structure. Here, we show that disordered solids can still be treated from an inverse self-assembly perspective by bypassing structure and directly targeting material properties. Using the Poisson’s ratio as a primary example, we demonstrate how differentiable programming links interaction parameters with emergent behavior, enabling iterative training to achieve the desired Poisson’s ratio. We also tune other properties, including pressure and local 8-fold structural order, and can even control multiple properties simultaneously. This robust, transferable, and scalable approach can handle a wide variety of systems and properties, demonstrating the utility of disordered solids as a practical avenue for self-assembly platforms.","lang":"eng"}],"_id":"17407","language":[{"iso":"eng"}]},{"quality_controlled":"1","type":"journal_article","external_id":{"pmid":["38097568"],"isi":["001125281300010"]},"_id":"14710","abstract":[{"lang":"eng","text":"The self-assembly of complex structures from a set of non-identical building blocks is a hallmark of soft matter and biological systems, including protein complexes, colloidal clusters, and DNA-based assemblies. Predicting the dependence of the equilibrium assembly yield on the concentrations and interaction energies of building blocks is highly challenging, owing to the difficulty of computing the entropic contributions to the free energy of the many structures that compete with the ground state configuration. While these calculations yield well known results for spherically symmetric building blocks, they do not hold when the building blocks have internal rotational degrees of freedom. Here we present an approach for solving this problem that works with arbitrary building blocks, including proteins with known structure and complex colloidal building blocks. Our algorithm combines classical statistical mechanics with recently developed computational tools for automatic differentiation. Automatic differentiation allows efficient evaluation of equilibrium averages over configurations that would otherwise be intractable. We demonstrate the validity of our framework by comparison to molecular dynamics simulations of simple examples, and apply it to calculate the yield curves for known protein complexes and for the assembly of colloidal shells."}],"language":[{"iso":"eng"}],"day":"01","citation":{"ista":"Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. 2023. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. 14, 8328.","ama":"Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. A computational toolbox for the assembly yield of complex and heterogeneous structures. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-43168-4\">10.1038/s41467-023-43168-4</a>","chicago":"Curatolo, Agnese I., Ofer Kimchi, Carl Peter Goodrich, Ryan K. Krueger, and Michael P. Brenner. “A Computational Toolbox for the Assembly Yield of Complex and Heterogeneous Structures.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-43168-4\">https://doi.org/10.1038/s41467-023-43168-4</a>.","short":"A.I. Curatolo, O. Kimchi, C.P. Goodrich, R.K. Krueger, M.P. Brenner, Nature Communications 14 (2023).","ieee":"A. I. Curatolo, O. Kimchi, C. P. Goodrich, R. K. Krueger, and M. P. Brenner, “A computational toolbox for the assembly yield of complex and heterogeneous structures,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","mla":"Curatolo, Agnese I., et al. “A Computational Toolbox for the Assembly Yield of Complex and Heterogeneous Structures.” <i>Nature Communications</i>, vol. 14, 8328, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-43168-4\">10.1038/s41467-023-43168-4</a>.","apa":"Curatolo, A. I., Kimchi, O., Goodrich, C. P., Krueger, R. K., &#38; Brenner, M. P. (2023). A computational toolbox for the assembly yield of complex and heterogeneous structures. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-43168-4\">https://doi.org/10.1038/s41467-023-43168-4</a>"},"has_accepted_license":"1","ddc":["530"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2023","intvolume":"        14","article_number":"8328","date_published":"2023-12-01T00:00:00Z","file_date_updated":"2023-12-27T08:40:43Z","isi":1,"publication":"Nature Communications","date_updated":"2025-09-09T14:02:41Z","status":"public","scopus_import":"1","publication_status":"published","file":[{"access_level":"open_access","date_created":"2023-12-27T08:40:43Z","file_size":1342319,"content_type":"application/pdf","success":1,"file_name":"2023_NatureComm_Curatolo.pdf","checksum":"fd9e9d527c2691f03fbc24031a75a3b3","creator":"kschuh","date_updated":"2023-12-27T08:40:43Z","file_id":"14714","relation":"main_file"}],"publication_identifier":{"eissn":["2041-1723"]},"oa_version":"Published Version","title":"A computational toolbox for the assembly yield of complex and heterogeneous structures","date_created":"2023-12-24T23:00:53Z","oa":1,"doi":"10.1038/s41467-023-43168-4","acknowledgement":"We thank Lucy Colwell for suggesting that we use covariance based methods to predict contacts and Yang Hsia, Scott Boyken, Zibo Chen, and David Baker for collaborations on designed protein complexes. We also thank Ned Wingreen for suggesting the alternative derivation of (11). This research was supported by the Office of Naval Research through ONR N00014-17-1-3029, the Simons Foundation the NSF-Simons Center for Mathematical and Statistical Analysis of Biology at Harvard (award number #1764269), the Peter B. Lewis ’55 Lewis-Sigler Institute/Genomics Fund through the Lewis-Sigler Institute of Integrative Genomics at Princeton University, and the National Science Foundation through the Center for the Physics of Biological Function (PHY-1734030).","department":[{"_id":"CaGo"}],"month":"12","article_type":"original","author":[{"full_name":"Curatolo, Agnese I.","last_name":"Curatolo","first_name":"Agnese I."},{"last_name":"Kimchi","full_name":"Kimchi, Ofer","first_name":"Ofer"},{"full_name":"Goodrich, Carl Peter","last_name":"Goodrich","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074"},{"first_name":"Ryan K.","last_name":"Krueger","full_name":"Krueger, Ryan K."},{"first_name":"Michael P.","full_name":"Brenner, Michael P.","last_name":"Brenner"}],"volume":14,"publisher":"Springer Nature","article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pmid":1},{"publication_status":"published","file":[{"date_updated":"2023-02-23T10:42:07Z","creator":"dernst","relation":"main_file","file_id":"12674","file_name":"2021_PNAS_Li.pdf","checksum":"702f7ec60ce6f2815104ab649dc661a4","file_size":3275944,"date_created":"2023-02-23T10:42:07Z","success":1,"content_type":"application/pdf","access_level":"open_access"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"date_created":"2023-02-21T08:51:04Z","title":"Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals","oa_version":"Published Version","oa":1,"doi":"10.1073/pnas.2107588118","author":[{"full_name":"Li, Ling","last_name":"Li","first_name":"Ling"},{"first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","last_name":"Goodrich","full_name":"Goodrich, Carl Peter"},{"first_name":"Haizhao","full_name":"Yang, Haizhao","last_name":"Yang"},{"first_name":"Katherine R.","full_name":"Phillips, Katherine R.","last_name":"Phillips"},{"first_name":"Zian","last_name":"Jia","full_name":"Jia, Zian"},{"full_name":"Chen, Hongshun","last_name":"Chen","first_name":"Hongshun"},{"first_name":"Lifeng","last_name":"Wang","full_name":"Wang, Lifeng"},{"first_name":"Jinjin","full_name":"Zhong, Jinjin","last_name":"Zhong"},{"first_name":"Anhua","full_name":"Liu, Anhua","last_name":"Liu"},{"full_name":"Lu, Jianfeng","last_name":"Lu","first_name":"Jianfeng"},{"first_name":"Jianwei","last_name":"Shuai","full_name":"Shuai, Jianwei"},{"last_name":"Brenner","full_name":"Brenner, Michael P.","first_name":"Michael P."},{"first_name":"Frans","full_name":"Spaepen, Frans","last_name":"Spaepen"},{"last_name":"Aizenberg","full_name":"Aizenberg, Joanna","first_name":"Joanna"}],"volume":118,"article_type":"original","month":"08","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"article_processing_charge":"No","publisher":"Proceedings of the National Academy of Sciences","extern":"1","pmid":1,"_id":"12667","language":[{"iso":"eng"}],"abstract":[{"text":"Unlike crystalline atomic and ionic solids, texture development due to crystallographically preferred growth in colloidal crystals is less studied. Here we investigate the underlying mechanisms of the texture evolution in an evaporation-induced colloidal assembly process through experiments, modeling, and theoretical analysis. In this widely used approach to obtain large-area colloidal crystals, the colloidal particles are driven to the meniscus via the evaporation of a solvent or matrix precursor solution where they close-pack to form a face-centered cubic colloidal assembly. Via two-dimensional large-area crystallographic mapping, we show that the initial crystal orientation is dominated by the interaction of particles with the meniscus, resulting in the expected coalignment of the close-packed direction with the local meniscus geometry. By combining with crystal structure analysis at a single-particle level, we further reveal that, at the later stage of self-assembly, however, the colloidal crystal undergoes a gradual rotation facilitated by geometrically necessary dislocations (GNDs) and achieves a large-area uniform crystallographic orientation with the close-packed direction perpendicular to the meniscus and parallel to the growth direction. Classical slip analysis, finite element-based mechanical simulation, computational colloidal assembly modeling, and continuum theory unequivocally show that these GNDs result from the tensile stress field along the meniscus direction due to the constrained shrinkage of the colloidal crystal during drying. The generation of GNDs with specific slip systems within individual grains leads to crystallographic rotation to accommodate the mechanical stress. The mechanistic understanding reported here can be utilized to control crystallographic features of colloidal assemblies, and may provide further insights into crystallographically preferred growth in synthetic, biological, and geological crystals.","lang":"eng"}],"external_id":{"pmid":["34341109"]},"type":"journal_article","quality_controlled":"1","has_accepted_license":"1","citation":{"apa":"Li, L., Goodrich, C. P., Yang, H., Phillips, K. R., Jia, Z., Chen, H., … Aizenberg, J. (2021). Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals. <i>PNAS</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2107588118\">https://doi.org/10.1073/pnas.2107588118</a>","mla":"Li, Ling, et al. “Microscopic Origins of the Crystallographically Preferred Growth in Evaporation-Induced Colloidal Crystals.” <i>PNAS</i>, vol. 118, no. 32, e2107588118, Proceedings of the National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2107588118\">10.1073/pnas.2107588118</a>.","short":"L. Li, C.P. Goodrich, H. Yang, K.R. Phillips, Z. Jia, H. Chen, L. Wang, J. Zhong, A. Liu, J. Lu, J. Shuai, M.P. Brenner, F. Spaepen, J. Aizenberg, PNAS 118 (2021).","ieee":"L. Li <i>et al.</i>, “Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals,” <i>PNAS</i>, vol. 118, no. 32. Proceedings of the National Academy of Sciences, 2021.","chicago":"Li, Ling, Carl Peter Goodrich, Haizhao Yang, Katherine R. Phillips, Zian Jia, Hongshun Chen, Lifeng Wang, et al. “Microscopic Origins of the Crystallographically Preferred Growth in Evaporation-Induced Colloidal Crystals.” <i>PNAS</i>. Proceedings of the National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2107588118\">https://doi.org/10.1073/pnas.2107588118</a>.","ama":"Li L, Goodrich CP, Yang H, et al. Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals. <i>PNAS</i>. 2021;118(32). doi:<a href=\"https://doi.org/10.1073/pnas.2107588118\">10.1073/pnas.2107588118</a>","ista":"Li L, Goodrich CP, Yang H, Phillips KR, Jia Z, Chen H, Wang L, Zhong J, Liu A, Lu J, Shuai J, Brenner MP, Spaepen F, Aizenberg J. 2021. Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals. PNAS. 118(32), e2107588118."},"day":"10","intvolume":"       118","article_number":"e2107588118","year":"2021","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-08-10T00:00:00Z","file_date_updated":"2023-02-23T10:42:07Z","publication":"PNAS","date_updated":"2023-02-23T10:45:44Z","status":"public","issue":"32","scopus_import":"1"},{"ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","intvolume":"       118","article_number":"e2024083118","date_published":"2021-03-09T00:00:00Z","quality_controlled":"1","type":"journal_article","external_id":{"isi":["000627429100097"],"pmid":["33653960"]},"_id":"9257","language":[{"iso":"eng"}],"abstract":[{"text":"The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing emergent kinetics, but this has received considerably less attention. Using recent advances in automatic differentiation, we show how kinetic pathways can be precisely designed by directly differentiating through statistical physics models, namely free energy calculations and molecular dynamics simulations. We consider two systems that are crucial to our understanding of structural self-assembly: bulk crystallization and small nanoclusters. In each case, we are able to assemble precise dynamical features. Using gradient information, we manipulate interactions among constituent particles to tune the rate at which these systems yield specific structures of interest. Moreover, we use this approach to learn nontrivial features about the high-dimensional design space, allowing us to accurately predict when multiple kinetic features can be simultaneously and independently controlled. These results provide a concrete and generalizable foundation for studying nonstructural self-assembly, including kinetic properties as well as other complex emergent properties, in a vast array of systems.","lang":"eng"}],"citation":{"apa":"Goodrich, C. P., King, E. M., Schoenholz, S. S., Cubuk, E. D., &#38; Brenner, M. P. (2021). Designing self-assembling kinetics with differentiable statistical physics models. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2024083118\">https://doi.org/10.1073/pnas.2024083118</a>","ieee":"C. P. Goodrich, E. M. King, S. S. Schoenholz, E. D. Cubuk, and M. P. Brenner, “Designing self-assembling kinetics with differentiable statistical physics models,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 10. National Academy of Sciences, 2021.","short":"C.P. Goodrich, E.M. King, S.S. Schoenholz, E.D. Cubuk, M.P. Brenner, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","mla":"Goodrich, Carl Peter, et al. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 10, e2024083118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2024083118\">10.1073/pnas.2024083118</a>.","chicago":"Goodrich, Carl Peter, Ella M. King, Samuel S. Schoenholz, Ekin D. Cubuk, and Michael P. Brenner. “Designing Self-Assembling Kinetics with Differentiable Statistical Physics Models.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2024083118\">https://doi.org/10.1073/pnas.2024083118</a>.","ista":"Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. 2021. Designing self-assembling kinetics with differentiable statistical physics models. Proceedings of the National Academy of Sciences of the United States of America. 118(10), e2024083118.","ama":"Goodrich CP, King EM, Schoenholz SS, Cubuk ED, Brenner MP. Designing self-assembling kinetics with differentiable statistical physics models. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(10). doi:<a href=\"https://doi.org/10.1073/pnas.2024083118\">10.1073/pnas.2024083118</a>"},"day":"09","has_accepted_license":"1","status":"public","scopus_import":"1","issue":"10","file_date_updated":"2021-03-22T12:23:54Z","isi":1,"publication":"Proceedings of the National Academy of Sciences of the United States of America","date_updated":"2025-05-14T10:58:42Z","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"oa_version":"Published Version","date_created":"2021-03-21T23:01:20Z","title":"Designing self-assembling kinetics with differentiable statistical physics models","publication_status":"published","file":[{"date_updated":"2021-03-22T12:23:54Z","relation":"main_file","file_id":"9278","creator":"dernst","file_name":"2021_PNAS_Goodrich.pdf","checksum":"5be8da2b1c0757feb1057f1a515cf9e0","date_created":"2021-03-22T12:23:54Z","file_size":1047954,"content_type":"application/pdf","success":1,"access_level":"open_access"}],"publisher":"National Academy of Sciences","article_processing_charge":"No","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"pmid":1,"oa":1,"doi":"10.1073/pnas.2024083118","acknowledgement":"We thank Agnese Curatolo, Megan Engel, Ofer Kimchi, Seong Ho Pahng, and Roy Frostig for helpful discussions. This material is based on work supported by NSF Graduate Research Fellowship Grant DGE1745303. This research was funded by NSF Grant DMS-1715477, Materials Research Science and Engineering Centers Grant DMR-1420570, and Office of Naval Research Grant N00014-17-1-3029. M.P.B. is an investigator of the Simons Foundation.","month":"03","department":[{"_id":"CaGo"}],"article_type":"original","author":[{"last_name":"Goodrich","full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","orcid":"0000-0002-1307-5074"},{"full_name":"King, Ella M.","last_name":"King","first_name":"Ella M."},{"first_name":"Samuel S.","last_name":"Schoenholz","full_name":"Schoenholz, Samuel S."},{"first_name":"Ekin D.","full_name":"Cubuk, Ekin D.","last_name":"Cubuk"},{"first_name":"Michael P.","last_name":"Brenner","full_name":"Brenner, Michael P."}],"volume":118},{"file_date_updated":"2021-04-12T08:33:23Z","publication":"Science Advances","date_updated":"2024-10-15T12:55:13Z","status":"public","DOAJ_listed":"1","issue":"51","language":[{"iso":"eng"}],"_id":"7778","abstract":[{"lang":"eng","text":"Recent advances in synthetic posttranslational protein circuits are substantially impacting the landscape of cellular engineering and offer several advantages compared to traditional gene circuits. However, engineering dynamic phenomena such as oscillations in protein-level circuits remains an outstanding challenge. Few examples of biological posttranslational oscillators are known, necessitating theoretical progress to determine realizable oscillators. We construct mathematical models for two posttranslational oscillators, using few components that interact only through reversible binding and phosphorylation/dephosphorylation reactions. Our designed oscillators rely on the self-assembly of two protein species into multimeric functional enzymes that respectively inhibit and enhance this self-assembly. We limit our analysis to within experimental constraints, finding (i) significant portions of the restricted parameter space yielding oscillations and (ii) that oscillation periods can be tuned by several orders of magnitude using recent advances in computational protein design. Our work paves the way for the rational design and realization of protein-based dynamic systems."}],"quality_controlled":"1","type":"journal_article","day":"16","citation":{"mla":"Kimchi, Ofer, et al. “Self-Assembly-Based Posttranslational Protein Oscillators.” <i>Science Advances</i>, vol. 6, no. 51, eabc1939, 2020, doi:<a href=\"https://doi.org/10.1126/sciadv.abc1939\">10.1126/sciadv.abc1939</a>.","short":"O. Kimchi, C.P. Goodrich, A. Courbet, A.I. Curatolo, N.B. Woodall, D. Baker, M.P. Brenner, Science Advances 6 (2020).","ieee":"O. Kimchi <i>et al.</i>, “Self-assembly-based posttranslational protein oscillators,” <i>Science Advances</i>, vol. 6, no. 51. 2020.","apa":"Kimchi, O., Goodrich, C. P., Courbet, A., Curatolo, A. I., Woodall, N. B., Baker, D., &#38; Brenner, M. P. (2020). Self-assembly-based posttranslational protein oscillators. <i>Science Advances</i>. <a href=\"https://doi.org/10.1126/sciadv.abc1939\">https://doi.org/10.1126/sciadv.abc1939</a>","ama":"Kimchi O, Goodrich CP, Courbet A, et al. Self-assembly-based posttranslational protein oscillators. <i>Science Advances</i>. 2020;6(51). doi:<a href=\"https://doi.org/10.1126/sciadv.abc1939\">10.1126/sciadv.abc1939</a>","ista":"Kimchi O, Goodrich CP, Courbet A, Curatolo AI, Woodall NB, Baker D, Brenner MP. 2020. Self-assembly-based posttranslational protein oscillators. Science Advances. 6(51), eabc1939.","chicago":"Kimchi, Ofer, Carl Peter Goodrich, Alexis Courbet, Agnese I. Curatolo, Nicholas B. Woodall, David Baker, and Michael P. Brenner. “Self-Assembly-Based Posttranslational Protein Oscillators.” <i>Science Advances</i>, 2020. <a href=\"https://doi.org/10.1126/sciadv.abc1939\">https://doi.org/10.1126/sciadv.abc1939</a>."},"has_accepted_license":"1","intvolume":"         6","article_number":"eabc1939","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","ddc":["570"],"year":"2020","OA_place":"publisher","date_published":"2020-12-16T00:00:00Z","oa":1,"doi":"10.1126/sciadv.abc1939","author":[{"first_name":"Ofer","full_name":"Kimchi, Ofer","last_name":"Kimchi"},{"orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter","last_name":"Goodrich"},{"first_name":"Alexis","last_name":"Courbet","full_name":"Courbet, Alexis"},{"last_name":"Curatolo","full_name":"Curatolo, Agnese I.","first_name":"Agnese I."},{"first_name":"Nicholas B.","last_name":"Woodall","full_name":"Woodall, Nicholas B."},{"last_name":"Baker","full_name":"Baker, David","first_name":"David"},{"full_name":"Brenner, Michael P.","last_name":"Brenner","first_name":"Michael P."}],"volume":6,"month":"12","article_type":"original","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"extern":"1","publication_status":"published","file":[{"relation":"main_file","file_id":"9320","creator":"dernst","date_updated":"2021-04-12T08:33:23Z","file_name":"2020_ScienceAdv_Kimchi.pdf","checksum":"eb6d950b6a68ddc4a2fb31ec80a2a1bd","file_size":1259758,"date_created":"2021-04-12T08:33:23Z","success":1,"content_type":"application/pdf","access_level":"open_access"}],"title":"Self-assembly-based posttranslational protein oscillators","date_created":"2020-04-30T12:07:55Z","OA_type":"gold","oa_version":"Published Version"},{"article_processing_charge":"No","publisher":"Springer Nature","status":"public","extern":"1","oa":1,"doi":"10.1038/s41467-018-06851-5","date_updated":"2021-01-12T08:15:18Z","publication":"Nature Communications","volume":9,"author":[{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","last_name":"Goodrich"},{"first_name":"Michael P.","last_name":"Brenner","full_name":"Brenner, Michael P."},{"last_name":"Ribbeck","full_name":"Ribbeck, Katharina","first_name":"Katharina"}],"article_type":"original","month":"10","article_number":"4348","intvolume":"         9","year":"2018","publication_identifier":{"issn":["2041-1723"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2018-10-19T00:00:00Z","date_created":"2020-04-30T11:38:01Z","title":"Enhanced diffusion by binding to the crosslinks of a polymer gel","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-018-06851-5"}],"_id":"7754","abstract":[{"lang":"eng","text":"Creating a selective gel that filters particles based on their interactions is a major goal of nanotechnology, with far-reaching implications from drug delivery to controlling assembly pathways. However, this is particularly difficult when the particles are larger than the gel’s characteristic mesh size because such particles cannot passively pass through the gel. Thus, filtering requires the interacting particles to transiently reorganize the gel’s internal structure. While significant advances, e.g., in DNA engineering, have enabled the design of nano-materials with programmable interactions, it is not clear what physical principles such a designer gel could exploit to achieve selective permeability. We present an equilibrium mechanism where crosslink binding dynamics are affected by interacting particles such that particle diffusion is enhanced. In addition to revealing specific design rules for manufacturing selective gels, our results have the potential to explain the origin of selective permeability in certain biological materials, including the nuclear pore complex."}],"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","publication_status":"published","day":"19","citation":{"ama":"Goodrich CP, Brenner MP, Ribbeck K. Enhanced diffusion by binding to the crosslinks of a polymer gel. <i>Nature Communications</i>. 2018;9. doi:<a href=\"https://doi.org/10.1038/s41467-018-06851-5\">10.1038/s41467-018-06851-5</a>","ista":"Goodrich CP, Brenner MP, Ribbeck K. 2018. Enhanced diffusion by binding to the crosslinks of a polymer gel. Nature Communications. 9, 4348.","chicago":"Goodrich, Carl Peter, Michael P. Brenner, and Katharina Ribbeck. “Enhanced Diffusion by Binding to the Crosslinks of a Polymer Gel.” <i>Nature Communications</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41467-018-06851-5\">https://doi.org/10.1038/s41467-018-06851-5</a>.","mla":"Goodrich, Carl Peter, et al. “Enhanced Diffusion by Binding to the Crosslinks of a Polymer Gel.” <i>Nature Communications</i>, vol. 9, 4348, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-06851-5\">10.1038/s41467-018-06851-5</a>.","ieee":"C. P. Goodrich, M. P. Brenner, and K. Ribbeck, “Enhanced diffusion by binding to the crosslinks of a polymer gel,” <i>Nature Communications</i>, vol. 9. Springer Nature, 2018.","short":"C.P. Goodrich, M.P. Brenner, K. Ribbeck, Nature Communications 9 (2018).","apa":"Goodrich, C. P., Brenner, M. P., &#38; Ribbeck, K. (2018). Enhanced diffusion by binding to the crosslinks of a polymer gel. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-018-06851-5\">https://doi.org/10.1038/s41467-018-06851-5</a>"}},{"extern":"1","article_processing_charge":"No","status":"public","page":"217-246","publisher":"Annual Reviews","volume":47,"author":[{"last_name":"Sethna","full_name":"Sethna, James P.","first_name":"James P."},{"first_name":"Matthew K.","last_name":"Bierbaum","full_name":"Bierbaum, Matthew K."},{"first_name":"Karin A.","last_name":"Dahmen","full_name":"Dahmen, Karin A."},{"orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","last_name":"Goodrich","full_name":"Goodrich, Carl Peter"},{"first_name":"Julia R.","full_name":"Greer, Julia R.","last_name":"Greer"},{"last_name":"Hayden","full_name":"Hayden, Lorien X.","first_name":"Lorien X."},{"last_name":"Kent-Dobias","full_name":"Kent-Dobias, Jaron P.","first_name":"Jaron P."},{"first_name":"Edward D.","full_name":"Lee, Edward D.","last_name":"Lee"},{"full_name":"Liarte, Danilo B.","last_name":"Liarte","first_name":"Danilo B."},{"last_name":"Ni","full_name":"Ni, Xiaoyue","first_name":"Xiaoyue"},{"last_name":"Quinn","full_name":"Quinn, Katherine N.","first_name":"Katherine N."},{"first_name":"Archishman","last_name":"Raju","full_name":"Raju, Archishman"},{"full_name":"Rocklin, D. Zeb","last_name":"Rocklin","first_name":"D. Zeb"},{"last_name":"Shekhawat","full_name":"Shekhawat, Ashivni","first_name":"Ashivni"},{"full_name":"Zapperi, Stefano","last_name":"Zapperi","first_name":"Stefano"}],"publication":"Annual Review of Materials Research","date_updated":"2021-01-12T08:15:18Z","month":"07","article_type":"original","doi":"10.1146/annurev-matsci-070115-032036","oa":1,"date_created":"2020-04-30T11:38:24Z","title":"Deformation of crystals: Connections with statistical physics","date_published":"2017-07-01T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1146/annurev-matsci-070115-032036","open_access":"1"}],"oa_version":"Published Version","intvolume":"        47","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","publication_identifier":{"issn":["1531-7331","1545-4118"]},"day":"01","citation":{"chicago":"Sethna, James P., Matthew K. Bierbaum, Karin A. Dahmen, Carl Peter Goodrich, Julia R. Greer, Lorien X. Hayden, Jaron P. Kent-Dobias, et al. “Deformation of Crystals: Connections with Statistical Physics.” <i>Annual Review of Materials Research</i>. Annual Reviews, 2017. <a href=\"https://doi.org/10.1146/annurev-matsci-070115-032036\">https://doi.org/10.1146/annurev-matsci-070115-032036</a>.","ista":"Sethna JP, Bierbaum MK, Dahmen KA, Goodrich CP, Greer JR, Hayden LX, Kent-Dobias JP, Lee ED, Liarte DB, Ni X, Quinn KN, Raju A, Rocklin DZ, Shekhawat A, Zapperi S. 2017. Deformation of crystals: Connections with statistical physics. Annual Review of Materials Research. 47, 217–246.","ama":"Sethna JP, Bierbaum MK, Dahmen KA, et al. Deformation of crystals: Connections with statistical physics. <i>Annual Review of Materials Research</i>. 2017;47:217-246. doi:<a href=\"https://doi.org/10.1146/annurev-matsci-070115-032036\">10.1146/annurev-matsci-070115-032036</a>","apa":"Sethna, J. P., Bierbaum, M. K., Dahmen, K. A., Goodrich, C. P., Greer, J. R., Hayden, L. X., … Zapperi, S. (2017). Deformation of crystals: Connections with statistical physics. <i>Annual Review of Materials Research</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-matsci-070115-032036\">https://doi.org/10.1146/annurev-matsci-070115-032036</a>","short":"J.P. Sethna, M.K. Bierbaum, K.A. Dahmen, C.P. Goodrich, J.R. Greer, L.X. Hayden, J.P. Kent-Dobias, E.D. Lee, D.B. Liarte, X. Ni, K.N. Quinn, A. Raju, D.Z. Rocklin, A. Shekhawat, S. Zapperi, Annual Review of Materials Research 47 (2017) 217–246.","ieee":"J. P. Sethna <i>et al.</i>, “Deformation of crystals: Connections with statistical physics,” <i>Annual Review of Materials Research</i>, vol. 47. Annual Reviews, pp. 217–246, 2017.","mla":"Sethna, James P., et al. “Deformation of Crystals: Connections with Statistical Physics.” <i>Annual Review of Materials Research</i>, vol. 47, Annual Reviews, 2017, pp. 217–46, doi:<a href=\"https://doi.org/10.1146/annurev-matsci-070115-032036\">10.1146/annurev-matsci-070115-032036</a>."},"language":[{"iso":"eng"}],"_id":"7755","abstract":[{"lang":"eng","text":"We give a bird's-eye view of the plastic deformation of crystals aimed at the statistical physics community, as well as a broad introduction to the statistical theories of forced rigid systems aimed at the plasticity community. Memory effects in magnets, spin glasses, charge density waves, and dilute colloidal suspensions are discussed in relation to the onset of plastic yielding in crystals. Dislocation avalanches and complex dislocation tangles are discussed via a brief introduction to the renormalization group and scaling. Analogies to emergent scale invariance in fracture, jamming, coarsening, and a variety of depinning transitions are explored. Dislocation dynamics in crystals challenge nonequilibrium statistical physics. Statistical physics provides both cautionary tales of subtle memory effects in nonequilibrium systems and systematic tools designed to address complex scale-invariant behavior on multiple length scales and timescales."}],"publication_status":"published","quality_controlled":"1","type":"journal_article"},{"doi":"10.1007/s10955-016-1703-9","article_type":"original","month":"01","publication":"Journal of Statistical Physics","date_updated":"2021-01-12T08:15:19Z","author":[{"first_name":"Marco","last_name":"Baity-Jesi","full_name":"Baity-Jesi, Marco"},{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","last_name":"Goodrich","full_name":"Goodrich, Carl Peter"},{"last_name":"Liu","full_name":"Liu, Andrea J.","first_name":"Andrea J."},{"first_name":"Sidney R.","last_name":"Nagel","full_name":"Nagel, Sidney R."},{"full_name":"Sethna, James P.","last_name":"Sethna","first_name":"James P."}],"volume":167,"publisher":"Springer Nature","page":"735-748","status":"public","article_processing_charge":"No","issue":"3-4","extern":"1","type":"journal_article","quality_controlled":"1","publication_status":"published","_id":"7756","abstract":[{"text":"We study the shear jamming of athermal frictionless soft spheres, and find that in the thermodynamic limit, a shear-jammed state exists with different elastic properties from the isotropically-jammed state. For example, shear-jammed states can have a non-zero residual shear stress in the thermodynamic limit that arises from long-range stress-stress correlations. As a result, the ratio of the shear and bulk moduli, which in isotropically-jammed systems vanishes as the jamming transition is approached from above, instead approaches a constant. Despite these striking differences, we argue that in a deeper sense, the shear jamming and isotropic jamming transitions actually have the same symmetry, and that the differences can be fully understood by rotating the six-dimensional basis of the elastic modulus tensor.","lang":"eng"}],"language":[{"iso":"eng"}],"day":"03","citation":{"ama":"Baity-Jesi M, Goodrich CP, Liu AJ, Nagel SR, Sethna JP. Emergent SO(3) symmetry of the frictionless shear jamming transition. <i>Journal of Statistical Physics</i>. 2017;167(3-4):735-748. doi:<a href=\"https://doi.org/10.1007/s10955-016-1703-9\">10.1007/s10955-016-1703-9</a>","ista":"Baity-Jesi M, Goodrich CP, Liu AJ, Nagel SR, Sethna JP. 2017. Emergent SO(3) symmetry of the frictionless shear jamming transition. Journal of Statistical Physics. 167(3–4), 735–748.","chicago":"Baity-Jesi, Marco, Carl Peter Goodrich, Andrea J. Liu, Sidney R. Nagel, and James P. Sethna. “Emergent SO(3) Symmetry of the Frictionless Shear Jamming Transition.” <i>Journal of Statistical Physics</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1007/s10955-016-1703-9\">https://doi.org/10.1007/s10955-016-1703-9</a>.","mla":"Baity-Jesi, Marco, et al. “Emergent SO(3) Symmetry of the Frictionless Shear Jamming Transition.” <i>Journal of Statistical Physics</i>, vol. 167, no. 3–4, Springer Nature, 2017, pp. 735–48, doi:<a href=\"https://doi.org/10.1007/s10955-016-1703-9\">10.1007/s10955-016-1703-9</a>.","short":"M. Baity-Jesi, C.P. Goodrich, A.J. Liu, S.R. Nagel, J.P. Sethna, Journal of Statistical Physics 167 (2017) 735–748.","ieee":"M. Baity-Jesi, C. P. Goodrich, A. J. Liu, S. R. Nagel, and J. P. Sethna, “Emergent SO(3) symmetry of the frictionless shear jamming transition,” <i>Journal of Statistical Physics</i>, vol. 167, no. 3–4. Springer Nature, pp. 735–748, 2017.","apa":"Baity-Jesi, M., Goodrich, C. P., Liu, A. J., Nagel, S. R., &#38; Sethna, J. P. (2017). Emergent SO(3) symmetry of the frictionless shear jamming transition. <i>Journal of Statistical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10955-016-1703-9\">https://doi.org/10.1007/s10955-016-1703-9</a>"},"year":"2017","publication_identifier":{"issn":["0022-4715","1572-9613"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       167","oa_version":"None","date_published":"2017-01-03T00:00:00Z","date_created":"2020-04-30T11:38:38Z","title":"Emergent SO(3) symmetry of the frictionless shear jamming transition"},{"doi":"10.1073/pnas.1612139114","article_type":"original","month":"03","date_updated":"2021-01-12T08:15:19Z","publication":"Proceedings of the National Academy of Sciences","volume":114,"author":[{"first_name":"Jason W.","full_name":"Rocks, Jason W.","last_name":"Rocks"},{"full_name":"Pashine, Nidhi","last_name":"Pashine","first_name":"Nidhi"},{"last_name":"Bischofberger","full_name":"Bischofberger, Irmgard","first_name":"Irmgard"},{"last_name":"Goodrich","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter"},{"first_name":"Andrea J.","last_name":"Liu","full_name":"Liu, Andrea J."},{"last_name":"Nagel","full_name":"Nagel, Sidney R.","first_name":"Sidney R."}],"publisher":"Proceedings of the National Academy of Sciences","page":"2520-2525","status":"public","article_processing_charge":"No","issue":"10","extern":"1","type":"journal_article","publication_status":"published","quality_controlled":"1","_id":"7757","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Recent advances in designing metamaterials have demonstrated that global mechanical properties of disordered spring networks can be tuned by selectively modifying only a small subset of bonds. Here, using a computationally efficient approach, we extend this idea to tune more general properties of networks. With nearly complete success, we are able to produce a strain between any two target nodes in a network in response to an applied source strain on any other pair of nodes by removing only ∼1% of the bonds. We are also able to control multiple pairs of target nodes, each with a different individual response, from a single source, and to tune multiple independent source/target responses simultaneously into a network. We have fabricated physical networks in macroscopic 2D and 3D systems that exhibit these responses. This work is inspired by the long-range coupled conformational changes that constitute allosteric function in proteins. The fact that allostery is a common means for regulation in biological molecules suggests that it is a relatively easy property to develop through evolution. In analogy, our results show that long-range coupled mechanical responses are similarly easy to achieve in disordered networks."}],"day":"07","citation":{"chicago":"Rocks, Jason W., Nidhi Pashine, Irmgard Bischofberger, Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel. “Designing Allostery-Inspired Response in Mechanical Networks.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1612139114\">https://doi.org/10.1073/pnas.1612139114</a>.","ista":"Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. 2017. Designing allostery-inspired response in mechanical networks. Proceedings of the National Academy of Sciences. 114(10), 2520–2525.","ama":"Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. Designing allostery-inspired response in mechanical networks. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(10):2520-2525. doi:<a href=\"https://doi.org/10.1073/pnas.1612139114\">10.1073/pnas.1612139114</a>","apa":"Rocks, J. W., Pashine, N., Bischofberger, I., Goodrich, C. P., Liu, A. J., &#38; Nagel, S. R. (2017). Designing allostery-inspired response in mechanical networks. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1612139114\">https://doi.org/10.1073/pnas.1612139114</a>","ieee":"J. W. Rocks, N. Pashine, I. Bischofberger, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Designing allostery-inspired response in mechanical networks,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 10. Proceedings of the National Academy of Sciences, pp. 2520–2525, 2017.","short":"J.W. Rocks, N. Pashine, I. Bischofberger, C.P. Goodrich, A.J. Liu, S.R. Nagel, Proceedings of the National Academy of Sciences 114 (2017) 2520–2525.","mla":"Rocks, Jason W., et al. “Designing Allostery-Inspired Response in Mechanical Networks.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 10, Proceedings of the National Academy of Sciences, 2017, pp. 2520–25, doi:<a href=\"https://doi.org/10.1073/pnas.1612139114\">10.1073/pnas.1612139114</a>."},"year":"2017","publication_identifier":{"issn":["0027-8424","1091-6490"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       114","oa_version":"None","date_published":"2017-03-07T00:00:00Z","date_created":"2020-04-30T11:38:53Z","title":"Designing allostery-inspired response in mechanical networks"},{"publisher":"Proceedings of the National Academy of Sciences","page":"257-262","status":"public","article_processing_charge":"No","issue":"2","extern":"1","doi":"10.1073/pnas.1608838114","article_type":"original","month":"01","publication":"Proceedings of the National Academy of Sciences","date_updated":"2021-01-12T08:15:20Z","author":[{"last_name":"Goodrich","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter"},{"full_name":"Brenner, Michael P.","last_name":"Brenner","first_name":"Michael P."}],"volume":114,"publication_identifier":{"issn":["0027-8424","1091-6490"]},"year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       114","oa_version":"None","date_published":"2017-01-10T00:00:00Z","title":"Using active colloids as machines to weave and braid on the micrometer scale","date_created":"2020-04-30T11:39:09Z","type":"journal_article","publication_status":"published","quality_controlled":"1","abstract":[{"lang":"eng","text":"Controlling motion at the microscopic scale is a fundamental goal in the development of biologically inspired systems. We show that the motion of active, self-propelled colloids can be sufficiently controlled for use as a tool to assemble complex structures such as braids and weaves out of microscopic filaments. Unlike typical self-assembly paradigms, these structures are held together by geometric constraints rather than adhesive bonds. The out-of-equilibrium assembly that we propose involves precisely controlling the 2D motion of active colloids so that their path has a nontrivial topology. We demonstrate with proof-of-principle Brownian dynamics simulations that, when the colloids are attached to long semiflexible filaments, this motion causes the filaments to braid. The ability of the active particles to provide sufficient force necessary to bend the filaments into a braid depends on a number of factors, including the self-propulsion mechanism, the properties of the filament, and the maximum curvature in the braid. Our work demonstrates that nonequilibrium assembly pathways can be designed using active particles."}],"_id":"7758","language":[{"iso":"eng"}],"day":"10","citation":{"apa":"Goodrich, C. P., &#38; Brenner, M. P. (2017). Using active colloids as machines to weave and braid on the micrometer scale. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1608838114\">https://doi.org/10.1073/pnas.1608838114</a>","mla":"Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as Machines to Weave and Braid on the Micrometer Scale.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 2, Proceedings of the National Academy of Sciences, 2017, pp. 257–62, doi:<a href=\"https://doi.org/10.1073/pnas.1608838114\">10.1073/pnas.1608838114</a>.","short":"C.P. Goodrich, M.P. Brenner, Proceedings of the National Academy of Sciences 114 (2017) 257–262.","ieee":"C. P. Goodrich and M. P. Brenner, “Using active colloids as machines to weave and braid on the micrometer scale,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 2. Proceedings of the National Academy of Sciences, pp. 257–262, 2017.","chicago":"Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as Machines to Weave and Braid on the Micrometer Scale.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1608838114\">https://doi.org/10.1073/pnas.1608838114</a>.","ama":"Goodrich CP, Brenner MP. Using active colloids as machines to weave and braid on the micrometer scale. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(2):257-262. doi:<a href=\"https://doi.org/10.1073/pnas.1608838114\">10.1073/pnas.1608838114</a>","ista":"Goodrich CP, Brenner MP. 2017. Using active colloids as machines to weave and braid on the micrometer scale. Proceedings of the National Academy of Sciences. 114(2), 257–262."}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2016","publication_identifier":{"issn":["0027-8424","1091-6490"]},"intvolume":"       113","oa_version":"None","date_created":"2020-04-30T11:39:53Z","title":"Scaling ansatz for the jamming transition","date_published":"2016-08-30T00:00:00Z","quality_controlled":"1","publication_status":"published","type":"journal_article","_id":"7760","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We propose a Widom-like scaling ansatz for the critical jamming transition. Our ansatz for the elastic energy shows that the scaling of the energy, compressive strain, shear strain, system size, pressure, shear stress, bulk modulus, and shear modulus are all related to each other via scaling relations, with only three independent scaling exponents. We extract the values of these exponents from already known numerical or theoretical results, and we numerically verify the resulting predictions of the scaling theory for the energy and residual shear stress. We also derive a scaling relation between pressure and residual shear stress that yields insight into why the shear and bulk moduli scale differently. Our theory shows that the jamming transition exhibits an emergent scale invariance, setting the stage for the potential development of a renormalization group theory for jamming."}],"day":"30","citation":{"apa":"Goodrich, C. P., Liu, A. J., &#38; Sethna, J. P. (2016). Scaling ansatz for the jamming transition. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1601858113\">https://doi.org/10.1073/pnas.1601858113</a>","mla":"Goodrich, Carl Peter, et al. “Scaling Ansatz for the Jamming Transition.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 35, Proceedings of the National Academy of Sciences, 2016, pp. 9745–50, doi:<a href=\"https://doi.org/10.1073/pnas.1601858113\">10.1073/pnas.1601858113</a>.","short":"C.P. Goodrich, A.J. Liu, J.P. Sethna, Proceedings of the National Academy of Sciences 113 (2016) 9745–9750.","ieee":"C. P. Goodrich, A. J. Liu, and J. P. Sethna, “Scaling ansatz for the jamming transition,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 35. Proceedings of the National Academy of Sciences, pp. 9745–9750, 2016.","chicago":"Goodrich, Carl Peter, Andrea J. Liu, and James P. Sethna. “Scaling Ansatz for the Jamming Transition.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1601858113\">https://doi.org/10.1073/pnas.1601858113</a>.","ama":"Goodrich CP, Liu AJ, Sethna JP. Scaling ansatz for the jamming transition. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(35):9745-9750. doi:<a href=\"https://doi.org/10.1073/pnas.1601858113\">10.1073/pnas.1601858113</a>","ista":"Goodrich CP, Liu AJ, Sethna JP. 2016. Scaling ansatz for the jamming transition. Proceedings of the National Academy of Sciences. 113(35), 9745–9750."},"status":"public","page":"9745-9750","publisher":"Proceedings of the National Academy of Sciences","article_processing_charge":"No","extern":"1","issue":"35","doi":"10.1073/pnas.1601858113","month":"08","article_type":"original","volume":113,"author":[{"last_name":"Goodrich","full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074"},{"full_name":"Liu, Andrea J.","last_name":"Liu","first_name":"Andrea J."},{"full_name":"Sethna, James P.","last_name":"Sethna","first_name":"James P."}],"date_updated":"2021-01-12T08:15:21Z","publication":"Proceedings of the National Academy of Sciences"},{"abstract":[{"text":"We study the effect of dilute pinning on the jamming transition. Pinning reduces the average contact number needed to jam unpinned particles and shifts the jamming threshold to lower densities, leading to a pinning susceptibility, χp. Our main results are that this susceptibility obeys scaling form and diverges in the thermodynamic limit as χp∝|ϕ−ϕ∞c|−γp where ϕ∞c is the jamming threshold in the absence of pins. Finite-size scaling arguments yield these values with associated statistical (systematic) errors γp=1.018±0.026(0.291) in d=2 and γp=1.534±0.120(0.822) in d=3. Logarithmic corrections raise the exponent in d=2 to close to the d=3 value, although the systematic errors are very large.","lang":"eng"}],"_id":"7761","language":[{"iso":"eng"}],"publication_status":"published","quality_controlled":"1","type":"journal_article","citation":{"mla":"Graves, Amy L., et al. “Pinning Susceptibility: The Effect of Dilute, Quenched Disorder on Jamming.” <i>Physical Review Letters</i>, vol. 116, no. 23, 235501, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/physrevlett.116.235501\">10.1103/physrevlett.116.235501</a>.","ieee":"A. L. Graves, S. Nashed, E. Padgett, C. P. Goodrich, A. J. Liu, and J. P. Sethna, “Pinning susceptibility: The effect of dilute, quenched disorder on jamming,” <i>Physical Review Letters</i>, vol. 116, no. 23. American Physical Society, 2016.","short":"A.L. Graves, S. Nashed, E. Padgett, C.P. Goodrich, A.J. Liu, J.P. Sethna, Physical Review Letters 116 (2016).","apa":"Graves, A. L., Nashed, S., Padgett, E., Goodrich, C. P., Liu, A. J., &#38; Sethna, J. P. (2016). Pinning susceptibility: The effect of dilute, quenched disorder on jamming. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.116.235501\">https://doi.org/10.1103/physrevlett.116.235501</a>","ama":"Graves AL, Nashed S, Padgett E, Goodrich CP, Liu AJ, Sethna JP. Pinning susceptibility: The effect of dilute, quenched disorder on jamming. <i>Physical Review Letters</i>. 2016;116(23). doi:<a href=\"https://doi.org/10.1103/physrevlett.116.235501\">10.1103/physrevlett.116.235501</a>","ista":"Graves AL, Nashed S, Padgett E, Goodrich CP, Liu AJ, Sethna JP. 2016. Pinning susceptibility: The effect of dilute, quenched disorder on jamming. Physical Review Letters. 116(23), 235501.","chicago":"Graves, Amy L., Samer Nashed, Elliot Padgett, Carl Peter Goodrich, Andrea J. Liu, and James P. Sethna. “Pinning Susceptibility: The Effect of Dilute, Quenched Disorder on Jamming.” <i>Physical Review Letters</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/physrevlett.116.235501\">https://doi.org/10.1103/physrevlett.116.235501</a>."},"day":"10","article_number":"235501","intvolume":"       116","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2016","publication_identifier":{"issn":["0031-9007","1079-7114"]},"date_created":"2020-04-30T11:40:10Z","title":"Pinning susceptibility: The effect of dilute, quenched disorder on jamming","date_published":"2016-06-10T00:00:00Z","oa_version":"None","doi":"10.1103/physrevlett.116.235501","volume":116,"author":[{"last_name":"Graves","full_name":"Graves, Amy L.","first_name":"Amy L."},{"first_name":"Samer","last_name":"Nashed","full_name":"Nashed, Samer"},{"first_name":"Elliot","last_name":"Padgett","full_name":"Padgett, Elliot"},{"full_name":"Goodrich, Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","orcid":"0000-0002-1307-5074"},{"last_name":"Liu","full_name":"Liu, Andrea J.","first_name":"Andrea J."},{"first_name":"James P.","full_name":"Sethna, James P.","last_name":"Sethna"}],"date_updated":"2021-01-12T08:15:21Z","publication":"Physical Review Letters","month":"06","article_type":"original","article_processing_charge":"No","status":"public","publisher":"American Physical Society","extern":"1","issue":"23"},{"month":"02","article_type":"original","volume":116,"author":[{"first_name":"Jennifer M.","last_name":"Rieser","full_name":"Rieser, Jennifer M."},{"full_name":"Goodrich, Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","orcid":"0000-0002-1307-5074"},{"last_name":"Liu","full_name":"Liu, Andrea J.","first_name":"Andrea J."},{"first_name":"Douglas J.","full_name":"Durian, Douglas J.","last_name":"Durian"}],"publication":"Physical Review Letters","date_updated":"2021-01-12T08:15:22Z","doi":"10.1103/physrevlett.116.088001","extern":"1","issue":"8","status":"public","publisher":"American Physical Society","article_processing_charge":"No","day":"23","citation":{"ama":"Rieser JM, Goodrich CP, Liu AJ, Durian DJ. Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials. <i>Physical Review Letters</i>. 2016;116(8). doi:<a href=\"https://doi.org/10.1103/physrevlett.116.088001\">10.1103/physrevlett.116.088001</a>","ista":"Rieser JM, Goodrich CP, Liu AJ, Durian DJ. 2016. Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials. Physical Review Letters. 116(8), 088001.","chicago":"Rieser, Jennifer M., Carl Peter Goodrich, Andrea J. Liu, and Douglas J. Durian. “Divergence of Voronoi Cell Anisotropy Vector: A Threshold-Free Characterization of Local Structure in Amorphous Materials.” <i>Physical Review Letters</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/physrevlett.116.088001\">https://doi.org/10.1103/physrevlett.116.088001</a>.","mla":"Rieser, Jennifer M., et al. “Divergence of Voronoi Cell Anisotropy Vector: A Threshold-Free Characterization of Local Structure in Amorphous Materials.” <i>Physical Review Letters</i>, vol. 116, no. 8, 088001, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/physrevlett.116.088001\">10.1103/physrevlett.116.088001</a>.","short":"J.M. Rieser, C.P. Goodrich, A.J. Liu, D.J. Durian, Physical Review Letters 116 (2016).","ieee":"J. M. Rieser, C. P. Goodrich, A. J. Liu, and D. J. Durian, “Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials,” <i>Physical Review Letters</i>, vol. 116, no. 8. American Physical Society, 2016.","apa":"Rieser, J. M., Goodrich, C. P., Liu, A. J., &#38; Durian, D. J. (2016). Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.116.088001\">https://doi.org/10.1103/physrevlett.116.088001</a>"},"publication_status":"published","quality_controlled":"1","type":"journal_article","_id":"7762","abstract":[{"text":"Characterizing structural inhomogeneity is an essential step in understanding the mechanical response of amorphous materials. We introduce a threshold-free measure based on the field of vectors pointing from the center of each particle to the centroid of the Voronoi cell in which the particle resides. These vectors tend to point in toward regions of high free volume and away from regions of low free volume, reminiscent of sinks and sources in a vector field. We compute the local divergence of these vectors, where positive values correspond to overpacked regions and negative values identify underpacked regions within the material. Distributions of this divergence are nearly Gaussian with zero mean, allowing for structural characterization using only the moments of the distribution. We explore how the standard deviation and skewness vary with the packing fraction for simulations of bidisperse systems and find a kink in these moments that coincides with the jamming transition.","lang":"eng"}],"language":[{"iso":"eng"}],"oa_version":"None","date_created":"2020-04-30T11:40:25Z","title":"Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials","date_published":"2016-02-23T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0031-9007","1079-7114"]},"year":"2016","intvolume":"       116","article_number":"088001 "},{"intvolume":"       305","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0021-9991"]},"year":"2016","title":"Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena","date_created":"2020-04-30T11:40:41Z","date_published":"2016-01-15T00:00:00Z","oa_version":"None","_id":"7763","language":[{"iso":"eng"}],"abstract":[{"text":"An orthogonal wavelet basis is characterized by its approximation order, which relates to the ability of the basis to represent general smooth functions on a given scale. It is known, though perhaps not widely known, that there are ways of exceeding the approximation order, i.e., achieving higher-order error in the discretized wavelet transform and its inverse. The focus here is on the development of a practical formulation to accomplish this first for 1D smooth functions, then for 1D functions with discontinuities and then for multidimensional (here 2D) functions with discontinuities. It is shown how to transcend both the wavelet approximation order and the 2D Gibbs phenomenon in representing electromagnetic fields at discontinuous dielectric interfaces that do not simply follow the wavelet-basis grid.","lang":"eng"}],"quality_controlled":"1","publication_status":"published","type":"journal_article","citation":{"chicago":"Lombardini, Richard, Ramiro Acevedo, Alexander Kuczala, Kerry P. Keys, Carl Peter Goodrich, and Bruce R. Johnson. “Higher-Order Wavelet Reconstruction/Differentiation Filters and Gibbs Phenomena.” <i>Journal of Computational Physics</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.jcp.2015.10.035\">https://doi.org/10.1016/j.jcp.2015.10.035</a>.","ama":"Lombardini R, Acevedo R, Kuczala A, Keys KP, Goodrich CP, Johnson BR. Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena. <i>Journal of Computational Physics</i>. 2016;305:244-262. doi:<a href=\"https://doi.org/10.1016/j.jcp.2015.10.035\">10.1016/j.jcp.2015.10.035</a>","ista":"Lombardini R, Acevedo R, Kuczala A, Keys KP, Goodrich CP, Johnson BR. 2016. Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena. Journal of Computational Physics. 305, 244–262.","apa":"Lombardini, R., Acevedo, R., Kuczala, A., Keys, K. P., Goodrich, C. P., &#38; Johnson, B. R. (2016). Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena. <i>Journal of Computational Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcp.2015.10.035\">https://doi.org/10.1016/j.jcp.2015.10.035</a>","mla":"Lombardini, Richard, et al. “Higher-Order Wavelet Reconstruction/Differentiation Filters and Gibbs Phenomena.” <i>Journal of Computational Physics</i>, vol. 305, Elsevier, 2016, pp. 244–62, doi:<a href=\"https://doi.org/10.1016/j.jcp.2015.10.035\">10.1016/j.jcp.2015.10.035</a>.","short":"R. Lombardini, R. Acevedo, A. Kuczala, K.P. Keys, C.P. Goodrich, B.R. Johnson, Journal of Computational Physics 305 (2016) 244–262.","ieee":"R. Lombardini, R. Acevedo, A. Kuczala, K. P. Keys, C. P. Goodrich, and B. R. Johnson, “Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena,” <i>Journal of Computational Physics</i>, vol. 305. Elsevier, pp. 244–262, 2016."},"day":"15","article_processing_charge":"No","status":"public","page":"244-262","publisher":"Elsevier","extern":"1","doi":"10.1016/j.jcp.2015.10.035","volume":305,"author":[{"first_name":"Richard","last_name":"Lombardini","full_name":"Lombardini, Richard"},{"full_name":"Acevedo, Ramiro","last_name":"Acevedo","first_name":"Ramiro"},{"last_name":"Kuczala","full_name":"Kuczala, Alexander","first_name":"Alexander"},{"last_name":"Keys","full_name":"Keys, Kerry P.","first_name":"Kerry P."},{"last_name":"Goodrich","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter"},{"full_name":"Johnson, Bruce R.","last_name":"Johnson","first_name":"Bruce R."}],"date_updated":"2021-01-12T08:15:22Z","publication":"Journal of Computational Physics","month":"01","article_type":"original"}]